Psyllid ID: psy1314

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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-----
Protein Sequence
MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAPY
Secondary Structure (PSIPRED)
ccccccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEEEEccccccccccEEEEEccHHHHHHHHHccccEEccEEEcccccccccccccccEEEccccccccHHHHHHHHHccccEEEEEEcccccccccccEEEEEEcccHHHHHHHHcccEEEcccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccHEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEccHHHHHHHHcccccEEccEEcEEEEccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccccEEEEEEEccHHHHHHHHHcccEEEcccEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mayrangtagpgrnderklfvgglhrntgekEINDYFSQygevesisikndphtgqsrgfAFVTFTTQKAVDDLLAAGdhyignkkidpkrvtkrvnplkckifvggltteiseQDVRDYFSqygsitefqqpfdksknmkkgfcfisfddqNVAEQVlanpkqvicgkevdvkrvkfnpetmgsvsgavrGAGArvasagtayaaapgrvvaypstyagyaatdygytagsydayataypgydysamgyaypaaatsygggkyreaaytrhapy
Flexible Loop (DISEMBL)
mayrangtagpgrnderklfvgglhrntgekEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDhyignkkidpkrvtkrvnplKCKIfvggltteiseqDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLanpkqvicgkevdVKRVKfnpetmgsvsgavrGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAPY
Low Complexity Region (SEG)
MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMgsvsgavrgagarvasagtayaaapgrVVAYPStyagyaatdygytagSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAPY
Disordered region (IsUnstruct)
******************LFVGGLHRNTGEKEINDYFSQYGEVESISIK*****GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYR**********
Disordered Region (DISOPRED)
********************VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP*RV******LK**IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDV******************************************************************************************************
Disordered Region (DISEMBL)
***********GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAPY
Disordered Region (DISPRO)
**************DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN****************RVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTR****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAPY
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	275	2.2.26 [Sep-21-2011]
Q08473	344	RNA-binding protein squid	no	N/A	0.632	0.505	0.541	9e-52
O43347	362	RNA-binding protein Musas	yes	N/A	0.8	0.607	0.354	1e-31
Q8K3P4	362	RNA-binding protein Musas	yes	N/A	0.8	0.607	0.354	1e-31
Q61474	362	RNA-binding protein Musas	yes	N/A	0.8	0.607	0.354	2e-31
Q920Q6	346	RNA-binding protein Musas	no	N/A	0.796	0.632	0.358	3e-31
Q96DH6	328	RNA-binding protein Musas	no	N/A	0.796	0.667	0.358	3e-31
Q99020	285	Heterogeneous nuclear rib	no	N/A	0.603	0.582	0.380	5e-31
Q60668	355	Heterogeneous nuclear rib	no	N/A	0.545	0.422	0.398	2e-30
Q14103	355	Heterogeneous nuclear rib	no	N/A	0.545	0.422	0.398	2e-30
O14979	420	Heterogeneous nuclear rib	no	N/A	0.603	0.395	0.378	5e-30

>sp|Q08473|SQD_DROME RNA-binding protein squid OS=Drosophila melanogaster GN=sqd PE=1 SV=3

 Score =  203 bits (517), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 97/179 (54%), Positives = 128/179 (71%), Gaps = 5/179 (2%)

Query: 6   NGTAGPG-RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
           N +A  G R+D+RKLFVGGL   T EKE+ D+F +YGE+ESI++K DP TG+SRGFAF+ 
Sbjct: 44  NQSAASGQRDDDRKLFVGGLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIV 103

Query: 65  FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQY 124
           FT  +A+D + AA +H I +KK+DPK+   R      KIFVGGLTTEIS+++++ YF Q+
Sbjct: 104 FTNTEAIDKVSAADEHIINSKKVDPKKAKAR----HGKIFVGGLTTEISDEEIKTYFGQF 159

Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETM 183
           G+I E + PFDK K+ +KGFCFI+FD + V   +L  PKQ I GKEVDVKR    PE  
Sbjct: 160 GNIVEVEMPFDKQKSQRKGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPENQ 218

This protein is a component of ribonucleosomes. Could be needed to organize a concentration gradient of a dorsalizing morphogen (Dm) originating in the germinal vesicle. At least one of the isoforms is essential in somatic tissues.
Drosophila melanogaster (taxid: 7227)

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

 Score =  136 bits (343), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           +D  K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD 
Sbjct: 17  HDPCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 76

Query: 74  LLAAGDHYIGNKKIDPK-RVTKRVNPLKC----KIFVGGLTTEISEQDVRDYFSQYGSIT 128
           +LA   H + +K IDPK    +R  P       KIFVGGL+   + +DV+ YF Q+G + 
Sbjct: 77  VLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKQYFEQFGKVD 136

Query: 129 EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSG 188
           +    FDK+ N  +GF F++F+ +++ E+V       I  K V+ K+ +  P+ + S +G
Sbjct: 137 DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQ--PKEVMSPTG 194

Query: 189 AVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDY 245
           + RG    +     A+    G ++ YP    G+ AT Y   + SY   A   PGY Y
Sbjct: 195 SARGRSRVMPYGMDAFMLGIG-MLGYP----GFQATTYA--SRSYTGLA---PGYTY 241

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

 Score =  136 bits (343), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           +D  K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD 
Sbjct: 17  HDPCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 76

Query: 74  LLAAGDHYIGNKKIDPK-RVTKRVNPLKC----KIFVGGLTTEISEQDVRDYFSQYGSIT 128
           +LA   H + +K IDPK    +R  P       KIFVGGL+   + +DV+ YF Q+G + 
Sbjct: 77  VLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKHYFEQFGKVD 136

Query: 129 EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSG 188
           +    FDK+ N  +GF F++F+ +++ E+V       I  K V+ K+ +  P+ + S +G
Sbjct: 137 DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQ--PKEVMSPTG 194

Query: 189 AVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDY 245
           + RG    +     A+    G ++ YP    G+ AT Y   + SY   A   PGY Y
Sbjct: 195 SARGRSRVMPYGMDAFMLGIG-MLGYP----GFQATTYA--SRSYTGLA---PGYTY 241

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

Rattus norvegicus (taxid: 10116)

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

 Score =  136 bits (343), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           +D  K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD 
Sbjct: 17  HDPCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDK 76

Query: 74  LLAAGDHYIGNKKIDPK-RVTKRVNPLKC----KIFVGGLTTEISEQDVRDYFSQYGSIT 128
           +LA   H + +K IDPK    +R  P       KIFVGGL+   + +DV+ YF Q+G + 
Sbjct: 77  VLAQSRHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSVNTTVEDVKHYFEQFGKVD 136

Query: 129 EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSG 188
           +    FDK+ N  +GF F++F+ +++ E+V       I  K V+ K+ +  P+ + S +G
Sbjct: 137 DAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKAQ--PKEVMSPTG 194

Query: 189 AVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYDY 245
           + RG    +     A+    G ++ YP    G+ AT Y   + SY   A   PGY Y
Sbjct: 195 SARGRSRVMPYGMDAFMLGIG-MLGYP----GFQATTYA--SRSYTGLA---PGYTY 241

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

 Score =  135 bits (341), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 120/234 (51%), Gaps = 15/234 (6%)

Query: 6   NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
           +G+A   ++D  K+F+GGL   T    + DYFS++GE+    +  DP T +SRGF FVTF
Sbjct: 10  SGSANDSQHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 69

Query: 66  TTQKAVDDLLAAGDHYIGNKKIDPK-RVTKRVNPLKC----KIFVGGLTTEISEQDVRDY 120
               +VD +L    H + +K IDPK    +R  P       KIFVGGL+     +DV+ Y
Sbjct: 70  ADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSANTVVEDVKQY 129

Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL------ANPKQVICGKEVDVK 174
           F Q+G + +    FDK+ N  +GF F++F++++V E+V        N K V C K+   K
Sbjct: 130 FEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVEC-KKAQPK 188

Query: 175 RVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGY 228
            V F P T G   G      A +   G      P  V  Y   Y G+A + YGY
Sbjct: 189 EVMFPPGTRGRARGLPYTMDAFM--LGMGMLGYPNFVATYGRGYPGFAPS-YGY 239

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 =  135 bits (340), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 120/234 (51%), Gaps = 15/234 (6%)

Query: 6   NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
           +G+A   ++D  K+F+GGL   T    + DYFS++GE+    +  DP T +SRGF FVTF
Sbjct: 10  SGSANDSQHDPGKMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTF 69

Query: 66  TTQKAVDDLLAAGDHYIGNKKIDPK-RVTKRVNPLKC----KIFVGGLTTEISEQDVRDY 120
               +VD +L    H + +K IDPK    +R  P       KIFVGGL+     +DV+ Y
Sbjct: 70  ADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGLSANTVVEDVKQY 129

Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL------ANPKQVICGKEVDVK 174
           F Q+G + +    FDK+ N  +GF F++F++++V E+V        N K V C K+   K
Sbjct: 130 FEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINNKMVEC-KKAQPK 188

Query: 175 RVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGY 228
            V F P T G   G      A +   G      P  V  Y   Y G+A + YGY
Sbjct: 189 EVMFPPGTRGRARGLPYTMDAFM--LGMGMLGYPNFVATYGRGYPGFAPS-YGY 239

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|Q99020|ROAA_MOUSE Heterogeneous nuclear ribonucleoprotein A/B OS=Mus musculus GN=Hnrnpab PE=1 SV=1

 Score =  134 bits (338), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 64/168 (38%), Positives = 105/168 (62%), Gaps = 2/168 (1%)

Query: 8   TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
            A     D  K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F  
Sbjct: 66  NASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKD 125

Query: 68  QKAVDDLLAAGDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             +V+ +L   +H +  + IDPK+ +  + +P+K KIFVGGL  E +E+ +R+YF Q+G 
Sbjct: 126 SSSVEKVLDQKEHRLDGRVIDPKKAMAMKKDPVK-KIFVGGLNPEATEEKIREYFGQFGE 184

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
           I   + P D   N ++GF FI+F +++  ++VL      + G + ++K
Sbjct: 185 IEAIELPIDPKLNKRRGFVFITFKEEDPVKKVLEKKFHTVSGSKCEIK 232

Transcriptional repressor. Binds to CArG box motifs, single-stranded and double-stranded DNA, and RNA. It may be that repression by CBF-A is a result of competitive binding of CBF, a putative positive factor, and CBF-A to the same or overlapping motifs around the CArG boxes.

Mus musculus (taxid: 10090)

>sp|Q60668|HNRPD_MOUSE Heterogeneous nuclear ribonucleoprotein D0 OS=Mus musculus GN=Hnrnpd PE=1 SV=2

 Score =  133 bits (334), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 61/153 (39%), Positives = 98/153 (64%), Gaps = 3/153 (1%)

Query: 9   AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
           A   + +E K+F+GGL  +T +K++ DYFS++GEV   ++K DP TG+SRGF FV F   
Sbjct: 89  AAAAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES 148

Query: 69  KAVDDLLAAGDHYIGNKKIDPKR--VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
           ++VD ++   +H +  K IDPKR    K   P+K KIFVGGL+ +  E+ +R+YF  +G 
Sbjct: 149 ESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPVK-KIFVGGLSPDTPEEKIREYFGGFGE 207

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           +   + P D   N ++GFCFI+F ++   ++++
Sbjct: 208 VESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 240

Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.

Mus musculus (taxid: 10090)

>sp|Q14103|HNRPD_HUMAN Heterogeneous nuclear ribonucleoprotein D0 OS=Homo sapiens GN=HNRNPD PE=1 SV=1

 Score =  132 bits (333), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 61/153 (39%), Positives = 98/153 (64%), Gaps = 3/153 (1%)

Query: 9   AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
           A   + +E K+F+GGL  +T +K++ DYFS++GEV   ++K DP TG+SRGF FV F   
Sbjct: 89  AATAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES 148

Query: 69  KAVDDLLAAGDHYIGNKKIDPKR--VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
           ++VD ++   +H +  K IDPKR    K   P+K KIFVGGL+ +  E+ +R+YF  +G 
Sbjct: 149 ESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPVK-KIFVGGLSPDTPEEKIREYFGGFGE 207

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           +   + P D   N ++GFCFI+F ++   ++++
Sbjct: 208 VESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 240

Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Also binds to double- and single-stranded DNA sequences in a specific manner and functions a transcription factor. Each of the RNA-binding domains specifically can bind solely to a single-stranded non-monotonous 5'-UUAG-3' sequence and also weaker to the single-stranded 5'-TTAGGG-3' telomeric DNA repeat. Binds RNA oligonucleotides with 5'-UUAGGG-3' repeats more tightly than the telomeric single-stranded DNA 5'-TTAGGG-3' repeats. Binding of RRM1 to DNA inhibits the formation of DNA quadruplex structure which may play a role in telomere elongation. May be involved in translationally coupled mRNA turnover. Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain.

Homo sapiens (taxid: 9606)

>sp|O14979|HNRDL_HUMAN Heterogeneous nuclear ribonucleoprotein D-like OS=Homo sapiens GN=HNRPDL PE=1 SV=3

 Score =  131 bits (330), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/169 (37%), Positives = 102/169 (60%), Gaps = 3/169 (1%)

Query: 8   TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
            A   + D+ K+F+GGL  +T +K++ +Y S++GEV   +IK DP TG+SRGF FV F  
Sbjct: 139 NASKNQQDDGKMFIGGLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKD 198

Query: 68  QKAVDDLLAAGDHYIGNKKIDPKR--VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYG 125
             +VD +L   +H +  K IDPKR    K   P K K+FVGGL+ + SE+ +++YF  +G
Sbjct: 199 AASVDKVLELKEHKLDGKLIDPKRAKALKGKEPPK-KVFVGGLSPDTSEEQIKEYFGAFG 257

Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
            I   + P D   N ++GFCFI++ D+   +++L +    I   + ++K
Sbjct: 258 EIENIELPMDTKTNERRGFCFITYTDEEPVKKLLESRYHQIGSGKCEIK 306

Acts as a transcriptional regulator. Promotes transcription repression. Promotes transcription activation in differentiated myotubes (By similarity). Binds to double- and single-stranded DNA sequences. Binds to the transcription suppressor CATR sequence of the COX5B promoter (By similarity). Binds with high affinity to RNA molecules that contain AU-rich elements (AREs) found within the 3'-UTR of many proto-oncogenes and cytokine mRNAs. Binds both to nuclear and cytoplasmic poly(A) mRNAs. Binds to poly(G) and poly(A), but not to poly(U) or poly(C) RNA homopolymers. Binds to the 5'-ACUAGC-3' RNA consensus sequence.

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	275
193716167	290	PREDICTED: RNA-binding protein squid-lik	0.981	0.931	0.610	2e-86
156548706	310	PREDICTED: RNA-binding protein squid-lik	0.905	0.803	0.458	4e-57
332016239	291	RNA-binding protein squid [Acromyrmex ec	0.876	0.828	0.498	4e-54
322783285	298	hypothetical protein SINV_13887 [Solenop	0.88	0.812	0.496	5e-54
307206491	311	RNA-binding protein squid [Harpegnathos	0.88	0.778	0.498	5e-54
328789356	314	PREDICTED: RNA-binding protein squid-lik	0.810	0.710	0.524	1e-52
380026397	314	PREDICTED: RNA-binding protein squid-lik	0.810	0.710	0.520	5e-52
307173016	288	RNA-binding protein squid [Camponotus fl	0.876	0.836	0.474	5e-52
270001992	344	hypothetical protein TcasGA2_TC000928 [T	0.607	0.485	0.549	1e-51
91076876	323	PREDICTED: similar to Bmsqd-2 isoform 3	0.607	0.517	0.549	1e-51

>gi|193716167|ref|XP_001946745.1| PREDICTED: RNA-binding protein squid-like [Acyrthosiphon pisum]

 Score =  324 bits (831), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 174/285 (61%), Positives = 205/285 (71%), Gaps = 15/285 (5%)

Query: 5   ANGTA-GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
           ANG + GPGR+D++KLFVGGL R   EKE+ +YF+QYGE+E+I+IK DP +GQSRGFAFV
Sbjct: 7   ANGRSNGPGRDDDKKLFVGGLGRTISEKELREYFTQYGEIENINIKTDPFSGQSRGFAFV 66

Query: 64  TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQ 123
            F   K VDDLLAAGDH+I NKK+DPKRVTK+VNPL+CKIFVGGLTTE++EQDVR+YF Q
Sbjct: 67  QFVNAKTVDDLLAAGDHFIANKKVDPKRVTKKVNPLRCKIFVGGLTTEMTEQDVRNYFVQ 126

Query: 124 YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETM 183
           +G I+E+QQPFDK KN KKGFCFI+F+D  V  QVL NPKQVI GKEVDVK+VKFNPETM
Sbjct: 127 FGQISEYQQPFDKMKNQKKGFCFITFEDSEVVNQVLKNPKQVINGKEVDVKKVKFNPETM 186

Query: 184 ---GSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAY 240
              G+ +G   GA    A A      A    +A  +      A DYGY A +YDAY  AY
Sbjct: 187 TAPGTRTGGPVGATRGGAPATFGLRPAYAGYMAPAAAAPYGTAADYGYAANAYDAYG-AY 245

Query: 241 PGYDYSAMGYAYPAA----------ATSYGGGKYREAAYTRHAPY 275
            GYDYSA+GY               A +YGGGKYRE  Y RHAPY
Sbjct: 246 GGYDYSAIGYGGGGGGGGGGGGGYPAQAYGGGKYRETTYPRHAPY 290

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156548706|ref|XP_001603011.1| PREDICTED: RNA-binding protein squid-like [Nasonia vitripennis]

 Score =  227 bits (579), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 126/275 (45%), Positives = 167/275 (60%), Gaps = 26/275 (9%)

Query: 4   RANGTAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
           +   TAG PG++DERKLFVGGL RNT E E+  YF ++GE+ES+SIK DP+TG SRGFAF
Sbjct: 59  KQQATAGIPGKDDERKLFVGGLTRNTTEAELKAYFGKFGEIESVSIKMDPYTGVSRGFAF 118

Query: 63  VTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFS 122
           + F   KA+D LLA+GDHY+  +K+DPKRV+K+      KIFVGGLT +I+++D++ YF 
Sbjct: 119 MVFQNPKAIDKLLASGDHYVNKRKVDPKRVSKKAQ--HGKIFVGGLTPDITDEDIKTYFG 176

Query: 123 QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPET 182
           QYG+I E Q PFDK+KN ++ +CF++FD ++V  ++L  PKQVI GKE+DVK+VK N + 
Sbjct: 177 QYGTIVEVQAPFDKTKNQRRSYCFVTFDSKDVVYKLLKTPKQVINGKEIDVKKVKVNQDQ 236

Query: 183 MGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYAT-AYP 241
                G   G        G         +  Y + Y GY            D YA   Y 
Sbjct: 237 RQGFWGPQYGGYGYGGGYGGY-------IPEYANGYGGYD-----------DMYANYDYS 278

Query: 242 GYD-YSAMGYAYPAAATSYGGGKYREAAYTRHAPY 275
           GYD Y  MGYA P    +   G      + RH PY
Sbjct: 279 GYDGYENMGYAMPGKPRN---GPQGPRQFQRHQPY 310

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332016239|gb|EGI57152.1| RNA-binding protein squid [Acromyrmex echinatior]

 Score =  217 bits (553), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 135/271 (49%), Positives = 169/271 (62%), Gaps = 30/271 (11%)

Query: 8   TAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           TAG PG++DERKLF+GGL RNT +KE+ D+F ++GE+ESIS+K DPHTG SRGFAF+ FT
Sbjct: 48  TAGIPGKDDERKLFIGGLSRNTTDKELRDHFGKFGEIESISVKVDPHTGISRGFAFMVFT 107

Query: 67  TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             K +D LLA+G+HYI  +K+DPKRV+K+  P   KIFVGGLT EIS+ D+++YFSQYG+
Sbjct: 108 NPKTIDKLLASGEHYINKRKVDPKRVSKK--PQHGKIFVGGLTPEISDDDIKNYFSQYGT 165

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I E Q PFDK KN +KGFCFI+FD + V  ++L  PKQ I GKEVDVK+VK NP+     
Sbjct: 166 IVELQAPFDKVKNQRKGFCFITFDSKEVVYKLLKTPKQTINGKEVDVKKVKVNPDP---- 221

Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYAT-AYPGYD- 244
               R  G      G  Y    G +      Y GY   D        D YA   Y GYD 
Sbjct: 222 ----RNQGFWAPGYGYGYGGGYGYI----PEYNGYHNYD--------DVYANYDYAGYDG 265

Query: 245 YSAMGYAYPAAATSYGGGKYREAAYTRHAPY 275
           Y  MGY         G  +++     RH PY
Sbjct: 266 YDNMGYGPKPRGNGPGPRQFQ-----RHQPY 291

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322783285|gb|EFZ10869.1| hypothetical protein SINV_13887 [Solenopsis invicta]

 Score =  217 bits (552), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 134/270 (49%), Positives = 170/270 (62%), Gaps = 28/270 (10%)

Query: 8   TAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           TAG PG++DERKLF+GGL RNT +KE+ D+F ++GE+ESIS+K DPHTG SRGFAF+ FT
Sbjct: 55  TAGIPGKDDERKLFIGGLSRNTTDKELRDHFGKFGEIESISVKVDPHTGVSRGFAFMVFT 114

Query: 67  TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             K +D LLA+G+HYI  +K+DPKRV+K+  P   KIFVGGLT EI++ D++ YFSQYG+
Sbjct: 115 NPKTIDKLLASGEHYINKRKVDPKRVSKK--PQHGKIFVGGLTPEITDDDIKSYFSQYGT 172

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I E Q PFDK KN +KGFCFI+FD + V  ++L  PKQ I GKEVDVK+VK NP+     
Sbjct: 173 IVELQAPFDKVKNQRKGFCFITFDSKEVVYKLLKTPKQTINGKEVDVKKVKVNPDP---- 228

Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYPGYD-Y 245
               R  G      G  Y    G +      Y GY + D  Y   +YD     Y GYD Y
Sbjct: 229 ----RNQGFWAPGYGYGYGGGYGYI----PEYNGYHSYDDMY--ANYD-----YAGYDGY 273

Query: 246 SAMGYAYPAAATSYGGGKYREAAYTRHAPY 275
             MGY         G  +++     RH PY
Sbjct: 274 DNMGYGPKPRGNGPGPRQFQ-----RHQPY 298

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307206491|gb|EFN84517.1| RNA-binding protein squid [Harpegnathos saltator]

 Score =  217 bits (552), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 135/271 (49%), Positives = 171/271 (63%), Gaps = 29/271 (10%)

Query: 8   TAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           TAG PG++DERKLFVGGL RNT +KE+ ++FS++GE+ESI++K DPHTG SRGFAF+ F 
Sbjct: 67  TAGIPGKDDERKLFVGGLSRNTTDKELREHFSKFGEIESITVKIDPHTGISRGFAFMVFA 126

Query: 67  TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             KA+D LLA+G+HYI  +K+DPKRV+K+  P   KIFVGGLT EI++ D++ YF QYG+
Sbjct: 127 NAKAIDKLLASGEHYINKRKVDPKRVSKK--PQHGKIFVGGLTPEITDDDIKTYFGQYGT 184

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I E Q PFDK KN +KGFCFI+FD + V  ++L  PKQ I GKEVDVK+VK NP+     
Sbjct: 185 IVELQAPFDKVKNQRKGFCFITFDSKEVVYKLLKTPKQTINGKEVDVKKVKVNPDP---- 240

Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYAT-AYPGYD- 244
               R  G      G  Y    G +  Y + Y GY            D YA   Y GYD 
Sbjct: 241 ----RSQGFWAPGYGYGYGGGYGYIPDY-NGYHGYE-----------DMYANYDYAGYDG 284

Query: 245 YSAMGYAYPAAATSYGGGKYREAAYTRHAPY 275
           Y  MGYA P    +  G +     + RH PY
Sbjct: 285 YDNMGYAQPKPRGNGPGPR----QFQRHQPY 311

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328789356|ref|XP_001121454.2| PREDICTED: RNA-binding protein squid-like [Apis mellifera]

 Score =  212 bits (540), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 129/246 (52%), Positives = 162/246 (65%), Gaps = 23/246 (9%)

Query: 8   TAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           TAG PG++DERKLFVGGL RNT +KE+ D+FS++GE+ESIS+K DP+TG SRGFAF+ FT
Sbjct: 49  TAGIPGKDDERKLFVGGLSRNTTDKELRDHFSKFGEIESISVKIDPYTGISRGFAFMVFT 108

Query: 67  TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             K +D LLA+G+HYI  +K+DPKRV+K+  P   KIFVGGLT EI+++D++ YF QYG+
Sbjct: 109 NPKTIDKLLASGEHYINKRKVDPKRVSKK--PQHGKIFVGGLTPEITDEDIKTYFGQYGT 166

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I E Q PFDK KN +KGFCFI+FD + V  ++L  PKQ I GKEVDVK+VK NP+     
Sbjct: 167 IVELQAPFDKVKNQRKGFCFITFDSKEVVYKLLKTPKQTINGKEVDVKKVKVNPDP---- 222

Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYAT-AYPGYD- 244
               R  G      G  Y    G +  Y +          GY  G  D YA   Y GYD 
Sbjct: 223 ----RNQGFWSPGYGYGYGGGYGYIPEYCN----------GYQGGYDDMYANYDYAGYDG 268

Query: 245 YSAMGY 250
           Y  MGY
Sbjct: 269 YDNMGY 274

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380026397|ref|XP_003696938.1| PREDICTED: RNA-binding protein squid-like [Apis florea]

 Score =  210 bits (535), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 128/246 (52%), Positives = 162/246 (65%), Gaps = 23/246 (9%)

Query: 8   TAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           TAG PG++DERKLFVGGL RNT +KE+ D+FS++GE+ESIS+K DP+TG SRGFAF+ FT
Sbjct: 49  TAGIPGKDDERKLFVGGLSRNTTDKELRDHFSKFGEIESISVKIDPYTGISRGFAFMVFT 108

Query: 67  TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             K +D LLA+G+HYI  +K+DPKRV+K+  P   KIFVGGLT EI+++D++ YF QYG+
Sbjct: 109 NPKTIDKLLASGEHYINKRKVDPKRVSKK--PQHGKIFVGGLTPEITDEDIKTYFGQYGT 166

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I E Q P+DK KN +KGFCFI+FD + V  ++L  PKQ I GKEVDVK+VK NP+     
Sbjct: 167 IVELQAPYDKVKNQRKGFCFITFDSKEVVYKLLKTPKQTINGKEVDVKKVKVNPDP---- 222

Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYAT-AYPGYD- 244
               R  G      G  Y    G +  Y +          GY  G  D YA   Y GYD 
Sbjct: 223 ----RNQGFWGPGYGYGYGGGYGYIPEYCN----------GYQGGYDDMYANYDYAGYDG 268

Query: 245 YSAMGY 250
           Y  MGY
Sbjct: 269 YDNMGY 274

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307173016|gb|EFN64158.1| RNA-binding protein squid [Camponotus floridanus]

 Score =  210 bits (534), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 129/272 (47%), Positives = 168/272 (61%), Gaps = 31/272 (11%)

Query: 8   TAG-PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           TAG PG++DERKLFVGGL R+T +KE++++FS++GE+ESIS+K DPHTG SRGFAF+ F 
Sbjct: 44  TAGIPGKDDERKLFVGGLSRSTTDKELHEHFSKFGEIESISVKVDPHTGVSRGFAFMVFA 103

Query: 67  TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             K +D LLA+G+HYI  +K+DPKRV+K+  P   K+FVGGLT EI+++D++ +F QYG+
Sbjct: 104 NPKTIDKLLASGEHYINKRKVDPKRVSKK--PQHGKVFVGGLTPEITDEDIKTHFGQYGT 161

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I E Q PFDK KN +KGFCFI+FD + V  ++L  PKQ I GKEVDVK+VK NP+     
Sbjct: 162 IVELQAPFDKVKNQRKGFCFITFDSKEVVYKLLKTPKQTINGKEVDVKKVKVNPDP---- 217

Query: 187 SGAVRGAGARVASAGTAYAAAPGRVVAYPSTYAGYAATDYGYTAGSYDAYATAYP--GYD 244
               R  G         +A   G        +  Y     GY +G YD   T Y   GYD
Sbjct: 218 ----RNQG--------FWAPGYGYGYGGGYYFPDYN----GYHSGGYDDMYTNYDYAGYD 261

Query: 245 -YSAMGYAYPAAATSYGGGKYREAAYTRHAPY 275
            Y  MGY         G        + RH PY
Sbjct: 262 GYDNMGYGPKPRGNGPG-----PRQFQRHQPY 288

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270001992|gb|EEZ98439.1| hypothetical protein TcasGA2_TC000928 [Tribolium castaneum]

 Score =  209 bits (531), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/171 (54%), Positives = 129/171 (75%), Gaps = 4/171 (2%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
           PGR+D+RKLFVGGL   T +KE+ D+F QYGE+ESI++K DP+TG+SRGFAF+ F   +A
Sbjct: 53  PGRDDDRKLFVGGLSWETTDKELRDHFGQYGEIESINVKTDPNTGRSRGFAFIVFNNAEA 112

Query: 71  VDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
           +D ++AAG+H I NKK+DPK+   R      KIFVGGLT E+S+ D++++FSQYG+I E 
Sbjct: 113 IDKVVAAGEHIINNKKVDPKKAKAR----HGKIFVGGLTNELSDDDIKNFFSQYGTIIEV 168

Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE 181
           + PFDK+KN +KGFCFI+F+ + V  ++L  PKQ I  KEVDVK+    P+
Sbjct: 169 EMPFDKTKNQRKGFCFITFESEQVVNELLKTPKQTIKDKEVDVKKATPKPD 219

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91076876|ref|XP_976197.1| PREDICTED: similar to Bmsqd-2 isoform 3 [Tribolium castaneum]

 Score =  209 bits (531), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 94/171 (54%), Positives = 129/171 (75%), Gaps = 4/171 (2%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
           PGR+D+RKLFVGGL   T +KE+ D+F QYGE+ESI++K DP+TG+SRGFAF+ F   +A
Sbjct: 53  PGRDDDRKLFVGGLSWETTDKELRDHFGQYGEIESINVKTDPNTGRSRGFAFIVFNNAEA 112

Query: 71  VDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
           +D ++AAG+H I NKK+DPK+   R      KIFVGGLT E+S+ D++++FSQYG+I E 
Sbjct: 113 IDKVVAAGEHIINNKKVDPKKAKAR----HGKIFVGGLTNELSDDDIKNFFSQYGTIIEV 168

Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE 181
           + PFDK+KN +KGFCFI+F+ + V  ++L  PKQ I  KEVDVK+    P+
Sbjct: 169 EMPFDKTKNQRKGFCFITFESEQVVNELLKTPKQTIKDKEVDVKKATPKPD 219

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

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	275
FB|FBgn0263396	344	sqd "squid" [Drosophila melano	0.625	0.5	0.548	3.7e-54
UNIPROTKB|E9PTS0	331	Hnrnpab "Protein Hnrnpab" [Rat	0.6	0.498	0.383	1e-36
UNIPROTKB|Q9QX81	332	Hnrnpab "RCG34663, isoform CRA	0.6	0.496	0.383	1e-36
ZFIN|ZDB-GENE-030131-185	366	hnrnpab "heterogeneous nuclear	0.578	0.434	0.403	3.5e-36
UNIPROTKB|D6RBZ0	327	HNRNPAB "Heterogeneous nuclear	0.6	0.504	0.377	4.4e-36
UNIPROTKB|Q99729	332	HNRNPAB "Heterogeneous nuclear	0.6	0.496	0.375	5e-35
UNIPROTKB|F1PA19	264	HNRNPAB "Uncharacterized prote	0.552	0.575	0.396	8.1e-35
UNIPROTKB|Q7ZYE9	324	hnrnpab "Hnrpab-prov protein"	0.567	0.481	0.386	1.7e-34
ZFIN|ZDB-GENE-040426-2516	309	zgc:77052 "zgc:77052" [Danio r	0.578	0.514	0.391	2.1e-34
ZFIN|ZDB-GENE-040426-2717	296	hnrpdl "heterogeneous nuclear	0.610	0.567	0.410	2.7e-34

FB|FBgn0263396 sqd "squid" [Drosophila melanogaster (taxid:7227)]

 Score = 515 (186.3 bits), Expect = 3.7e-54, Sum P(2) = 3.7e-54
 Identities = 97/177 (54%), Positives = 128/177 (72%)

Query:     6 NGTAGPG-RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
             N +A  G R+D+RKLFVGGL   T EKE+ D+F +YGE+ESI++K DP TG+SRGFAF+ 
Sbjct:    44 NQSAASGQRDDDRKLFVGGLSWETTEKELRDHFGKYGEIESINVKTDPQTGRSRGFAFIV 103

Query:    65 FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQY 124
             FT  +A+D + AA +H I +KK+DPK+   R      KIFVGGLTTEIS+++++ YF Q+
Sbjct:   104 FTNTEAIDKVSAADEHIINSKKVDPKKAKARHG----KIFVGGLTTEISDEEIKTYFGQF 159

Query:   125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE 181
             G+I E + PFDK K+ +KGFCFI+FD + V   +L  PKQ I GKEVDVKR    PE
Sbjct:   160 GNIVEVEMPFDKQKSQRKGFCFITFDSEQVVTDLLKTPKQKIAGKEVDVKRATPKPE 216

GO:0005634 "nucleus" evidence=IC;IDA;TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005703 "polytene chromosome puff" evidence=IDA

GO:0008069 "dorsal/ventral axis specification, ovarian follicular epithelium" evidence=IMP

GO:0007297 "ovarian follicle cell migration" evidence=IMP

GO:0048477 "oogenesis" evidence=IMP;TAS

GO:0008298 "intracellular mRNA localization" evidence=NAS;TAS

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

GO:0003730 "mRNA 3'-UTR binding" evidence=TAS

GO:0009953 "dorsal/ventral pattern formation" evidence=IMP;TAS

GO:0006405 "RNA export from nucleus" evidence=TAS

GO:0030529 "ribonucleoprotein complex" evidence=ISS;NAS

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

GO:0035062 "omega speckle" evidence=IDA

GO:0000785 "chromatin" evidence=IDA

GO:0005737 "cytoplasm" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0019094 "pole plasm mRNA localization" evidence=IMP

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

GO:0030720 "oocyte localization involved in germarium-derived egg chamber formation" evidence=IMP

GO:0016325 "oocyte microtubule cytoskeleton organization" evidence=IMP

GO:0007293 "germarium-derived egg chamber formation" evidence=IMP

GO:0007314 "oocyte anterior/posterior axis specification" evidence=IMP

GO:0045451 "pole plasm oskar mRNA localization" evidence=IEP

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

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

GO:0033119 "negative regulation of RNA splicing" evidence=IMP

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

 Score = 345 (126.5 bits), Expect = 1.0e-36, Sum P(2) = 1.0e-36
 Identities = 64/167 (38%), Positives = 105/167 (62%)

Query:     9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             A     D  K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   
Sbjct:    66 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDS 125

Query:    69 KAVDDLLAAGDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
              +V+ +L   +H +  + IDPK+ +  + +P+K KIFVGGL  E +E+ +R+YF Q+G I
Sbjct:   126 SSVEKVLDQKEHRLDGRVIDPKKAMAMKKDPVK-KIFVGGLNPEATEEKIREYFGQFGEI 184

Query:   128 TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
                + P D   N ++GF FI+F +++  ++VL      + G + ++K
Sbjct:   185 EAIELPIDPKLNKRRGFVFITFKEEDPVKKVLEKKFHTVSGSKCEIK 231

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 345 (126.5 bits), Expect = 1.0e-36, Sum P(2) = 1.0e-36
 Identities = 64/167 (38%), Positives = 105/167 (62%)

Query:     9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             A     D  K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   
Sbjct:    67 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDS 126

Query:    69 KAVDDLLAAGDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
              +V+ +L   +H +  + IDPK+ +  + +P+K KIFVGGL  E +E+ +R+YF Q+G I
Sbjct:   127 SSVEKVLDQKEHRLDGRVIDPKKAMAMKKDPVK-KIFVGGLNPEATEEKIREYFGQFGEI 185

Query:   128 TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
                + P D   N ++GF FI+F +++  ++VL      + G + ++K
Sbjct:   186 EAIELPIDPKLNKRRGFVFITFKEEDPVKKVLEKKFHTVSGSKCEIK 232

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

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

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

ZFIN|ZDB-GENE-030131-185 hnrnpab "heterogeneous nuclear ribonucleoprotein A/B" [Danio rerio (taxid:7955)]

 Score = 348 (127.6 bits), Expect = 3.5e-36, Sum P(2) = 3.5e-36
 Identities = 65/161 (40%), Positives = 100/161 (62%)

Query:     9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             A  G  D  K+FVGGL  +T +K++ DYFS++GEV   +IK DP+TG+SRGF F+ F   
Sbjct:    87 ASKGEEDAGKMFVGGLSWDTSKKDLKDYFSKFGEVTDCTIKMDPNTGRSRGFGFILFKEP 146

Query:    69 KAVDDLLAAGDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
               VD +LA  +H +  ++IDPK+ +  +  P+K KIFVGGL  E +E+ +R+YF  +G I
Sbjct:   147 SGVDKVLAQKEHRLDGRQIDPKKAMAMKKEPVK-KIFVGGLNPETTEERIREYFGAFGEI 205

Query:   128 TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG 168
                + P D   N ++GF FI+F ++   +++L      + G
Sbjct:   206 ETIELPMDPKSNKRRGFVFITFKEEEAVKKILEKKYHNVSG 246

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

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

 Score = 339 (124.4 bits), Expect = 4.4e-36, Sum P(2) = 4.4e-36
 Identities = 63/167 (37%), Positives = 104/167 (62%)

Query:     9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             A     D  K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   
Sbjct:    62 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 121

Query:    69 KAVDDLLAAGDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
              +V+ +L   +H +  + IDPK+ +  + +P+K KIFVGGL  E +E+ +R+YF ++G I
Sbjct:   122 ASVEKVLDQKEHRLDGRVIDPKKAMAMKKDPVK-KIFVGGLNPEATEEKIREYFGEFGEI 180

Query:   128 TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
                + P D   N ++GF FI+F ++   ++VL      + G + ++K
Sbjct:   181 EAIELPMDPKLNKRRGFVFITFKEEEPVKKVLEKKFHTVSGSKCEIK 227

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|Q99729 HNRNPAB "Heterogeneous nuclear ribonucleoprotein A/B" [Homo sapiens (taxid:9606)]

 Score = 329 (120.9 bits), Expect = 5.0e-35, Sum P(2) = 5.0e-35
 Identities = 63/168 (37%), Positives = 104/168 (61%)

Query:     9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             A     D  K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   
Sbjct:    61 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 120

Query:    69 KAVDDLLAAGDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEI-SEQDVRDYFSQYGS 126
              +V+ +L   +H +  + IDPK+ +  + +P+K KIFVGGL  E  +E+ +R+YF ++G 
Sbjct:   121 ASVEKVLDQKEHRLDGRVIDPKKAMAMKKDPVK-KIFVGGLNPESPTEEKIREYFGEFGE 179

Query:   127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
             I   + P D   N ++GF FI+F ++   ++VL      + G + ++K
Sbjct:   180 IEAIELPMDPKLNKRRGFVFITFKEEEPVKKVLEKKFHTVSGSKCEIK 227

GO:0000166 "nucleotide binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IDA

GO:0003723 "RNA binding" evidence=TAS

GO:0003729 "mRNA binding" evidence=TAS

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

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

GO:0005634 "nucleus" evidence=ISS;IDA

GO:0005737 "cytoplasm" evidence=ISS

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

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

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|F1PA19 HNRNPAB "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 327 (120.2 bits), Expect = 8.1e-35, Sum P(2) = 8.1e-35
 Identities = 61/154 (39%), Positives = 99/154 (64%)

Query:    18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
             K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F    +V+ +L  
Sbjct:     1 KMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ 60

Query:    78 GDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
              +H +  + IDPK+ +  + +P+K KIFVGGL  E +E+ +R+YF ++G I   + P D 
Sbjct:    61 KEHRLDGRVIDPKKAMAMKKDPVK-KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDP 119

Query:   137 SKNMKKGFCFISFDDQNVAEQVLANPKQVICGKE 170
               N ++GF FI+F ++   ++VL      I G +
Sbjct:   120 KSNKRRGFVFITFKEEEPVKKVLEKKFHTISGSK 153

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|Q7ZYE9 hnrnpab "Hnrpab-prov protein" [Xenopus laevis (taxid:8355)]

 Score = 335 (123.0 bits), Expect = 1.7e-34, Sum P(2) = 1.7e-34
 Identities = 61/158 (38%), Positives = 101/158 (63%)

Query:    18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
             K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   ++VD +L  
Sbjct:    65 KMFVGGLSWDTSKKDLKDYFAKFGEVSDCTIKMDPNTGRSRGFGFILFKDAESVDKVLEH 124

Query:    78 GDHYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
              +H +  + IDPK+ +  + +P+K KIFVGGL  E  E  +R+YF  +G I   + P D 
Sbjct:   125 KEHRLDGRLIDPKKAMAMKKDPIK-KIFVGGLNPEAGEDQIREYFETFGEIEAIELPMDP 183

Query:   137 SKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
               N ++GF FI+F +++  +++L      + G + ++K
Sbjct:   184 KTNKRRGFVFITFKEEDPVKKILEKKFHNVSGSKCEIK 221

GO:0005515 "protein binding" evidence=IPI

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

 Score = 337 (123.7 bits), Expect = 2.1e-34, Sum P(2) = 2.1e-34
 Identities = 63/161 (39%), Positives = 101/161 (62%)

Query:    15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
             D  K+FVGGL  +T +K++ DYFS++GEV   +IK D +TG+SRGF F+ F    +VD +
Sbjct:    43 DAGKMFVGGLSWDTSKKDLKDYFSKFGEVMDCTIKMDSNTGRSRGFGFILFKESDSVDRV 102

Query:    75 LAAGDHYIGNKKIDPKRVTK-RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
             L   +H +  ++IDPKR    +  P+K KIFVGGL  E +E+ +R+YF  +G I   + P
Sbjct:   103 LQQKEHRLDGRQIDPKRAMAIKKEPVK-KIFVGGLNPETTEEKIREYFGSFGEIETIELP 161

Query:   134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK 174
              D   + ++GF FI+F ++   +++L      +CG + ++K
Sbjct:   162 TDPKTSKRRGFVFITFKEEFAVKKILEKKYHNVCGSKCEIK 202

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-040426-2717 hnrpdl "heterogeneous nuclear ribonucleoprotein D-like" [Danio rerio (taxid:7955)]

 Score = 341 (125.1 bits), Expect = 2.7e-34, Sum P(2) = 2.7e-34
 Identities = 71/173 (41%), Positives = 107/173 (61%)

Query:     9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             A   + D+ K+F+GGL  +T +K++ DY S++GEV   +IK DP TG+SRGF FV F   
Sbjct:    22 ASKNQEDDGKMFIGGLSWDTSKKDLTDYLSRFGEVLDCTIKTDPLTGRSRGFGFVLFKDA 81

Query:    69 KAVDDLLAAGDHYIGNKKIDPKRVT--KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
             ++VD +L   +H +  K IDPKR    K   P K K+FVGGL+ +I+E+ +R+YF  YG 
Sbjct:    82 ESVDRVLELTEHKLDGKLIDPKRAKAIKGKEPPK-KVFVGGLSPDITEEQLREYFGVYGE 140

Query:   127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGK-EVDVKRVK 177
             I   + P D   N ++GFCF++F  +   +++L N   Q+  GK E+ V + K
Sbjct:   141 IESIELPTDTKTNERRGFCFVTFALEEPVQKLLENRYHQIGSGKCEIKVAQPK 193

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8K3P4	MSI1H_RAT	No assigned EC number	0.3544	0.8	0.6077	yes	N/A
O43347	MSI1H_HUMAN	No assigned EC number	0.3544	0.8	0.6077	yes	N/A
Q61474	MSI1H_MOUSE	No assigned EC number	0.3544	0.8	0.6077	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	275
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	5e-29
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	7e-29
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	7e-20
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	1e-19
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-19
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	1e-19
smart00360	73	smart00360, RRM, RNA recognition motif	2e-19
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-19
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	2e-19
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-19
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	5e-19
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-19
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-18
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-18
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	9e-18
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-17
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-17
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	6e-17
smart00360	73	smart00360, RRM, RNA recognition motif	7e-17
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	7e-17
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-16
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-16
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	7e-16
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	7e-16
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-15
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	2e-15
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-15
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-15
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-15
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-15
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	1e-14
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-14
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-14
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	2e-14
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-14
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-14
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	3e-14
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	3e-14
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	3e-14
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	5e-14
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	5e-14
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-13
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-13
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-13
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-13
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	2e-13
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-13
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	4e-13
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-13
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	5e-13
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	9e-13
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-12
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	1e-12
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	1e-12
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	2e-12
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-12
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-12
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-12
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-12
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	7e-12
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	7e-12
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	8e-12
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	9e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	9e-12
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-11
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	2e-11
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	3e-11
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	3e-11
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-11
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-11
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	5e-11
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	5e-11
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-11
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	7e-11
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	7e-11
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	7e-11
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	9e-11
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	2e-10
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-10
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-10
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	3e-10
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-10
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	4e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	5e-10
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	5e-10
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	5e-10
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	5e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	6e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	9e-10
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	1e-09
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	2e-09
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	2e-09
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-09
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-09
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-09
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	4e-09
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-09
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	5e-09
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	5e-09
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	6e-09
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	6e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	6e-09
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	7e-09
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	7e-09
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-09
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	8e-09
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	8e-09
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	9e-09
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	9e-09
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	1e-08
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	1e-08
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	1e-08
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-08
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	2e-08
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	2e-08
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-08
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	3e-08
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	3e-08
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	3e-08
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	6e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	7e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	7e-08
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	7e-08
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	7e-08
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	7e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-08
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	8e-08
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	8e-08
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-07
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	1e-07
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	1e-07
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	1e-07
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	2e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	3e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	3e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	3e-07
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	3e-07
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-07
cd12635	81	cd12635, RRM2_CELF3_4_5_6, RNA recognition motif 2	4e-07
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	4e-07
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	5e-07
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	5e-07
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	5e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-07
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-07
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	6e-07
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	6e-07
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	7e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	9e-07
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	9e-07
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	9e-07
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	9e-07
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-06
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-06
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	1e-06
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	2e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	2e-06
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	2e-06
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-06
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	2e-06
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	2e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	3e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	3e-06
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	3e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-06
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	3e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-06
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	4e-06
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	4e-06
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	4e-06
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	5e-06
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	5e-06
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-06
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	6e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	6e-06
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-06
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	6e-06
cd12279	74	cd12279, RRM_TUT1, RNA recognition motif in speckl	7e-06
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	7e-06
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-06
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	8e-06
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	8e-06
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	8e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	9e-06
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	9e-06
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-06
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	9e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	1e-05
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-05
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	1e-05
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-05
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	1e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	1e-05
cd12586	71	cd12586, RRM1_PSP1, RNA recognition motif 1 in ver	1e-05
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	1e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	1e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-05
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	2e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	2e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	2e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	2e-05
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	3e-05
cd12724	92	cd12724, RRM1_CPEB2_like, RNA recognition motif 1	3e-05
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	3e-05
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	3e-05
cd12587	71	cd12587, RRM1_PSF, RNA recognition motif 1 in vert	3e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	3e-05
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	3e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	4e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	4e-05
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	4e-05
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	4e-05
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	4e-05
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	4e-05
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	5e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	5e-05
cd12571	79	cd12571, RRM6_RBM19, RNA recognition motif 6 in RN	5e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	5e-05
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	5e-05
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-05
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	5e-05
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	5e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-05
cd12636	81	cd12636, RRM2_Bruno_like, RNA recognition motif 2	6e-05
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	6e-05
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	6e-05
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	6e-05
cd12303	86	cd12303, RRM_spSet1p_like, RNA recognition motif i	6e-05
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	7e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	7e-05
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	7e-05
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	7e-05
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	8e-05
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	8e-05
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	9e-05
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	9e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	9e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	1e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	1e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	1e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	1e-04
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	1e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	1e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	1e-04
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-04
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	2e-04
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	2e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	2e-04
cd12348	75	cd12348, RRM1_SHARP, RNA recognition motif 1 in SM	2e-04
cd12488	85	cd12488, RRM2_hnRNPR, RNA recognition motif 2 in v	2e-04
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	2e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	2e-04
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	2e-04
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	2e-04
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	2e-04
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	2e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-04
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	3e-04
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	3e-04
cd12302	110	cd12302, RRM_scSet1p_like, RNA recognition motif i	3e-04
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	3e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	3e-04
cd12556	85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	3e-04
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	3e-04
cd12304	93	cd12304, RRM_Set1, RNA recognition motif in the Se	3e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	4e-04
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-04
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	4e-04
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-04
cd12238	73	cd12238, RRM1_RBM40_like, RNA recognition motif 1	4e-04
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	5e-04
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	5e-04
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	5e-04
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	6e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	6e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	6e-04
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	6e-04
cd12444	112	cd12444, RRM1_CPEBs, RNA recognition motif 1 in cy	6e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	6e-04
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	6e-04
cd12368	75	cd12368, RRM3_RBM45, RNA recognition motif 3 in RN	6e-04
cd12489	85	cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in v	6e-04
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	6e-04
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	8e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-04
cd12723	100	cd12723, RRM1_CPEB1, RNA recognition motif 1 in cy	8e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	8e-04
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	9e-04
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	9e-04
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.001
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	0.001
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.001
cd12472	80	cd12472, RRM1_RBMS3, RNA recognition motif 1 found	0.001
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	0.001
cd12265	86	cd12265, RRM_SLT11, RNA recognition motif of pre-m	0.001
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	0.001
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	0.001
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	0.001
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	0.001
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	0.001
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.001
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	0.001
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	0.001
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.001
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	0.001
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	0.001
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.002
cd12634	81	cd12634, RRM2_CELF1_2, RNA recognition motif 2 in	0.002
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	0.002
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.002
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.002
cd12444	112	cd12444, RRM1_CPEBs, RNA recognition motif 1 in cy	0.002
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	0.002
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	0.002
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.002
cd12360	78	cd12360, RRM_cwf2, RNA recognition motif in yeast	0.002
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.002
cd12596	70	cd12596, RRM1_SRSF6, RNA recognition motif 1 in ve	0.002
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.002
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.002
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.002
cd12470	86	cd12470, RRM1_MSSP1, RNA recognition motif 1 in ve	0.002
cd12269	69	cd12269, RRM_Vip1_like, RNA recognition motif in a	0.002
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	0.002
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	0.002
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.002
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	0.002
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.003
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	0.003
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.003
cd12342	71	cd12342, RRM_Nab3p, RNA recognition motif in yeast	0.003
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	0.003
cd12597	73	cd12597, RRM1_SRSF1, RNA recognition motif 1 in se	0.004
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.004
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	0.004

>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 =  105 bits (263), Expect = 5e-29
 Identities = 34/74 (45%), Positives = 53/74 (71%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+ E +E+ +R+YF ++G+I E + P DK  N ++GFCFI+FD +   +++L  
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 162 PKQVICGKEVDVKR 175
              VI GK+V+VK+
Sbjct: 61  QFHVIGGKKVEVKK 74

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

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

 Score =  104 bits (262), Expect = 7e-29
 Identities = 37/72 (51%), Positives = 49/72 (68%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          LF+GGL  +T E+ + +YFS+YGEV    I  DP TG+SRGF FVTF    +VD +LAA 
Sbjct: 1  LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 79 DHYIGNKKIDPK 90
           H +  ++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|241201 cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 81.2 bits (200), Expect = 7e-20
 Identities = 33/74 (44%), Positives = 52/74 (70%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F    +V+ +L  
Sbjct: 1  KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 78 GDHYIGNKKIDPKR 91
           +H +  + IDPK+
Sbjct: 61 KEHRLDGRLIDPKK 74

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

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

 Score = 80.5 bits (199), Expect = 1e-19
 Identities = 29/74 (39%), Positives = 46/74 (62%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL   T E++I +YF ++G +  I +  D  T + RGF F+TF +++ V  +L  
Sbjct: 1  KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKILET 60

Query: 78 GDHYIGNKKIDPKR 91
            H IG KK++ K+
Sbjct: 61 QFHVIGGKKVEVKK 74

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

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

 Score = 80.6 bits (199), Expect = 1e-19
 Identities = 33/72 (45%), Positives = 48/72 (66%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +F+GGL   T  + + +YFS++GE++   +  DP T +SRGF FVTF+   +VD +LA G
Sbjct: 1  MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 79 DHYIGNKKIDPK 90
           H +  KKIDPK
Sbjct: 61 PHELDGKKIDPK 72

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

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

 Score = 80.5 bits (199), Expect = 1e-19
 Identities = 32/78 (41%), Positives = 48/78 (61%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLF+GGL   T +  + +YFSQ+GE+    +  DP+T +SRGF FVTF +   VD  + A
Sbjct: 1  KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 78 GDHYIGNKKIDPKRVTKR 95
            H +  ++++PKR   R
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|214636 smart00360, RRM, RNA recognition motif

 Score = 79.9 bits (198), Expect = 2e-19
 Identities = 26/72 (36%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           LFVG L  +T E+E+ + FS++G+VES+ +  D  TG+S+GFAFV F +++  +  L A
Sbjct: 1  TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 78 GD-HYIGNKKID 88
           +   +  + + 
Sbjct: 61 LNGKELDGRPLK 72

Length = 73

>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 = 80.0 bits (197), Expect = 2e-19
 Identities = 35/74 (47%), Positives = 50/74 (67%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL  +T +K++ +Y S++GEV   +IK DP TG+SRGF FV F    +VD +L  
Sbjct: 1  KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 78 GDHYIGNKKIDPKR 91
           +H +  K IDPKR
Sbjct: 61 KEHKLDGKLIDPKR 74

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

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

 Score = 79.9 bits (197), Expect = 2e-19
 Identities = 34/73 (46%), Positives = 50/73 (68%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +FVGGL  +T +K++ +YFS++GEV   +IK DP TG+SRGF FV F    +V+ +L   
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 79 DHYIGNKKIDPKR 91
          +H +  + IDPKR
Sbjct: 61 EHKLDGRVIDPKR 73

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

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

 Score = 79.7 bits (197), Expect = 2e-19
 Identities = 33/74 (44%), Positives = 50/74 (67%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  +  E+E  +YFSQ+G+V    +  D  TG+SRGF FVTF ++ AV+ + +A
Sbjct: 1  KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 78 GDHYIGNKKIDPKR 91
          G   +G K+++ KR
Sbjct: 61 GMLELGGKQVEVKR 74

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

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

 Score = 78.8 bits (194), Expect = 5e-19
 Identities = 31/77 (40%), Positives = 49/77 (63%), Gaps = 1/77 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +F+GGL+  T +  + +YF Q+GEV   ++  D  TG+SRGF F+TF   K+V++++   
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKK- 59

Query: 79 DHYIGNKKIDPKRVTKR 95
          +H +  K IDPKR   R
Sbjct: 60 EHILDGKIIDPKRAIPR 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|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily

 Score = 78.5 bits (194), Expect = 5e-19
 Identities = 34/73 (46%), Positives = 46/73 (63%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLFVGGL  +  E+++ +YFSQYG VES+ I  D  TG+ RGFAFVTF     VD ++  
Sbjct: 1  KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 78 GDHYIGNKKIDPK 90
            H I   +++ 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|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 77.9 bits (192), Expect = 1e-18
 Identities = 37/78 (47%), Positives = 44/78 (56%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLFVGGL   T ++ +  YFSQYGEV    I  D  T +SRGF FV F     V  +LA 
Sbjct: 1  KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 78 GDHYIGNKKIDPKRVTKR 95
          G H +  + IDPK  T R
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|241200 cd12756, RRM1_hnRNPD, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 77.0 bits (189), Expect = 2e-18
 Identities = 34/73 (46%), Positives = 51/73 (69%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +F+GGL  +T +K++ DYFS++GEV   ++K DP TG+SRGF FV F   ++VD ++   
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 79 DHYIGNKKIDPKR 91
          +H +  K IDPKR
Sbjct: 61 EHKLNGKVIDPKR 73

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

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

 Score = 75.5 bits (186), Expect = 9e-18
 Identities = 33/74 (44%), Positives = 49/74 (66%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL   ++E D+R YFSQ+G++TE    +D  K   +GF FI+F+ ++  +QV+  
Sbjct: 4   KIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNE 63

Query: 162 PKQVICGKEVDVKR 175
               I GK+V+VKR
Sbjct: 64  HFHDINGKKVEVKR 77

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

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

 Score = 75.5 bits (186), Expect = 1e-17
 Identities = 28/74 (37%), Positives = 48/74 (64%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL  +++E++ ++YFSQ+G + + Q   D      +GF F++FD ++  E+V + 
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 162 PKQVICGKEVDVKR 175
               + GK+V+VKR
Sbjct: 61  GMLELGGKQVEVKR 74

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

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

 Score = 75.4 bits (185), Expect = 1e-17
 Identities = 34/73 (46%), Positives = 47/73 (64%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD +LA 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 78 GDHYIGNKKIDPK 90
            H + +K IDPK
Sbjct: 62 SRHELDSKTIDPK 74

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

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

 Score = 74.6 bits (184), Expect = 2e-17
 Identities = 29/73 (39%), Positives = 48/73 (65%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL  +++E+D+R+YFSQYG++   +   DK    K+GF F++FDD +  ++++  
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQ 60

Query: 162 PKQVICGKEVDVK 174
               I G  V+VK
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|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins

 Score = 73.4 bits (181), Expect = 6e-17
 Identities = 28/56 (50%), Positives = 36/56 (64%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          KLFV GL   T EKE+   FS++G VE + +  DP TG+SRGF FVTF + +  D 
Sbjct: 3  KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADA 58

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|214636 smart00360, RRM, RNA recognition motif

 Score = 73.0 bits (180), Expect = 7e-17
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-A 160
            +FVG L  + +E+++R+ FS++G +   +   DK     KGF F+ F+ +  AE+ L A
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 161 NPKQVICGKEVDV 173
              + + G+ + V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 73.0 bits (180), Expect = 7e-17
 Identities = 28/70 (40%), Positives = 45/70 (64%), Gaps = 2/70 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          LFVG L  +T E+++ D FS++G +ESI I  D  TG+S+GFAFV F  ++  +  L A 
Sbjct: 1  LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 79 D-HYIGNKKI 87
          +   +G +++
Sbjct: 60 NGKELGGREL 69

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

 Score = 71.7 bits (176), Expect = 2e-16
 Identities = 29/74 (39%), Positives = 45/74 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+   +E DV+ YFSQ+G + +    FDK  N  +GF F++F+ ++V ++V   
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 162 PKQVICGKEVDVKR 175
               I  K V+ K+
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|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins

 Score = 70.9 bits (174), Expect = 5e-16
 Identities = 29/75 (38%), Positives = 45/75 (60%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGGL  N  E ++  YFSQ+G V  + +  D    + RGF F+TF ++ +VD ++ 
Sbjct: 3  KKIFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVN 62

Query: 77 AGDHYIGNKKIDPKR 91
             H I  KK++ KR
Sbjct: 63 EHFHDINGKKVEVKR 77

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

 Score = 70.2 bits (172), Expect = 7e-16
 Identities = 32/74 (43%), Positives = 45/74 (60%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  NT E ++  YFSQ+G+VE   +  D  T + RGF FVTF ++  VD +   
Sbjct: 1  KIFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEI 60

Query: 78 GDHYIGNKKIDPKR 91
            H I NK ++ K+
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|241204 cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins

 Score = 70.5 bits (172), Expect = 7e-16
 Identities = 33/73 (45%), Positives = 45/73 (61%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL   T    + DYFS++GE+    +  DP T +SRGF FVTF    +VD +LA 
Sbjct: 1  KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 78 GDHYIGNKKIDPK 90
            H + +K IDPK
Sbjct: 61 PHHELDSKTIDPK 73

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

 Score = 69.7 bits (171), Expect = 1e-15
 Identities = 30/76 (39%), Positives = 40/76 (52%), Gaps = 7/76 (9%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT---TQKAVDDL 74
           L V GL   T E+++ DYFS +GE+  + +K DP TGQS+GF FV F     Q  V   
Sbjct: 1  DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKV--- 57

Query: 75 LAAGDHYIGNKKIDPK 90
            +  H I  +  D K
Sbjct: 58 -LSQRHMIDGRWCDVK 72

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

 Score = 69.8 bits (170), Expect = 2e-15
 Identities = 32/79 (40%), Positives = 48/79 (60%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          RKLF+GGL   T E+ + +Y+ Q+G++    +  DP + +SRGF FVTF+    VD  +A
Sbjct: 3  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA 62

Query: 77 AGDHYIGNKKIDPKRVTKR 95
          A  H I  + ++PKR   R
Sbjct: 63 ARPHTIDGRVVEPKRAVAR 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|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins

 Score = 68.4 bits (168), Expect = 3e-15
 Identities = 25/72 (34%), Positives = 45/72 (62%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +F+GGL+ + +E+ +R+YFS+YG + +     D      +GF F++F D +  ++VLA  
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAK 60

Query: 163 KQVICGKEVDVK 174
             V+ G+E+D 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|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins

 Score = 68.9 bits (168), Expect = 3e-15
 Identities = 32/73 (43%), Positives = 48/73 (65%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  +T E++I +YF  +GE+E+I +  D  T + RGF FVT+T ++ V  LL +
Sbjct: 1  KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 78 GDHYIGNKKIDPK 90
            H IG+ K + K
Sbjct: 61 RYHQIGSGKCEIK 73

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

 Score = 68.4 bits (168), Expect = 4e-15
 Identities = 25/61 (40%), Positives = 34/61 (55%), Gaps = 4/61 (6%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
           L+VG L  N  E+++ D F Q+GEV S  +  D  TG+SRGF FV   T      A++ 
Sbjct: 1  NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 74 L 74
          L
Sbjct: 61 L 61

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

 Score = 67.7 bits (166), Expect = 7e-15
 Identities = 26/70 (37%), Positives = 44/70 (62%), Gaps = 2/70 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          LFVG L  +T E+++ + FS++GE+ES+ I  D   G+S+GFAFV F + +  +  L A 
Sbjct: 1  LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKD-GKSKGFAFVEFESPEDAEKALEAL 59

Query: 79 DHY-IGNKKI 87
          +   +  +K+
Sbjct: 60 NGKELDGRKL 69

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

 Score = 66.9 bits (164), Expect = 1e-14
 Identities = 24/73 (32%), Positives = 43/73 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVG L   +  +++++YFSQ+G +     PFDK   + KG+ F+SF  ++  E  L  
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 162 PKQVICGKEVDVK 174
            K ++ G ++ V+
Sbjct: 61  QKHILEGNKLQVQ 73

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

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

 Score = 66.1 bits (162), Expect = 2e-14
 Identities = 23/70 (32%), Positives = 42/70 (60%), Gaps = 2/70 (2%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
           +FVG L  + +E+D++D FS++G I   +   D++    KGF F+ F+D+  AE+ L   
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGR-SKGFAFVEFEDEEDAEKALEAL 59

Query: 162 PKQVICGKEV 171
             + + G+E+
Sbjct: 60  NGKELGGREL 69

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

 Score = 67.0 bits (163), Expect = 2e-14
 Identities = 29/79 (36%), Positives = 48/79 (60%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+++ + VD  + 
Sbjct: 3  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMN 62

Query: 77 AGDHYIGNKKIDPKRVTKR 95
          A  H +  + ++PKR   R
Sbjct: 63 ARPHKVDGRVVEPKRAVSR 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|241028 cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins

 Score = 66.9 bits (163), Expect = 2e-14
 Identities = 28/74 (37%), Positives = 45/74 (60%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGGL+    E++I +YF ++GE+E+I +  DP T + RGF F+TF  +  V  +L 
Sbjct: 5  KKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLE 64

Query: 77 AGDHYIGNKKIDPK 90
             H +   K + K
Sbjct: 65 KKFHNVSGSKCEIK 78

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

 Score = 71.5 bits (174), Expect = 2e-14
 Identities = 33/164 (20%), Positives = 67/164 (40%), Gaps = 26/164 (15%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
           + +   LFVG L  +  E+++ + F ++G V+ + +  D  TG+SRGFAFV F ++++ +
Sbjct: 112 KEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAE 171

Query: 73  D-LLAAGDHYIGNKKIDPKRVTKRVNPLK-------------------------CKIFVG 106
             +       +  + +  ++      P                             ++VG
Sbjct: 172 KAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVG 231

Query: 107 GLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
            L  + +E+++ D F   G I     P  K   + K   F+  +
Sbjct: 232 NLPLKTAEEELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNE 275

Length = 306

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

 Score = 66.4 bits (163), Expect = 2e-14
 Identities = 26/61 (42%), Positives = 39/61 (63%), Gaps = 4/61 (6%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
          KLFVG L +   E+++   F +YG +E ++I  D  TGQS+G AFV F++    QKA++ 
Sbjct: 1  KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEA 60

Query: 74 L 74
          L
Sbjct: 61 L 61

This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. . Length = 77

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

 Score = 66.2 bits (161), Expect = 3e-14
 Identities = 29/68 (42%), Positives = 42/68 (61%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGG+  +T E  + DYF QYG++E I I  D  +G+ RGFAFVTF    +VD ++ 
Sbjct: 1  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 60

Query: 77 AGDHYIGN 84
             H +  
Sbjct: 61 QKYHTVNG 68

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

 Score = 66.2 bits (161), Expect = 3e-14
 Identities = 29/75 (38%), Positives = 45/75 (60%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGG+  +T E  + DYF +YG++E+I +  D  +G+ RGFAFVTF     VD ++ 
Sbjct: 1  KKIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVV 60

Query: 77 AGDHYIGNKKIDPKR 91
             H I     + K+
Sbjct: 61 QKYHTINGHNCEVKK 75

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

 Score = 66.1 bits (162), Expect = 3e-14
 Identities = 28/71 (39%), Positives = 47/71 (66%), Gaps = 1/71 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          ++FVGG+  +T E+E+ D+FS++G V+ + I  D   G S+G+ FVTF TQ+  + +LA 
Sbjct: 4  RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITD-RAGVSKGYGFVTFETQEDAEKILAM 62

Query: 78 GDHYIGNKKID 88
          G+     KK++
Sbjct: 63 GNLNFRGKKLN 73

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

 Score = 65.5 bits (159), Expect = 5e-14
 Identities = 28/79 (35%), Positives = 47/79 (59%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          RKLF+GGL   T +  + ++F ++G +    +  DP T +SRGF FVT++  + VD  ++
Sbjct: 3  RKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMS 62

Query: 77 AGDHYIGNKKIDPKRVTKR 95
          A  H +  + ++PKR   R
Sbjct: 63 ARPHKVDGRVVEPKRAVSR 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|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 65.4 bits (160), Expect = 5e-14
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQSR-GFAFVTFTTQKAVDD 73
          R+++V  L     E ++   FS++GEVESI I  K D   G+   GFAFVTF    + ++
Sbjct: 1  REIYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAEN 60

Query: 74 LLAAGDHYIGNKKID 88
           L      +G +KI 
Sbjct: 61 ALQLNGTELGGRKIS 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|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily

 Score = 64.2 bits (157), Expect = 1e-13
 Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 2/73 (2%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-AN 161
           +FVG L  + +E+D+R+ FS++G I   +   DK     KGF F+ F+    AE+ L A 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 162 PKQVICGKEVDVK 174
             + + G+++ V 
Sbjct: 60  NGKELDGRKLKVS 72

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

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

 Score = 64.2 bits (157), Expect = 1e-13
 Identities = 26/73 (35%), Positives = 41/73 (56%), Gaps = 6/73 (8%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+FVG LT +++E+D+R YFSQ+G +T+   P        + F F++F D  VA+ +  
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFADPEVAQSLCG 55

Query: 161 NPKQVICGKEVDV 173
               +I G  V V
Sbjct: 56  E-DHIIKGVSVHV 67

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

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

 Score = 63.5 bits (155), Expect = 2e-13
 Identities = 27/71 (38%), Positives = 45/71 (63%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLFVG L    G KE+ +YFSQ+G+V+S ++  D  TG S+G+ FV+F+++  +++ L  
Sbjct: 1  KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK 60

Query: 78 GDHYIGNKKID 88
            H +   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|241025 cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins

 Score = 63.9 bits (155), Expect = 2e-13
 Identities = 29/79 (36%), Positives = 45/79 (56%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +KLFVGG+  +T E  + DYF +YG++++I I  D  +G+ RGF FVTF     VD ++ 
Sbjct: 1  KKLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVL 60

Query: 77 AGDHYIGNKKIDPKRVTKR 95
             H I     + ++   R
Sbjct: 61 QKYHTINGHNAEVRKALSR 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|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins

 Score = 63.5 bits (154), Expect = 2e-13
 Identities = 30/73 (41%), Positives = 45/73 (61%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  +T E++I +YF  +GEVESI +  D  T + RGF F+TF  ++ V  ++  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 78 GDHYIGNKKIDPK 90
            H +G  K + K
Sbjct: 61 KYHNVGLSKCEIK 73

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

 Score = 63.1 bits (153), Expect = 3e-13
 Identities = 22/73 (30%), Positives = 45/73 (61%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL+ + +E+ +++YF  +G I   + P D   N ++GFCF+++ D+   +++L +
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLLES 60

Query: 162 PKQVICGKEVDVK 174
               I   + ++K
Sbjct: 61  RYHQIGSGKCEIK 73

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 = 63.1 bits (154), Expect = 4e-13
 Identities = 24/72 (33%), Positives = 50/72 (69%), Gaps = 1/72 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +IFVGG+  + +E+++RD+FS++GS+ + +   D++  + KG+ F++F+ Q  AE++LA 
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDRA-GVSKGYGFVTFETQEDAEKILAM 62

Query: 162 PKQVICGKEVDV 173
                 GK++++
Sbjct: 63  GNLNFRGKKLNI 74

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

 Score = 68.4 bits (167), Expect = 4e-13
 Identities = 45/162 (27%), Positives = 73/162 (45%), Gaps = 13/162 (8%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
               D+R +FV  L     E+++ ++FS+ G+V  +    D ++ +S+G A+V F   ++
Sbjct: 84  EAERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVES 143

Query: 71  VDDLLAA-GDHYIG------------NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDV 117
           V   LA  G   +G            N+            P   K++VG L   I+EQ++
Sbjct: 144 VIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQEL 203

Query: 118 RDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           R  F  +G I + Q   D      KGF FI F D   A++ L
Sbjct: 204 RQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEAL 245

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

 Score = 62.7 bits (152), Expect = 5e-13
 Identities = 26/74 (35%), Positives = 42/74 (56%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGG+  +  E  +RDYF +YG I   +   D+    K+GF F++FDD +  ++++  
Sbjct: 2   KIFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQ 61

Query: 162 PKQVICGKEVDVKR 175
               I G   +VK+
Sbjct: 62  KYHTINGHNCEVKK 75

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

 Score = 61.9 bits (151), Expect = 9e-13
 Identities = 26/74 (35%), Positives = 42/74 (56%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            KIFVGGL    ++  +R YFSQ+G I E     D+     +G+ F++F D+  AE+   
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACK 60

Query: 161 NPKQVICGKEVDVK 174
           +P  +I G++ +V 
Sbjct: 61  DPNPIIDGRKANVN 74

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 = 61.3 bits (149), Expect = 1e-12
 Identities = 24/72 (33%), Positives = 43/72 (59%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +F+GGL+ + + + +R+YFS++G I E     D +    +GF F++F D    ++VLA  
Sbjct: 1   MFIGGLSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQG 60

Query: 163 KQVICGKEVDVK 174
              + GK++D K
Sbjct: 61  PHELDGKKIDPK 72

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

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

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 28/78 (35%), Positives = 49/78 (62%), Gaps = 1/78 (1%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +P+K KIFVGGL  E +E+ +R+YF ++G I   + P D   N ++GF FI+F +++  +
Sbjct: 2   DPVK-KIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVK 60

Query: 157 QVLANPKQVICGKEVDVK 174
           +VL      + G + ++K
Sbjct: 61  KVLEKKFHNVSGSKCEIK 78

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

 Score = 62.0 bits (150), Expect = 1e-12
 Identities = 29/75 (38%), Positives = 44/75 (58%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGGL  NT  +++  YF Q+G+VE   +  D  T + RGF FVTF  +  V+ +  
Sbjct: 4  KKIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCE 63

Query: 77 AGDHYIGNKKIDPKR 91
             H I NK ++ K+
Sbjct: 64 IHFHEINNKMVECKK 78

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

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

 Score = 61.2 bits (148), Expect = 2e-12
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 6/74 (8%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
           KIFVGGL+   + +DV+ YF Q+G + +    FDK+ N  +GF F++F+ +++ E+V   
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 161 -----NPKQVICGK 169
                N K V C K
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|241023 cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 61.1 bits (148), Expect = 2e-12
 Identities = 28/74 (37%), Positives = 41/74 (55%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLFVGGL  + GE ++ ++FSQ+G VE   +  D  TG+ RGF FV F    + D     
Sbjct: 1  KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 78 GDHYIGNKKIDPKR 91
            H I   +++ K+
Sbjct: 61 KFHPINGHRVEVKK 74

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

 Score = 59.8 bits (145), Expect = 6e-12
 Identities = 31/82 (37%), Positives = 45/82 (54%), Gaps = 2/82 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL+ E +++ +R YFSQYG + +     DK+ N  +GF F+ F D N    VLA 
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAG 60

Query: 162 PKQVICGKEVDVKRVKFNPETM 183
               + G+ +D K     P  M
Sbjct: 61  GPHTLDGRTIDPKPC--TPRGM 80

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

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

 Score = 59.8 bits (145), Expect = 6e-12
 Identities = 28/76 (36%), Positives = 46/76 (60%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
            KLFVGGL+  T +  +  +F++YG++    +  DP+T +SRGF F+TF++    D+ +
Sbjct: 2  LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAM 61

Query: 76 AAGDHYIGNKKIDPKR 91
           A  H I   +I+ KR
Sbjct: 62 EAQPHSIDGNQIELKR 77

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

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

 Score = 64.2 bits (155), Expect = 7e-12
 Identities = 19/101 (18%), Positives = 48/101 (47%), Gaps = 3/101 (2%)

Query: 84  NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
           + +    R   +       +FVG L  +++E+D+R+ F ++G +   +   D+     +G
Sbjct: 101 SSESPKSRQKSKEE--NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRG 158

Query: 144 FCFISFDDQNVAEQVL-ANPKQVICGKEVDVKRVKFNPETM 183
           F F+ F+ +  AE+ +     + + G+ + V++ +   +  
Sbjct: 159 FAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPR 199

Length = 306

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

 Score = 59.6 bits (144), Expect = 7e-12
 Identities = 21/58 (36%), Positives = 38/58 (65%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           KIFVGGL+ +  E+ +R+YF  +G +   + P D   N ++GFCFI+F ++   ++++
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

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

 Score = 59.5 bits (144), Expect = 7e-12
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLF+GGL  +T E+ +   FS+YG++  + +  D  T +SRGF FVTF       D + A
Sbjct: 2  KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMA 61

Query: 78 GDHYIGNKKIDPKRV 92
              +  K +D +++
Sbjct: 62 ----MNGKSVDGRQI 72

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

 Score = 59.3 bits (143), Expect = 8e-12
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  NT  +++  YF Q+G+V+   +  D  T + RGF FVTF ++  V+ +   
Sbjct: 1  KIFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 78 GDHYIGNKKIDPKR 91
            H I NK ++ K+
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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 59.3 bits (143), Expect = 9e-12
 Identities = 28/74 (37%), Positives = 45/74 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+     +DV+ YF Q+G + +    FDK+ N  +GF F++F++++V E+V   
Sbjct: 5   KIFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEI 64

Query: 162 PKQVICGKEVDVKR 175
               I  K V+ K+
Sbjct: 65  HFHEINNKMVECKK 78

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

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

 Score = 59.1 bits (144), Expect = 9e-12
 Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA- 77
          L+V  L  +  E+++ ++FS YG+VE + +  +    + RGFAFV F + +  +  L   
Sbjct: 1  LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKD--RPRGFAFVEFASPEDAEAALKKL 58

Query: 78 GDHYIGNKKI 87
              +  + +
Sbjct: 59 NGLVLDGRTL 68

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

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 24/51 (47%), Positives = 33/51 (64%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
           K+FVGGL  +T +  +  YFSQ+GE+E   +  D  TG+SRG+ FVTF  
Sbjct: 1  TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKD 51

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 58.7 bits (143), Expect = 1e-11
 Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 3/70 (4%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-N 161
           ++V  L   ++E+D+R++FS YG +   +    ++K+  +GF F+ F     AE  L   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVR--LVRNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 162 PKQVICGKEV 171
              V+ G+ +
Sbjct: 59  NGLVLDGRTL 68

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

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

 Score = 58.3 bits (141), Expect = 2e-11
 Identities = 26/77 (33%), Positives = 45/77 (58%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+FVGGL  + S+  +R +F++YG +TE     D +    +GF FI+F   + A++ + 
Sbjct: 3   CKLFVGGLNLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAME 62

Query: 161 NPKQVICGKEVDVKRVK 177
                I G ++++KR K
Sbjct: 63  AQPHSIDGNQIELKRAK 79

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 = 57.7 bits (139), Expect = 3e-11
 Identities = 26/74 (35%), Positives = 47/74 (63%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL+ + S++D++DYF+++G +T+     D +    +GF FI F D +  E+VL  
Sbjct: 1   KMFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ 60

Query: 162 PKQVICGKEVDVKR 175
            +  + G+ +D K+
Sbjct: 61  KEHRLDGRLIDPKK 74

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

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

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 6/71 (8%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          RK+FVG L  +  E+++  YFSQ+GEV  + I         R FAFVTF   +    L  
Sbjct: 1  RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLCG 55

Query: 77 AGDHYIGNKKI 87
            DH I    +
Sbjct: 56 E-DHIIKGVSV 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|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins

 Score = 58.4 bits (142), Expect = 3e-11
 Identities = 28/76 (36%), Positives = 45/76 (59%), Gaps = 4/76 (5%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          + LFV  L+ +T E ++   F +YG ++ I +  D  TG+ RG+AF+ F  ++   D+ A
Sbjct: 2  KTLFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER---DMKA 58

Query: 77 AGDHYIGNKKIDPKRV 92
          A  +  G KKID +RV
Sbjct: 59 AYKYADG-KKIDGRRV 73

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

 Score = 57.3 bits (139), Expect = 4e-11
 Identities = 19/47 (40%), Positives = 31/47 (65%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+VG LH N  E ++   F  +GE+E + ++ DP TG+S+G+ F+ F
Sbjct: 1  LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQF 47

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

 Score = 57.3 bits (138), Expect = 5e-11
 Identities = 25/74 (33%), Positives = 42/74 (56%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGG+  +  E  +RDYF QYG I   +   D+    K+GF F++FDD +  ++++  
Sbjct: 2   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 61

Query: 162 PKQVICGKEVDVKR 175
               + G   +V++
Sbjct: 62  KYHTVNGHNCEVRK 75

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

 Score = 57.4 bits (138), Expect = 5e-11
 Identities = 24/74 (32%), Positives = 42/74 (56%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGG+  +  E  +RDYF +YG I   +   D+    K+GF F++FDD +  ++++  
Sbjct: 2   KLFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQ 61

Query: 162 PKQVICGKEVDVKR 175
               I G   +V++
Sbjct: 62  KYHTINGHNAEVRK 75

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

 Score = 61.8 bits (150), Expect = 7e-11
 Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 5   ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
           A    G   N   KL+VG LH N  E+E+   F  +G++E + +  DP TG+S+GF F+ 
Sbjct: 176 ATHQPGDIPNF-LKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQ 234

Query: 65  F 65
           F
Sbjct: 235 F 235

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

 Score = 56.8 bits (137), Expect = 7e-11
 Identities = 25/74 (33%), Positives = 43/74 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL  ++ E D+ ++FSQ+G + + +   DK    K+GF F+ F + + A++    
Sbjct: 1   KLFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVV 60

Query: 162 PKQVICGKEVDVKR 175
               I G  V+VK+
Sbjct: 61  KFHPINGHRVEVKK 74

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

 Score = 56.8 bits (138), Expect = 7e-11
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
          FVG L  +  E+E+  +F   G+VE++ I  D  TG  +GF +V F T+ +V   L    
Sbjct: 3  FVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLNG 62

Query: 80 HYIGNKKIDPKRVT 93
            +  +KI   RV 
Sbjct: 63 IKLKGRKI---RVK 73

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

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

 Score = 56.9 bits (138), Expect = 7e-11
 Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 3/61 (4%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L V GL   T E+++ + FS+YG +E + +  D  TG+SRGF FV F +   V+D   A 
Sbjct: 2  LGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VEDAKEAK 58

Query: 79 D 79
          +
Sbjct: 59 E 59

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

 Score = 56.6 bits (136), Expect = 9e-11
 Identities = 25/74 (33%), Positives = 44/74 (59%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+F+GGL+ + +++ +R+YF Q+G + E     D      +GF F++F DQ   ++VLA
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 161 NPKQVICGKEVDVK 174
             +  +  K +D K
Sbjct: 61  QSRHELDSKTIDPK 74

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

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

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 1/55 (1%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          ERKLFVG L +   E ++   F+ +G +E  ++  D   GQSRG AFVTF +++ 
Sbjct: 1  ERKLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRD-QNGQSRGCAFVTFASRQC 54

This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 81

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

 Score = 60.0 bits (145), Expect = 2e-10
 Identities = 58/248 (23%), Positives = 96/248 (38%), Gaps = 18/248 (7%)

Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
           L V  L +   ++EI   F+  GE+ES  +  D  TGQS G+ FV +   +   D   A 
Sbjct: 6   LIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPE---DAEKAV 62

Query: 79  DHYIG----NKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
           +   G    NK I         + +K   ++V GL   +++ ++   FS +G I   +  
Sbjct: 63  NSLNGLRLQNKTIKVSYARPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRIL 122

Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGA 193
            D    + KG  FI FD ++ A++ +            +   VKF      S S  +   
Sbjct: 123 SDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQ 182

Query: 194 GARVASAGTAYAAAPGRVVAYPSTYAG-----YAATDYGYTAGSYDAYATAYPGYDYSAM 248
              V +  T         ++   T AG     +AA  +  +AG + A           A 
Sbjct: 183 LEAVQNPQT-----TRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQ 237

Query: 249 GYAYPAAA 256
            +A   A+
Sbjct: 238 QHAAQRAS 245

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

 Score = 55.4 bits (134), Expect = 2e-10
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI---KNDPHTGQSRGFAFVTFTTQKAVDD- 73
          +L++G L     E  +   FS+YG+++       K+ P  GQ RG+ FVTF T++  +  
Sbjct: 1  RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 74 LLAAGDHYIGNKKI 87
          L +        KK+
Sbjct: 61 LKSLNGKTALGKKL 74

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

 Score = 55.3 bits (133), Expect = 3e-10
 Identities = 22/73 (30%), Positives = 41/73 (56%), Gaps = 1/73 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +F+GGL  E ++  +R+YF Q+G +T+     D +    +GF F++F       +V+   
Sbjct: 1   MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKK- 59

Query: 163 KQVICGKEVDVKR 175
           + ++ GK +D KR
Sbjct: 60  EHILDGKIIDPKR 72

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

 Score = 60.2 bits (146), Expect = 3e-10
 Identities = 45/164 (27%), Positives = 77/164 (46%), Gaps = 32/164 (19%)

Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
           L+V  L  +  E ++ + F+++GE+ S ++  D  +G+SRGFAFV F       KAV+++
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 75  LAAGDHYIGNKKIDPK----RVTKRV---NPLKCK----------------IFVGGLTTE 111
                  IG  K   K    R  KR      L+ K                ++V  L   
Sbjct: 240 ---NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDT 296

Query: 112 ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
           ++++ +R+ FS+ G IT  +   D+ K + +GF F+ F +   A
Sbjct: 297 VTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEA 339

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

 Score = 54.7 bits (131), Expect = 4e-10
 Identities = 27/73 (36%), Positives = 42/73 (57%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ + S   +RDYFS++G I E     D +    +GF F++F D    ++VLA 
Sbjct: 1   KMFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 60

Query: 162 PKQVICGKEVDVK 174
           P   +  K +D K
Sbjct: 61  PHHELDSKTIDPK 73

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

 Score = 54.3 bits (131), Expect = 5e-10
 Identities = 23/74 (31%), Positives = 43/74 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ E ++  +++YFSQ+G IT+     D +    +GF F++F   +  +  +  
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNA 60

Query: 162 PKQVICGKEVDVKR 175
               + G+EV+ KR
Sbjct: 61  RPHKVDGREVEPKR 74

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

 Score = 54.5 bits (131), Expect = 5e-10
 Identities = 27/61 (44%), Positives = 34/61 (55%), Gaps = 5/61 (8%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDD 73
          KLFVG L++   EKE+ + FS YG VE I +  D    QSRG AFV +      Q A+  
Sbjct: 1  KLFVGCLNKQATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKA 59

Query: 74 L 74
          L
Sbjct: 60 L 60

This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. . Length = 80

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

 Score = 54.6 bits (132), Expect = 5e-10
 Identities = 25/60 (41%), Positives = 38/60 (63%), Gaps = 4/60 (6%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK----AVDDL 74
          +++GGL     E +I   FSQYGE+  I++  D  TG+S+GFAF+ +  Q+    AVD+L
Sbjct: 12 IYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRSTILAVDNL 71

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

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 19/54 (35%), Positives = 32/54 (59%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          LFVG L   T E+ + + FS+YG++  + +  D  TG S+G+AFV +  ++   
Sbjct: 6  LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDAL 59

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

 Score = 54.5 bits (132), Expect = 6e-10
 Identities = 25/63 (39%), Positives = 37/63 (58%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          R +F+  L  +  E+E+ + FSQ+GEV+   I  D  TG S+G AFV F T+++    L 
Sbjct: 1  RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 77 AGD 79
          A D
Sbjct: 61 AAD 63

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

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L+VGGL     EK ++  F  +G+++ I I  D  T + RGFAFV F      +D  AA 
Sbjct: 1  LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEP---EDAAAAI 57

Query: 79 D 79
          D
Sbjct: 58 D 58

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

 Score = 53.3 bits (128), Expect = 1e-09
 Identities = 22/64 (34%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +IFVGG+  + +E D+R +FSQYG++ E +   D++  + KG+ F++F+ Q  A+++L  
Sbjct: 4   RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQE 62

Query: 162 PKQV 165
             ++
Sbjct: 63  ANRL 66

This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 81

>gnl|CDD|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 = 52.9 bits (128), Expect = 2e-09
 Identities = 20/50 (40%), Positives = 26/50 (52%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
           K+FVG L    +E+DVR  F +YG+I E     DK     KG  F+ F  
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSS 50

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 21/50 (42%), Positives = 31/50 (62%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
           I++GGL  E++E D+   FSQYG I +     DK     KGF F++++DQ
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|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins

 Score = 53.1 bits (128), Expect = 2e-09
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 2/71 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          LF+G L     EK + D FS +G  +++  I  DP TG S+GFAF+++ + +A D  + A
Sbjct: 4  LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 78 -GDHYIGNKKI 87
              Y+ N+ I
Sbjct: 64 MNGQYLCNRPI 74

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

 Score = 52.4 bits (126), Expect = 2e-09
 Identities = 23/69 (33%), Positives = 36/69 (52%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          LFVG L  +T  +++  +F   G   S+ +  D  TG+S+G AFV F T +A+   L   
Sbjct: 3  LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 79 DHYIGNKKI 87
             +  +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|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

 Score = 51.8 bits (124), Expect = 4e-09
 Identities = 23/73 (31%), Positives = 43/73 (58%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +FVGGL+ + +++D+++YFS++G + +     D      +GF F+ F D    E+VL   
Sbjct: 1   MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQK 60

Query: 163 KQVICGKEVDVKR 175
           +  + G+ +D KR
Sbjct: 61  EHKLDGRVIDPKR 73

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

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

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            + V GL  + +EQD++DYFS +G +   Q   D      KGF F+ F D     +VL+ 
Sbjct: 1   DLIVLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQ 60

Query: 162 PKQVICGKEVDVK 174
            + +I G+  DVK
Sbjct: 61  -RHMIDGRWCDVK 72

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

 Score = 52.1 bits (125), Expect = 4e-09
 Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          ++FVGG+   T E ++  +FSQYG V+ + I ND   G S+G+ FVTF TQ+    +L  
Sbjct: 4  RIFVGGIDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQE 62

Query: 78 GD 79
           +
Sbjct: 63 AN 64

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

 Score = 51.9 bits (124), Expect = 5e-09
 Identities = 21/73 (28%), Positives = 43/73 (58%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +F+GGL+ + +++D++DYFS++G + +     D      +GF F+ F +    ++V+   
Sbjct: 1   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 60

Query: 163 KQVICGKEVDVKR 175
           +  + GK +D KR
Sbjct: 61  EHKLNGKVIDPKR 73

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

>gnl|CDD|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 = 51.8 bits (125), Expect = 5e-09
 Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
           KIF+GGL   +SE  V++    +G +  F    D +  + KG+ F  + D +V +Q +A 
Sbjct: 2   KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 161 -NPKQVICGKEVDVKR 175
            N  Q +  K++ V+R
Sbjct: 62  LNGMQ-LGDKKLTVQR 76

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

 Score = 51.5 bits (123), Expect = 6e-09
 Identities = 24/76 (31%), Positives = 43/76 (56%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ + S++D+ +Y S++G + +     D      +GF F+ F D    ++VL  
Sbjct: 1   KMFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLEL 60

Query: 162 PKQVICGKEVDVKRVK 177
            +  + GK +D KR K
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|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 = 51.7 bits (124), Expect = 6e-09
 Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKA 70
          K+FVG + R+  EK++ + F QYG V  I++  D      QS+G  FVTF T+KA
Sbjct: 3  KMFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57

This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 84

>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 51.5 bits (124), Expect = 6e-09
 Identities = 19/48 (39%), Positives = 30/48 (62%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +LFV  L   T E+E+ + F  +GE+  + +  D  T +S+GFAFV+F
Sbjct: 1  RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSF 48

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

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

 Score = 51.6 bits (123), Expect = 7e-09
 Identities = 24/74 (32%), Positives = 43/74 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ E +E+ +R+Y+ Q+G +T+     D +    +GF F++F   N  +  +A 
Sbjct: 4   KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMAA 63

Query: 162 PKQVICGKEVDVKR 175
               I G+ V+ KR
Sbjct: 64  RPHTIDGRVVEPKR 77

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|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 = 51.6 bits (124), Expect = 7e-09
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          D  KLFVG + RN  EK++   F Q+G++  +++  D +TG  +G AF+T+
Sbjct: 4  DAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 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|240752 cd12306, RRM_II_PABPs, RNA recognition motif in type II polyadenylate-binding proteins

 Score = 51.1 bits (123), Expect = 7e-09
 Identities = 20/68 (29%), Positives = 37/68 (54%)

Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
          FVG +   T  +E+ ++F   G +  I+I  D  TGQ +GFA++ F  + +V++ L   +
Sbjct: 3  FVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLNE 62

Query: 80 HYIGNKKI 87
               ++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|240717 cd12271, RRM1_PHIP1, RNA recognition motif 1 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 50.8 bits (122), Expect = 8e-09
 Identities = 23/52 (44%), Positives = 34/52 (65%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          ++VGG+   + E EI  YFS  GE+E + +   P TG+ RG AF+TF T++A
Sbjct: 1  VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEA 52

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

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

 Score = 55.5 bits (133), Expect = 8e-09
 Identities = 56/238 (23%), Positives = 97/238 (40%), Gaps = 31/238 (13%)

Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA- 76
           +++VG +     E  I   F  +G ++SI++  DP TG+ +GFAFV +   +A    LA 
Sbjct: 109 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAA--QLAL 166

Query: 77  --AGDHYIGNKKIDPKR-------------VTKRVNPLKCKIFVGGLTTEISEQDVRDYF 121
                  +G + I   R             V +       +I+V  +  ++SE D++  F
Sbjct: 167 EQMNGQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFN-RIYVASVHPDLSETDIKSVF 225

Query: 122 SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-------PKQVICGKEVDVK 174
             +G I + Q     +    KG+ FI +++     + +A+        + +  GK V   
Sbjct: 226 EAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP 285

Query: 175 RVKFNPETMGSVSGAVRGAGARV-----ASAGTAYAAAPGRVVAYPSTYAGYAATDYG 227
                P T+ ++  A   A A       A+   A AA  G     P+T +    TD G
Sbjct: 286 DALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGAAVLGPRAQSPATPSSSLPTDIG 343

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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 50.7 bits (122), Expect = 9e-09
 Identities = 22/52 (42%), Positives = 33/52 (63%), Gaps = 6/52 (11%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          L+VGGL     EK++ D+F Q+GE+ SI++         +  AFVTFTT++A
Sbjct: 4  LYVGGLGERVTEKDLRDHFYQFGEIRSITVV------PRQQCAFVTFTTREA 49

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 50.9 bits (122), Expect = 9e-09
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 9/83 (10%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D  +LFVG L  +  E E+ ++F ++G V  + I +    G+   F FV F   +AV  +
Sbjct: 2  DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKI 61

Query: 75 LAA------GDHYIGNKKIDPKR 91
          LA       GDH +    ++ K+
Sbjct: 62 LANKPIYFRGDHRL---NVEEKK 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|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 = 50.7 bits (122), Expect = 1e-08
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 9/73 (12%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ--V 158
             ++VG L   ++E++++  FS +G+I E +          KG+ F+ FD    A    V
Sbjct: 1   TTVYVGNLPHGLTEEELQRTFSPFGAIEEVRV------FKDKGYAFVRFDTHEAAATAIV 54

Query: 159 LANPKQVICGKEV 171
             N    I G+ V
Sbjct: 55  AVN-GTSINGQTV 66

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

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

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 4/79 (5%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
          ++V  L +N   + +   FS+YG V  +S+    HTG  +GFAF+ F T    QKA   L
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 75 LAAGDHYIGNKKIDPKRVT 93
              +         PK V 
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|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 21/58 (36%), Positives = 36/58 (62%), Gaps = 6/58 (10%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           +C++FVG L  +I+E++ ++ FS+YG ++E         N +KGF FI  D +  AE+
Sbjct: 1   RCRLFVGNLPNDITEEEFKELFSKYGEVSEV------FLNKEKGFGFIRLDTRTNAEK 52

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 4/73 (5%)

Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ 164
           V GL+   +E+D+R+ FS+YG I + Q  +D+     +GF F+ F+  +V +   A  K+
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFE--SVEDAKEA--KE 59

Query: 165 VICGKEVDVKRVK 177
            + G E+D +R++
Sbjct: 60  RLNGMEIDGRRIR 72

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

 Score = 54.8 bits (132), Expect = 2e-08
 Identities = 44/173 (25%), Positives = 75/173 (43%), Gaps = 34/173 (19%)

Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
           L+VG L  +  E ++ D F  +G V S+ +  D  T +S G+ +V F      ++A++  
Sbjct: 3   LYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALE-- 60

Query: 75  LAAGDHYIGNKKI-------DP-KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS 126
                  +G K I       DP  R +   N     IFV  L   +  + + D FS++G+
Sbjct: 61  -TMNFKRLGGKPIRIMWSQRDPSLRRSGVGN-----IFVKNLDKSVDNKALFDTFSKFGN 114

Query: 127 ITE---FQQPFDKSKNMKKGFCFISFDDQNVAEQ-------VLANPKQVICGK 169
           I           KS    +G+ F+ F+ +  A+        +L N K+V  G+
Sbjct: 115 ILSCKVATDENGKS----RGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGR 163

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

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 18/59 (30%), Positives = 30/59 (50%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++VGGL  E+ E+ +   F  +G I + Q P D      +GF F+ F++   A   + N
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDN 59

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

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
          L+VG LH +  E  + + FS  G V SI +  D  T +S G+A+V F      ++A+D L
Sbjct: 2  LYVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTL 61

Query: 75 LAAGDHYIGNKKI 87
                 I  K I
Sbjct: 62 ---NFDVIKGKPI 71

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

 Score = 50.4 bits (120), Expect = 2e-08
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
          +RKLF+G + +   E +I   FS +G++E   I   P  G SRG AFVTFTT+      +
Sbjct: 1  DRKLFIGMVSKKCNENDIRVMFSPFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAI 59

Query: 76 AA 77
           A
Sbjct: 60 KA 61

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

 Score = 50.1 bits (120), Expect = 2e-08
 Identities = 23/77 (29%), Positives = 42/77 (54%), Gaps = 7/77 (9%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG-FAFVTFTTQKAVDDL 74
          ER +FV G  R T E+++ DYFS +G V ++ +  D      +G +A V F +++ VD +
Sbjct: 2  ERSVFVSGFKRGTSEEQLMDYFSAFGPVMNVIMDKD------KGVYAIVEFDSKEGVDKV 55

Query: 75 LAAGDHYIGNKKIDPKR 91
          L+   H +   ++  + 
Sbjct: 56 LSEPQHTLNGHRLRVRP 72

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 19/67 (28%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +FVG + R+  E E+   F + G +  + +  D  +G +RG+AFVT+T ++A    +   
Sbjct: 4  VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDF-SGLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 79 DHYIGNK 85
           +Y    
Sbjct: 63 HNYEIRP 69

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

 Score = 50.0 bits (119), Expect = 3e-08
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          KLFVG + R   E+E+   F ++G V  ++I  D  TG  +G  FV ++T+   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|240672 cd12226, RRM_NOL8, RNA recognition motif in nucleolar protein 8 (NOL8) and similar proteins

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 18/49 (36%), Positives = 27/49 (55%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
          LFVGGL  +  E ++ + FS++G V  + I      G  RGFA++   T
Sbjct: 2  LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRT 50

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 22/61 (36%), Positives = 35/61 (57%), Gaps = 5/61 (8%)

Query: 27 NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDLLAAG-DHY 81
          +  E ++ + F  +G +  + +  D  TGQSRGFAFVTF T    ++A++ L   G D+ 
Sbjct: 10 DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLNGFGYDNL 69

Query: 82 I 82
          I
Sbjct: 70 I 70

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|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 = 48.8 bits (117), Expect = 6e-08
 Identities = 20/75 (26%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL     E ++ +    +G++++ ++  D  TG S+G+AF  +      D  +A 
Sbjct: 2  KIFIGGLPNYLSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAG 61

Query: 78 -GDHYIGNKKIDPKR 91
               +G+KK+  +R
Sbjct: 62 LNGMQLGDKKLTVQR 76

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|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 = 7e-08
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L VG L RN  +  + + FS YG V+ + +  D      RG+A+V F + +  +  +   
Sbjct: 1  LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 79 DH 80
          D 
Sbjct: 61 DG 62

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|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 = 48.4 bits (116), Expect = 7e-08
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF-TTQKAVDDLLAA 77
          LF+  L     ++++   F+ +G V S  +  D +TGQS+ F FV++   + A   + A 
Sbjct: 1  LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAM 60

Query: 78 GDHYIGNKKI 87
              +G K++
Sbjct: 61 NGFQVGGKRL 70

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

 Score = 50.4 bits (120), Expect = 7e-08
 Identities = 25/111 (22%), Positives = 52/111 (46%), Gaps = 4/111 (3%)

Query: 99  LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
           +  K+F+GGL+    +  +RD F+ +G + + +   D+     +GF F++F+D+  A   
Sbjct: 33  MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAA 92

Query: 159 LANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPG 209
           ++     + GKE++ + ++ NP      +    G G   +  G  Y     
Sbjct: 93  ISE----MDGKELNGRHIRVNPANDRPSAPRAYGGGGGYSGGGGGYGGGGD 139

Length = 144

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

 Score = 52.6 bits (126), Expect = 7e-08
 Identities = 38/203 (18%), Positives = 78/203 (38%), Gaps = 43/203 (21%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG---------QSRGFAFVTFTT 67
           R+L+VGG+     E+ + D+F+    +   +  +    G         + + FAF+ F T
Sbjct: 176 RRLYVGGIPPEFVEEAVVDFFND---LMIATGYHKAEDGKHVSSVNINKEKNFAFLEFRT 232

Query: 68  QK------AVDDLLAAG--------DHYIGNKKIDPKRVTKRVN---------------- 97
            +      A+D ++ +           YI   +I P+   K  +                
Sbjct: 233 VEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVL 292

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             K +I++G L   + E  +++    +G +  F    D +  + KG+ F  + D +V + 
Sbjct: 293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDV 352

Query: 158 VLANPKQVICG-KEVDVKRVKFN 179
            +A       G  ++ V+R    
Sbjct: 353 AIAALNGKDTGDNKLHVQRACVG 375

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

 Score = 48.3 bits (115), Expect = 7e-08
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          LFV  L  +  ++++ D+FS    ++   +  DP TG+SRG+ FVTF 
Sbjct: 2  LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFA 49

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

 Score = 48.1 bits (115), Expect = 8e-08
 Identities = 23/61 (37%), Positives = 33/61 (54%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L V  L   T   ++   F +YGEV  + I  D +T +SRGFAFV F  ++  +D + A 
Sbjct: 1  LKVDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

Query: 79 D 79
          D
Sbjct: 61 D 61

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|240897 cd12451, RRM2_NUCLs, RNA recognition motif 2 in nucleolin-like proteins mainly from plants

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 4/62 (6%)

Query: 18 KLFVGGLHRNTGEKEIND----YFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           +FV G   + GE +I      +FS  GE+  +SI  D  TG S+GFA++ F +   V+ 
Sbjct: 1  TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 74 LL 75
           L
Sbjct: 61 AL 62

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

 Score = 48.5 bits (116), Expect = 8e-08
 Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 3/74 (4%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           IFVG L+ +++++++ + FS++G I E      K  N    F FI F+ +  A + + + 
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVN--LIKRANHTNAFAFIKFEREQAAARAVESE 63

Query: 163 K-QVICGKEVDVKR 175
              ++  K + V+ 
Sbjct: 64  NHSMLKNKTMHVQY 77

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|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 = 47.6 bits (114), Expect = 1e-07
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FV GL+T  +E+++   FS++G + E     D      +GF F++F+    A+  + +
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 162 -PKQVICGKEVDVKRVK 177
              + + G+ + V++ K
Sbjct: 63  LNGKELEGRVIKVEKAK 79

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

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 17/60 (28%), Positives = 35/60 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++FVG L  +I+E +++++F ++G++ E +            F F+ FDD    +++LAN
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

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

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

 Score = 47.7 bits (114), Expect = 1e-07
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 6/82 (7%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPHTGQSRGFAFVTFTTQKAVDD 73
          D+  +FVG L  +  ++E+N+ FS++G++  ++ IK   HT     FAF+ F  ++A   
Sbjct: 2  DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHT---NAFAFIKFEREQAAAR 58

Query: 74 LLAAGDHYIGNKKIDPKRVTKR 95
           + + +H +   K     V  +
Sbjct: 59 AVESENHSMLKNK--TMHVQYK 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|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 4/60 (6%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ----KAVDDL 74
          LFVG L  +  E  I + F +YGE+ S+ +  DP +G+ +GF +V F++Q     A+D L
Sbjct: 1  LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

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|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 = 48.0 bits (115), Expect = 1e-07
 Identities = 16/59 (27%), Positives = 30/59 (50%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +FVG +  + +E+ + + FS+ G +  F+   D+     KG+ F  F+D   A   + N
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRN 59

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

 Score = 48.0 bits (114), Expect = 1e-07
 Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
           +FV  +  +   +D+R  F +YG I +   P D      +GF ++ F+D   AE  L N 
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 162 PKQVICGKEVDVK 174
            ++ ICG++++++
Sbjct: 63  DRKWICGRQIEIQ 75

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 1/70 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           IFVG L+ EI  + +R  F+ +G I++ +   D      KG+ F+SF  +  AE  + + 
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 163 K-QVICGKEV 171
             Q + G+ +
Sbjct: 62  NGQWLGGRAI 71

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

>gnl|CDD|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 20/52 (38%), Positives = 29/52 (55%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          L++G L     E  I   F++ GEV S+ I  +  TG+S G+ FV F T +A
Sbjct: 2  LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEA 53

This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 81

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

 Score = 48.5 bits (115), Expect = 3e-07
 Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 6/81 (7%)

Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           KLF+GGL   T +  + D F+ +G+V    +  D  TG+SRGF FV F  + A    ++ 
Sbjct: 36  KLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISE 95

Query: 78  GDHYIGNKKIDPKRVTKRVNP 98
            D     K+++ + +  RVNP
Sbjct: 96  MD----GKELNGRHI--RVNP 110

Length = 144

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          FV  L     E+++ ++FS+ G+V  + I  D ++ +S+G A+V F  +++V
Sbjct: 3  FVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 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|240770 cd12324, RRM_RBM8, RNA recognition motif in RNA-binding protein RBM8A, RBM8B nd similar proteins

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 16/51 (31%), Positives = 35/51 (68%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          +FV G+H    E++++D F+++GE++++ +  D  TG  +G+A + + T+K
Sbjct: 9  IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKK 59

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

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

 Score = 46.8 bits (112), Expect = 3e-07
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 5/60 (8%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
          ++V  L  +  ++++ + F +YG++ S  +  D   G+S+GF FV F      QKAV++L
Sbjct: 4  VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDD-EGKSKGFGFVNFENHEAAQKAVEEL 62

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

 Score = 46.5 bits (111), Expect = 3e-07
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 7/63 (11%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI-KNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          K++VG L     ++E+ D F +YG + S+ + +N P      GFAFV F   +  +D + 
Sbjct: 1  KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP------GFAFVEFEDPRDAEDAVR 54

Query: 77 AGD 79
          A D
Sbjct: 55 ALD 57

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|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 = 46.4 bits (110), Expect = 4e-07
 Identities = 23/76 (30%), Positives = 45/76 (59%), Gaps = 4/76 (5%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ + +EQ +   FS+YG I+E     D+     +GF F++F++ + A+  +  
Sbjct: 2   KLFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAM-- 59

Query: 162 PKQVICGKEVDVKRVK 177
               + GK VD ++++
Sbjct: 60  --MAMNGKSVDGRQIR 73

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

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 17/59 (28%), Positives = 27/59 (45%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           ++FV  L     E D+   FS++G ++E     DK     KGF ++ F D   A +   
Sbjct: 4   RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYK 62

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|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 = 46.7 bits (111), Expect = 4e-07
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          +RKLFVG L +   E ++   F  +G +E  +I   P  G S+G AFV F++ 
Sbjct: 1  DRKLFVGMLSKQQTEDDVRRLFEPFGTIEECTILRGPD-GNSKGCAFVKFSSH 52

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|240926 cd12482, RRM1_hnRNPR, RNA recognition motif 1 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 46.5 bits (110), Expect = 4e-07
 Identities = 21/64 (32%), Positives = 39/64 (60%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          ++FVG + R+  E E+   F + G +  + +  DP +GQ+RG+AF+TF  ++A  + +  
Sbjct: 3  EVFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITFCGKEAAQEAVKL 62

Query: 78 GDHY 81
           D+Y
Sbjct: 63 CDNY 66

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

 Score = 45.8 bits (109), Expect = 5e-07
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          +FVG L      + +   F+ +GE+    +  D  TG+S+G+ FV+F  +
Sbjct: 2  IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKK 51

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

 Score = 46.2 bits (110), Expect = 5e-07
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +LFV  L  +  E ++   FS++GE+  + +  D  +G+S+GFA+V F
Sbjct: 4  RLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLF 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|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           C+++VG ++ E+ E  +R  FS +G I      +D      KGF F+ ++
Sbjct: 1   CRVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYE 50

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

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 17/67 (25%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +FV  L   + E ++R  FS+ G IT+ +   +  K   KG+ ++ F+++   ++ L   
Sbjct: 2   VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNY-KGKSKGYAYVEFENEESVQEALKLD 60

Query: 163 KQVICGK 169
           +++I 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|240837 cd12391, RRM1_SART3, RNA recognition motif 1 in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins

 Score = 45.7 bits (109), Expect = 5e-07
 Identities = 17/58 (29%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +FV  L  +  E E+   FS+ GE+  + +  + + G+S+G+A+V F  +++V + L 
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALK 58

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

 Score = 45.6 bits (108), Expect = 6e-07
 Identities = 20/60 (33%), Positives = 33/60 (55%), Gaps = 8/60 (13%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVG L  E +EQ++R  F QYG + E         ++ K + F+  DD+  A++ + N
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLEC--------DIIKNYGFVHMDDKTAADEAIRN 53

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

 Score = 50.0 bits (119), Expect = 6e-07
 Identities = 50/193 (25%), Positives = 89/193 (46%), Gaps = 31/193 (16%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
           PGR  E  +FVG + R+  E E+   F + G +  + +  D  +GQ+RG+AFVTF  ++ 
Sbjct: 55  PGRGCE--VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEE 111

Query: 71  VDDLLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSI 127
             + +   ++Y    +I P R   V   V+   C++FVGG+      +++ + FS+   +
Sbjct: 112 AKEAVKLLNNY----EIRPGRLLGVCISVD--NCRLFVGGIPKNKKREEILEEFSK---V 162

Query: 128 TE-------FQQPFDKSKNMKKGFCFISFDDQNVAEQV---LANPKQVICGKEVDVK--- 174
           TE       +    DK KN  +GF F+ ++    A      L   +  + G  + V    
Sbjct: 163 TEGVVDVIVYHSAADKKKN--RGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAE 220

Query: 175 -RVKFNPETMGSV 186
              + + + M  V
Sbjct: 221 PEEEVDEDVMAKV 233

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

>gnl|CDD|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 = 45.7 bits (109), Expect = 7e-07
 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVDDL 74
          FVG +  +  E+++ + FS+ G V S  +  D  TG+ +G+ F  F    T   A+ +L
Sbjct: 2  FVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

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

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

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 22/69 (31%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK---GFCFISFDDQNVAEQV 158
           ++++G L + ++E  +   FS+YG I +F   F KS  +K    G+CF++F+ +  AE+ 
Sbjct: 1   RLWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKA 60

Query: 159 L--ANPKQV 165
           L   N K  
Sbjct: 61  LKSLNGKTA 69

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

 Score = 45.4 bits (107), Expect = 9e-07
 Identities = 21/56 (37%), Positives = 35/56 (62%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          ++FVG + R+  E E+   F + G +  + +  DP TG +RG+AFVTF T++A  +
Sbjct: 3  EIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTFCTKEAAQE 58

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

 Score = 45.5 bits (108), Expect = 9e-07
 Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 98  PLKCK-IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           P  CK +FVGGL    +E+ +R+ F Q G I   +         KK FC I F ++   +
Sbjct: 3   PPGCKTVFVGGLPENATEEIIREVFEQCGEIIAIRMS-------KKNFCHIRFAEEFAVD 55

Query: 157 QVLA 160
           + + 
Sbjct: 56  KAIY 59

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

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

 Score = 45.6 bits (109), Expect = 9e-07
 Identities = 21/71 (29%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 23 GLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTF-TTQKA---VDDLLA 76
          GL   T E++I    S      ++ + +  D  TG SRGFAFV F + + A   +D L  
Sbjct: 9  GLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDALNN 68

Query: 77 AGDHYIGNKKI 87
               I  + +
Sbjct: 69 LDPFVIDGRVV 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|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 21/76 (27%), Positives = 42/76 (55%), Gaps = 10/76 (13%)

Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD-QNVAEQV 158
            ++FVG L T+ +S++D+ + FS+YG I           ++ KG+ F+ FD+ ++    V
Sbjct: 1   SRVFVGNLNTDKVSKEDLEEIFSKYGKILGI--------SLHKGYGFVQFDNEEDARAAV 52

Query: 159 LANPKQVICGKEVDVK 174
                + I G+++D+ 
Sbjct: 53  AGENGREIAGQKLDIN 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|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 = 45.3 bits (108), Expect = 1e-06
 Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 5/62 (8%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQSRGFAFVTFTTQKAVDDLL 75
          KL V  +     +KE+ + FS +G+V+S+ +  K D   G  RGFAFV F T++   + +
Sbjct: 2  KLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKFD---GSHRGFAFVEFVTKQEAQNAM 58

Query: 76 AA 77
           A
Sbjct: 59 EA 60

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

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
           ++F+  L    +E+D+   FS+YG ++E   P DK     KGF F+++
Sbjct: 4   RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 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|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 17/78 (21%), Positives = 36/78 (46%), Gaps = 4/78 (5%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++VG L   ++E+D++D F Q+G +T  +   D+     +GF F+  +    A   +  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 162 PKQVICGKEVDVKRVKFN 179
               + G +   + +  N
Sbjct: 61  ----LNGTDFGGRTLTVN 74

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

 Score = 44.3 bits (105), Expect = 2e-06
 Identities = 15/57 (26%), Positives = 25/57 (43%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           +FVG L  + + +D+  +F   G+    +   DK     KG  F+ FD      + L
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL 59

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

>gnl|CDD|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 = 44.2 bits (105), Expect = 2e-06
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
           ++FV  L    +E+++R+ F  +G I+E   P DK     KGF F+SF  
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMF 50

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

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

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 24/65 (36%), Positives = 30/65 (46%), Gaps = 10/65 (15%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          KLFVG L     E+EI   F QYG+V E   IKN         + FV    + A D+ + 
Sbjct: 2  KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKN---------YGFVHMDDKTAADEAIR 52

Query: 77 AGDHY 81
             HY
Sbjct: 53 NLHHY 57

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|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 6/70 (8%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            L++G L +   E+++ + F +YGE++SI +         RG A+V   T++     L 
Sbjct: 3  TTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRALQ 56

Query: 77 AGDHYIGNKK 86
             +     K
Sbjct: 57 KLRNVKLAGK 66

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 45.0 bits (106), Expect = 2e-06
 Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 5/86 (5%)

Query: 95  RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           R NP   C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ +
Sbjct: 3   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 62

Query: 154 VAEQVLANPKQVICGKEVDVKRVKFN 179
            A++     K+   G E+D +R++ +
Sbjct: 63  DAKEA----KERANGMELDGRRIRVD 84

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

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 5/59 (8%)

Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKI 87
          E+++++YF Q+G V  + I       Q R F FVTF   + V  +L+ G+ H+I   ++
Sbjct: 13 EEDVSEYFGQFGPVLDVRIPY----QQKRMFGFVTFENAETVKRILSKGNPHFICGSRV 67

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

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 5/58 (8%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVD 72
          +FVGG+     E EI  +F++YG V+ + I  D  TG S+G+ FV+F      QK V+
Sbjct: 8  VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITD-RTGVSKGYGFVSFYDDVDVQKIVE 64

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

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 20/59 (33%), Positives = 28/59 (47%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++VG L   I+E D+R  F  +G I   Q   D      KG+ FI F D   A++ L  
Sbjct: 1   LYVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59

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

 Score = 44.2 bits (104), Expect = 3e-06
 Identities = 27/72 (37%), Positives = 44/72 (61%), Gaps = 4/72 (5%)

Query: 21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH 80
          V GL   T E+++ + FS+YG +  +++  D  TG+SRGFAFV F   + +DD   A +H
Sbjct: 4  VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYF---ERIDDSKEAMEH 60

Query: 81 YIGNKKIDPKRV 92
            G  ++D +R+
Sbjct: 61 ANG-MELDGRRI 71

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

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 5/61 (8%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
          +L V  L     E ++   FS +G V  ++I   P  G+ +GFAFV FT+    +KA+  
Sbjct: 1  RLIVRNLPFKCTEADLKKLFSPFGFVWEVTIPRKPD-GKKKGFAFVQFTSKADAEKAIKG 59

Query: 74 L 74
          +
Sbjct: 60 V 60

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 19/52 (36%), Positives = 30/52 (57%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           +IFVG L  E++++ +   FS+Y S  + +   DK     KG+ F+SF D N
Sbjct: 8   RIFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPN 59

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

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          ND R +FVG L     ++ +   FS+Y   +   +  D  TG+S+G+ FV+F      +D
Sbjct: 5  NDFR-IFVGDLGNEVTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSF---SDPND 60

Query: 74 LLAA----GDHYIGNKKIDPKR 91
           L A       Y+GN+ I  ++
Sbjct: 61 YLKAMKEMNGKYVGNRPIKLRK 82

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|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 16 ERKLFVGGLHRNTGEKEINDYF-SQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          E  +FVG L     E ++   F S++   +S  I  DP TG SRG+ FV F+ + 
Sbjct: 1  EYSIFVGDLSPEVNESDLVSLFQSRFPSCKSAKIMTDPVTGVSRGYGFVRFSDEN 55

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

 Score = 43.9 bits (104), Expect = 4e-06
 Identities = 12/41 (29%), Positives = 25/41 (60%)

Query: 26 RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          ++  E ++ + F+ +GE++ I +  D  T +S+G A+V F 
Sbjct: 12 KSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 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|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 1/57 (1%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          +R LFVG L     E+ + + F Q G +E + I  DP+ G+ + FAFVTF  + +V 
Sbjct: 1  DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPN-GKPKSFAFVTFKHEVSVP 56

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 8/55 (14%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           ++++G L     E+DV  +F  YG I E         N+K GF F+ F+D   A+
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREI--------NLKNGFGFVEFEDPRDAD 47

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

 Score = 43.5 bits (103), Expect = 4e-06
 Identities = 22/49 (44%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          R LFVG L     E+E+   F +YG VE + IK  P  GQ   +AFV F
Sbjct: 3  RTLFVGNLEITITEEELRRAFERYGVVEDVDIKR-PPRGQGNAYAFVKF 50

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

>gnl|CDD|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 = 43.6 bits (103), Expect = 5e-06
 Identities = 20/50 (40%), Positives = 32/50 (64%), Gaps = 2/50 (4%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN--MKKGFCFISF 149
           K+FVG +    SE+D+R+ F QYG++ +     D+S+N    KG CF++F
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|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 14/79 (17%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNM--KKGFCFISFDDQNVAEQV 158
             ++VGGL   ++E+D+RD+F Q+G I        +S  +  ++   F++F  +  AE+ 
Sbjct: 2   TTLYVGGLGERVTEKDLRDHFYQFGEI--------RSITVVPRQQCAFVTFTTREAAEKA 53

Query: 159 ---LANPKQVICGKEVDVK 174
              L N K +I G+ + +K
Sbjct: 54  AERLFN-KLIINGRRLKLK 71

This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. Length = 74

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

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            L V  L ++  ++E+   F   G +ES  I  D  TGQS G+ FV +  +      + 
Sbjct: 1  TNLIVNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

Query: 77 AGDHY-IGNKKI 87
            + + I NK++
Sbjct: 61 TLNGFEIRNKRL 72

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

 Score = 42.7 bits (101), Expect = 6e-06
 Identities = 21/70 (30%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-AN 161
           +FVG L+ +  E  + + F +YG I+  + P D      KGF ++ F  Q  A+  L A 
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 162 PKQVICGKEV 171
               + G+ V
Sbjct: 61  GGTDLLGRPV 70

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

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

 Score = 42.9 bits (102), Expect = 6e-06
 Identities = 18/56 (32%), Positives = 31/56 (55%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
           +++G L     E ++R YFSQ+G++T  +    K     KG+ F+ F+   VA+ V
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIV 57

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

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          LFV  L  +T ++++ ++FS+ G ++   +  D  + + RGF +VTF  +   +D   A
Sbjct: 2  LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALE---EDAKRA 57

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|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 43.6 bits (103), Expect = 6e-06
 Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 10/67 (14%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSR------GFAFVTFTTQKA 70
          RK+FVGGL  +  E EI   F ++G +    + + PH  +S+      G+AF+ F  + +
Sbjct: 1  RKVFVGGLPPDIDEDEITASFRRFGPL----VVDWPHKAESKSYFPPKGYAFLLFQEESS 56

Query: 71 VDDLLAA 77
          V  L+ A
Sbjct: 57 VQALIDA 63

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

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

 Score = 42.8 bits (101), Expect = 7e-06
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +FV G     SE+ + DYFS +G +       DK    K  +  + FD +   ++VL+ P
Sbjct: 5   VFVSGFKRGTSEEQLMDYFSAFGPVMNVI--MDKD---KGVYAIVEFDSKEGVDKVLSEP 59

Query: 163 KQVICGKEVDVKR 175
           +  + G  + V+ 
Sbjct: 60  QHTLNGHRLRVRP 72

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

 Score = 42.9 bits (101), Expect = 7e-06
 Identities = 17/58 (29%), Positives = 31/58 (53%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           IFVG L+ E+++  +   FS + S ++ +  +D      +G+ F+SF  Q  AE  + 
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAIN 59

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 7/77 (9%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK-----GFCFISFDDQNVAE 156
           +I+V  L  ++ E D+R  FS++G +   + P  K ++ K+     GF F++F D + AE
Sbjct: 2   EIYVRNLDFKLDEDDLRGIFSKFGEVESIRIP--KKQDEKQGRLNNGFAFVTFKDASSAE 59

Query: 157 QVLANPKQVICGKEVDV 173
             L      + G+++ V
Sbjct: 60  NALQLNGTELGGRKISV 76

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

>gnl|CDD|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 = 42.7 bits (101), Expect = 8e-06
 Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH--TGQSRGFAFVTFTTQKA 70
          L+VG L   T ++++    ++ G V+  SIK   H   G+S+GFA+V F ++ A
Sbjct: 1  LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAA 54

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

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 3/64 (4%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          +++VG L  +  E++I D F +YG +++I +KN     +   FAFV F   +  +D +  
Sbjct: 1  RIYVGNLPGDIRERDIEDLFYKYGPIKAIDLKNRR---RGPPFAFVEFEDPRDAEDAVRG 57

Query: 78 GDHY 81
           D Y
Sbjct: 58 RDGY 61

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

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

 Score = 42.8 bits (101), Expect = 8e-06
 Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 4/59 (6%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
           LFVG L  +  ++ +   F ++G V    +  D  TG+SRGF +V F +    +KA++
Sbjct: 1  TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIE 59

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

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

 Score = 42.6 bits (101), Expect = 8e-06
 Identities = 17/52 (32%), Positives = 32/52 (61%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          LFV  L+  T ++++   FS++G+++S  +  D  TG S  +AF+ F T++ 
Sbjct: 6  LFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED 57

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

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

 Score = 42.3 bits (100), Expect = 9e-06
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ-QPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           ++VGG+    +E ++R YFS  G I E     F  +    +G  FI+F  +  A++ LA
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRF-RGIAFITFKTEEAAKRALA 58

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

 Score = 42.6 bits (100), Expect = 9e-06
 Identities = 18/58 (31%), Positives = 35/58 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K+FVG +   I+EQ+VR  F ++G++ E     DK    ++G CF+ +  ++ A++ +
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKYSTRDEADRAI 58

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

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 18/47 (38%), Positives = 28/47 (59%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +++G L     E E+  YFSQ+G V  + +     TG+S+G+AFV F
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEF 48

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

 Score = 42.6 bits (101), Expect = 9e-06
 Identities = 16/60 (26%), Positives = 36/60 (60%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          +++V  +H +  E +I   F  +G+++S S+  DP TG+ +G+ F+ +   ++  D +A+
Sbjct: 2  RIYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIAS 61

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

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 19/74 (25%), Positives = 41/74 (55%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ E +++ +R +F Q+G++T+     D +    +GF F+++      +  +  
Sbjct: 4   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNA 63

Query: 162 PKQVICGKEVDVKR 175
               + G+ V+ KR
Sbjct: 64  RPHKVDGRVVEPKR 77

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

 Score = 42.1 bits (100), Expect = 1e-05
 Identities = 15/53 (28%), Positives = 27/53 (50%)

Query: 108 LTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           L+ +  E D+R+ F  +G I+      DK     +GF F++F  +  AE+ + 
Sbjct: 7   LSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIE 59

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

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 15/55 (27%), Positives = 33/55 (60%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           + VG LT  +++  +++ FS YG++ +   P D+  N+ +G+ ++ F+    AE+
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEK 55

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

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 19/53 (35%), Positives = 31/53 (58%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          +++VG +    GE  I   FS +G ++SI +  DP T + +GFAFV +   +A
Sbjct: 2  RVYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEA 54

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

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 14/50 (28%), Positives = 26/50 (52%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          L VG L     +++  +  S +G VE   +     TG+S+G+ FV + ++
Sbjct: 2  LCVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASK 51

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

 Score = 42.6 bits (100), Expect = 1e-05
 Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 6/84 (7%)

Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
           +FVG L     E+ +   F + G +E + I  DP T   +GFA+V F  + AV+  L   
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKAL--- 58

Query: 79  DHYIGNKKIDPKRVTKRVNPLKCK 102
              + N+K  P  + + +   +CK
Sbjct: 59  ---LLNEKKFPPMLPRELRVSRCK 79

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 6/57 (10%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +C++FVG L T+I+E+D +  F +YG      +P +   N  +GF FI  + + +AE
Sbjct: 1   RCRLFVGNLPTDITEEDFKKLFEKYG------EPSEVFINRDRGFGFIRLESRTLAE 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|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins

 Score = 42.1 bits (99), Expect = 1e-05
 Identities = 16/47 (34%), Positives = 28/47 (59%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +++G L     EKE+  YFSQ+G V+++ +     TG S+ + F+ F
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQF 48

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

 Score = 42.0 bits (99), Expect = 1e-05
 Identities = 14/37 (37%), Positives = 27/37 (72%)

Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          E+++ + F ++G++E +SI  D +TG+S+GF +V F 
Sbjct: 14 EEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFH 50

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 17/59 (28%), Positives = 36/59 (61%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +++ GL   ++++DV D FS++G I   +   D++  + +G  FI FD ++ AE+ + +
Sbjct: 3   LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAITS 61

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 14/48 (29%), Positives = 29/48 (60%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           +FVGGL+  ++E D+ + FS++G++++ +    K     +GF +I   
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLR 49

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +LF+  L     E+++   FS+YG +  + +  D  T + +GFAFVT+
Sbjct: 4  RLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 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|241114 cd12670, RRM2_Nop12p_like, RNA recognition motif 2 in yeast nucleolar protein 12 (Nop12p) and similar proteins

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 3/78 (3%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--- 159
           +FVG L  E  E+ +   F + G I   +   D   N+ KGF ++ F D+N  E+ L   
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 160 ANPKQVICGKEVDVKRVK 177
                 +  +E+ V R K
Sbjct: 62  EKKFPPMLPRELRVSRCK 79

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

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 20/47 (42%), Positives = 27/47 (57%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F
Sbjct: 3  LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRF 49

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

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 9/51 (17%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESI--SIKNDPHTGQSRGFAFVTF 65
          R LFV  ++ N  ++E+   F Q+G++ ++  + K+       RGF  V++
Sbjct: 2  RTLFVRNINSNVEDEELRALFEQFGDIRTLYTACKH-------RGFIMVSY 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|241207 cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins

 Score = 41.2 bits (96), Expect = 3e-05
 Identities = 22/75 (29%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD-DQNVAEQVLA 160
           K+F+GGL+ E ++  +R++F ++G++T+     D      +GF F+++   + V   + A
Sbjct: 4   KLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSA 63

Query: 161 NPKQVICGKEVDVKR 175
            P +V  G+ V+ KR
Sbjct: 64  RPHKVD-GRVVEPKR 77

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|241168 cd12724, RRM1_CPEB2_like, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 2/60 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEF--QQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K+FVGGL  +I E ++   F ++G +      +   KS    KG+ F+ F +++  + ++
Sbjct: 2   KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 61

This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. . Length = 92

>gnl|CDD|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 = 41.1 bits (97), Expect = 3e-05
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK-NMK-KGFCFISFDDQNVAEQVLA 160
           ++VG LT   +++D+    ++ G +      F + K N K KGF ++ F  +  A  V  
Sbjct: 1   LYVGNLTWWTTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKE 60

Query: 161 N-PKQVICGKEVDVK 174
               +   GK+  V 
Sbjct: 61  KLEGREFNGKKCVVT 75

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

 Score = 41.5 bits (97), Expect = 3e-05
 Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P  C +F+  L  E ++ D+   F  +G++   +   DK  N+ K F F+S+D+ + A+ 
Sbjct: 2   PEGCNLFIYHLPQEFTDTDLAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQA 61

Query: 158 VLANPKQVICGKEVDVKRVK 177
            +    Q + G ++  KR+K
Sbjct: 62  AI----QAMNGFQIGTKRLK 77

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

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

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 19/57 (33%), Positives = 33/57 (57%), Gaps = 6/57 (10%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +C++FVG L  +I+E + +  F++YG      +P +   N  KGF FI  + + +AE
Sbjct: 1   RCRLFVGNLPADITEDEFKKLFAKYG------EPGEVFINKGKGFGFIKLESRALAE 51

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

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

 Score = 41.3 bits (97), Expect = 3e-05
 Identities = 23/60 (38%), Positives = 32/60 (53%), Gaps = 4/60 (6%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
          L V  L +N  + EI   FS  GE+ES  +  D  TGQS G+ FV +      +KA++ L
Sbjct: 4  LIVNYLPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL 63

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

 Score = 41.1 bits (96), Expect = 3e-05
 Identities = 20/47 (42%), Positives = 27/47 (57%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRF 50

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLAN 161
           +F+G L  E+ E+ + D FS +G I +  +          KGF FIS+D    ++  +  
Sbjct: 4   LFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEA 63

Query: 162 PK-QVICGKEVDV 173
              Q +C + + V
Sbjct: 64  MNGQYLCNRPITV 76

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 6/50 (12%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
          +LFVG L  +  E+E  + FS+YGEV  + +  +      +GF F+   T
Sbjct: 3  RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNKE------KGFGFIRLDT 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|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 = 40.3 bits (95), Expect = 4e-05
 Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 4/75 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +F+  L  E ++QD+   F+ +G++   +   DK+    K F F+S+D+   A       
Sbjct: 1   LFIYHLPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESA----QAA 56

Query: 163 KQVICGKEVDVKRVK 177
            + + G +V  KR+K
Sbjct: 57  IKAMNGFQVGGKRLK 71

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           V  LT   +  D+R  F +YG + +   P D+     +GF F+ F D+  AE
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAE 54

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

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 5/59 (8%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAEQ 157
           +FVGG+   + E ++R +F++YGS+ E +   D++  + KG+ F+SF    D Q + E 
Sbjct: 8   VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDRT-GVSKGYGFVSFYDDVDVQKIVES 65

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

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 1/73 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
           +FV  +      +D+R  F +YG I +   P D      +GF +I F+D   AE  L N 
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNL 62

Query: 162 PKQVICGKEVDVK 174
            ++ +CG++++++
Sbjct: 63  NRKWVCGRQIEIQ 75

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 43.9 bits (103), Expect = 4e-05
 Identities = 38/160 (23%), Positives = 69/160 (43%), Gaps = 8/160 (5%)

Query: 12  GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
             N    L V  L ++  ++E+   F   G + +  I  D  TG S G+AFV F +    
Sbjct: 103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADS 162

Query: 68  QKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGS 126
           Q+A+ +L       + NK++           +K   ++V  L   I++  +   F +YG 
Sbjct: 163 QRAIKNLNGIT---VRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQ 219

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
           I +     DK     +G  F+ F+ +  A++ ++    VI
Sbjct: 220 IVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVI 259

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

 Score = 40.5 bits (95), Expect = 4e-05
 Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 1/71 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +++G L  +I+E DVR++F     IT  +   DK     KGF  + F D+   +  L   
Sbjct: 2   VYIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 163 KQVICGKEVDV 173
             V+CG+ + +
Sbjct: 61  GTVLCGRPIRI 71

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|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 = 40.8 bits (96), Expect = 5e-05
 Identities = 19/55 (34%), Positives = 29/55 (52%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           K+FVG +   + E+D+R  F Q+G I E     DK   M KG  F+++  +  A 
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTYCARESAL 61

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          R ++VG L   T   ++ ++FSQ GEV+ + +  D    Q   +AFV F  Q +V + L 
Sbjct: 5  RTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDE--TQPTRYAFVEFAEQTSVINALK 62

Query: 77 AGDHYIGNKKI 87
                G + +
Sbjct: 63 LNGAMFGGRPL 73

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

 Score = 40.5 bits (95), Expect = 5e-05
 Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 1/38 (2%)

Query: 31 KEINDYFSQYGEVESISI-KNDPHTGQSRGFAFVTFTT 67
          KE+ + FS +GE++++ + K    TG  RGF FV F T
Sbjct: 15 KELRELFSTFGELKTVRLPKKMTGTGSHRGFGFVDFIT 52

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

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 18/47 (38%), Positives = 26/47 (55%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+V GL +   ++E+   FS YG + +  I  D  TG SRG  F+ F
Sbjct: 3  LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF 49

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|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 4/80 (5%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P  C +F+  L  E  + ++   F  +G++   +   D++ N  K F F+SFD+   A+ 
Sbjct: 2   PEGCNLFIYHLPQEFGDAELMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQA 61

Query: 158 VLANPKQVICGKEVDVKRVK 177
            +    Q + G ++ +KR+K
Sbjct: 62  AI----QAMNGFQIGMKRLK 77

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 18/59 (30%), Positives = 32/59 (54%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +FVG +  E +E+ ++D FS+ G +  F+  +D+     KG+ F  + DQ  A   + N
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRN 59

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

 Score = 40.1 bits (94), Expect = 5e-05
 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQ-QPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +FVG L+ E +E ++R +F + G I   +   F+ S    KGF F+ F++   A   L  
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKC-KGFAFVDFEEIEFATNALKG 59

Query: 162 P 162
            
Sbjct: 60  K 60

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

 Score = 40.7 bits (95), Expect = 5e-05
 Identities = 20/63 (31%), Positives = 30/63 (47%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D  +LFVG L  +  E E+ ++F  +G V  + I      G+   F FV F   + V  +
Sbjct: 4  DSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRI 63

Query: 75 LAA 77
          L A
Sbjct: 64 LGA 66

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

 Score = 40.2 bits (95), Expect = 6e-05
 Identities = 18/72 (25%), Positives = 36/72 (50%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +FVG L  +I E+++R +F   G +   +   D+   + KGF ++ F  ++     L   
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 163 KQVICGKEVDVK 174
              + G+++ VK
Sbjct: 62  GIKLKGRKIRVK 73

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

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

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
           K+FVG L+ + +E DVR  F+ +GSI E     D++    +G  F++F  +  A
Sbjct: 3   KLFVGMLSKKCNENDVRIMFAPFGSIEECTVLRDQN-GQSRGCAFVTFASRQCA 55

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

 Score = 40.0 bits (94), Expect = 6e-05
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 8/56 (14%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          ++++G L     E+++  +F  YG +  I++KN        GF FV F   +  DD
Sbjct: 1  RVYIGRLPYRARERDVERFFKGYGRIREINLKN--------GFGFVEFEDPRDADD 48

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

 Score = 40.3 bits (94), Expect = 6e-05
 Identities = 18/64 (28%), Positives = 36/64 (56%), Gaps = 3/64 (4%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P   ++FVG L  ++ + +++++F QYG++ E +     S      F F+ FDD    ++
Sbjct: 1   PDSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRI---NSGGKLPNFGFVVFDDSEPVQK 57

Query: 158 VLAN 161
           +L+N
Sbjct: 58  ILSN 61

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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 40.1 bits (94), Expect = 6e-05
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 3/63 (4%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          ++VG L  +  E+E+ D F +YG +  I +K  P   +  G+AF+ F   +  +D +   
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVDIDLKLPP---RPPGYAFIEFEDARDAEDAIRGR 58

Query: 79 DHY 81
          D Y
Sbjct: 59 DGY 61

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>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 = 40.4 bits (95), Expect = 6e-05
 Identities = 20/47 (42%), Positives = 27/47 (57%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          + + GL   T  K+I  +F  +GE+E   +K DP TGQS G   VTF
Sbjct: 1  ILITGLSPLTTPKQIRMHFRPFGEIEESELKLDPRTGQSLGICRVTF 47

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 19/71 (26%), Positives = 35/71 (49%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           IFVG +    + ++++++F   G+I       DK     KGF +I F D++  E  L   
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61

Query: 163 KQVICGKEVDV 173
           +    G+++ V
Sbjct: 62  ESEFRGRQIKV 72

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

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

 Score = 40.2 bits (94), Expect = 7e-05
 Identities = 15/50 (30%), Positives = 25/50 (50%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          +FVG L     +  +   FS +       +  D  +G+SRG+ FV+F +Q
Sbjct: 2  IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQ 51

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

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 18/58 (31%), Positives = 33/58 (56%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          L++ GL R   +K++ D FS++G + +  +  D  TG SRG AF+ F  +   ++ + 
Sbjct: 3  LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60

This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 1/69 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          LFVG L  +  + ++ ++F + GEV  + I  D   G+S+GF  V F T++     L   
Sbjct: 2  LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 79 DHYIGNKKI 87
             +  ++I
Sbjct: 61 GEELLGREI 69

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

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 15/48 (31%), Positives = 25/48 (52%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          +FV  L  +  E  +   FS +G V ++ +  D  T + +G+ FVT T
Sbjct: 4  IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMT 51

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

 Score = 39.5 bits (93), Expect = 8e-05
 Identities = 16/66 (24%), Positives = 31/66 (46%), Gaps = 4/66 (6%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVD 72
            +++ GL  NT ++++      +G++ S     D  T + +G+ FV F       KA++
Sbjct: 1  TNVYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIE 60

Query: 73 DLLAAG 78
           L   G
Sbjct: 61 GLNGRG 66

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

 Score = 39.9 bits (94), Expect = 9e-05
 Identities = 15/51 (29%), Positives = 25/51 (49%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           +FV  L  + +E  +R  F +YG I   +   DK     +G+ FI F+ + 
Sbjct: 4   LFVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHER 54

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

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

 Score = 40.0 bits (93), Expect = 9e-05
 Identities = 21/47 (44%), Positives = 30/47 (63%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L V GL   T E+++ + FS+YG +  +SI  D  + +SRGFAFV F
Sbjct: 12 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 58

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

 Score = 39.6 bits (93), Expect = 9e-05
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           ++ V  L   I E  +R  F  +G+IT+ Q  + K    +K F F+ +  +  A++ L 
Sbjct: 2   RLIVKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRK-FGFVGYKTEEEAQKALK 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|233516 TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing factor

 Score = 42.2 bits (99), Expect = 1e-04
 Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 1   MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF 60
           +A  A   A  G      +FV  L  +T E  +   F  +G V+++ I  D  T Q +G+
Sbjct: 256 LAAGAQIAASDGAG--YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGY 313

Query: 61  AFVTFTT-QKAVDDLLAAGDHYIGNK 85
            FV+ T   +A   +L+   + +GN+
Sbjct: 314 GFVSMTNYDEAAMAILSLNGYTLGNR 339

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

 Score = 43.0 bits (101), Expect = 1e-04
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 16  ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
           + ++++G L    GE +I +    +G++++ ++  D  TG S+G+AF  +      D  +
Sbjct: 295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAI 354

Query: 76  AAGDHY-IGNKKIDPKRVTKRVNP 98
           AA +    G+ K+  +R     N 
Sbjct: 355 AALNGKDTGDNKLHVQRACVGANQ 378

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 19/74 (25%), Positives = 40/74 (54%), Gaps = 10/74 (13%)

Query: 17 RKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
           ++FVG L+ +   ++++ + FS+YG++  IS+    H    +G+ FV F  ++     +
Sbjct: 1  SRVFVGNLNTDKVSKEDLEEIFSKYGKILGISL----H----KGYGFVQFDNEEDARAAV 52

Query: 76 AAGD-HYIGNKKID 88
          A  +   I  +K+D
Sbjct: 53 AGENGREIAGQKLD 66

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

 Score = 39.3 bits (92), Expect = 1e-04
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +I+VG L  +I E+D+ D F +YG I        K++     F F+ F+D   AE
Sbjct: 1   RIYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRDAE 52

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

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

 Score = 39.2 bits (91), Expect = 1e-04
 Identities = 18/57 (31%), Positives = 32/57 (56%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           ++V GL   +S++++   FSQYG I   +   D+   + +G  FI FD +  AE+ +
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|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen D (HuD)

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 20/47 (42%), Positives = 27/47 (57%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F
Sbjct: 5  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 51

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-QKAVDD 73
          ++ KLFV GL  +  ++E+   F ++G V+S+ +  +  +G+ +G A+V +     A   
Sbjct: 1  EKHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTN-RSGKPKGLAYVEYENESSASQA 59

Query: 74 LLAAGDHYIGNKKI 87
          +L      I  K I
Sbjct: 60 VLKMDGTEIKEKTI 73

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

 Score = 39.1 bits (92), Expect = 1e-04
 Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 9/65 (13%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQ---SRGFAFVTF----TTQK 69
          LFV  L+  T E+ +  +F + G V S++I  K DP       S G+ FV F      QK
Sbjct: 3  LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 70 AVDDL 74
          A+  L
Sbjct: 63 ALKRL 67

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

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 20/47 (42%), Positives = 27/47 (57%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F
Sbjct: 8  LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 54

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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 14/57 (24%), Positives = 26/57 (45%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           +++G L   + E  +   F++ G +T  +   +K      G+ F+ F     AEQ L
Sbjct: 2   LWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQAL 58

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
           IFV G+  E  E+DV D F+++G I       D+     KG+  I ++ +  A+  +   
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 162 PKQVICGKEVDV 173
             + + G+ + V
Sbjct: 69  NGKELLGQTISV 80

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

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          LFVG L   T E E+  +F + G +  + +     +G+ +GFAFV F   +   + L  G
Sbjct: 1  LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNAL-KG 59

Query: 79 DHYIGNK 85
           H  G  
Sbjct: 60 KHLNGRA 66

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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           ++VG L  +I E++V D F +YG I +      K      G+ FI F+D   AE
Sbjct: 2   VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARDAE 52

This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. . Length = 72

>gnl|CDD|240794 cd12348, RRM1_SHARP, RNA recognition motif 1 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 23/58 (39%), Positives = 31/58 (53%), Gaps = 9/58 (15%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISI--KNDPHTGQSRGFAFVTFT----TQKA 70
          L+VG L  N  E+ I+++F +YG VES+ I  K     G +   AFV F      QKA
Sbjct: 2  LWVGNLPENVREERISEHFKRYGRVESVKILPKRGSDGGVA---AFVDFVDIKSAQKA 56

This subfamily corresponds to the RRM1 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 = 75

>gnl|CDD|240932 cd12488, RRM2_hnRNPR, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 20/63 (31%), Positives = 36/63 (57%), Gaps = 12/63 (19%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE-------FQQPFDKSKNMKKGFCFISFDDQNV 154
           ++FVG +    +++++ + FS+   +TE       + QP DK KN  +GFCF+ ++D   
Sbjct: 4   RLFVGSIPKNKTKENILEEFSK---VTEGLVDVILYHQPDDKKKN--RGFCFLEYEDHKS 58

Query: 155 AEQ 157
           A Q
Sbjct: 59  AAQ 61

This subgroup corresponds to the RRM2 of hnRNP R, a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. It contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif. hnRNP R binds RNA through its RRM domains. . Length = 85

>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 = 38.9 bits (91), Expect = 2e-04
 Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 9/84 (10%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           R + VGG+  +  E ++ ++FS  GEV  + +  D     S  FAFV F   ++    L 
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQ--HSARFAFVEFADAESALSALN 58

Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK 100
                +G   +       RV+P K
Sbjct: 59  LSGTLLGGHPL-------RVSPSK 75

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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 15/84 (17%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITE-------FQQPFDKSKNMKKGFCFISFDDQ 152
            C++FVGG+    +++++ + FS+   +TE       ++ P DK+KN  +GF F+ ++  
Sbjct: 1   NCRLFVGGIPKTKTKEEILEEFSK---VTEGVVDVIVYRSPDDKNKN--RGFAFVEYESH 55

Query: 153 NVAEQV---LANPKQVICGKEVDV 173
             A      L   + ++ G EV V
Sbjct: 56  RAAAMARRKLVPGRILLWGHEVAV 79

This subfamily corresponds to the RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

>gnl|CDD|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 22/84 (26%), Positives = 43/84 (51%), Gaps = 4/84 (4%)

Query: 94  KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           ++  P    +F+  L  E  +QD+   F  +G++   +   DK  N+ K F F+S+D+  
Sbjct: 1   QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 60

Query: 154 VAEQVLANPKQVICGKEVDVKRVK 177
            A+  +    Q + G ++ +KR+K
Sbjct: 61  SAQAAI----QAMNGFQIGMKRLK 80

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 36/59 (61%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +FVG L+ EI+ +D++  F+ +G I++ +   D +    KG+ F+SF ++  AE  + +
Sbjct: 4   VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

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

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +I+VG L +++ E+D+ D F +YG I + +    K++     F F+ F+D   AE
Sbjct: 1   RIYVGNLPSDVREKDLEDLFYKYGRIRDIEL---KNRRGLVPFAFVRFEDPRDAE 52

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

>gnl|CDD|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 = 2e-04
 Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          + + GL  +  E++I D+FS      + I I  D   G+  G A+V F + +     L  
Sbjct: 2  VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALRK 60

Query: 78 GDHYIGNKKI 87
           ++ +G + I
Sbjct: 61 HNNKMGGRYI 70

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 14/51 (27%), Positives = 23/51 (45%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
            +I V G     SE  +++YFS +G I E +   D +  +  G   I +  
Sbjct: 3   VEIVVWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYYG 53

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p 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 = 110

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 18/79 (22%), Positives = 31/79 (39%), Gaps = 4/79 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
           ++V  L    + + ++  FS+YG++     P  K     KGF FI F+    A++     
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEEAQKACKHL 61

Query: 161 --NPKQVICGKEVDVKRVK 177
              P+          K V 
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|240718 cd12272, RRM2_PHIP1, RNA recognition motif 2 in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 1/68 (1%)

Query: 20 FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
          ++G L  +  E ++ ++F    E+ S+ +  D  TG+ +GF  V F  ++++D  L    
Sbjct: 3  YIGNLAWDITEDDVREFFKG-CEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLDG 61

Query: 80 HYIGNKKI 87
            +  + I
Sbjct: 62 TVLCGRPI 69

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

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D  +LFVG L  +  + E+ ++F QYG V  + I +    G+   F FV F   + V  +
Sbjct: 2  DSHQLFVGNLPHDVDKSELKEFFQQYGNVVELRINSG---GKLPNFGFVVFDDSEPVQKI 58

Query: 75 LA 76
          L+
Sbjct: 59 LS 60

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|240748 cd12302, RRM_scSet1p_like, RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins

 Score = 38.9 bits (91), Expect = 3e-04
 Identities = 16/46 (34%), Positives = 23/46 (50%)

Query: 21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          V G   +T E  I +YFS +GE+  I   NDP+T    G   + + 
Sbjct: 7  VWGFQPSTSEDIIKNYFSSFGEIAEIRNFNDPNTAVPLGIYLIKYY 52

This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p 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 = 110

>gnl|CDD|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 4/61 (6%)

Query: 27 NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK 86
           T EK+I+D+FS  G++ ++ + ND  +      A +TF    A    L   +  +G K 
Sbjct: 9  KTTEKQISDFFSFCGKISNLDLTNDGESQT----ATITFEKPSAAKTALLLDNALLGGKV 64

Query: 87 I 87
          I
Sbjct: 65 I 65

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 24/80 (30%), Positives = 41/80 (51%), Gaps = 10/80 (12%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           + ++FVG L  +I+E+++R  F +YG   E         +  KGF FI  + + +AE   
Sbjct: 1   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEI------FIHKDKGFGFIRLETRTLAEIAK 54

Query: 160 ANPKQVIC-GKEVDVKRVKF 178
           A    +   GK++   RV+F
Sbjct: 55  AELDNMPLRGKQL---RVRF 71

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|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          R LF+G L  N  E E+   F +YG +E + IK  P  GQ   +AF+ F
Sbjct: 9  RNLFIGNLDHNVSEVELRRAFDKYGIIEEVVIKR-PARGQGGAYAFLKF 56

This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B 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. RBM15B belongs 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 = 85

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

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 12/75 (16%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++F+G L     E+DV  +F  YG I +         ++K+GF F+ FDD   A+  +  
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDI--------DLKRGFGFVEFDDPRDADDAVYE 52

Query: 162 PKQVICGKEVDVKRV 176
               + GKE+  +RV
Sbjct: 53  ----LDGKELCNERV 63

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

 Score = 38.4 bits (90), Expect = 3e-04
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 12/90 (13%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
           R++    L+ N  E  + D   +YGEVE + I   P T +  G A V F + K+    +
Sbjct: 2  PREVTFSNLNDNIDEGFLKDMCKKYGEVEEVKIYFHPKTNKHLGLARVVFDSVKSAKRCV 61

Query: 76 AAGDHY--------IGNKKIDPK-RVTKRV 96
             +          I    +DPK  + KR+
Sbjct: 62 ---EKLNQTSVMGKIIKVFLDPKGEIRKRL 88

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

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

 Score = 40.9 bits (96), Expect = 4e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)

Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
           L+V  L     ++++ + FS+ GE+ S  +  D   G SRGF FV F+  +  +  +
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAV 343

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

 Score = 37.9 bits (89), Expect = 4e-04
 Identities = 21/77 (27%), Positives = 43/77 (55%), Gaps = 11/77 (14%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD---KSKNMKKGFCFISFDDQNVAEQVL 159
           ++V  L  ++ ++ +++ F +YG IT  +   D   KS    KGF F++F++   A++ +
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKS----KGFGFVNFENHEAAQKAV 59

Query: 160 ANPKQVICGKEVDVKRV 176
                 + GKEV+ K++
Sbjct: 60  EE----LNGKEVNGKKL 72

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 37.9 bits (89), Expect = 4e-04
 Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 16/82 (19%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPF-------DKSKNMKKGFCFISFDDQNVA 155
           + + GL    +E+D+    S   S+     P        DK     +GF F+ F     A
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASV-----PIKDVRLIRDKLTGTSRGFAFVEFPSLEDA 59

Query: 156 EQVL----ANPKQVICGKEVDV 173
            Q +         VI G+ V V
Sbjct: 60  TQWMDALNNLDPFVIDGRVVRV 81

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

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

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 16/54 (29%), Positives = 28/54 (51%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           I++G L     E++++ YFSQ+G++   +    K     K + FI F +  VA 
Sbjct: 2   IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAA 55

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

 Score = 38.0 bits (88), Expect = 4e-04
 Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 1/56 (1%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          +R LFVG L     E+ I + F Q G V  + I  D   G+ + FAFV F  + +V
Sbjct: 1  DRTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKD-KDGKPKQFAFVNFKHEVSV 55

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

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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          R LF+G L + T   ++ + F ++GE+  I IK          +AF+ +    +V   + 
Sbjct: 3  RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKKQGGNPA---YAFIQYADIASVVKAMR 59

Query: 77 AGD-HYIGNKKI 87
            D  Y+GN ++
Sbjct: 60 KMDGEYLGNNRV 71

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

 Score = 38.0 bits (89), Expect = 4e-04
 Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 5/61 (8%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ----KAVDD 73
           L+V  L  +  ++ + + FS +G + S  +  D   G+S+GF FV F++     KAV +
Sbjct: 3  NLYVKNLDDSIDDERLREEFSPFGTITSAKVMTDE-KGRSKGFGFVCFSSPEEATKAVTE 61

Query: 74 L 74
          +
Sbjct: 62 M 62

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

 Score = 37.6 bits (88), Expect = 4e-04
 Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 3/49 (6%)

Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           E+SE D  D    +G  +  +      +   K   F +FD++  A Q L
Sbjct: 10  ELSEDDKEDLLKHFG-ASSVR--VMSRRGKLKNTAFATFDNEQAASQAL 55

This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. . Length = 73

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

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 7/63 (11%)

Query: 114 EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA--NPKQVICGKEV 171
           E+DV +YF Q+G + + + P+ +    K+ F F++F++    +++L+  NP   ICG  V
Sbjct: 13  EEDVSEYFGQFGPVLDVRIPYQQ----KRMFGFVTFENAETVKRILSKGNP-HFICGSRV 67

Query: 172 DVK 174
            VK
Sbjct: 68  RVK 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|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 14/73 (19%)

Query: 34  NDY---FSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK 90
           ND    FS+YG+V  ++I  D  T +S+G AF+ F  ++         D +   K ++ K
Sbjct: 16  NDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDRE---------DAHKCVKALNNK 66

Query: 91  RVTKRVNPLKCKI 103
            +  R   LKC I
Sbjct: 67  ELFGRT--LKCSI 77

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

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 16/54 (29%), Positives = 26/54 (48%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          L+V GL   T   ++   FS+YG+V    I  +  +  +R F FVT  + +   
Sbjct: 2  LWVSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAA 55

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

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 4/75 (5%)

Query: 105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ 164
           V GL+   +E+D+R+ FS+YG +      +D+     +GF F+ F+  + +++ + +   
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHAN- 62

Query: 165 VICGKEVDVKRVKFN 179
              G E+D +R++ +
Sbjct: 63  ---GMELDGRRIRVD 74

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

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

 Score = 37.6 bits (87), Expect = 6e-04
 Identities = 16/62 (25%), Positives = 32/62 (51%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P   ++FVG L  +I E +++++F  +G++ E +            F F+ FDD    ++
Sbjct: 3   PDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQR 62

Query: 158 VL 159
           +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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQ-SRGFAFVTFTTQKA 70
          +LFVGG+ +   ++EI + FS+  E V  + +   P     +RGFAFV + + +A
Sbjct: 3  RLFVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRA 57

This subfamily corresponds to the RRM2 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 bind 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), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. . Length = 82

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          +++VG L  +  EK++ D F +YG +  I +KN         FAFV F   +  +D
Sbjct: 1  RIYVGNLPSDVREKDLEDLFYKYGRIRDIELKNR---RGLVPFAFVRFEDPRDAED 53

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

>gnl|CDD|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 38.4 bits (89), Expect = 6e-04
 Identities = 25/109 (22%), Positives = 44/109 (40%), Gaps = 29/109 (26%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSIT------EFQQPFDKSK---------------- 138
            K+FVGGL  +I+E D+ + F ++GS+        ++   D                   
Sbjct: 1   RKVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60

Query: 139 NMKKGFCFISFDDQ-NVAEQVLA------NPKQVICGKEVDVKRVKFNP 180
              KG+ F+ F+ + +V   +LA         ++      D KRV+  P
Sbjct: 61  QHPKGYVFLLFEKERSVRSLLLACSEEEGGLFRITSSSSTDSKRVQIRP 109

This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 112

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

 Score = 37.5 bits (87), Expect = 6e-04
 Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          ++VG +   +  +E+  +FS  G +  ++I  D  +G  +G+A++ F T+ +V+  +A  
Sbjct: 2  VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAAVALD 61

Query: 79 DHYIGNK--KIDPKR 91
          +     +  K+ PKR
Sbjct: 62 ESSFRGRVIKVLPKR 76

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

 Score = 37.7 bits (88), Expect = 6e-04
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L+V  +   T   ++   F +YG +  + I  D +T + RGFA+V F   +  +D L   
Sbjct: 3  LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 79 DH 80
          D 
Sbjct: 63 DR 64

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|240814 cd12368, RRM3_RBM45, RNA recognition motif 3 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 16/55 (29%), Positives = 35/55 (63%), Gaps = 1/55 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          ++LFV  + ++  +++++  F     +E   +K DP+TG+S+GFA+VT++   + 
Sbjct: 1  QRLFVV-VSKSVTQEQLHRLFDIIPGLEYCDLKRDPYTGKSKGFAYVTYSNPASA 54

This subfamily corresponds to the RRM3 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 = 75

>gnl|CDD|240933 cd12489, RRM2_hnRNPQ, RNA recognition motif 2 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 37.8 bits (87), Expect = 6e-04
 Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 6/60 (10%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQ----YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           ++FVG +    +++ + + FS+       +  + QP DK KN  +GFCF+ ++D   A Q
Sbjct: 4   RLFVGSIPKSKTKEQIVEEFSKVTEGLTDVILYHQPDDKKKN--RGFCFLEYEDHKTAAQ 61

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 85

>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 = 6e-04
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 1/51 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          +FV  L  +   +++ D F + G V    +K D   G+S+GF  V F + +
Sbjct: 1  IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDN-DGRSKGFGTVLFESPE 50

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

 Score = 36.8 bits (86), Expect = 8e-04
 Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 14/77 (18%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE----FQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           K++VG L    +++++ D F +YG +         P         GF F+ F+D   AE 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPP---------GFAFVEFEDPRDAED 51

Query: 158 -VLANPKQVICGKEVDV 173
            V A   + ICG  V V
Sbjct: 52  AVRALDGRRICGNRVRV 68

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 36.3 bits (85), Expect = 8e-04
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 6/56 (10%)

Query: 33 INDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKI 87
          +   FS +G VE I +          GFAFV F+T++A +  +   +    G + +
Sbjct: 1  LYKLFSPFGNVEKIKLLKK-----KPGFAFVEFSTEEAAEKAVQYLNGVLFGGRPL 51

(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|241167 cd12723, RRM1_CPEB1, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 5/74 (6%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP---FDKSKNMKKGFCFISFD-DQNVAE 156
           CK+F+GG+  +I+E  + + F  +GS++  + P       ++  KG+ ++ F+ +++V  
Sbjct: 3   CKVFLGGVPWDITEAGLINTFKPFGSVS-VEWPGKDGKHPRHPPKGYVYLIFESEKSVKA 61

Query: 157 QVLANPKQVICGKE 170
            + A     + G E
Sbjct: 62  LLQACTHDFLNGGE 75

This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins. . Length = 100

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

 Score = 37.4 bits (86), Expect = 8e-04
 Identities = 25/81 (30%), Positives = 33/81 (40%), Gaps = 21/81 (25%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L V  L +N  ++E    F   GE+ES  +  D  TGQS G+ FV +             
Sbjct: 5  LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY------------- 51

Query: 79 DHYIGNKKIDPKRVTKRVNPL 99
                  IDPK   K +N L
Sbjct: 52 --------IDPKDAEKAINTL 64

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

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

 Score = 36.9 bits (86), Expect = 9e-04
 Identities = 17/54 (31%), Positives = 28/54 (51%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           ++V GL   +++Q++   FS YG I   +   D    + +G  FI FD +  AE
Sbjct: 3   LYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAE 56

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

 Score = 36.9 bits (85), Expect = 9e-04
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 11/78 (14%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-- 159
           ++++G L+ +  E+DV  +F  YG I E         ++K G+ F+ FDD   A+  +  
Sbjct: 1   RVYIGRLSYQARERDVERFFKGYGKILEV--------DLKNGYGFVEFDDLRDADDAVYE 52

Query: 160 ANPKQVICGKEVDVKRVK 177
            N K  +CG+ V V+  +
Sbjct: 53  LNGKD-LCGERVIVEHAR 69

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

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 15/64 (23%), Positives = 31/64 (48%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +F+  L  + +E+++++ FSQ+G +   +   DK     KG  F+ F  +  A++ L 
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLE 60

Query: 161 NPKQ 164
               
Sbjct: 61  AADN 64

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ-KAVDDLLAA 77
          +FVG L      ++I   F+ +G++    +  D  TG+S+G+ FV+F  +  A + ++  
Sbjct: 4  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 63

Query: 78 GDHYIGNKKIDPKRVTK 94
          G  ++G ++I     T+
Sbjct: 64 GGQWLGGRQIRTNWATR 80

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

 Score = 36.4 bits (84), Expect = 0.001
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 6/55 (10%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          +LFVG L  +  E+E+   F +YG+   I I  D      +GF F+   T+   +
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|241120 cd12676, RRM3_Nop4p, RNA recognition motif 3 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 37.6 bits (87), Expect = 0.001
 Identities = 19/61 (31%), Positives = 29/61 (47%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +FV  L  + +E+ +  +FS++GS+       DKS    KG  F+ F DQ      L N 
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 163 K 163
            
Sbjct: 64  P 64

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|240916 cd12472, RRM1_RBMS3, RNA recognition motif 1 found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3)

 Score = 37.1 bits (85), Expect = 0.001
 Identities = 19/64 (29%), Positives = 33/64 (51%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  +++ GL    ++QD+      YG I   +   DK+ N  KG+ F+ FD    A++ +
Sbjct: 4   KTNLYIRGLPPGTTDQDLIKLCQPYGKIVSTKAILDKNTNQCKGYGFVDFDSPAAAQKAV 63

Query: 160 ANPK 163
           A+ K
Sbjct: 64  ASLK 67

This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. . Length = 80

>gnl|CDD|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 = 36.5 bits (85), Expect = 0.001
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           +FVGGL   ++E ++R  F  +G I   + P        KG  F+ F  +  AE  + 
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPG------KGCGFVQFVHRAAAEAAIQ 55

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|240711 cd12265, RRM_SLT11, RNA recognition motif of pre-mRNA-splicing factor SLT11 and similar proteins

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 6/54 (11%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          +  F+ G+  +  E +I DYF Q+G+ +S+ + +           FV F T++A
Sbjct: 3  KSFFLFGVEDDLPEYKIRDYFEQFGKSKSVIVNHRAK------CGFVRFETREA 50

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 19/51 (37%), Positives = 25/51 (49%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          L V  L +N  + E+   FS  GEVES  +  D   G S G+ FV +   K
Sbjct: 4  LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAK 54

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|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C ++ GG+T+ ++EQ +R  FS +G I E +   D      KG+ F+ F+    A   + 
Sbjct: 1   CTVYCGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIV 54

Query: 161 N 161
           +
Sbjct: 55  S 55

This subgroup corresponds to the RRM3 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 = 74

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 9/64 (14%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEF--QQPF------DKSKNMKKGFCFISFDDQNV 154
           I++ GL  +++E  + + F   G I       P       DK     KG   +++DD + 
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKETE-PKGEATVTYDDPSA 59

Query: 155 AEQV 158
           A+  
Sbjct: 60  AQAA 63

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

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

 Score = 36.9 bits (85), Expect = 0.001
 Identities = 17/64 (26%), Positives = 36/64 (56%), Gaps = 1/64 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          ++F+G L R+  E E+     + G++  + +  D   G +RG+AFVTF+ ++   + +  
Sbjct: 3  EIFIGKLPRDLFEDELIPLCEKIGKIYEMRMMMD-FNGNNRGYAFVTFSNKQEAKNAIKQ 61

Query: 78 GDHY 81
           ++Y
Sbjct: 62 LNNY 65

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
          +L V  LH +  E+++ + F + GEV+ + I  D  +G+S G A V F      ++A+ 
Sbjct: 2  RLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          +F+  L ++   K + D FS +G + S  +  D   G S+G+ FV F T++A  
Sbjct: 5  IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDE-NGGSKGYGFVHFETEEAAV 57

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

>gnl|CDD|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 17/78 (21%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-----------------HTGQSRG 59
          R +FVG L   T +K++   F Q+G +ES+  ++ P                 H  +   
Sbjct: 1  RTVFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNV 60

Query: 60 FAFVTFTTQKAVDDLLAA 77
           A+V F  +++ +  L  
Sbjct: 61 NAYVVFKEEESAEKALKL 78

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 8/66 (12%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG--FAFVTFTTQKAVDDLL 75
          +++VG L  +   K+I D F +YG +  I +KN       RG  FAFV F   +  +D +
Sbjct: 1  RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDLKN------RRGPPFAFVEFEDPRDAEDAV 54

Query: 76 AAGDHY 81
             D Y
Sbjct: 55 YGRDGY 60

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 18/81 (22%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++ V  +     + D+R  F Q+G I + +  F++  +  KGF F++F +   A++    
Sbjct: 2   RLHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS--KGFGFVTFANSADADRA--- 56

Query: 162 PKQVICGKEVDVKRVKFNPET 182
            ++ + G  V+ ++++ N  T
Sbjct: 57  -REKLHGTVVEGRKIEVNNAT 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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 2/75 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          ++VG +      +E+  +F   G V  ++I  D  +G  +GFA++ F+ +++V   LA  
Sbjct: 2  VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 79 DHYIGNK--KIDPKR 91
          +     +  K+ PKR
Sbjct: 62 ESLFRGRQIKVMPKR 76

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

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
          +FV  L    G K++ + F   G+V    IK D   G+SRG   V F  
Sbjct: 1  IFVANLDYKVGWKKLKEVFKLAGKVVRADIKED-KEGKSRGMGVVQFEH 48

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

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

 Score = 36.5 bits (85), Expect = 0.002
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 3/79 (3%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
              +FVG L+ + +E+ +R+ FS+YG I   +   D      KG+ F+ ++ +  A +  
Sbjct: 3   YLTLFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAY 62

Query: 160 -ANPKQVICGKE--VDVKR 175
               K VI G E  VD +R
Sbjct: 63  RDAHKLVIDGSEIFVDFER 81

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 15/58 (25%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K+F+G ++ + +E D+R  FS +G I E  +       + +G  F++F  + +A+  +
Sbjct: 3   KLFIGMVSKKCNENDIRVMFSPFGQIEE-CRILRGPDGLSRGCAFVTFTTRAMAQTAI 59

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           ++V GL   ++++++   FSQYG I   +   D+   + +G  FI FD +  AE+ +
Sbjct: 3   LYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAI 59

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

 Score = 35.9 bits (82), Expect = 0.002
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           ++V GL   ++++++   FSQYG I   +   D+   + +G  FI FD +  AE+ +
Sbjct: 5   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 61

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 12/76 (15%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          ++F+G L+    EK++  +F  YG +  I +K        RGF FV F   +  DD +  
Sbjct: 1  RVFIGRLNPAAREKDVERFFKGYGRIRDIDLK--------RGFGFVEFDDPRDADDAV-- 50

Query: 78 GDHYIGNKKIDPKRVT 93
            + +  K++  +RVT
Sbjct: 51 --YELDGKELCNERVT 64

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|240890 cd12444, RRM1_CPEBs, RNA recognition motif 1 in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens

 Score = 36.9 bits (85), Expect = 0.002
 Identities = 26/105 (24%), Positives = 41/105 (39%), Gaps = 29/105 (27%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYG--EVE--------------------SISIKNDPHT 54
           RK+FVGGL  +  E +I + F ++G  +V+                    S    N    
Sbjct: 1   RKVFVGGLPWDITEADILNSFRRFGSLQVDWPGKHYECKSDSDPSLCNEKSDGSINGDKG 60

Query: 55  GQSRGFAFVTFTTQKAVDDLLAAGDHYIG-------NKKIDPKRV 92
              +G+ F+ F  +++V  LL A     G       +   D KRV
Sbjct: 61  QHPKGYVFLLFEKERSVRSLLLACSEEEGGLFRITSSSSTDSKRV 105

This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. . Length = 112

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

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 5/50 (10%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQP--FDKSKNMKKGFCFISF 149
           KI V  L  E +++DVR  FS YG +   + P  FD+S    +GF F+ F
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKFDQS---ARGFAFVEF 48

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 6/73 (8%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
           ++VG L   ++E  + + FSQ G I   +   +   +    + F+ + D   A   L   
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGND---PYAFVEYYDHRSAAAALQTM 57

Query: 161 NPKQVICGKEVDV 173
           N +  I G+E+ V
Sbjct: 58  NGRL-ILGQEIKV 69

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

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 36.6 bits (84), Expect = 0.002
 Identities = 18/58 (31%), Positives = 34/58 (58%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           +FVG L+ EI+  D++  F+ +G I++ +   D +    KG+ F+SF ++  AE  + 
Sbjct: 4   VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 61

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|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 10/56 (17%)

Query: 17 RKLFVGGLHRNTGEKEIND----YFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          R L+VGG+   +  K+I +    +F ++G++E I          S+G AFV +  +
Sbjct: 2  RTLYVGGIKAGSALKQIEEILRRHFGEWGDIEDI------RVLPSKGIAFVRYKYR 51

This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. Length = 78

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

 Score = 36.2 bits (83), Expect = 0.002
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 4/65 (6%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQK 69
          + +  L V  L +N  ++E+   F   GE+ES  +  D  TGQS G+ FV +      +K
Sbjct: 2  DSKTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEK 61

Query: 70 AVDDL 74
          A++ L
Sbjct: 62 AINTL 66

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

 Score = 36.1 bits (83), Expect = 0.002
 Identities = 20/78 (25%), Positives = 42/78 (53%), Gaps = 11/78 (14%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL-- 159
           ++++G L+  + E+D++ +F  YG + E         ++K G+ F+ F+D   A+  +  
Sbjct: 1   RVYIGRLSYHVREKDIQRFFGGYGKLLEI--------DLKNGYGFVEFEDSRDADDAVYE 52

Query: 160 ANPKQVICGKEVDVKRVK 177
            N K  +CG+ V V+  +
Sbjct: 53  LNGKD-LCGERVIVEHAR 69

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

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

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSR-GFAFVTFTTQKAVDD 73
          + R ++VG +  +T   E+   F  +GE+E I++    H       + FVT+        
Sbjct: 1  ERRVIYVGKIPIDTTRSELRQRFQPFGEIEEITL----HFRDDGDNYGFVTYRYACDAFR 56

Query: 74 LLAAGDH 80
           +  G+ 
Sbjct: 57 AIEHGND 63

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 11/28 (39%), Positives = 19/28 (67%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE 129
           K+FVG L    + +++R  F +YG++TE
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTE 28

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 10/66 (15%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          KLFVG L   T  +E+   F +YG V E   +KN         + FV    ++  +D + 
Sbjct: 1  KLFVGNLPDATTSEELRALFEKYGTVTECDVVKN---------YGFVHMEEEEDAEDAIK 51

Query: 77 AGDHYI 82
          A + Y 
Sbjct: 52 ALNGYE 57

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|240914 cd12470, RRM1_MSSP1, RNA recognition motif 1 in vertebrate single-stranded DNA-binding protein MSSP-1

 Score = 36.3 bits (83), Expect = 0.002
 Identities = 18/64 (28%), Positives = 32/64 (50%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  +++ GL    ++QD+      YG I   +   DK+ N  KG+ F+ FD    A++ +
Sbjct: 7   KTNLYIRGLPPNTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPAAAQKAV 66

Query: 160 ANPK 163
           +  K
Sbjct: 67  SALK 70

This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. . Length = 86

>gnl|CDD|240715 cd12269, RRM_Vip1_like, RNA recognition motif in a group of uncharacterized plant proteins similar to fission yeast Vip1

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 4/59 (6%)

Query: 21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD-LLAAG 78
          V  L     E++I D+FS  G++E + I+     G+    A+VTF   +A +  LL +G
Sbjct: 3  VTNLSPKATERDIYDFFSFSGDIEYVEIQRS---GEQSQTAYVTFKDPQAQETALLLSG 58

This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 69

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 10/62 (16%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF---CFISFDDQNVAEQVL 159
           +FV  L    +E+++R  FS+       Q  F + K   KG    CF+ F+D + A Q L
Sbjct: 5   LFVANLGPNTTEEELRQLFSR-------QPGFRRLKMHNKGGGPVCFVEFEDVSFATQAL 57

Query: 160 AN 161
            +
Sbjct: 58  NS 59

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          R L+V  L      +E+ D F +YG +  I I N   T   RG AFV +   + + D   
Sbjct: 3  RILYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVY---EDIYDAKN 56

Query: 77 AGDHYIG 83
          A DH  G
Sbjct: 57 ACDHLSG 63

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

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

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 6/58 (10%)

Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI 87
            ++N++FS++G + +I +  +P +      A V F+T +       + +    N+ I
Sbjct: 16 ITKLNEHFSKFGTIVNIQVNYNPES------ALVQFSTSEEAKKAYRSPEAVFNNRFI 67

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

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 35.6 bits (83), Expect = 0.002
 Identities = 12/55 (21%), Positives = 26/55 (47%), Gaps = 6/55 (10%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           ++VGGL    S  ++   F ++G+I      +D  +N    + +I ++    A+ 
Sbjct: 1   LWVGGLGPWTSLAELEREFDRFGAIRRID--YDPGRN----YAYIEYESIEAAQA 49

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

 Score = 35.9 bits (82), Expect = 0.003
 Identities = 17/57 (29%), Positives = 32/57 (56%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           ++V GL   ++++++   FSQYG I   +   D+   + +G  FI FD +  AE+ +
Sbjct: 8   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAI 64

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|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 = 35.4 bits (82), Expect = 0.003
 Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 2/49 (4%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
           I VGG+   +SE D++++FS  G +T  +   D+  + +  F F+ F D
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSAR--FAFVEFAD 49

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|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 9/61 (14%)

Query: 18 KLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +LF+G L  +   ++++   FS YGE+  I +KN         + FV F + ++  + + 
Sbjct: 1  RLFIGNLPTKRVSKEDLFRIFSTYGELAQIVLKN--------AYGFVQFDSPESCANAIN 52

Query: 77 A 77
           
Sbjct: 53 C 53

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240788 cd12342, RRM_Nab3p, RNA recognition motif in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 9/50 (18%)

Query: 102 KIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           ++F+G L T+ +S++D+   FS YG + +          +K  + F+ FD
Sbjct: 1   RLFIGNLPTKRVSKEDLFRIFSTYGELAQI--------VLKNAYGFVQFD 42

This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. . Length = 71

>gnl|CDD|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 16/53 (30%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
           ++FVG + R+  E E+   F + G++    +  +  +G++RG+AFV +TT++
Sbjct: 2  CEVFVGKIPRDMYEDELVPLFERAGKIYEFRLMME-FSGENRGYAFVMYTTKE 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|241041 cd12597, RRM1_SRSF1, RNA recognition motif 1 in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins

 Score = 35.1 bits (81), Expect = 0.004
 Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 6/56 (10%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG-FCFISFDDQNVAE 156
           +I+VG L  +I  +D+ D F +YG+I +        KN +   F F+ F+D   AE
Sbjct: 1   RIYVGNLPPDIRTKDIEDLFYKYGAIRDIDL-----KNRRGPPFAFVEFEDPRDAE 51

This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. . Length = 73

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 1/77 (1%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA- 77
          +FVG L       +I   F+ +G +    +  D  TG+S+G+ FV+F  +   ++ +   
Sbjct: 4  VFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 63

Query: 78 GDHYIGNKKIDPKRVTK 94
          G  ++G ++I     T+
Sbjct: 64 GGQWLGGRQIRTNWATR 80

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

 Score = 35.1 bits (80), Expect = 0.004
 Identities = 19/59 (32%), Positives = 28/59 (47%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          + +  L V  L +N  ++E    F   GE+ES  +  D  TGQS G+ FV +      D
Sbjct: 1  DSKTNLIVNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDAD 59

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	275
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0148|consensus	321		100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.98
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.98
KOG0117|consensus	506		99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
KOG0144|consensus	510		99.97
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG4205|consensus	311		99.96
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.96
KOG0145|consensus	360		99.96
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.95
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.95
KOG0131|consensus	203		99.95
KOG0127|consensus	678		99.94
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.94
KOG0109|consensus	346		99.93
KOG0124|consensus	544		99.93
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.93
KOG0127|consensus	678		99.93
KOG0145|consensus	360		99.91
KOG4211|consensus	510		99.91
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.9
KOG0123|consensus	369		99.9
KOG0147|consensus	549		99.89
KOG0148|consensus	321		99.89
KOG0110|consensus	725		99.88
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.86
KOG0146|consensus	371		99.86
KOG0144|consensus	510		99.85
KOG0105|consensus	241		99.85
KOG0123|consensus	369		99.83
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.78
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.77
KOG4212|consensus	608		99.73
KOG4211|consensus	510		99.71
KOG0149|consensus	247		99.71
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.71
KOG0149|consensus	247		99.69
KOG4206|consensus	221		99.66
KOG0110|consensus	725		99.65
KOG0106|consensus	216		99.64
KOG0122|consensus	270		99.64
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.63
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.63
KOG0147|consensus	549		99.62
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.6
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.6
KOG0113|consensus	335		99.59
PLN03120	260	nucleic acid binding protein; Provisional	99.59
KOG0122|consensus	270		99.59
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.58
KOG1548|consensus	382		99.57
KOG0125|consensus	376		99.56
KOG0121|consensus	153		99.56
KOG0125|consensus	376		99.56
KOG0121|consensus	153		99.56
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.55
KOG1457|consensus	284		99.54
KOG1365|consensus	508		99.54
KOG0107|consensus	195		99.54
PLN03121	243	nucleic acid binding protein; Provisional	99.53
KOG4207|consensus	256		99.53
PLN03120	260	nucleic acid binding protein; Provisional	99.52
KOG0105|consensus	241		99.49
KOG0129|consensus	520		99.49
KOG0130|consensus	170		99.48
KOG0113|consensus	335		99.47
KOG0107|consensus	195		99.47
KOG4212|consensus	608		99.45
smart00362	72	RRM_2 RNA recognition motif.	99.45
KOG4207|consensus	256		99.45
KOG0124|consensus	544		99.45
KOG0111|consensus	298		99.44
KOG0120|consensus	500		99.44
KOG1190|consensus	492		99.42
PLN03121	243	nucleic acid binding protein; Provisional	99.41
KOG0126|consensus	219		99.41
smart00360	71	RRM RNA recognition motif.	99.41
KOG0117|consensus	506		99.41
smart00362	72	RRM_2 RNA recognition motif.	99.39
KOG1190|consensus	492		99.39
KOG0126|consensus	219		99.39
KOG0130|consensus	170		99.39
smart00360	71	RRM RNA recognition motif.	99.38
PLN03213	759	repressor of silencing 3; Provisional	99.38
KOG0131|consensus	203		99.38
KOG0120|consensus	500		99.38
KOG0114|consensus	124		99.38
PLN03213	759	repressor of silencing 3; Provisional	99.37
KOG1456|consensus	494		99.36
KOG0114|consensus	124		99.35
KOG0108|consensus	435		99.35
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.34
KOG0116|consensus	419		99.33
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.3
KOG0415|consensus	479		99.28
KOG4210|consensus	285		99.28
KOG0111|consensus	298		99.28
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.27
KOG0108|consensus	435		99.26
KOG0128|consensus	881		99.24
KOG4205|consensus	311		99.24
KOG0415|consensus	479		99.22
smart00361	70	RRM_1 RNA recognition motif.	99.21
KOG0132|consensus	894		99.17
smart00361	70	RRM_1 RNA recognition motif.	99.17
KOG0109|consensus	346		99.14
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.14
KOG4454|consensus	267		99.1
KOG1365|consensus	508		99.09
KOG0153|consensus	377		99.07
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.06
KOG0226|consensus	290		99.05
KOG0153|consensus	377		99.05
KOG0112|consensus	975		98.97
KOG0132|consensus	894		98.95
KOG4208|consensus	214		98.93
KOG0146|consensus	371		98.93
KOG4661|consensus	940		98.85
KOG4208|consensus	214		98.84
KOG0116|consensus	419		98.81
KOG1456|consensus	494		98.81
KOG4661|consensus	940		98.78
KOG4307|consensus	944		98.73
KOG0533|consensus	243		98.7
KOG2193|consensus	584		98.66
KOG4209|consensus	231		98.66
KOG4676|consensus	479		98.66
KOG4206|consensus	221		98.65
KOG4209|consensus	231		98.64
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.61
KOG0226|consensus	290		98.61
KOG0533|consensus	243		98.57
KOG4307|consensus	944		98.55
KOG4660|consensus	549		98.55
KOG0106|consensus	216		98.54
KOG1995|consensus	351		98.47
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.35
KOG4454|consensus	267		98.34
KOG1457|consensus	284		98.32
KOG0128|consensus	881		98.31
KOG1548|consensus	382		98.3
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.23
KOG1995|consensus	351		98.22
KOG4660|consensus	549		98.19
KOG0151|consensus	877		98.12
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.02
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.97
KOG0151|consensus	877		97.97
KOG4849|consensus	498		97.95
KOG4210|consensus	285		97.91
KOG0129|consensus	520		97.89
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.87
KOG4849|consensus	498		97.84
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.74
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.63
KOG0921|consensus	1282		97.62
KOG1855|consensus	484		97.57
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.53
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.51
KOG1855|consensus	484		97.27
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.11
KOG2314|consensus	698		97.1
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.05
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.0
KOG2314|consensus	698		96.94
COG5175	480	MOT2 Transcriptional repressor [Transcription]	96.93
KOG4676|consensus	479		96.83
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.78
KOG0115|consensus	275		96.74
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.7
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.56
KOG2202|consensus	260		96.49
KOG3152|consensus	278		96.47
KOG2135|consensus	526		96.31
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	96.26
KOG0115|consensus	275		96.11
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	96.1
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.08
KOG2591|consensus	684		95.96
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.81
KOG1996|consensus	378		95.69
KOG3152|consensus	278		95.52
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.52
KOG2202|consensus	260		95.35
KOG1996|consensus	378		95.24
KOG2591|consensus	684		95.16
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.88
KOG2193|consensus	584		94.82
KOG2416|consensus	718		94.45
KOG0112|consensus	975		94.39
KOG0804|consensus	493		94.31
KOG2135|consensus	526		94.25
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	93.92
KOG2416|consensus	718		93.91
KOG4285|consensus	350		93.88
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	93.88
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.09
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	92.27
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	90.53
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	90.18
KOG4285|consensus	350		90.05
KOG2068|consensus	327		89.92
KOG2068|consensus	327		89.56
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	88.53
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	87.85
KOG4410|consensus	396		87.85
KOG4574|consensus	1007		87.69
KOG4483|consensus	528		87.52
KOG2253|consensus	668		86.48
KOG2253|consensus	668		86.1
KOG4574|consensus	1007		84.47
KOG2318|consensus	650		83.88
KOG4213|consensus	205		83.85
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	81.26

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=3.1e-38  Score=275.75  Aligned_cols=172  Identities=20%  Similarity=0.349  Sum_probs=154.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      .+....++|||++||+++|+++|+++|++||+|++|+|+.++.|++++|||||+|.++++|++||+. ++..+.+++|.|
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            3456788999999999999999999999999999999999999999999999999999999999975 677999999999


Q ss_pred             cccccccC-CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeC
Q psy1314          90 KRVTKRVN-PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVIC  167 (275)
Q Consensus        90 ~~~~~~~~-~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~  167 (275)
                      .++.+... ....+|||+|||+.+|+++|+++|++||+|+.|+|+.++.+++++|||||+|++.++|++||+.++ ..+.
T Consensus       182 ~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~  261 (346)
T TIGR01659       182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPE  261 (346)
T ss_pred             ecccccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccC
Confidence            98765432 345789999999999999999999999999999999999999999999999999999999999985 6665


Q ss_pred             C--eEEEEEEeeeCCCC
Q psy1314         168 G--KEVDVKRVKFNPET  182 (275)
Q Consensus       168 g--~~i~v~~~~~~~~~  182 (275)
                      +  ++|+|.+++.....
T Consensus       262 g~~~~l~V~~a~~~~~~  278 (346)
T TIGR01659       262 GGSQPLTVRLAEEHGKA  278 (346)
T ss_pred             CCceeEEEEECCccccc
Confidence            5  68888888765443

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

>KOG0148|consensus

Probab=100.00  E-value=2.3e-32  Score=220.62  Aligned_cols=171  Identities=23%  Similarity=0.518  Sum_probs=154.3

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCe
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNK   85 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~   85 (275)
                      ..++++......|||+.|+++++-++|++.|.+||+|.+++|++|..|++||||+||.|.+.++|++||.. ++++|..|
T Consensus        53 nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R  132 (321)
T KOG0148|consen   53 NQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRR  132 (321)
T ss_pred             cCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccc
Confidence            33455556677899999999999999999999999999999999999999999999999999999999985 57899999


Q ss_pred             eecccccccccC-----------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEE
Q psy1314          86 KIDPKRVTKRVN-----------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS  148 (275)
Q Consensus        86 ~i~v~~~~~~~~-----------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~  148 (275)
                      .|+..|+..+..                 ..+++|||+||+..+++++|++.|++||+|.+|+|.++      +||+||.
T Consensus       133 ~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVr  206 (321)
T KOG0148|consen  133 TIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVR  206 (321)
T ss_pred             eeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEE
Confidence            999999876642                 34589999999999999999999999999999999987      7899999


Q ss_pred             ECCHHHHHHHHhcC-CceeCCeEEEEEEeeeCCCCC
Q psy1314         149 FDDQNVAEQVLANP-KQVICGKEVDVKRVKFNPETM  183 (275)
Q Consensus       149 f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~~~~~  183 (275)
                      |++.|.|.+||..+ +.+|.|..|+|.|-+......
T Consensus       207 F~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~~  242 (321)
T KOG0148|consen  207 FETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDGI  242 (321)
T ss_pred             ecchhhHHHHHHHhcCceeCceEEEEeccccCCCCC
Confidence            99999999999998 599999999999988766543

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

Probab=100.00  E-value=7.1e-32  Score=247.21  Aligned_cols=164  Identities=21%  Similarity=0.379  Sum_probs=134.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceec-Ceee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIG-NKKI   87 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~-g~~i   87 (275)
                      ...+...++|||+|||++++|++|+++|++||+|.+|+|++| .+++++|||||+|.+.|+|++||+.++ ..+. ++.|
T Consensus        52 ~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l  130 (578)
T TIGR01648        52 GVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLL  130 (578)
T ss_pred             CCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccc
Confidence            444556789999999999999999999999999999999999 889999999999999999999998653 3332 2222


Q ss_pred             ccc-----------------------------------------------------------------------------
Q psy1314          88 DPK-----------------------------------------------------------------------------   90 (275)
Q Consensus        88 ~v~-----------------------------------------------------------------------------   90 (275)
                      .+.                                                                             
T Consensus       131 ~V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~  210 (578)
T TIGR01648       131 GVCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLW  210 (578)
T ss_pred             cccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEec
Confidence            111                                                                             


Q ss_pred             -------ccccccC------CCcceeeecCCCCCCCHHHHHHhcccC--CCeEEEEeccCCCCCCeeeEEEEEECCHHHH
Q psy1314          91 -------RVTKRVN------PLKCKIFVGGLTTEISEQDVRDYFSQY--GSITEFQQPFDKSKNMKKGFCFISFDDQNVA  155 (275)
Q Consensus        91 -------~~~~~~~------~~~~~l~V~~l~~~~~~~~l~~~F~~~--G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a  155 (275)
                             |+.+...      ....+|||+||++++++++|+++|++|  |+|+.|+++        ++||||+|++.++|
T Consensus       211 Gr~I~VdwA~p~~~~d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A  282 (578)
T TIGR01648       211 GHVIAVDWAEPEEEVDEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDA  282 (578)
T ss_pred             CceEEEEeecccccccccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHH
Confidence                   1110000      012569999999999999999999999  999999875        45999999999999


Q ss_pred             HHHHhcCC-ceeCCeEEEEEEeeeCCCC
Q psy1314         156 EQVLANPK-QVICGKEVDVKRVKFNPET  182 (275)
Q Consensus       156 ~~Ai~~~~-~~~~g~~i~v~~~~~~~~~  182 (275)
                      ++||+.++ ..|.|++|+|.+++++...
T Consensus       283 ~kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       283 VKAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             HHHHHHhCCCEECCEEEEEEEccCCCcc
Confidence            99999885 8999999999999876543

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

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

Probab=100.00  E-value=2e-32  Score=251.18  Aligned_cols=170  Identities=23%  Similarity=0.442  Sum_probs=154.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ...++|||+|||+++++++|+++|++||+|.+|.|+.|+.|++++|||||+|.+.++|++||+. ++..+.|+.|.|.+.
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp  184 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  184 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccc
Confidence            4568999999999999999999999999999999999999999999999999999999999975 678999999998765


Q ss_pred             cccc------------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHh
Q psy1314          93 TKRV------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA  160 (275)
Q Consensus        93 ~~~~------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~  160 (275)
                      ....            ....++|||+|||+++++++|+++|+.||.|..|+|.+++.++.++|||||+|.+.++|.+||+
T Consensus       185 ~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~  264 (612)
T TIGR01645       185 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIA  264 (612)
T ss_pred             ccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHH
Confidence            4221            1123789999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC-ceeCCeEEEEEEeeeCCCCC
Q psy1314         161 NPK-QVICGKEVDVKRVKFNPETM  183 (275)
Q Consensus       161 ~~~-~~~~g~~i~v~~~~~~~~~~  183 (275)
                      .++ ..|+|+.|+|.++..+|...
T Consensus       265 amNg~elgGr~LrV~kAi~pP~~~  288 (612)
T TIGR01645       265 SMNLFDLGGQYLRVGKCVTPPDAL  288 (612)
T ss_pred             HhCCCeeCCeEEEEEecCCCcccc
Confidence            996 88999999999999776543

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.98  E-value=2.9e-31  Score=235.45  Aligned_cols=167  Identities=23%  Similarity=0.420  Sum_probs=150.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ++..+|||+|||.++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++||+. ++..+.++.|.|+++
T Consensus         1 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a   80 (352)
T TIGR01661         1 ESKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYA   80 (352)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEee
Confidence            3578999999999999999999999999999999999999999999999999999999999975 577999999999988


Q ss_pred             ccccCC-CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC--
Q psy1314          93 TKRVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICG--  168 (275)
Q Consensus        93 ~~~~~~-~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g--  168 (275)
                      .+.... ..++|||+|||..+++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++||+.++ ..+.+  
T Consensus        81 ~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~  160 (352)
T TIGR01661        81 RPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCT  160 (352)
T ss_pred             cccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCc
Confidence            765443 45789999999999999999999999999999999998888899999999999999999999885 66655  


Q ss_pred             eEEEEEEeeeCC
Q psy1314         169 KEVDVKRVKFNP  180 (275)
Q Consensus       169 ~~i~v~~~~~~~  180 (275)
                      .+|.|.++....
T Consensus       161 ~~i~v~~a~~~~  172 (352)
T TIGR01661       161 EPITVKFANNPS  172 (352)
T ss_pred             eeEEEEECCCCC
Confidence            677887776543

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

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

Probab=99.98  E-value=7.5e-31  Score=240.50  Aligned_cols=168  Identities=27%  Similarity=0.446  Sum_probs=153.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ..+.++|||+|||.++++++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||.+++..+.+++|.|..+
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            44578999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             ccccC-------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHH
Q psy1314          93 TKRVN-------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL  159 (275)
Q Consensus        93 ~~~~~-------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai  159 (275)
                      .....             ...++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|+
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            43211             12478999999999999999999999999999999999998899999999999999999999


Q ss_pred             hcC-CceeCCeEEEEEEeeeCC
Q psy1314         160 ANP-KQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       160 ~~~-~~~~~g~~i~v~~~~~~~  180 (275)
                      +.| +..|.|++|.|.++....
T Consensus       246 ~~l~g~~i~g~~i~v~~a~~~~  267 (457)
T TIGR01622       246 EVMNGFELAGRPIKVGYAQDST  267 (457)
T ss_pred             HhcCCcEECCEEEEEEEccCCC
Confidence            988 489999999999987543

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.

>KOG0117|consensus

Probab=99.97  E-value=3.9e-30  Score=220.50  Aligned_cols=167  Identities=22%  Similarity=0.433  Sum_probs=141.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-Ccee-cCe
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYI-GNK   85 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~-~g~   85 (275)
                      +..+.+..-+.|||+.||.++.|++|.-+|++.|+|-+++|+.|+.+|.+||||||+|++.++|++||+.+ +++| .|+
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK  154 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK  154 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC
Confidence            45555667789999999999999999999999999999999999999999999999999999999999864 4433 344


Q ss_pred             eecccccc------------------------------------------------------------------------
Q psy1314          86 KIDPKRVT------------------------------------------------------------------------   93 (275)
Q Consensus        86 ~i~v~~~~------------------------------------------------------------------------   93 (275)
                      .|.|..+.                                                                        
T Consensus       155 ~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrKl~~g~~k  234 (506)
T KOG0117|consen  155 LLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRKLMPGKIK  234 (506)
T ss_pred             EeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhhccCCcee
Confidence            44332221                                                                        


Q ss_pred             ------------cccCC------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHH
Q psy1314          94 ------------KRVNP------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA  155 (275)
Q Consensus        94 ------------~~~~~------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a  155 (275)
                                  +.+..      .-..|||+||+.++|++.|+++|++||.|+.|+.++|        ||||.|.++++|
T Consensus       235 lwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~da  306 (506)
T KOG0117|consen  235 LWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDA  306 (506)
T ss_pred             ecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHH
Confidence                        11110      1156999999999999999999999999999998865        999999999999


Q ss_pred             HHHHhcCC-ceeCCeEEEEEEeeeCCCC
Q psy1314         156 EQVLANPK-QVICGKEVDVKRVKFNPET  182 (275)
Q Consensus       156 ~~Ai~~~~-~~~~g~~i~v~~~~~~~~~  182 (275)
                      .+|++.++ ++|+|..|+|..|++..+.
T Consensus       307 vkAm~~~ngkeldG~~iEvtLAKP~~k~  334 (506)
T KOG0117|consen  307 VKAMKETNGKELDGSPIEVTLAKPVDKK  334 (506)
T ss_pred             HHHHHHhcCceecCceEEEEecCChhhh
Confidence            99999995 9999999999999987554

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=3.5e-30  Score=228.53  Aligned_cols=168  Identities=20%  Similarity=0.318  Sum_probs=145.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecC--eeeccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGN--KKIDPK   90 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g--~~i~v~   90 (275)
                      ....+|||+|||.++++++|+++|++||+|..+.++.+..++.++|||||+|.+.++|++||+.+ +..+.+  .+|.+.
T Consensus        87 ~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~ai~~l~g~~~~g~~~~i~v~  166 (352)
T TIGR01661        87 IKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVK  166 (352)
T ss_pred             cccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            35678999999999999999999999999999999999888999999999999999999999854 555554  455554


Q ss_pred             cccccc--------------------------------------------------------------------------
Q psy1314          91 RVTKRV--------------------------------------------------------------------------   96 (275)
Q Consensus        91 ~~~~~~--------------------------------------------------------------------------   96 (275)
                      ++....                                                                          
T Consensus       167 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  246 (352)
T TIGR01661       167 FANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLAHQQQQHAVAQQHAAQRASP  246 (352)
T ss_pred             ECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhhhhhhhcccccccccccCCC
Confidence            432111                                                                          


Q ss_pred             -------------------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHH
Q psy1314          97 -------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ  157 (275)
Q Consensus        97 -------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~  157 (275)
                                         .....+|||+|||+.+++++|+++|++||.|..|+|+.|..++.++|||||+|.+.++|.+
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~  326 (352)
T TIGR01661       247 PATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAM  326 (352)
T ss_pred             ccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHH
Confidence                               0001259999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcC-CceeCCeEEEEEEeeeCCC
Q psy1314         158 VLANP-KQVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       158 Ai~~~-~~~~~g~~i~v~~~~~~~~  181 (275)
                      ||+.| +..|.|+.|+|.++..++.
T Consensus       327 Ai~~lnG~~~~gr~i~V~~~~~~~~  351 (352)
T TIGR01661       327 AILSLNGYTLGNRVLQVSFKTNKAY  351 (352)
T ss_pred             HHHHhCCCEECCeEEEEEEccCCCC
Confidence            99988 5899999999999988764

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

>KOG0144|consensus

Probab=99.97  E-value=3.2e-31  Score=226.23  Aligned_cols=170  Identities=28%  Similarity=0.501  Sum_probs=150.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC--CceecC--eeecc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG--DHYIGN--KKIDP   89 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~--~~~~~g--~~i~v   89 (275)
                      .+.-+|||+.||..++|.||+++|++||.|.+|.|++|+.|+.++|||||+|.+.++|.+|+..+  .+.|.|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            55668999999999999999999999999999999999999999999999999999999999864  335554  57778


Q ss_pred             cccccccCCC--cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC--ce
Q psy1314          90 KRVTKRVNPL--KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK--QV  165 (275)
Q Consensus        90 ~~~~~~~~~~--~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~--~~  165 (275)
                      +.+....+..  +++|||+-|+..+||.+|+++|++||.|++|.|++|.. +.+||||||+|.+.|.|..||+.++  ..
T Consensus       112 k~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~-~~sRGcaFV~fstke~A~~Aika~ng~~t  190 (510)
T KOG0144|consen  112 KYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPD-GLSRGCAFVKFSTKEMAVAAIKALNGTQT  190 (510)
T ss_pred             cccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheeccc-ccccceeEEEEehHHHHHHHHHhhcccee
Confidence            8777665543  78999999999999999999999999999999999864 7899999999999999999999985  45


Q ss_pred             eCC--eEEEEEEeeeCCCCCC
Q psy1314         166 ICG--KEVDVKRVKFNPETMG  184 (275)
Q Consensus       166 ~~g--~~i~v~~~~~~~~~~~  184 (275)
                      +.|  .+|.|+|++++.++..
T Consensus       191 meGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  191 MEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             eccCCCceEEEecccCCCchH
Confidence            555  7899999999877643

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

Probab=99.96  E-value=4.1e-29  Score=234.30  Aligned_cols=161  Identities=24%  Similarity=0.415  Sum_probs=144.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeeccccccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRVTKRV   96 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~~~~~   96 (275)
                      +|||+|||.++||++|+++|++||+|++|+|++|+.|++++|||||+|.+.++|++||+.+ ...+.++.|.|.|+....
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~   81 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDP   81 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeecccccc
Confidence            7999999999999999999999999999999999999999999999999999999999865 557999999998875432


Q ss_pred             C---CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEE
Q psy1314          97 N---PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD  172 (275)
Q Consensus        97 ~---~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~  172 (275)
                      .   ....+|||+|||.++++++|+++|+.||.|..|+|+.+. +++++|||||+|.+.++|++|+++++ ..+.++.|.
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~-~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~  160 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVY  160 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecC-CCCcccEEEEEECCHHHHHHHHHHhcccEecCceEE
Confidence            2   224679999999999999999999999999999999874 57789999999999999999999985 889999998


Q ss_pred             EEEeeeC
Q psy1314         173 VKRVKFN  179 (275)
Q Consensus       173 v~~~~~~  179 (275)
                      |.....+
T Consensus       161 v~~~~~~  167 (562)
T TIGR01628       161 VGRFIKK  167 (562)
T ss_pred             Eeccccc
Confidence            8665443

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

>KOG4205|consensus

Probab=99.96  E-value=8.3e-29  Score=210.57  Aligned_cols=173  Identities=38%  Similarity=0.700  Sum_probs=161.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ..+.++|||++|+++++++.|+++|.+||+|.+|.+++++.+++++||+||+|++.+.+.++|....+.|.++.|+++.+
T Consensus         3 ~~~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~a   82 (311)
T KOG4205|consen    3 SGESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRA   82 (311)
T ss_pred             ccCCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceec
Confidence            34889999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccccCCC-------cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCce
Q psy1314          93 TKRVNPL-------KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQV  165 (275)
Q Consensus        93 ~~~~~~~-------~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~  165 (275)
                      .++....       ..+|||++||..+++++|++.|++||.|..+.++.|..+.++++|+||+|.+++++++++....+.
T Consensus        83 v~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~  162 (311)
T KOG4205|consen   83 VSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHD  162 (311)
T ss_pred             cCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceee
Confidence            8775432       358999999999999999999999999999999999999999999999999999999999998999


Q ss_pred             eCCeEEEEEEeeeCCCCCCC
Q psy1314         166 ICGKEVDVKRVKFNPETMGS  185 (275)
Q Consensus       166 ~~g~~i~v~~~~~~~~~~~~  185 (275)
                      |++++++|++|.++......
T Consensus       163 ~~gk~vevkrA~pk~~~~~~  182 (311)
T KOG4205|consen  163 FNGKKVEVKRAIPKEVMQST  182 (311)
T ss_pred             ecCceeeEeeccchhhcccc
Confidence            99999999999999776543

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

Probab=99.96  E-value=5.1e-28  Score=226.96  Aligned_cols=167  Identities=26%  Similarity=0.512  Sum_probs=147.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceec----Ceee
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIG----NKKI   87 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~----g~~i   87 (275)
                      ....++|||+|||.++|+++|+++|++||+|+++.++.+ .+++++|||||+|.+.++|.+|++. ++..+.    ++.+
T Consensus       175 ~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~-~~g~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l  253 (562)
T TIGR01628       175 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKD-GSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKL  253 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEEC-CCCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceee
Confidence            345678999999999999999999999999999999998 4789999999999999999999985 566787    8888


Q ss_pred             cccccccccC-------------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEE
Q psy1314          88 DPKRVTKRVN-------------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS  148 (275)
Q Consensus        88 ~v~~~~~~~~-------------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~  148 (275)
                      .+.++..+..                   ...++|||+||++.+++++|+++|++||.|++|+|+.+ .++.++|||||+
T Consensus       254 ~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~  332 (562)
T TIGR01628       254 YVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVC  332 (562)
T ss_pred             EeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEE
Confidence            8876644322                   23467999999999999999999999999999999998 678899999999


Q ss_pred             ECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeCCC
Q psy1314         149 FDDQNVAEQVLANPK-QVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       149 f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~~  181 (275)
                      |.+.++|++|+..++ ..|.|++|.|.++..+..
T Consensus       333 f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k~~  366 (562)
T TIGR01628       333 FSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQ  366 (562)
T ss_pred             eCCHHHHHHHHHHhcCCeeCCceeEEEeccCcHH
Confidence            999999999999884 899999999999987643

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=2.9e-28  Score=195.96  Aligned_cols=169  Identities=24%  Similarity=0.425  Sum_probs=151.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~   91 (275)
                      .+....|.|..||.++|+|||+.+|...|+|++|++++|+.+|+|.||+||.|.+++||++|+..+ +..+..+.|+|+.
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            344566999999999999999999999999999999999999999999999999999999999964 6689999999999


Q ss_pred             cccccCC-CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee--C
Q psy1314          92 VTKRVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI--C  167 (275)
Q Consensus        92 ~~~~~~~-~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~--~  167 (275)
                      +.+.... ....|||++||..+|..+|+++|++||.|...+|+.|..++.+||.+||.|+..++|+.||+.++ +.-  +
T Consensus       118 ARPSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~  197 (360)
T KOG0145|consen  118 ARPSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGC  197 (360)
T ss_pred             ccCChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCC
Confidence            8876544 34789999999999999999999999999999999999999999999999999999999999975 332  3


Q ss_pred             CeEEEEEEeeeCCC
Q psy1314         168 GKEVDVKRVKFNPE  181 (275)
Q Consensus       168 g~~i~v~~~~~~~~  181 (275)
                      -.+|.|+++.....
T Consensus       198 tepItVKFannPsq  211 (360)
T KOG0145|consen  198 TEPITVKFANNPSQ  211 (360)
T ss_pred             CCCeEEEecCCccc
Confidence            36899999876543

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

Probab=99.95  E-value=3.4e-27  Score=219.12  Aligned_cols=162  Identities=22%  Similarity=0.434  Sum_probs=137.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhc------------CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQY------------GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD   79 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~------------G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~   79 (275)
                      .....++|||+|||+++|+++|+++|.++            ..|..+.+.      +.+|||||+|.+.++|.+||++++
T Consensus       171 ~~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~------~~kg~afVeF~~~e~A~~Al~l~g  244 (509)
T TIGR01642       171 ATRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNIN------KEKNFAFLEFRTVEEATFAMALDS  244 (509)
T ss_pred             CCccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEEC------CCCCEEEEEeCCHHHHhhhhcCCC
Confidence            44567899999999999999999999985            234344443      347899999999999999998888


Q ss_pred             ceecCeeeccccccccc------------------------------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE
Q psy1314          80 HYIGNKKIDPKRVTKRV------------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE  129 (275)
Q Consensus        80 ~~~~g~~i~v~~~~~~~------------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~  129 (275)
                      ..|.+++|.|.......                              .....+|||+|||..+++++|+++|+.||.|..
T Consensus       245 ~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~  324 (509)
T TIGR01642       245 IIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKA  324 (509)
T ss_pred             eEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeE
Confidence            89999998876432111                              112368999999999999999999999999999


Q ss_pred             EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       130 v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      +.|+.+..++.++|||||+|.+.++|.+||+.|+ ..|.+++|.|.++...
T Consensus       325 ~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       325 FNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             EEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            9999999999999999999999999999999884 8999999999998654

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

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

Probab=99.95  E-value=1.6e-26  Score=212.35  Aligned_cols=155  Identities=14%  Similarity=0.151  Sum_probs=132.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh---CCceecCeeecccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA---GDHYIGNKKIDPKR   91 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~---~~~~~~g~~i~v~~   91 (275)
                      ++++|||+|||+++|+++|+++|++||+|.+|.|+.+      +++|||+|.+.++|++||+.   +...+.+++|.|++
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            4789999999999999999999999999999999864      57999999999999999984   46789999999998


Q ss_pred             cccccC-------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHH
Q psy1314          92 VTKRVN-------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV  158 (275)
Q Consensus        92 ~~~~~~-------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~A  158 (275)
                      +..+..             ....+|+|.||++.+|+++|+++|++||.|..|.|.++..    +++|||+|.+.++|.+|
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            754321             1124789999999999999999999999999999887643    46899999999999999


Q ss_pred             HhcCC-ceeCC--eEEEEEEeeeC
Q psy1314         159 LANPK-QVICG--KEVDVKRVKFN  179 (275)
Q Consensus       159 i~~~~-~~~~g--~~i~v~~~~~~  179 (275)
                      ++.|+ ..|.+  ..|+|.+++..
T Consensus       151 ~~~Lng~~i~~~~~~l~v~~sk~~  174 (481)
T TIGR01649       151 KAALNGADIYNGCCTLKIEYAKPT  174 (481)
T ss_pred             HHHhcCCcccCCceEEEEEEecCC
Confidence            99885 77754  47888887754

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).

>KOG0131|consensus

Probab=99.95  E-value=2.3e-27  Score=181.42  Aligned_cols=170  Identities=23%  Similarity=0.389  Sum_probs=152.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v   89 (275)
                      .+.+...+|||+||+..++++.|.|+|-+.|+|.++.|.+++.+...+|||||+|.++|+|+-|++.+ ..++-+++|.|
T Consensus         4 ~~rnqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv   83 (203)
T KOG0131|consen    4 IERNQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRV   83 (203)
T ss_pred             cccCCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEE
Confidence            34567889999999999999999999999999999999999999999999999999999999999964 45889999999


Q ss_pred             ccccccc--CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE-EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ce
Q psy1314          90 KRVTKRV--NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE-FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QV  165 (275)
Q Consensus        90 ~~~~~~~--~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~  165 (275)
                      ..+....  .....+|||+||.+.+++..|.+.|+.||.+.. -+|+++..|+.+++|+||.|.+.|.+.+|+..++ ..
T Consensus        84 ~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~  163 (203)
T KOG0131|consen   84 NKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQY  163 (203)
T ss_pred             EecccccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccch
Confidence            9887332  234578999999999999999999999998765 4788999999999999999999999999999985 88


Q ss_pred             eCCeEEEEEEeeeCC
Q psy1314         166 ICGKEVDVKRVKFNP  180 (275)
Q Consensus       166 ~~g~~i~v~~~~~~~  180 (275)
                      ++.++++|..+..+.
T Consensus       164 l~nr~itv~ya~k~~  178 (203)
T KOG0131|consen  164 LCNRPITVSYAFKKD  178 (203)
T ss_pred             hcCCceEEEEEEecC
Confidence            999999999988764

>KOG0127|consensus

Probab=99.94  E-value=2.1e-26  Score=201.96  Aligned_cols=163  Identities=24%  Similarity=0.438  Sum_probs=147.7

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~~~~   95 (275)
                      .||||++||+.++.++|.++|+.+|+|..|.++.++.+..++||+||+|+-.|+++.|+... +..|.|+.|.|..+..+
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            89999999999999999999999999999999999999999999999999999999999875 66899999988876544


Q ss_pred             cCC---------------------------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEE
Q psy1314          96 VNP---------------------------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS  148 (275)
Q Consensus        96 ~~~---------------------------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~  148 (275)
                      ...                           ...+|.|.||||.+.+.+|+.+|+.||.|.+|.|++...... .|||||+
T Consensus        86 ~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgkl-cGFaFV~  164 (678)
T KOG0127|consen   86 ARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKL-CGFAFVQ  164 (678)
T ss_pred             ccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCc-cceEEEE
Confidence            211                           146799999999999999999999999999999997766554 5999999


Q ss_pred             ECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeCC
Q psy1314         149 FDDQNVAEQVLANPK-QVICGKEVDVKRVKFNP  180 (275)
Q Consensus       149 f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~  180 (275)
                      |....+|.+||+.+| +.|.|++|-|.||.++.
T Consensus       165 fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  165 FKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             EeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            999999999999996 89999999999998874

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

Probab=99.94  E-value=2.1e-25  Score=204.98  Aligned_cols=159  Identities=14%  Similarity=0.261  Sum_probs=134.0

Q ss_pred             CCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          14 NDERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      .+.++|||+|||+ .+|+++|+++|++||.|.+|+|+.++     +|+|||+|.+.++|++||+ +++..|.+++|.|..
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            4678999999998 69999999999999999999999873     5899999999999999998 467799999998876


Q ss_pred             ccccc--------------------------------------CCCcceeeecCCCCCCCHHHHHHhcccCCC--eEEEE
Q psy1314          92 VTKRV--------------------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGS--ITEFQ  131 (275)
Q Consensus        92 ~~~~~--------------------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~--v~~v~  131 (275)
                      +....                                      ..++.+|||.|||.++++++|+++|++||.  |+.|+
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            53210                                      012357999999999999999999999998  88888


Q ss_pred             eccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeE------EEEEEeeeC
Q psy1314         132 QPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKE------VDVKRVKFN  179 (275)
Q Consensus       132 i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~------i~v~~~~~~  179 (275)
                      +...+.  .++++|||+|.+.++|.+||..++ ..|.++.      |+|.+++++
T Consensus       428 ~~~~~~--~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs~~~  480 (481)
T TIGR01649       428 FFPKDN--ERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFSTSR  480 (481)
T ss_pred             EecCCC--CcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEeccCC
Confidence            765432  257899999999999999999985 7888875      888777653

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=99.93  E-value=5.2e-26  Score=185.65  Aligned_cols=149  Identities=25%  Similarity=0.440  Sum_probs=136.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~~~~   95 (275)
                      .+|||+|||.++++.+|+.+|++||+|.+|.|+++        |+||..++...++.||..+ +-+|++..|.|+.++.+
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            47999999999999999999999999999999987        9999999999999999955 55999999999999877


Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                       ...+.+|+|+||.+.++.++|+..|++||+|++|+|++|        |+||.|+-.++|..|+..| +.++.|++++|.
T Consensus        75 -sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq  145 (346)
T KOG0109|consen   75 -SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQ  145 (346)
T ss_pred             -CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeee
Confidence             456789999999999999999999999999999999855        8999999999999999998 599999999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      .+..+-..
T Consensus       146 ~stsrlrt  153 (346)
T KOG0109|consen  146 LSTSRLRT  153 (346)
T ss_pred             eecccccc
Confidence            88876543

>KOG0124|consensus

Probab=99.93  E-value=5e-26  Score=190.95  Aligned_cols=167  Identities=23%  Similarity=0.454  Sum_probs=152.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~   94 (275)
                      -++|||+.|++++.|+.|+..|..||+|++|.|-+|+.|++.||||||+|+-+|.|..|++. ++..+.|+.|.|-....
T Consensus       113 McRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsN  192 (544)
T KOG0124|consen  113 MCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSN  192 (544)
T ss_pred             hHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCC
Confidence            36899999999999999999999999999999999999999999999999999999999986 56799999999886544


Q ss_pred             ccC------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314          95 RVN------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus        95 ~~~------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      -..            ..-.+|||..+.++++++||+.+|+.||+|..|.+.++.....++||+||+|.+..+...||..|
T Consensus       193 mpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasM  272 (544)
T KOG0124|consen  193 MPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASM  272 (544)
T ss_pred             CcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhc
Confidence            322            12378999999999999999999999999999999999999999999999999999999999999


Q ss_pred             C-ceeCCeEEEEEEeeeCCCC
Q psy1314         163 K-QVICGKEVDVKRVKFNPET  182 (275)
Q Consensus       163 ~-~~~~g~~i~v~~~~~~~~~  182 (275)
                      | ..|.|..|+|-++...|..
T Consensus       273 NlFDLGGQyLRVGk~vTPP~a  293 (544)
T KOG0124|consen  273 NLFDLGGQYLRVGKCVTPPDA  293 (544)
T ss_pred             chhhcccceEecccccCCCch
Confidence            8 7899999999888777654

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

Probab=99.93  E-value=7.8e-25  Score=203.35  Aligned_cols=166  Identities=20%  Similarity=0.357  Sum_probs=139.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      .+..++|||+|||..+|+++|+++|+.||.|..+.|+.++.++.++|||||+|.+.++|.+||+. ++..|.++.|.|.+
T Consensus       292 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~  371 (509)
T TIGR01642       292 LDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQR  371 (509)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            34568999999999999999999999999999999999999999999999999999999999975 57799999998877


Q ss_pred             ccccc-----------------------------CCCcceeeecCCCCCC----------CHHHHHHhcccCCCeEEEEe
Q psy1314          92 VTKRV-----------------------------NPLKCKIFVGGLTTEI----------SEQDVRDYFSQYGSITEFQQ  132 (275)
Q Consensus        92 ~~~~~-----------------------------~~~~~~l~V~~l~~~~----------~~~~l~~~F~~~G~v~~v~i  132 (275)
                      +....                             ......|+|.||....          ..++|+++|++||.|+.|.|
T Consensus       372 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i  451 (509)
T TIGR01642       372 ACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVI  451 (509)
T ss_pred             CccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEe
Confidence            53211                             0123567888885321          23689999999999999999


Q ss_pred             ccCC---CCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         133 PFDK---SKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       133 ~~~~---~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      +++.   .+....|++||+|.++++|++||..|+ ..|.|+.|.|.+...
T Consensus       452 ~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       452 PRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             eccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            8652   334567999999999999999999995 899999999988654

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

>KOG0127|consensus

Probab=99.93  E-value=8.3e-25  Score=191.96  Aligned_cols=166  Identities=21%  Similarity=0.359  Sum_probs=146.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      +..+|.|.|||+.+.+.+|+.+|+.||.|.+|.|.+.+..+.. |||||.|.+..+|++||+. +.++|.+++|-|.|+.
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklc-GFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLC-GFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCcc-ceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            3778999999999999999999999999999999987665555 9999999999999999996 5779999999999975


Q ss_pred             cccC-----------------------------------------------C----------------------------
Q psy1314          94 KRVN-----------------------------------------------P----------------------------   98 (275)
Q Consensus        94 ~~~~-----------------------------------------------~----------------------------   98 (275)
                      ++..                                               .                            
T Consensus       195 ~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~  274 (678)
T KOG0127|consen  195 DKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKK  274 (678)
T ss_pred             ccccccccchhhhhhhhhccchhhhcccccccccccchhcccccccccccccccchhhhccccccccccccccccccccC
Confidence            4310                                               0                            


Q ss_pred             ----------------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314          99 ----------------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus        99 ----------------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                                      ...+|||.|||+++|+++|.++|++||+|..+.|+.++.|+.++|.|||.|.+..+|.+||+..
T Consensus       275 ~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~A  354 (678)
T KOG0127|consen  275 ESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAA  354 (678)
T ss_pred             cccchhccccccccccccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhc
Confidence                            0167999999999999999999999999999999999999999999999999999999999874


Q ss_pred             ------C-ceeCCeEEEEEEeeeCCC
Q psy1314         163 ------K-QVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       163 ------~-~~~~g~~i~v~~~~~~~~  181 (275)
                            . ..|.|+.|.|..+..+.+
T Consensus       355 spa~e~g~~ll~GR~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  355 SPASEDGSVLLDGRLLKVTLAVTRKE  380 (678)
T ss_pred             CccCCCceEEEeccEEeeeeccchHH
Confidence                  2 578999999998887644

>KOG0145|consensus

Probab=99.91  E-value=9e-24  Score=170.12  Aligned_cols=167  Identities=22%  Similarity=0.335  Sum_probs=143.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecC--eeeccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGN--KKIDPK   90 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g--~~i~v~   90 (275)
                      -....|||.+||+.+|..||+++|++||.|..-+|+.|..|+.+||.+||.|...++|+.||..+ +++-.+  .+|.|+
T Consensus       125 Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVK  204 (360)
T KOG0145|consen  125 IKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVK  204 (360)
T ss_pred             hcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEE
Confidence            34557999999999999999999999999999999999999999999999999999999999864 333222  455555


Q ss_pred             ccccccCC----------------------------------------------------------------Ccceeeec
Q psy1314          91 RVTKRVNP----------------------------------------------------------------LKCKIFVG  106 (275)
Q Consensus        91 ~~~~~~~~----------------------------------------------------------------~~~~l~V~  106 (275)
                      .+......                                                                ...+|||-
T Consensus       205 FannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l~~~~lp~~~~~g~ciFvY  284 (360)
T KOG0145|consen  205 FANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGLAGVNLPGGPGGGWCIFVY  284 (360)
T ss_pred             ecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCccccccceeeeeccCCCCCCeeEEEEE
Confidence            54322100                                                                11779999


Q ss_pred             CCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeCC
Q psy1314         107 GLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFNP  180 (275)
Q Consensus       107 ~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~  180 (275)
                      ||.++++|..|-++|.+||.|.+|+|++|-.|.+-+||+||++.+-++|..||..++ ..|.++.|.|.+...++
T Consensus       285 NLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKtnk~  359 (360)
T KOG0145|consen  285 NLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKTNKA  359 (360)
T ss_pred             ecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEecCCC
Confidence            999999999999999999999999999999999999999999999999999999985 88999999999876553

>KOG4211|consensus

Probab=99.91  E-value=1.5e-22  Score=176.21  Aligned_cols=167  Identities=22%  Similarity=0.316  Sum_probs=139.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ++.++...|.+.+|||++|++||.+||+.+ .|+++.+.+  .+++..|-|||+|.++|++++||+++...+..+.|+|-
T Consensus         5 ~e~~~~~~vr~rGLPwsat~~ei~~Ff~~~-~I~~~~~~r--~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf   81 (510)
T KOG4211|consen    5 NEGSTAFEVRLRGLPWSATEKEILDFFSNC-GIENLEIPR--RNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVF   81 (510)
T ss_pred             cCCCcceEEEecCCCccccHHHHHHHHhcC-ceeEEEEec--cCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEE
Confidence            356677889999999999999999999999 577866655  47999999999999999999999999889999999887


Q ss_pred             ccccccCC------------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHH
Q psy1314          91 RVTKRVNP------------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV  158 (275)
Q Consensus        91 ~~~~~~~~------------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~A  158 (275)
                      .+...+.+            ....|.+.+||+.||++||.++|+..-.|....++.....+++.|-|||+|++.+.|++|
T Consensus        82 ~~~~~e~d~~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~A  161 (510)
T KOG4211|consen   82 TAGGAEADWVMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQESAEIA  161 (510)
T ss_pred             ccCCccccccccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHHHHHH
Confidence            76433221            346789999999999999999999886555533233334567899999999999999999


Q ss_pred             HhcCCceeCCeEEEEEEeeeCC
Q psy1314         159 LANPKQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       159 i~~~~~~~~g~~i~v~~~~~~~  180 (275)
                      +..+...|..+.|+|-++....
T Consensus       162 l~rhre~iGhRYIEvF~Ss~~e  183 (510)
T KOG4211|consen  162 LGRHRENIGHRYIEVFRSSRAE  183 (510)
T ss_pred             HHHHHHhhccceEEeehhHHHH
Confidence            9999999999999998766543

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

Probab=99.90  E-value=1.3e-22  Score=186.04  Aligned_cols=161  Identities=22%  Similarity=0.411  Sum_probs=134.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      ..++|||+|||.++|+++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|.+||+. ++..|.+++|.|.++.
T Consensus       185 ~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       185 NFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            368999999999999999999999999999999999999999999999999999999999985 5779999999888732


Q ss_pred             ccc-----------------------------------------------------------------------------
Q psy1314          94 KRV-----------------------------------------------------------------------------   96 (275)
Q Consensus        94 ~~~-----------------------------------------------------------------------------   96 (275)
                      ...                                                                             
T Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  344 (457)
T TIGR01622       265 DSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGAL  344 (457)
T ss_pred             CCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCCCccchhhhhcccccccccccccccccccccc
Confidence            100                                                                             


Q ss_pred             --------------CCCcceeeecCCCCCCC----------HHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCH
Q psy1314          97 --------------NPLKCKIFVGGLTTEIS----------EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ  152 (275)
Q Consensus        97 --------------~~~~~~l~V~~l~~~~~----------~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~  152 (275)
                                    .....+|+|.||....+          .+||++.|++||.|+.|.|...    ...|++||+|.++
T Consensus       345 ~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~----~~~G~~fV~F~~~  420 (457)
T TIGR01622       345 AIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEECSKYGGVVHIYVDTK----NSAGKIYLKFSSV  420 (457)
T ss_pred             ccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHHHhcCCeeEEEEeCC----CCceeEEEEECCH
Confidence                          01224567777744433          3689999999999999988643    3478999999999


Q ss_pred             HHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         153 NVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       153 e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      ++|.+|++.|+ ..++|+.|.+.+....
T Consensus       421 e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       421 DAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             HHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            99999999995 8999999999887643

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=99.90  E-value=4.3e-23  Score=181.52  Aligned_cols=154  Identities=25%  Similarity=0.429  Sum_probs=140.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~v~~~~~~   95 (275)
                      ..|||+   +++|+..|.++|+++|+|.++++.+|. |  +-|||||.|.++++|++||..++ ..+.+++|++.|+...
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   999999999999999999999999997 7  99999999999999999999765 5899999999999653


Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVK  174 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~  174 (275)
                      ..    .|||.||+++++..+|.++|+.||.|.+|++.++.+.  ++|| ||+|+++++|++||++++ ..+.+++|.|.
T Consensus        76 ~~----~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g--~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg  148 (369)
T KOG0123|consen   76 PS----LVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENG--SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVG  148 (369)
T ss_pred             Cc----eeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCC--ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEe
Confidence            32    3999999999999999999999999999999998654  8999 999999999999999985 88999999999


Q ss_pred             EeeeCCCCC
Q psy1314         175 RVKFNPETM  183 (275)
Q Consensus       175 ~~~~~~~~~  183 (275)
                      ....+.++.
T Consensus       149 ~~~~~~er~  157 (369)
T KOG0123|consen  149 LFERKEERE  157 (369)
T ss_pred             eccchhhhc
Confidence            888877654

>KOG0147|consensus

Probab=99.89  E-value=1.2e-23  Score=185.41  Aligned_cols=175  Identities=25%  Similarity=0.410  Sum_probs=156.8

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      .-..++.+.++||+-.|+..+++.+|.+||+.+|+|.+|.||.|+.+.+++|.+||+|.+.+.+..||.+.++.+.+.+|
T Consensus       171 ~l~~eERd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv  250 (549)
T KOG0147|consen  171 ILSPEERDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPV  250 (549)
T ss_pred             cCCchHHhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCcee
Confidence            33455677889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccccccCC---------------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCH
Q psy1314          88 DPKRVTKRVNP---------------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ  152 (275)
Q Consensus        88 ~v~~~~~~~~~---------------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~  152 (275)
                      .|+.....++.               +-.+|||+||.+++++++|+.+|++||.|..|.+.+|..|++++||+||+|.+.
T Consensus       251 ~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~  330 (549)
T KOG0147|consen  251 IVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNK  330 (549)
T ss_pred             EecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecH
Confidence            98876433221               113499999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCC-ceeCCeEEEEEEeeeCCCC
Q psy1314         153 NVAEQVLANPK-QVICGKEVDVKRVKFNPET  182 (275)
Q Consensus       153 e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~~~  182 (275)
                      ++|++|++.+| ..|-|+.|+|.....+...
T Consensus       331 ~~ar~a~e~lngfelAGr~ikV~~v~~r~~~  361 (549)
T KOG0147|consen  331 EDARKALEQLNGFELAGRLIKVSVVTERVDT  361 (549)
T ss_pred             HHHHHHHHHhccceecCceEEEEEeeeeccc
Confidence            99999999985 8899999999887776543

>KOG0148|consensus

Probab=99.89  E-value=7.3e-23  Score=165.77  Aligned_cols=138  Identities=25%  Similarity=0.454  Sum_probs=118.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ++++.++|||+||+.++||+-|..+|++.|+|++|+|+.+.                                  |.|.+
T Consensus         2 ~~~~prtlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e----------------------------------~~v~w   47 (321)
T KOG0148|consen    2 GSDEPRTLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDE----------------------------------LKVNW   47 (321)
T ss_pred             CCCCCceEEeeccChhhHHHHHHHHHHhccccccceeehhh----------------------------------hcccc
Confidence            46778999999999999999999999999999999999871                                  11111


Q ss_pred             ccc------ccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c
Q psy1314          92 VTK------RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q  164 (275)
Q Consensus        92 ~~~------~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~  164 (275)
                      +..      ........+||+.|...++-++|++.|.+||+|.+++|++|..|+++|||+||.|...++|+.||..|+ .
T Consensus        48 a~~p~nQsk~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGq  127 (321)
T KOG0148|consen   48 ATAPGNQSKPTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQ  127 (321)
T ss_pred             ccCcccCCCCccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCe
Confidence            111      111124568999999999999999999999999999999999999999999999999999999999996 8


Q ss_pred             eeCCeEEEEEEeeeCCCCC
Q psy1314         165 VICGKEVDVKRVKFNPETM  183 (275)
Q Consensus       165 ~~~g~~i~v~~~~~~~~~~  183 (275)
                      -|..|.|+..|+..||..+
T Consensus       128 WlG~R~IRTNWATRKp~e~  146 (321)
T KOG0148|consen  128 WLGRRTIRTNWATRKPSEM  146 (321)
T ss_pred             eeccceeeccccccCcccc
Confidence            8999999999999998543

>KOG0110|consensus

Probab=99.88  E-value=2e-22  Score=182.16  Aligned_cols=164  Identities=26%  Similarity=0.422  Sum_probs=142.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC---CCcccEEEEEEccHHHHHHHHHhCC-ceecCeeecccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT---GQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKR   91 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~t---g~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~v~~   91 (275)
                      .++|||.||++++|.++|..+|.+.|.|.+|.|...+.-   -.|.||+||+|.++++|++|++.++ +.+.|+.|.++.
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            334999999999999999999999999999988765432   1367999999999999999999875 899999999888


Q ss_pred             cc--------cccCC--CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc
Q psy1314          92 VT--------KRVNP--LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus        92 ~~--------~~~~~--~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      +.        .....  ...+|+|.|||+.++..+|+++|..||.|..|+|+.......++|||||+|-++.+|..|+..
T Consensus       595 S~~k~~~~~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~a  674 (725)
T KOG0110|consen  595 SENKPASTVGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDA  674 (725)
T ss_pred             ccCccccccccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHh
Confidence            76        11111  235899999999999999999999999999999998755667799999999999999999999


Q ss_pred             C-CceeCCeEEEEEEeeeC
Q psy1314         162 P-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       162 ~-~~~~~g~~i~v~~~~~~  179 (275)
                      + .+.|.|+.|.+.|+...
T Consensus       675 l~STHlyGRrLVLEwA~~d  693 (725)
T KOG0110|consen  675 LGSTHLYGRRLVLEWAKSD  693 (725)
T ss_pred             hcccceechhhheehhccc
Confidence            8 58899999999998765

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

Probab=99.86  E-value=1.2e-20  Score=145.45  Aligned_cols=87  Identities=22%  Similarity=0.537  Sum_probs=80.2

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      .....++|||+|||+++++++|+++|++||+|..|.|+.|..+++++|||||+|.+.++|++||+.+ ++.|++++|+|.
T Consensus        30 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~  109 (144)
T PLN03134         30 LRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVN  109 (144)
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3445688999999999999999999999999999999999999999999999999999999999987 589999999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      ++..++..
T Consensus       110 ~a~~~~~~  117 (144)
T PLN03134        110 PANDRPSA  117 (144)
T ss_pred             eCCcCCCC
Confidence            99876654

>KOG0146|consensus

Probab=99.86  E-value=1.2e-21  Score=158.59  Aligned_cols=168  Identities=25%  Similarity=0.450  Sum_probs=138.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC--ceecC--eeec
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD--HYIGN--KKID   88 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~--~~~~g--~~i~   88 (275)
                      ..+.++|||+-|.+.-.|||++.+|..||+|++|.+++.+ ++.+|||+||+|.+..+|..||..+.  ..+-|  ..+.
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLV   94 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLV   94 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceE
Confidence            3478899999999999999999999999999999999985 69999999999999999999998642  12222  1222


Q ss_pred             cccccccc------------------------------------------------------------------------
Q psy1314          89 PKRVTKRV------------------------------------------------------------------------   96 (275)
Q Consensus        89 v~~~~~~~------------------------------------------------------------------------   96 (275)
                      |+.+...+                                                                        
T Consensus        95 VK~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl  174 (371)
T KOG0146|consen   95 VKFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGL  174 (371)
T ss_pred             EEeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhccc
Confidence            22221110                                                                        


Q ss_pred             --------------------------------------------------------------------------------
Q psy1314          97 --------------------------------------------------------------------------------   96 (275)
Q Consensus        97 --------------------------------------------------------------------------------   96 (275)
                                                                                                      
T Consensus       175 ~A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~  254 (371)
T KOG0146|consen  175 AAAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYA  254 (371)
T ss_pred             ccCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHh
Confidence                                                                                            


Q ss_pred             ---------------------------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEE
Q psy1314          97 ---------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF  149 (275)
Q Consensus        97 ---------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f  149 (275)
                                                 .+..|.|||-.||.+..+.+|-+.|-+||.|++.+|..|+.|+.+|+|+||.|
T Consensus       255 Aaypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSf  334 (371)
T KOG0146|consen  255 AAYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSF  334 (371)
T ss_pred             hhcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEec
Confidence                                       00128899999999999999999999999999999999999999999999999


Q ss_pred             CCHHHHHHHHhcCC-ceeCCeEEEEEEeeeCCC
Q psy1314         150 DDQNVAEQVLANPK-QVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       150 ~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~~  181 (275)
                      +++.+|+.||..|| ..|.=++|+|....++..
T Consensus       335 DNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkda  367 (371)
T KOG0146|consen  335 DNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDA  367 (371)
T ss_pred             CCchhHHHHHHHhcchhhhhhhhhhhhcCcccc
Confidence            99999999999986 667778888876666644

>KOG0144|consensus

Probab=99.85  E-value=3.3e-21  Score=165.22  Aligned_cols=167  Identities=28%  Similarity=0.442  Sum_probs=143.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc--eecC--eeecc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH--YIGN--KKIDP   89 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~--~~~g--~~i~v   89 (275)
                      .++++|||+.|++.+||.+|+++|++||.|++|.|+++. .+.+||||||+|.+.|.|..||+.++.  ++.|  .+|.|
T Consensus       122 ~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVV  200 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVV  200 (510)
T ss_pred             ccchhhhhhhccccccHHHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEE
Confidence            458899999999999999999999999999999999994 699999999999999999999997543  4443  56666


Q ss_pred             cccccccCC-----------------------------------------------------------------------
Q psy1314          90 KRVTKRVNP-----------------------------------------------------------------------   98 (275)
Q Consensus        90 ~~~~~~~~~-----------------------------------------------------------------------   98 (275)
                      +++.++++.                                                                       
T Consensus       201 kFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~g~~~L~~l~a~~~qq~~~~  280 (510)
T KOG0144|consen  201 KFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLGGLPPLGPLNATQLQQAAAL  280 (510)
T ss_pred             EecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccccccCCCCcchhHHHHHHHh
Confidence            665433110                                                                       


Q ss_pred             --------------------------------------------------------------------------------
Q psy1314          99 --------------------------------------------------------------------------------   98 (275)
Q Consensus        99 --------------------------------------------------------------------------------   98 (275)
                                                                                                      
T Consensus       281 ~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t~~~~n~~~~~a~a~~~sp~  360 (510)
T KOG0144|consen  281 AAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGTPANYNLAGGMAGAGTTSPV  360 (510)
T ss_pred             hhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCCchhcccccccccccccCcc
Confidence                                                                                            


Q ss_pred             --------------------------------------------------------------CcceeeecCCCCCCCHHH
Q psy1314          99 --------------------------------------------------------------LKCKIFVGGLTTEISEQD  116 (275)
Q Consensus        99 --------------------------------------------------------------~~~~l~V~~l~~~~~~~~  116 (275)
                                                                                    ....|||.+||.+.-+.+
T Consensus       361 aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eGpeGanlfiyhlPqefgdq~  440 (510)
T KOG0144|consen  361 AASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEGPEGANLFIYHLPQEFGDQD  440 (510)
T ss_pred             cccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccCCCccceeeeeCchhhhhHH
Confidence                                                                          004589999999999999


Q ss_pred             HHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeCCC
Q psy1314         117 VRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       117 l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~~  181 (275)
                      |-..|..||.|...++..|+.|+.+++|+||.|++..+|..||..|+ ..|..++++|....++-+
T Consensus       441 l~~~f~pfG~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQlk~~~~n  506 (510)
T KOG0144|consen  441 LIATFQPFGGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQLKRDRNN  506 (510)
T ss_pred             HHHHhccccceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEEeeeccCC
Confidence            99999999999999999999999999999999999999999999986 788999998877766543

>KOG0105|consensus

Probab=99.85  E-value=4.7e-20  Score=141.66  Aligned_cols=141  Identities=23%  Similarity=0.372  Sum_probs=121.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ...+++|||+|||.++.+.+|+++|.+||.|.+|.|...+   ....||||+|+++.+|+.||.- ++-.+.+-.|.|+.
T Consensus         3 gr~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEf   79 (241)
T KOG0105|consen    3 GRNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEF   79 (241)
T ss_pred             CcccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEe
Confidence            3567899999999999999999999999999999997653   3456999999999999999986 45688898998887


Q ss_pred             cccc---------------------------cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeE
Q psy1314          92 VTKR---------------------------VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF  144 (275)
Q Consensus        92 ~~~~---------------------------~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~  144 (275)
                      +..-                           ......+|.|++||.+.+|+||+++..+-|.|....+.+|       |.
T Consensus        80 prggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~  152 (241)
T KOG0105|consen   80 PRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GV  152 (241)
T ss_pred             ccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cc
Confidence            6432                           1234578999999999999999999999999999998876       36


Q ss_pred             EEEEECCHHHHHHHHhcCC
Q psy1314         145 CFISFDDQNVAEQVLANPK  163 (275)
Q Consensus       145 afV~f~~~e~a~~Ai~~~~  163 (275)
                      +.|+|...|+.+-||.++.
T Consensus       153 GvV~~~r~eDMkYAvr~ld  171 (241)
T KOG0105|consen  153 GVVEYLRKEDMKYAVRKLD  171 (241)
T ss_pred             eeeeeeehhhHHHHHHhhc
Confidence            8999999999999999874

>KOG0123|consensus

Probab=99.83  E-value=6.9e-20  Score=161.30  Aligned_cols=157  Identities=25%  Similarity=0.486  Sum_probs=137.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccccccC
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKRVN   97 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~~~   97 (275)
                      |||.||++++|.++|.++|+.||.|.+|++.++.. + ++|| ||+|+++++|++|+++ ++..+.+++|.|-....+..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            99999999999999999999999999999999854 5 9999 9999999999999997 46688889888765544332


Q ss_pred             ---------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeC
Q psy1314          98 ---------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVIC  167 (275)
Q Consensus        98 ---------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~  167 (275)
                               ..-..++|.+++.+++++.|+.+|..+|.|..+.++.+.. +.+++|+||.|.++++|..|++.++ ..+.
T Consensus       156 r~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~-g~~~~~gfv~f~~~e~a~~av~~l~~~~~~  234 (369)
T KOG0123|consen  156 REAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSI-GKSKGFGFVNFENPEDAKKAVETLNGKIFG  234 (369)
T ss_pred             hcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCC-CCCCCccceeecChhHHHHHHHhccCCcCC
Confidence                     2235689999999999999999999999999999998865 4489999999999999999999986 6666


Q ss_pred             CeEEEEEEeeeC
Q psy1314         168 GKEVDVKRVKFN  179 (275)
Q Consensus       168 g~~i~v~~~~~~  179 (275)
                      +..+.|..+..+
T Consensus       235 ~~~~~V~~aqkk  246 (369)
T KOG0123|consen  235 DKELYVGRAQKK  246 (369)
T ss_pred             ccceeecccccc
Confidence            788888877764

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

Probab=99.78  E-value=2.6e-18  Score=132.45  Aligned_cols=86  Identities=30%  Similarity=0.548  Sum_probs=78.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .......++|||+|||+++|+++|+++|++||+|++|.|+.++.|++++|||||+|.+.++|++||+. +++.|.+++|.
T Consensus        28 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~  107 (144)
T PLN03134         28 GSLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR  107 (144)
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34456678999999999999999999999999999999999999999999999999999999999974 67899999999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++..+
T Consensus       108 V~~a~~~  114 (144)
T PLN03134        108 VNPANDR  114 (144)
T ss_pred             EEeCCcC
Confidence            9988643

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

Probab=99.77  E-value=2.6e-17  Score=151.87  Aligned_cols=79  Identities=15%  Similarity=0.425  Sum_probs=71.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~   92 (275)
                      ...++|||+|||+++++++|+++|++||+|++|+|++++.+++++|||||+|.+.++|.+||+.+ +..+.|+.|.|.++
T Consensus       202 ~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kA  281 (612)
T TIGR01645       202 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  281 (612)
T ss_pred             cccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEec
Confidence            45679999999999999999999999999999999999999999999999999999999999864 56788888876553

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.

>KOG4212|consensus

Probab=99.73  E-value=9.8e-17  Score=138.13  Aligned_cols=160  Identities=22%  Similarity=0.393  Sum_probs=134.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHh-hcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeecccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFS-QYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~-~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~v~~   91 (275)
                      ...+.|||.|||++...++|+++|. +.|+|+.|.++.| .+++++|+|.|+|+++|.+++|++.++ +.+.+++|.|+.
T Consensus        42 ~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKE  120 (608)
T KOG4212|consen   42 ARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKE  120 (608)
T ss_pred             cccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEec
Confidence            3445699999999999999999996 5799999999999 579999999999999999999999764 589999998776


Q ss_pred             ccccc---------------------------------------------------------------------------
Q psy1314          92 VTKRV---------------------------------------------------------------------------   96 (275)
Q Consensus        92 ~~~~~---------------------------------------------------------------------------   96 (275)
                      ....+                                                                           
T Consensus       121 d~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~  200 (608)
T KOG4212|consen  121 DHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLS  200 (608)
T ss_pred             cCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccch
Confidence            43210                                                                           


Q ss_pred             -----------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c
Q psy1314          97 -----------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q  164 (275)
Q Consensus        97 -----------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~  164 (275)
                                 .+...++||.||...+....|++.|.--|.|+.|.+-.|++. .++|+|.++|..+-+|..||.+++ .
T Consensus       201 ~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG-~s~G~~vi~y~hpveavqaIsml~~~  279 (608)
T KOG4212|consen  201 ASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEG-NSRGFAVIEYDHPVEAVQAISMLDRQ  279 (608)
T ss_pred             hhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeecccc-ccCCeeEEEecchHHHHHHHHhhccC
Confidence                       001156899999999999999999999999999999888774 789999999999999999999985 4


Q ss_pred             eeCCeEEEEEE
Q psy1314         165 VICGKEVDVKR  175 (275)
Q Consensus       165 ~~~g~~i~v~~  175 (275)
                      -+..++.++..
T Consensus       280 g~~~~~~~~Rl  290 (608)
T KOG4212|consen  280 GLFDRRMTVRL  290 (608)
T ss_pred             CCccccceeec
Confidence            55556655543

>KOG4211|consensus

Probab=99.71  E-value=1e-15  Score=133.90  Aligned_cols=160  Identities=19%  Similarity=0.285  Sum_probs=127.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVES-ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~-~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      .....|.+.+||+.||++||.+||+-.-.|.. |.++.++ -+++.|.|||.|++.++|++||..+.+.|..+-|+|..+
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            56778999999999999999999998865555 5555554 477999999999999999999999888888887776543


Q ss_pred             cccc----------------------------------------------------------------------------
Q psy1314          93 TKRV----------------------------------------------------------------------------   96 (275)
Q Consensus        93 ~~~~----------------------------------------------------------------------------   96 (275)
                      ...+                                                                            
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            2110                                                                            


Q ss_pred             -C-----------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHH
Q psy1314          97 -N-----------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV  158 (275)
Q Consensus        97 -~-----------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~A  158 (275)
                       .                 .....++.++||+..++.+|..+|+..-.+ .|+|... .+++..|-|+|+|.+.++|..|
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                 001558889999999999999999977554 5555544 4578889999999999999999


Q ss_pred             HhcCCceeCCeEEEEEEe
Q psy1314         159 LANPKQVICGKEVDVKRV  176 (275)
Q Consensus       159 i~~~~~~~~g~~i~v~~~  176 (275)
                      +.+.+..+..+.|++...
T Consensus       338 mskd~anm~hrYVElFln  355 (510)
T KOG4211|consen  338 MGKDGANMGHRYVELFLN  355 (510)
T ss_pred             hccCCcccCcceeeeccc
Confidence            999888888888877543

>KOG0149|consensus

Probab=99.71  E-value=3.1e-17  Score=131.00  Aligned_cols=82  Identities=29%  Similarity=0.515  Sum_probs=76.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      .-..++|||++|+|++++++|+++|++||+|++..|+.|+.|++||||+||+|++.|+|.+|++..+-.|+||+..+..+
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            33567899999999999999999999999999999999999999999999999999999999998899999999888776


Q ss_pred             cc
Q psy1314          93 TK   94 (275)
Q Consensus        93 ~~   94 (275)
                      .-
T Consensus        89 ~l   90 (247)
T KOG0149|consen   89 SL   90 (247)
T ss_pred             hh
Confidence            43

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

Probab=99.71  E-value=2.7e-16  Score=144.98  Aligned_cols=75  Identities=21%  Similarity=0.335  Sum_probs=66.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQY--GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~--G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      ...++|||+|||.++|+++|+++|++|  |+|++|.+++        +||||+|.+.++|++||+ +++..|.++.|+|+
T Consensus       231 ~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~  302 (578)
T TIGR01648       231 AKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVT  302 (578)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999999999999999999  9999998764        499999999999999998 46789999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++.+..
T Consensus       303 ~Akp~~  308 (578)
T TIGR01648       303 LAKPVD  308 (578)
T ss_pred             EccCCC
Confidence            987643

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.

>KOG0149|consensus

Probab=99.69  E-value=4.4e-17  Score=130.17  Aligned_cols=81  Identities=32%  Similarity=0.578  Sum_probs=76.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ..-.+|||++|+|.+..+.|+++|++||+|++..|+.|+.++++|||+||+|.|.|+|.+|++..+..|+||+..|..|.
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            34578999999999999999999999999999999999999999999999999999999999999999999999998876


Q ss_pred             e
Q psy1314         178 F  178 (275)
Q Consensus       178 ~  178 (275)
                      .
T Consensus        90 l   90 (247)
T KOG0149|consen   90 L   90 (247)
T ss_pred             h
Confidence            5

>KOG4206|consensus

Probab=99.66  E-value=3.4e-15  Score=119.06  Aligned_cols=156  Identities=21%  Similarity=0.310  Sum_probs=124.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeee
Q psy1314          13 RNDERKLFVGGLHRNTGEKEIND----YFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKI   87 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~----~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i   87 (275)
                      ..+..||||.||+..+..++|+.    +|++||+|.+|....   |.+.+|-|||.|.+.+.|..|+..+ +-.+-++++
T Consensus         6 ~~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    6 VNPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             cCCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            34555999999999999999988    999999999888875   4678999999999999999999865 557778888


Q ss_pred             ccccccccc---------------------------------------------------CCCcceeeecCCCCCCCHHH
Q psy1314          88 DPKRVTKRV---------------------------------------------------NPLKCKIFVGGLTTEISEQD  116 (275)
Q Consensus        88 ~v~~~~~~~---------------------------------------------------~~~~~~l~V~~l~~~~~~~~  116 (275)
                      .++++....                                                   ..++..|++.|||..++.+.
T Consensus        83 riqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~  162 (221)
T KOG4206|consen   83 RIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEM  162 (221)
T ss_pred             heecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHH
Confidence            776654321                                                   12346789999999999999


Q ss_pred             HHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC-CeEEEEEEe
Q psy1314         117 VRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC-GKEVDVKRV  176 (275)
Q Consensus       117 l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~-g~~i~v~~~  176 (275)
                      |..+|++|.-...|+++...     .+.|||+|.+...|..|...+ +..+. ...+.|..+
T Consensus       163 l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a  219 (221)
T KOG4206|consen  163 LSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFA  219 (221)
T ss_pred             HHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEeccc
Confidence            99999999988999887643     568999999998888888875 23332 445555443

>KOG0110|consensus

Probab=99.65  E-value=1.9e-15  Score=137.32  Aligned_cols=164  Identities=20%  Similarity=0.332  Sum_probs=128.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc-eecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH-YIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~-~~~g~~i~v~   90 (275)
                      .....+.|+|+|||..+..++|.++|..||+|..+.|...   |.   -++|+|.++.+|++|+..+.. .+..-++.+.
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---GT---GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLE  454 (725)
T ss_pred             hhhhcceeeeccCccccccHHHHHHhhcccccceeecCcc---cc---eeeeeecCccchHHHHHHhchhhhccCccccc
Confidence            3455678999999999999999999999999999966532   11   499999999999999986532 3433344333


Q ss_pred             cccccc---------------------------------------------------CCCcceeeecCCCCCCCHHHHHH
Q psy1314          91 RVTKRV---------------------------------------------------NPLKCKIFVGGLTTEISEQDVRD  119 (275)
Q Consensus        91 ~~~~~~---------------------------------------------------~~~~~~l~V~~l~~~~~~~~l~~  119 (275)
                      |+....                                                   ....++|||.||++.+|.++|..
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            321000                                                   00114499999999999999999


Q ss_pred             hcccCCCeEEEEeccCCCC---CCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeCCC
Q psy1314         120 YFSQYGSITEFQQPFDKSK---NMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       120 ~F~~~G~v~~v~i~~~~~~---~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~~~  181 (275)
                      +|...|.|..+.|...++.   -.+.||+||+|.++++|+.|++.|. +.|+|+.|.|.++..++.
T Consensus       535 ~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~  600 (725)
T KOG0110|consen  535 LFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPA  600 (725)
T ss_pred             HHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccc
Confidence            9999999999988865432   1345999999999999999999996 999999999999984443

>KOG0106|consensus

Probab=99.64  E-value=3.2e-16  Score=126.08  Aligned_cols=141  Identities=23%  Similarity=0.513  Sum_probs=119.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~   95 (275)
                      ..|||++||+.+.+++|.++|..||.|.+|.|+.        ||+||+|.+..+|+.|+.. ++..|.+..+.++++...
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~--------gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKN--------GFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeec--------ccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            4799999999999999999999999999999865        4899999999999999875 456777766666665521


Q ss_pred             ---------------------cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHH
Q psy1314          96 ---------------------VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV  154 (275)
Q Consensus        96 ---------------------~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~  154 (275)
                                           .....+.|.|.+++..+.+++|+++|.++|.+....+        .++++||+|.+.++
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                                 0123478999999999999999999999999855443        25689999999999


Q ss_pred             HHHHHhcC-CceeCCeEEEE
Q psy1314         155 AEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus       155 a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      |.+||.++ +..+.++.|++
T Consensus       146 a~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen  146 AKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             hhhcchhccchhhcCceeee
Confidence            99999998 58899999999

>KOG0122|consensus

Probab=99.64  E-value=1e-15  Score=122.81  Aligned_cols=86  Identities=24%  Similarity=0.387  Sum_probs=78.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~   88 (275)
                      ..+.+++.+|.|.|||.+++|++|+++|.+||.|..|.|.+|+.||.+||||||.|.+.++|.+||+.+ +.-++.--|.
T Consensus       183 ~R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILr  262 (270)
T KOG0122|consen  183 MRERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILR  262 (270)
T ss_pred             cccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEE
Confidence            346678999999999999999999999999999999999999999999999999999999999999964 6678888889


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+|+.++
T Consensus       263 vEwskP~  269 (270)
T KOG0122|consen  263 VEWSKPS  269 (270)
T ss_pred             EEecCCC
Confidence            9998764

>PF00076 RRM_1: RNA recognition motif

Probab=99.63  E-value=1.9e-15  Score=102.03  Aligned_cols=69  Identities=36%  Similarity=0.744  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      |||+|||.++|+++|+++|++||+|..+.++.+ .++.++++|||+|.+.++|++|++ +++..+.++.|+
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 678899999999999999999999 577888888763

(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 ....

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.63  E-value=1.1e-15  Score=134.13  Aligned_cols=82  Identities=16%  Similarity=0.301  Sum_probs=76.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||++||+++|+++|+++|++||+|+.|+|++|..+++++|||||+|.++++|++||+.| +..|.+++|+|.+
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            345689999999999999999999999999999999999999999999999999999999999987 4889999999988


Q ss_pred             eee
Q psy1314         176 VKF  178 (275)
Q Consensus       176 ~~~  178 (275)
                      +.+
T Consensus       184 a~p  186 (346)
T TIGR01659       184 ARP  186 (346)
T ss_pred             ccc
Confidence            764

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

>KOG0147|consensus

Probab=99.62  E-value=2.2e-15  Score=133.41  Aligned_cols=158  Identities=21%  Similarity=0.415  Sum_probs=122.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~   95 (275)
                      .+|+|+||.+++++++|+.+|+.||+|+.|.++.+..||+++||+||+|.+.++|++|++. ++-.+-|+.|.|.....+
T Consensus       279 ~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  279 RRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             hhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeee
Confidence            3499999999999999999999999999999999988999999999999999999999765 566888888875443211


Q ss_pred             cC------------------------------------------------------------------------------
Q psy1314          96 VN------------------------------------------------------------------------------   97 (275)
Q Consensus        96 ~~------------------------------------------------------------------------------   97 (275)
                      ..                                                                              
T Consensus       359 ~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~  438 (549)
T KOG0147|consen  359 VDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPA  438 (549)
T ss_pred             cccccccccccccchhhccccccccccHHHHHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccc
Confidence            00                                                                              


Q ss_pred             --CCcceeeecCCC--CCCC--------HHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c
Q psy1314          98 --PLKCKIFVGGLT--TEIS--------EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q  164 (275)
Q Consensus        98 --~~~~~l~V~~l~--~~~~--------~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~  164 (275)
                        ..+.++.+.|+=  ...|        .+|+.+...+||.|..|.|-+.     +-|+.||.|.+.+.|..|+..++ .
T Consensus       439 ~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~g~v~hi~vd~n-----s~g~VYvrc~s~~~A~~a~~alhgr  513 (549)
T KOG0147|consen  439 FDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKHGKVCHIFVDKN-----SAGCVYVRCPSAEAAGTAVKALHGR  513 (549)
T ss_pred             cCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhcCCeeEEEEccC-----CCceEEEecCcHHHHHHHHHHHhhh
Confidence              001223333331  1111        2677778889999988876543     34899999999999999999985 8


Q ss_pred             eeCCeEEEEEEeeeC
Q psy1314         165 VICGKEVDVKRVKFN  179 (275)
Q Consensus       165 ~~~g~~i~v~~~~~~  179 (275)
                      .+.|+.|+..+....
T Consensus       514 WF~gr~Ita~~~~~~  528 (549)
T KOG0147|consen  514 WFAGRMITAKYLPLE  528 (549)
T ss_pred             hhccceeEEEEeehh
Confidence            899999998876544

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.60  E-value=4.9e-15  Score=100.19  Aligned_cols=69  Identities=30%  Similarity=0.648  Sum_probs=62.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeec
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKID   88 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~   88 (275)
                      |+|+|||+++++++|+++|+.+|.|..+.+..++. ++++++|||+|.++++|.+|++.++ ..+.++.|+
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            79999999999999999999999999999999977 8999999999999999999999876 789998763

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 ....

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

Probab=99.60  E-value=3.2e-14  Score=120.97  Aligned_cols=124  Identities=25%  Similarity=0.517  Sum_probs=107.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeecccccc-
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVT-   93 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~v~~~~-   93 (275)
                      .++|||+|||.++|+++|.++|.+||+|..+.+..++.+++++|+|||+|.+.++|..|++.++ ..|.+++|.|.+.. 
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            6999999999999999999999999999999999998899999999999999999999999875 79999999998843 


Q ss_pred             ---cccCC---------------------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCC
Q psy1314          94 ---KRVNP---------------------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN  139 (275)
Q Consensus        94 ---~~~~~---------------------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~  139 (275)
                         .+...                     ....+++.+++..++..++...|..++.+..+.+.......
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPSKDGK  264 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhccccccceeeeccCCCCCc
Confidence               21111                     12568999999999999999999999999777776554433

>KOG0113|consensus

Probab=99.59  E-value=6.1e-15  Score=121.55  Aligned_cols=92  Identities=22%  Similarity=0.415  Sum_probs=82.9

Q ss_pred             cccCCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCc
Q psy1314           2 AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDH   80 (275)
Q Consensus         2 a~~~~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~   80 (275)
                      -|+.+.+.....++-+||||+-|+.+++|.+|++.|+.||+|+.|.|++++.|++++|||||+|+++.+..+|.+. .+.
T Consensus        87 ~wdP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~  166 (335)
T KOG0113|consen   87 LWDPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGI  166 (335)
T ss_pred             hcCCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCc
Confidence            3566667777779999999999999999999999999999999999999999999999999999999999999885 577


Q ss_pred             eecCeeecccccc
Q psy1314          81 YIGNKKIDPKRVT   93 (275)
Q Consensus        81 ~~~g~~i~v~~~~   93 (275)
                      +|+++.|.|..-.
T Consensus       167 ~Idgrri~VDvER  179 (335)
T KOG0113|consen  167 KIDGRRILVDVER  179 (335)
T ss_pred             eecCcEEEEEecc
Confidence            9999998877543

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.59  E-value=9e-15  Score=120.77  Aligned_cols=80  Identities=18%  Similarity=0.328  Sum_probs=72.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~   94 (275)
                      ..++|||+|||+++|+++|+++|+.||+|++|.|+.++.   ++|||||+|.++++|+.||.+++..|.++.|.|.++..
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            367999999999999999999999999999999998853   57899999999999999999889999999999998865


Q ss_pred             ccC
Q psy1314          95 RVN   97 (275)
Q Consensus        95 ~~~   97 (275)
                      ...
T Consensus        80 ~~~   82 (260)
T PLN03120         80 YQL   82 (260)
T ss_pred             CCC
Confidence            443

>KOG0122|consensus

Probab=99.59  E-value=5.3e-15  Score=118.78  Aligned_cols=82  Identities=23%  Similarity=0.389  Sum_probs=76.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~  176 (275)
                      ...++|.|.||+.++++++|+++|.+||.|..|.|.+|++|+.+||||||+|.+.++|.+||..|+ .-++.--|.|.|+
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            356789999999999999999999999999999999999999999999999999999999999985 7788889999999


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      +++
T Consensus       267 kP~  269 (270)
T KOG0122|consen  267 KPS  269 (270)
T ss_pred             CCC
Confidence            875

>PF00076 RRM_1: RNA recognition motif

Probab=99.58  E-value=8.1e-15  Score=98.85  Aligned_cols=69  Identities=30%  Similarity=0.681  Sum_probs=64.1

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEE
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVD  172 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~  172 (275)
                      |||+|||.++++++|+++|++||.|..+.+..+ .++.++++|||+|.+.++|++|++.+ +..+.+++|+
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            799999999999999999999999999999987 67888999999999999999999976 5889998874

(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 ....

>KOG1548|consensus

Probab=99.57  E-value=1.6e-13  Score=115.38  Aligned_cols=165  Identities=15%  Similarity=0.257  Sum_probs=130.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-Cc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DH   80 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~--------~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~   80 (275)
                      ..++.-+..|||.+||.++|.+++.++|++||.|..        |+|.++. .|..+|-+.+.|-..|+++.|++.+ ..
T Consensus       128 ~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~  206 (382)
T KOG1548|consen  128 NPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDED  206 (382)
T ss_pred             CcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCcc
Confidence            344556677999999999999999999999998763        7788874 4999999999999999999999976 55


Q ss_pred             eecCeeecccccccc---------------------------------------cCCCcceeeecCCCC----CCC----
Q psy1314          81 YIGNKKIDPKRVTKR---------------------------------------VNPLKCKIFVGGLTT----EIS----  113 (275)
Q Consensus        81 ~~~g~~i~v~~~~~~---------------------------------------~~~~~~~l~V~~l~~----~~~----  113 (275)
                      .+.++.|.|+.+.-.                                       .....++|.|.|+=.    ..+    
T Consensus       207 ~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~  286 (382)
T KOG1548|consen  207 ELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLL  286 (382)
T ss_pred             cccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHH
Confidence            888999988876421                                       011236788888732    223    


Q ss_pred             ---HHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         114 ---EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       114 ---~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                         .++|++-.++||.|..|.|.-.    .+.|.+.|.|.+.++|..||+.| +..+.|+.|+......+
T Consensus       287 ~dlkedl~eec~K~G~v~~vvv~d~----hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  287 NDLKEDLTEECEKFGQVRKVVVYDR----HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHHHHHhCCcceEEEecc----CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence               3566777889999999987633    35788999999999999999999 58899999988765543

>KOG0125|consensus

Probab=99.56  E-value=6.8e-15  Score=122.74  Aligned_cols=96  Identities=18%  Similarity=0.402  Sum_probs=79.7

Q ss_pred             ecCeeeccccccccc-CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHh
Q psy1314          82 IGNKKIDPKRVTKRV-NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA  160 (275)
Q Consensus        82 ~~g~~i~v~~~~~~~-~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~  160 (275)
                      ..+.++.+..+...+ ....++|+|+|||+...+.||+..|++||.|.+|+|+.+.  .-+|||+||+|++.+||++|-+
T Consensus        77 t~g~~~~~~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa  154 (376)
T KOG0125|consen   77 TDGQPIQTQPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARA  154 (376)
T ss_pred             CCCCccccCCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHH
Confidence            344444444443332 2345899999999999999999999999999999999874  3479999999999999999999


Q ss_pred             cCC-ceeCCeEEEEEEeeeC
Q psy1314         161 NPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       161 ~~~-~~~~g~~i~v~~~~~~  179 (275)
                      +++ ..|.||+|+|..+..+
T Consensus       155 ~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen  155 ELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             HhhcceeeceEEEEeccchh
Confidence            985 8999999999988766

>KOG0121|consensus

Probab=99.56  E-value=6.4e-15  Score=106.91  Aligned_cols=83  Identities=23%  Similarity=0.418  Sum_probs=76.1

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .+++|||+||++.++|++|.++|+++|+|..|.+-.|+.+..+.|||||+|-+.++|+.|++-+ ++.|+.++|.+.+..
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            4789999999999999999999999999999999999999999999999999999999999988 588999999988765


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      --.+
T Consensus       115 GF~e  118 (153)
T KOG0121|consen  115 GFVE  118 (153)
T ss_pred             cchh
Confidence            4443

>KOG0125|consensus

Probab=99.56  E-value=1.5e-14  Score=120.66  Aligned_cols=96  Identities=23%  Similarity=0.378  Sum_probs=83.3

Q ss_pred             CCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceec
Q psy1314           5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIG   83 (275)
Q Consensus         5 ~~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~   83 (275)
                      ...+..+..+..++|+|.|||+...|-||+..|++||+|.+|.||.+.  .-||||+||+|++.+||++|-++ ++..+.
T Consensus        85 ~~st~s~s~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VE  162 (376)
T KOG0125|consen   85 QPSTNSSSKDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVE  162 (376)
T ss_pred             CCCCcCCCCCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceee
Confidence            345556667788999999999999999999999999999999999873  56899999999999999999876 588999


Q ss_pred             CeeecccccccccCCCcce
Q psy1314          84 NKKIDPKRVTKRVNPLKCK  102 (275)
Q Consensus        84 g~~i~v~~~~~~~~~~~~~  102 (275)
                      ||+|+|..+..+....+.+
T Consensus       163 GRkIEVn~ATarV~n~K~~  181 (376)
T KOG0125|consen  163 GRKIEVNNATARVHNKKKK  181 (376)
T ss_pred             ceEEEEeccchhhccCCcc
Confidence            9999999998876555443

>KOG0121|consensus

Probab=99.56  E-value=9.7e-15  Score=105.95  Aligned_cols=82  Identities=22%  Similarity=0.379  Sum_probs=74.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      ....+++|||+||+..++||+|.++|+++|+|..|.|=.|+.+..+=|||||+|.+.++|+.||+. ++..+..++|.+.
T Consensus        32 a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   32 ALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             HHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            346789999999999999999999999999999999999999999999999999999999999996 4678888888887


Q ss_pred             ccc
Q psy1314          91 RVT   93 (275)
Q Consensus        91 ~~~   93 (275)
                      |..
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            753

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.55  E-value=2.9e-14  Score=96.39  Aligned_cols=69  Identities=23%  Similarity=0.578  Sum_probs=63.2

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEE
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD  172 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~  172 (275)
                      |+|+|||+++++++|+++|+.+|.|..+.+..++. +.++++|||+|.++++|++|++.++ ..++|++|+
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            78999999999999999999999999999999877 8899999999999999999999986 899999874

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 ....

>KOG1457|consensus

Probab=99.54  E-value=1.1e-13  Score=109.85  Aligned_cols=149  Identities=17%  Similarity=0.275  Sum_probs=109.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEee-CCCCCCcccEEEEEEccHHHHHHHHHhCC-ceec---C
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-DPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIG---N   84 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~-~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~---g   84 (275)
                      ..++..-+||||.+||.++...+|..+|..|--.+.+.|.. ++.....+-++||+|.+..+|.+|+++++ ..|+   +
T Consensus        28 ~~~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~  107 (284)
T KOG1457|consen   28 ADEPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETG  107 (284)
T ss_pred             cccccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccC
Confidence            34456689999999999999999999999997777776654 33333456799999999999999998753 3333   1


Q ss_pred             eeeccccccc--ccC-----------------------------------------------------------------
Q psy1314          85 KKIDPKRVTK--RVN-----------------------------------------------------------------   97 (275)
Q Consensus        85 ~~i~v~~~~~--~~~-----------------------------------------------------------------   97 (275)
                      ..+.++.++.  +..                                                                 
T Consensus       108 stLhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~  187 (284)
T KOG1457|consen  108 STLHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPD  187 (284)
T ss_pred             ceeEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhh
Confidence            2222222211  000                                                                 


Q ss_pred             --------------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHH
Q psy1314          98 --------------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ  157 (275)
Q Consensus        98 --------------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~  157 (275)
                                          ....+|||.||..+++|++|+.+|+.|--...++|...  .+  ...||++|++.+.|..
T Consensus       188 ~~~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~  263 (284)
T KOG1457|consen  188 SKAPSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATD  263 (284)
T ss_pred             hcCCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHH
Confidence                                00156999999999999999999999977666666432  12  4468999999999999


Q ss_pred             HHhcC
Q psy1314         158 VLANP  162 (275)
Q Consensus       158 Ai~~~  162 (275)
                      |+..+
T Consensus       264 am~~l  268 (284)
T KOG1457|consen  264 AMNHL  268 (284)
T ss_pred             HHHHh
Confidence            99884

>KOG1365|consensus

Probab=99.54  E-value=1.3e-14  Score=123.21  Aligned_cols=163  Identities=19%  Similarity=0.304  Sum_probs=128.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhc----CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQY----GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~----G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      +.-.|.+++||+++++.|+.+||..-    +.++.|.+++.+ +++..|-|||.|..+++|+.||.++...+..|.|++.
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            34568888999999999999999632    346677777764 6899999999999999999999998878877777655


Q ss_pred             ccccc--------------------------------cCCCcceeeecCCCCCCCHHHHHHhcccCCC-eEE--EEeccC
Q psy1314          91 RVTKR--------------------------------VNPLKCKIFVGGLTTEISEQDVRDYFSQYGS-ITE--FQQPFD  135 (275)
Q Consensus        91 ~~~~~--------------------------------~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~-v~~--v~i~~~  135 (275)
                      .+...                                ....+.+|.+++||+.++.++|-++|..|-. |..  |.++.+
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            44321                                1122467999999999999999999998853 333  666655


Q ss_pred             CCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         136 KSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       136 ~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                       ..+++.|-|||+|.+.|+|.+|..+. ++....+.|+|-.+...
T Consensus       319 -~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~S~e  362 (508)
T KOG1365|consen  319 -GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPCSVE  362 (508)
T ss_pred             -CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeeccHH
Confidence             45888999999999999999998887 45556888988766543

>KOG0107|consensus

Probab=99.54  E-value=4.1e-14  Score=108.27  Aligned_cols=78  Identities=26%  Similarity=0.514  Sum_probs=71.3

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      ..++|||+||+..+++.+|+.+|..||+|..|+|...     +.|||||||+++.+|+.|+..|+ ..|+|..|.|...+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            4689999999999999999999999999999998764     57999999999999999999995 89999999999888


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      -.+.
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            7654

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.53  E-value=5.7e-14  Score=114.24  Aligned_cols=79  Identities=22%  Similarity=0.281  Sum_probs=71.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~   94 (275)
                      ...+|||+||++.+|+++|+++|+.||+|++|.|+++.   +.+++|||+|+++++++.||.+++..|.+++|.|..+..
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            45799999999999999999999999999999999884   456799999999999999999999999999999887654


Q ss_pred             cc
Q psy1314          95 RV   96 (275)
Q Consensus        95 ~~   96 (275)
                      ..
T Consensus        81 y~   82 (243)
T PLN03121         81 YE   82 (243)
T ss_pred             cc
Confidence            33

>KOG4207|consensus

Probab=99.53  E-value=3.5e-14  Score=111.37  Aligned_cols=83  Identities=28%  Similarity=0.487  Sum_probs=77.7

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      -...|.|-||.+.++.++|+.+|++||.|-+|.|+.|+.|..++|||||.|.+..+|+.|++.|+ .+|+|+.|.|.+|.
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            34679999999999999999999999999999999999999999999999999999999999995 89999999999988


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      ....
T Consensus        92 ygr~   95 (256)
T KOG4207|consen   92 YGRP   95 (256)
T ss_pred             cCCC
Confidence            6654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.52  E-value=7.5e-14  Score=115.33  Aligned_cols=77  Identities=18%  Similarity=0.332  Sum_probs=70.3

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      .++|||+|||+.+++++|+++|+.||.|.+|+|+.++.   +++||||+|.++++|+.||...+..|.++.|.|.++..-
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            46899999999999999999999999999999998864   478999999999999999986679999999999998744

>KOG0105|consensus

Probab=99.49  E-value=1.6e-13  Score=105.87  Aligned_cols=79  Identities=25%  Similarity=0.381  Sum_probs=68.8

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ..+++|||+|||.++.+.+|+++|-+||.|.+|++...   .....||||+|+++.+|+.||.-- ...+++..|.|.++
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            34689999999999999999999999999999987543   234679999999999999999987 48899999999987


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      ..-
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            643

>KOG0129|consensus

Probab=99.49  E-value=8.9e-13  Score=116.43  Aligned_cols=165  Identities=23%  Similarity=0.412  Sum_probs=123.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC-CC--Cccc---EEEEEEccHHHHHHHHHhCCc-----
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH-TG--QSRG---FAFVTFTTQKAVDDLLAAGDH-----   80 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~-tg--~~~G---~afV~f~~~e~a~~al~~~~~-----   80 (275)
                      ...-+++|||++||++++|++|...|..||.+. +....... .+  .++|   |+|+.|+++..+++.|...-.     
T Consensus       255 ~~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~  333 (520)
T KOG0129|consen  255 SPRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNY  333 (520)
T ss_pred             ccccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccce
Confidence            345578899999999999999999999999863 33332111 11  2466   999999999999988875321     


Q ss_pred             -------eecCeeecccccc----------cccCCCcceeeecCCCCCCCHHHHHHhcc-cCCCeEEEEeccCCCCCCee
Q psy1314          81 -------YIGNKKIDPKRVT----------KRVNPLKCKIFVGGLTTEISEQDVRDYFS-QYGSITEFQQPFDKSKNMKK  142 (275)
Q Consensus        81 -------~~~g~~i~v~~~~----------~~~~~~~~~l~V~~l~~~~~~~~l~~~F~-~~G~v~~v~i~~~~~~~~~~  142 (275)
                             .+..+.++|..+.          ....+..++|||++||-.++.++|..+|+ .||.|..+-|-+|.+-+.++
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                   1122223332221          22344568999999999999999999999 79999999999998889999


Q ss_pred             eEEEEEECCHHHHHHHHhcCCceeC----CeEEEEEEee
Q psy1314         143 GFCFISFDDQNVAEQVLANPKQVIC----GKEVDVKRVK  177 (275)
Q Consensus       143 G~afV~f~~~e~a~~Ai~~~~~~~~----g~~i~v~~~~  177 (275)
                      |-+-|+|.+..+-.+||.+--..|.    .++|+|+.-.
T Consensus       414 GaGRVtFsnqqsYi~AIsarFvql~h~d~~KRVEIkPYv  452 (520)
T KOG0129|consen  414 GAGRVTFSNQQAYIKAISARFVQLDHTDIDKRVEIKPYV  452 (520)
T ss_pred             CcceeeecccHHHHHHHhhheEEEeccccceeeeeccee
Confidence            9999999999999999988543333    3456665433

>KOG0130|consensus

Probab=99.48  E-value=1e-13  Score=101.60  Aligned_cols=84  Identities=23%  Similarity=0.447  Sum_probs=79.3

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      ...|||+++...+++++|.+.|..||+|+++.+-.|+-|+..+|||+|+|++.+.|++||..+| ..|.+.+|.|.|+..
T Consensus        72 GwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   72 GWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             eEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            4679999999999999999999999999999999999999999999999999999999999997 899999999999998


Q ss_pred             CCCCC
Q psy1314         179 NPETM  183 (275)
Q Consensus       179 ~~~~~  183 (275)
                      +.+..
T Consensus       152 ~gp~~  156 (170)
T KOG0130|consen  152 KGPER  156 (170)
T ss_pred             cCCcc
Confidence            86643

>KOG0113|consensus

Probab=99.47  E-value=2.4e-13  Score=112.23  Aligned_cols=82  Identities=23%  Similarity=0.362  Sum_probs=75.4

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ++-++|||..|+.+++|..|+..|+.||+|+.|.|+.|+.|++++|||||+|+++.+..+|.+.. +.+|+++.|.|..-
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            34589999999999999999999999999999999999999999999999999999999999887 68999999998765


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      .-+
T Consensus       179 RgR  181 (335)
T KOG0113|consen  179 RGR  181 (335)
T ss_pred             ccc
Confidence            433

>KOG0107|consensus

Probab=99.47  E-value=1.2e-13  Score=105.80  Aligned_cols=77  Identities=30%  Similarity=0.529  Sum_probs=68.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~   92 (275)
                      .-.++|||+||+.++++.||+.+|..||+|.+|+|-.++     .|||||+|++..+|+.|+..+ ++.|.+..|.|+.+
T Consensus         8 ~~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S   82 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELS   82 (195)
T ss_pred             CCCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEEEee
Confidence            447899999999999999999999999999999998875     589999999999999999864 67899988888877


Q ss_pred             ccc
Q psy1314          93 TKR   95 (275)
Q Consensus        93 ~~~   95 (275)
                      .-.
T Consensus        83 ~G~   85 (195)
T KOG0107|consen   83 TGR   85 (195)
T ss_pred             cCC
Confidence            543

>KOG4212|consensus

Probab=99.45  E-value=1.4e-12  Score=112.75  Aligned_cols=70  Identities=23%  Similarity=0.318  Sum_probs=63.5

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      |+|+|.|||+++||+.|++.|..+|.|..++|+.   .++++|  .|.|.++++|+.|+..++ ..|+|+.|+|..
T Consensus       537 ~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y  607 (608)
T KOG4212|consen  537 CQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTY  607 (608)
T ss_pred             cEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeee
Confidence            8899999999999999999999999999999953   356665  899999999999999985 889999999975

>smart00362 RRM_2 RNA recognition motif

Probab=99.45  E-value=8e-13  Score=88.77  Aligned_cols=70  Identities=33%  Similarity=0.700  Sum_probs=63.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeecc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDP   89 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~v   89 (275)
                      +|+|.|||..+++++|+++|++||+|..+.+..++  +.++++|||+|.+.++|++|++.++ ..+.++++.+
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            58999999999999999999999999999999876  6788999999999999999998754 7888887765

>KOG4207|consensus

Probab=99.45  E-value=2e-13  Score=107.18  Aligned_cols=84  Identities=29%  Similarity=0.449  Sum_probs=77.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~   88 (275)
                      .++-+.-.+|.|-||...++.++|+.+|++||.|-+|.|.+|+.|+.++|||||.|.+..+|+.||+.+ +.+++++.|.
T Consensus         7 PPdv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelr   86 (256)
T KOG4207|consen    7 PPDVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELR   86 (256)
T ss_pred             CCCcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceee
Confidence            455677789999999999999999999999999999999999999999999999999999999999975 6789999988


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      |+.+.
T Consensus        87 Vq~ar   91 (256)
T KOG4207|consen   87 VQMAR   91 (256)
T ss_pred             ehhhh
Confidence            87664

>KOG0124|consensus

Probab=99.45  E-value=2.6e-12  Score=108.88  Aligned_cols=77  Identities=16%  Similarity=0.445  Sum_probs=67.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc-eecCeeecc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH-YIGNKKIDP   89 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~-~~~g~~i~v   89 (275)
                      ...-++|||..+.++++|+||+..|+.||+|..|++-+.+.++..|||+||+|.+..+...|+..++. .+.|..++|
T Consensus       207 Ak~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRV  284 (544)
T KOG0124|consen  207 AKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV  284 (544)
T ss_pred             HHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEec
Confidence            34567999999999999999999999999999999999998899999999999999988888886553 566655553

>KOG0111|consensus

Probab=99.44  E-value=1.2e-13  Score=109.30  Aligned_cols=85  Identities=26%  Similarity=0.509  Sum_probs=79.5

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~  176 (275)
                      ..+++|||++|..++++..|...|-+||.|..|.++.|..+.+.|||+||+|...|+|.+||..|+ .+|.|+.|+|..+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            456899999999999999999999999999999999999999999999999999999999999997 8999999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      ++....
T Consensus        88 kP~kik   93 (298)
T KOG0111|consen   88 KPEKIK   93 (298)
T ss_pred             CCcccc
Confidence            876443

>KOG0120|consensus

Probab=99.44  E-value=1.2e-12  Score=117.36  Aligned_cols=167  Identities=20%  Similarity=0.379  Sum_probs=125.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v   89 (275)
                      ......+.+||++||..+++.++.|+++.||++....++.+..++.++||||.+|.+......|+..+ +..+.++.+.|
T Consensus       284 ~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvv  363 (500)
T KOG0120|consen  284 DVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVV  363 (500)
T ss_pred             CcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEe
Confidence            34466788999999999999999999999999999999999999999999999999999998888864 45666677766


Q ss_pred             cccccccCC-------------------------CcceeeecCC--CCCC-CH-------HHHHHhcccCCCeEEEEecc
Q psy1314          90 KRVTKRVNP-------------------------LKCKIFVGGL--TTEI-SE-------QDVRDYFSQYGSITEFQQPF  134 (275)
Q Consensus        90 ~~~~~~~~~-------------------------~~~~l~V~~l--~~~~-~~-------~~l~~~F~~~G~v~~v~i~~  134 (275)
                      +.+......                         .+..|.+.|+  |.++ ++       ++++..+.+||.|..|.|++
T Consensus       364 q~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr  443 (500)
T KOG0120|consen  364 QRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPR  443 (500)
T ss_pred             ehhhccchhccccCCccccccccchhhhcccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCC
Confidence            654322110                         0111222221  0111 11       45666778899999999987


Q ss_pred             CC---CCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314         135 DK---SKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus       135 ~~---~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      +.   ......|..||+|.+.+++++|++.| +.++.++.|....-.
T Consensus       444 ~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  444 PYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             CCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            72   22234667899999999999999999 589999998776543

>KOG1190|consensus

Probab=99.42  E-value=6.7e-12  Score=107.80  Aligned_cols=154  Identities=16%  Similarity=0.245  Sum_probs=123.3

Q ss_pred             CCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccccc
Q psy1314          16 ERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRVT   93 (275)
Q Consensus        16 ~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~~   93 (275)
                      +..|.|.||..+ +|++.|..+|..||.|..|+|+.++.     -.|.|+|.+...|+-|++.+ ++++.+++|+|..++
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            678999999766 79999999999999999999999864     37999999999999999864 779999999887764


Q ss_pred             cccC------------------------------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCC
Q psy1314          94 KRVN------------------------------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS  137 (275)
Q Consensus        94 ~~~~------------------------------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~  137 (275)
                      ....                                    +++.+|++.|+|.+++||+|+.+|.+-|-..+......  
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            3210                                    12357999999999999999999998876554433222  


Q ss_pred             CCCeeeEEEEEECCHHHHHHHHhcC-CceeCCe-EEEEEEeee
Q psy1314         138 KNMKKGFCFISFDDQNVAEQVLANP-KQVICGK-EVDVKRVKF  178 (275)
Q Consensus       138 ~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~-~i~v~~~~~  178 (275)
                        ..+-++++.+++.|+|..|+..+ ++.+... .++|++.+.
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              12458999999999999999887 5666654 788887763

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.41  E-value=1.5e-12  Score=106.09  Aligned_cols=77  Identities=21%  Similarity=0.264  Sum_probs=70.1

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      ..+|+|+||++.+|+++|+++|+.||+|.+|+|+.+..   .+++|||+|+++++|+.|+...+..|.+++|.|..+...
T Consensus         5 g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~y   81 (243)
T PLN03121          5 GYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQY   81 (243)
T ss_pred             ceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCccc
Confidence            46899999999999999999999999999999998853   457999999999999999988889999999999887644

>KOG0126|consensus

Probab=99.41  E-value=3.4e-14  Score=109.31  Aligned_cols=82  Identities=30%  Similarity=0.490  Sum_probs=74.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      .++.-|||++||.++||.||.-.|++||+|++|.+++|+.||+|+||||+.|++..+...|+.. ++..|.++.|.|...
T Consensus        33 kdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            5677899999999999999999999999999999999999999999999999999988888875 577999999999876


Q ss_pred             ccc
Q psy1314          93 TKR   95 (275)
Q Consensus        93 ~~~   95 (275)
                      ...
T Consensus       113 ~~Y  115 (219)
T KOG0126|consen  113 SNY  115 (219)
T ss_pred             ccc
Confidence            544

>smart00360 RRM RNA recognition motif

Probab=99.41  E-value=1.6e-12  Score=86.91  Aligned_cols=69  Identities=32%  Similarity=0.642  Sum_probs=62.6

Q ss_pred             EcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeecc
Q psy1314          21 VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDP   89 (275)
Q Consensus        21 v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~v   89 (275)
                      |+|||..+++++|+++|++||.|..+.+..++.+++++++|||+|.+.++|.+|++.++ ..+.++.+.|
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            67999999999999999999999999999988889999999999999999999998754 6778877765

>KOG0117|consensus

Probab=99.41  E-value=1.7e-12  Score=112.52  Aligned_cols=82  Identities=24%  Similarity=0.453  Sum_probs=73.7

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee-CCeEEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI-CGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~-~g~~i~v~~  175 (275)
                      ...|.|||+.||.++.|++|..+|++.|+|-+++++.|+.++.+||||||+|.+.++|++||+.++ ++| .|+.|.|..
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            446899999999999999999999999999999999999999999999999999999999999984 544 578888876


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +..+
T Consensus       161 Svan  164 (506)
T KOG0117|consen  161 SVAN  164 (506)
T ss_pred             eeec
Confidence            6554

>smart00362 RRM_2 RNA recognition motif

Probab=99.39  E-value=2.4e-12  Score=86.46  Aligned_cols=70  Identities=30%  Similarity=0.680  Sum_probs=64.2

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEE
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDV  173 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v  173 (275)
                      +|+|+|||..+++++|+++|++||.|..+.+..+.  +.++++|||+|.+.++|++|++.++ ..+.+++|.|
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            58999999999999999999999999999988776  5678999999999999999999885 8899998876

>KOG1190|consensus

Probab=99.39  E-value=9.6e-13  Score=112.89  Aligned_cols=154  Identities=10%  Similarity=0.112  Sum_probs=113.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecCee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGNKK   86 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g~~   86 (275)
                      .....+++.|.++|||++++|+||.+++.+||+|+.+.++.-++      -|||+|+++++|...+...   .-.+.+++
T Consensus        22 ~~~~~pSkV~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGkn------QAflem~d~~sAvtmv~~y~~~~p~lr~~~   95 (492)
T KOG1190|consen   22 RSMAEPSKVVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKN------QAFLEMADEESAVTMVNYYTSVTPVLRGQP   95 (492)
T ss_pred             ccccCCcceeEeccCCccccHHHHHHhcccccceeeeeeeccch------hhhhhhcchhhhhheeecccccCccccCcc
Confidence            34455889999999999999999999999999999999987654      7999999999888754421   22445555


Q ss_pred             eccccccccc-----------------------------------------CCCcceeeecCCCCCCCHHHHHHhcccCC
Q psy1314          87 IDPKRVTKRV-----------------------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYG  125 (275)
Q Consensus        87 i~v~~~~~~~-----------------------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G  125 (275)
                      |.++.+....                                         ...-.+++|.++-..++-+-|.++|++||
T Consensus        96 ~yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG  175 (492)
T KOG1190|consen   96 IYIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFG  175 (492)
T ss_pred             eeehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcc
Confidence            5544432110                                         01125678899999999999999999999


Q ss_pred             CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314         126 SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus       126 ~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      .|.+|.-.....+-    -|+|+|.+.+.|..|...+ +..|..-.+.+
T Consensus       176 ~VlKIiTF~Knn~F----QALvQy~d~~sAq~AK~aLdGqnIyngcCtL  220 (492)
T KOG1190|consen  176 FVLKIITFTKNNGF----QALVQYTDAVSAQAAKLALDGQNIYNGCCTL  220 (492)
T ss_pred             eeEEEEEEecccch----hhhhhccchhhHHHHHHhccCCcccCceeEE
Confidence            99887544332221    2899999999999998887 45554433333

>KOG0126|consensus

Probab=99.39  E-value=1e-13  Score=106.70  Aligned_cols=80  Identities=33%  Similarity=0.538  Sum_probs=74.5

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      +.-|||++||+.+||.||--+|++||+|++|.+++|+.||+++||||+.|++..+..-|+..++ ..|.|+.|+|.....
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~  114 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSN  114 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeeccc
Confidence            4679999999999999999999999999999999999999999999999999999999999985 899999999987654


Q ss_pred             C
Q psy1314         179 N  179 (275)
Q Consensus       179 ~  179 (275)
                      .
T Consensus       115 Y  115 (219)
T KOG0126|consen  115 Y  115 (219)
T ss_pred             c
Confidence            3

>KOG0130|consensus

Probab=99.39  E-value=1.2e-12  Score=96.06  Aligned_cols=85  Identities=25%  Similarity=0.433  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~   91 (275)
                      +.+-..|||.++..++||++|.+.|..||+|++|.+..|+.|+-.+|||+|+|++.++|++|+..+ +..+.+..|.|.|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            344557999999999999999999999999999999999999999999999999999999999975 5799999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +..+..
T Consensus       149 ~Fv~gp  154 (170)
T KOG0130|consen  149 CFVKGP  154 (170)
T ss_pred             EEecCC
Confidence            865433

>smart00360 RRM RNA recognition motif

Probab=99.38  E-value=2.3e-12  Score=86.16  Aligned_cols=69  Identities=30%  Similarity=0.625  Sum_probs=64.0

Q ss_pred             ecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEE
Q psy1314         105 VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDV  173 (275)
Q Consensus       105 V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v  173 (275)
                      |+|||..+++++|+++|++||.|..+.+..++.++.++++|||+|.+.++|.+|++.++ ..+.+++|.|
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            57999999999999999999999999999888778899999999999999999999885 8889988876

>PLN03213 repressor of silencing 3; Provisional

Probab=99.38  E-value=1.2e-12  Score=114.86  Aligned_cols=77  Identities=21%  Similarity=0.421  Sum_probs=70.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCH--HHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ--NVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~--e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ...+|||+||++.+++++|+.+|++||.|..|.|+  +.++  ||||||+|.+.  +++.+||..++ ..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            35789999999999999999999999999999999  4566  99999999987  78999999985 899999999999


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      |++.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8765

>KOG0131|consensus

Probab=99.38  E-value=4.5e-13  Score=103.21  Aligned_cols=82  Identities=20%  Similarity=0.417  Sum_probs=77.1

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~  176 (275)
                      ....+|||+||+..++++.|.++|-+.|+|.++.|++|+.+...+|||||+|.++|+|+-||+.++ ..|.|++|+|..+
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            456789999999999999999999999999999999999999999999999999999999999997 7899999999998


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      ...
T Consensus        87 s~~   89 (203)
T KOG0131|consen   87 SAH   89 (203)
T ss_pred             ccc
Confidence            833

>KOG0120|consensus

Probab=99.38  E-value=9.9e-13  Score=117.96  Aligned_cols=161  Identities=24%  Similarity=0.456  Sum_probs=133.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhc-----------CC-eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQY-----------GE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH   80 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~-----------G~-v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~   80 (275)
                      ....+.++|++||+.++++.+..+|..-           |+ +..+.+...+      .||||+|.+.++|..|+..+..
T Consensus       172 t~q~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~------nfa~ie~~s~~~at~~~~~~~~  245 (500)
T KOG0120|consen  172 TRQARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEK------NFAFIEFRSISEATEAMALDGI  245 (500)
T ss_pred             hhhhhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeecccc------cceeEEecCCCchhhhhcccch
Confidence            3456789999999999999999999865           33 6666666553      4999999999999999988777


Q ss_pred             eecCeeecccccccc------------------------cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCC
Q psy1314          81 YIGNKKIDPKRVTKR------------------------VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK  136 (275)
Q Consensus        81 ~~~g~~i~v~~~~~~------------------------~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~  136 (275)
                      .+.+.++.+......                        .....++++|++||..+++++++++.+.||++....++.+.
T Consensus       246 ~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~  325 (500)
T KOG0120|consen  246 IFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDS  325 (500)
T ss_pred             hhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeeccc
Confidence            777766654332211                        12234789999999999999999999999999999999999


Q ss_pred             CCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         137 SKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       137 ~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      .++.++||||.+|.+......|+..++ ..+.++++.|..+...
T Consensus       326 ~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g  369 (500)
T KOG0120|consen  326 ATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVG  369 (500)
T ss_pred             ccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhcc
Confidence            999999999999999999999999986 7788899998877654

>KOG0114|consensus

Probab=99.38  E-value=3.2e-12  Score=89.50  Aligned_cols=87  Identities=20%  Similarity=0.253  Sum_probs=72.7

Q ss_pred             CCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-Cceec
Q psy1314           5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIG   83 (275)
Q Consensus         5 ~~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~   83 (275)
                      ...+..-.++..+.|||+|||+++|.+++.++|.+||.|.+|+|=..+.   .+|.|||.|++..+|++|+..+ +..+.
T Consensus         7 ~~~~~rlppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~   83 (124)
T KOG0114|consen    7 KKQNIRLPPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVD   83 (124)
T ss_pred             ccCCCCCChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccC
Confidence            3445555667788899999999999999999999999999999977655   4899999999999999999864 55777


Q ss_pred             Ceeeccccccc
Q psy1314          84 NKKIDPKRVTK   94 (275)
Q Consensus        84 g~~i~v~~~~~   94 (275)
                      ++.+.|...++
T Consensus        84 ~ryl~vlyyq~   94 (124)
T KOG0114|consen   84 NRYLVVLYYQP   94 (124)
T ss_pred             CceEEEEecCH
Confidence            88877776643

>PLN03213 repressor of silencing 3; Provisional

Probab=99.37  E-value=2.2e-12  Score=113.19  Aligned_cols=79  Identities=20%  Similarity=0.473  Sum_probs=69.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccH--HHHHHHHHh-CCceecCeeec
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ--KAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~--e~a~~al~~-~~~~~~g~~i~   88 (275)
                      +.....+|||+||++++++++|+.+|..||.|.+|.|++  .|+  ||||||+|.+.  +++.+||+. ++..+.|+.|.
T Consensus         6 s~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpR--ETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LK   81 (759)
T PLN03213          6 SGGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVR--TKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLR   81 (759)
T ss_pred             cCCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEec--ccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeE
Confidence            345567899999999999999999999999999999994  466  89999999987  678899985 57799999999


Q ss_pred             cccccc
Q psy1314          89 PKRVTK   94 (275)
Q Consensus        89 v~~~~~   94 (275)
                      |..+.+
T Consensus        82 VNKAKP   87 (759)
T PLN03213         82 LEKAKE   87 (759)
T ss_pred             EeeccH
Confidence            888754

>KOG1456|consensus

Probab=99.36  E-value=2.1e-10  Score=97.65  Aligned_cols=163  Identities=14%  Similarity=0.161  Sum_probs=120.8

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---Ccee
Q psy1314           6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYI   82 (275)
Q Consensus         6 ~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~   82 (275)
                      +.........+-.|.|++|-..++|.+|.+.++.||+|..+.++..+      .-|.|+|++.+.|++++...   ...+
T Consensus        21 ~~~dphk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~------r~alvefedi~~akn~Vnfaa~n~i~i   94 (494)
T KOG1456|consen   21 DNADPHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHK------RQALVEFEDIEGAKNCVNFAADNQIYI   94 (494)
T ss_pred             cCCCCCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEecccc------ceeeeeeccccchhhheehhccCcccc
Confidence            34444556778899999999999999999999999999888887653      37999999999999998752   3456


Q ss_pred             cCeeeccccccccc--------CCCcceee--ecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCH
Q psy1314          83 GNKKIDPKRVTKRV--------NPLKCKIF--VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ  152 (275)
Q Consensus        83 ~g~~i~v~~~~~~~--------~~~~~~l~--V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~  152 (275)
                      .+..-.+..+..+.        ...+..|.  |-|--..+|.+-|..+....|.|..|.|.+.  ++   --|.|||++.
T Consensus        95 ~gq~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv  169 (494)
T KOG1456|consen   95 AGQQALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSV  169 (494)
T ss_pred             cCchhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--cc---eeeEEeechh
Confidence            66655555443221        11223333  3455567899999999999999999988865  22   2499999999


Q ss_pred             HHHHHHHhcCC-ceeCC--eEEEEEEeeeC
Q psy1314         153 NVAEQVLANPK-QVICG--KEVDVKRVKFN  179 (275)
Q Consensus       153 e~a~~Ai~~~~-~~~~g--~~i~v~~~~~~  179 (275)
                      +.|++|.+.|+ ..|..  ..|+|..|++.
T Consensus       170 ~~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  170 EVAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             HHHHHHHhhcccccccccceeEEEEecCcc
Confidence            99999999985 55443  45566666544

>KOG0114|consensus

Probab=99.35  E-value=3.9e-12  Score=89.07  Aligned_cols=78  Identities=17%  Similarity=0.304  Sum_probs=69.6

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .++.|||.|||+++|.+++.++|.+||+|..|+|-..+.|   +|.|||.|++..+|++|++.| ...++++.+.|....
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            3577999999999999999999999999999999877654   899999999999999999998 588999999987665


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      +.
T Consensus        94 ~~   95 (124)
T KOG0114|consen   94 PE   95 (124)
T ss_pred             HH
Confidence            43

>KOG0108|consensus

Probab=99.35  E-value=2.8e-12  Score=114.39  Aligned_cols=80  Identities=24%  Similarity=0.426  Sum_probs=75.5

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~~~~   95 (275)
                      +.|||+|||+++++++|.++|+..|.|.+++++.|+.||+++||+|++|.+.++|+.|++.+ +.++.+++|+|.++...
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            89999999999999999999999999999999999999999999999999999999999976 57999999999988654


Q ss_pred             c
Q psy1314          96 V   96 (275)
Q Consensus        96 ~   96 (275)
                      +
T Consensus        99 ~   99 (435)
T KOG0108|consen   99 K   99 (435)
T ss_pred             c
Confidence            3

>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=99.34  E-value=1.1e-11  Score=83.67  Aligned_cols=72  Identities=35%  Similarity=0.655  Sum_probs=63.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc-eecCeeeccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH-YIGNKKIDPK   90 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~-~~~g~~i~v~   90 (275)
                      +|+|++||..+++++|+++|+.+|.|..+.+..++.+ .++++|||+|.+.++|..|++.+.. .+.++.+.+.
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            5899999999999999999999999999999988655 7789999999999999999987544 5888877664

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).

>KOG0116|consensus

Probab=99.33  E-value=1.2e-11  Score=109.82  Aligned_cols=81  Identities=19%  Similarity=0.356  Sum_probs=70.0

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeCC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~~  180 (275)
                      ..|||.|||.++++++|+++|.+||+|+...|....-.+...+|+||+|.+.++++.||+.....|.+++|.|.......
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~~~  368 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRPGF  368 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccccc
Confidence            55999999999999999999999999999888765433334499999999999999999999899999999998766554


Q ss_pred             C
Q psy1314         181 E  181 (275)
Q Consensus       181 ~  181 (275)
                      .
T Consensus       369 ~  369 (419)
T KOG0116|consen  369 R  369 (419)
T ss_pred             c
Confidence            3

>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=99.30  E-value=2.2e-11  Score=82.10  Aligned_cols=72  Identities=32%  Similarity=0.673  Sum_probs=65.3

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEE
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVK  174 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~  174 (275)
                      +|+|++||..+++++|+++|+.+|.|..+.+..+..+ .++++|||+|.+.++|..|++.++ ..+.++++.|.
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            4899999999999999999999999999999987655 668999999999999999999985 66999999875

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).

>KOG0415|consensus

Probab=99.28  E-value=6e-12  Score=106.24  Aligned_cols=84  Identities=23%  Similarity=0.397  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ....+.+.|||+.|.+-+|+++|.-+|+.||+|.+|.|+++..|+.+.-||||+|.+.++|++|.- +.+..|..+.|.|
T Consensus       234 d~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  234 DVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             ccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            345778999999999999999999999999999999999999999999999999999999999965 4578999999999


Q ss_pred             ccccc
Q psy1314          90 KRVTK   94 (275)
Q Consensus        90 ~~~~~   94 (275)
                      ..++.
T Consensus       314 DFSQS  318 (479)
T KOG0415|consen  314 DFSQS  318 (479)
T ss_pred             ehhhh
Confidence            88754

>KOG4210|consensus

Probab=99.28  E-value=9.6e-12  Score=106.07  Aligned_cols=170  Identities=23%  Similarity=0.336  Sum_probs=139.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc-eecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH-YIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~-~~~g~~i~v~~~~   93 (275)
                      ...++|++++..++.+.++..++...|.+..+.+........+++++.|.|+..+.+..+|.+... .+..+.+......
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            588999999999999999999999999888888877667788999999999999999999998654 4444444333322


Q ss_pred             ccc-----------CCCcceee-ecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc
Q psy1314          94 KRV-----------NPLKCKIF-VGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus        94 ~~~-----------~~~~~~l~-V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      ...           .....+++ |.+|++.+++++|+.+|..++.|..++++.++.++..++|++|.|.+...+.+++..
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            221           11234455 999999999999999999999999999999999999999999999999999999887


Q ss_pred             CCceeCCeEEEEEEeeeCCCCCC
Q psy1314         162 PKQVICGKEVDVKRVKFNPETMG  184 (275)
Q Consensus       162 ~~~~~~g~~i~v~~~~~~~~~~~  184 (275)
                      ....+.++++.+....+.+....
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~~  269 (285)
T KOG4210|consen  247 QTRSIGGRPLRLEEDEPRPKSDG  269 (285)
T ss_pred             ccCcccCcccccccCCCCccccc
Confidence            44778899999988887766543

>KOG0111|consensus

Probab=99.28  E-value=4.6e-12  Score=100.45  Aligned_cols=85  Identities=25%  Similarity=0.423  Sum_probs=78.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~   91 (275)
                      ....++|||++|..++||.-|...|-+||.|.+|++..|-.+.+.|||+||+|...|+|.+||..+ ..++.|+.|+|..
T Consensus         7 a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~   86 (298)
T KOG0111|consen    7 ANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNL   86 (298)
T ss_pred             cccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEee
Confidence            456789999999999999999999999999999999999999999999999999999999999864 6699999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.+.+.
T Consensus        87 AkP~ki   92 (298)
T KOG0111|consen   87 AKPEKI   92 (298)
T ss_pred             cCCccc
Confidence            876543

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

Probab=99.27  E-value=1.9e-11  Score=103.85  Aligned_cols=79  Identities=23%  Similarity=0.582  Sum_probs=75.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      .++|||+|||..+++++|.++|.+||.|..+.+..++.++.++|+|||+|.+.++|..|++.++ ..|.+++|.|.++..
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            5899999999999999999999999999999999999899999999999999999999999996 999999999999653

>KOG0108|consensus

Probab=99.26  E-value=1.1e-11  Score=110.55  Aligned_cols=82  Identities=27%  Similarity=0.481  Sum_probs=78.3

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      +.|||+|||+++++++|.++|+..|.|..++++.|+.|++++||+|++|.+.++|++|++.++ .++.+++|+|.++...
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            789999999999999999999999999999999999999999999999999999999999996 9999999999998877


Q ss_pred             CCC
Q psy1314         180 PET  182 (275)
Q Consensus       180 ~~~  182 (275)
                      ..+
T Consensus        99 ~~~  101 (435)
T KOG0108|consen   99 KNA  101 (435)
T ss_pred             chh
Confidence            654

>KOG0128|consensus

Probab=99.24  E-value=3.7e-13  Score=124.86  Aligned_cols=149  Identities=19%  Similarity=0.259  Sum_probs=126.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      .+..++||.||+..+.+.+|.+.|..++.+..+++...+.+++.+|+|||+|.+++++.+||......+.+         
T Consensus       665 R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g---------  735 (881)
T KOG0128|consen  665 RDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG---------  735 (881)
T ss_pred             HHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh---------
Confidence            45567999999999999999999999998888888766778999999999999999999999986665555         


Q ss_pred             cccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEE
Q psy1314          94 KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD  172 (275)
Q Consensus        94 ~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~  172 (275)
                            +..|+|.|+|+..|.++|+.++..+|.+..+.++..+ .++++|.++|.|.++.++.+++.+.. ..+.-..+.
T Consensus       736 ------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~  808 (881)
T KOG0128|consen  736 ------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGE  808 (881)
T ss_pred             ------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCcc
Confidence                  3579999999999999999999999999999877664 47899999999999999999988864 445555555


Q ss_pred             EEEeee
Q psy1314         173 VKRVKF  178 (275)
Q Consensus       173 v~~~~~  178 (275)
                      |....+
T Consensus       809 v~vsnp  814 (881)
T KOG0128|consen  809 VQVSNP  814 (881)
T ss_pred             ccccCC
Confidence            555444

>KOG4205|consensus

Probab=99.24  E-value=1.4e-11  Score=105.47  Aligned_cols=114  Identities=33%  Similarity=0.558  Sum_probs=95.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~   94 (275)
                      ...+|||+.||.++++++|+++|++||.|..+.++.|..+.+++||+||+|.+++++++++...-+.|.++.++|..+.+
T Consensus        96 ~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   96 RTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQKFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             ceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceecccceeeecCceeeEeeccc
Confidence            35589999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             ccCCCcceeeecC------CCCCCCHHHHHHhcccCCCeE
Q psy1314          95 RVNPLKCKIFVGG------LTTEISEQDVRDYFSQYGSIT  128 (275)
Q Consensus        95 ~~~~~~~~l~V~~------l~~~~~~~~l~~~F~~~G~v~  128 (275)
                      +.......+.+..      +....+.-.|..+|..|+.+.
T Consensus       176 k~~~~~~~~~~~~~~~~~~~g~~~~~~~l~~~~~g~~~~~  215 (311)
T KOG4205|consen  176 KEVMQSTKSSVSTRGKGNNLGNGRTGFFLKKYFKGYGPVG  215 (311)
T ss_pred             hhhccccccccccccccccccccccccccchhccccCccc
Confidence            8776655443333      333334445666676666543

>KOG0415|consensus

Probab=99.22  E-value=2e-11  Score=103.19  Aligned_cols=83  Identities=20%  Similarity=0.341  Sum_probs=77.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      .++...|||.-|.+-++++||.-+|+.||.|..|.|++|..|+.+-.||||+|++.+++++|.-+| |..|++++|+|.+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDF  315 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDF  315 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeeh
Confidence            456688999999999999999999999999999999999999999999999999999999999888 7999999999988


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +..-
T Consensus       316 SQSV  319 (479)
T KOG0415|consen  316 SQSV  319 (479)
T ss_pred             hhhh
Confidence            7644

>smart00361 RRM_1 RNA recognition motif

Probab=99.21  E-value=5.7e-11  Score=80.14  Aligned_cols=60  Identities=22%  Similarity=0.432  Sum_probs=53.0

Q ss_pred             HHHHHHhcc----cCCCeEEEE-eccCCCC--CCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314         114 EQDVRDYFS----QYGSITEFQ-QPFDKSK--NMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus       114 ~~~l~~~F~----~~G~v~~v~-i~~~~~~--~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      +++|+++|+    +||.|.+|. |+.++.+  +.++|++||+|.+.++|.+|++.| +..+.|+.|.+
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            578888998    999999995 7777666  889999999999999999999998 48899999876

>KOG0132|consensus

Probab=99.17  E-value=4.5e-11  Score=110.10  Aligned_cols=101  Identities=22%  Similarity=0.393  Sum_probs=83.9

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~~~   94 (275)
                      ++||||+.|+.+++|.||.++|+.||+|++|.++..      ++||||.+....+|++||.++ +..+..+.|++.|+..
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g  494 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVG  494 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeecc
Confidence            689999999999999999999999999999999876      579999999999999999875 6789999999999876


Q ss_pred             ccCCC------cceeeecCCCCCCCHHHHHHhcc
Q psy1314          95 RVNPL------KCKIFVGGLTTEISEQDVRDYFS  122 (275)
Q Consensus        95 ~~~~~------~~~l~V~~l~~~~~~~~l~~~F~  122 (275)
                      +-...      ...|=|+-||+..-.++|+.+.+
T Consensus       495 ~G~kse~k~~wD~~lGVt~IP~~kLt~dl~~~~e  528 (894)
T KOG0132|consen  495 KGPKSEYKDYWDVELGVTYIPWEKLTDDLEAWCE  528 (894)
T ss_pred             CCcchhhhhhhhcccCeeEeehHhcCHHHHHhhh
Confidence            54433      34455666787765555666654

>smart00361 RRM_1 RNA recognition motif

Probab=99.17  E-value=1.5e-10  Score=78.14  Aligned_cols=60  Identities=22%  Similarity=0.458  Sum_probs=52.0

Q ss_pred             HHHHHHHHh----hcCCeeEEE-EeeCCCC--CCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          30 EKEINDYFS----QYGEVESIS-IKNDPHT--GQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        30 ~~~l~~~f~----~~G~v~~~~-i~~~~~t--g~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      +++|+++|+    +||.|.+|. |+.++.+  ++++|++||+|.+.++|.+|++. ++..+.++.|.+
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            678888888    999999995 6666666  89999999999999999999986 577899988765

>KOG0109|consensus

Probab=99.14  E-value=6e-11  Score=97.91  Aligned_cols=71  Identities=30%  Similarity=0.567  Sum_probs=66.2

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      .+|||+|||.++++.+|+.+|++||.|.+|+|+++        |+||..++...|+.||..| +-.|+|..|.|+.++.|
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            47999999999999999999999999999999954        8999999999999999987 58899999999988877

>PF13893 RRM_5: RNA recognition motif

Probab=99.14  E-value=2.1e-10  Score=73.76  Aligned_cols=55  Identities=20%  Similarity=0.446  Sum_probs=48.3

Q ss_pred             HHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314         117 VRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus       117 l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      |.++|++||+|..+.+..+.     +++|||+|.+.++|++|++.+ +..+.|++|+|.++
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            68899999999999997653     579999999999999999987 58899999999875

(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 ....

>KOG4454|consensus

Probab=99.10  E-value=2.5e-11  Score=96.24  Aligned_cols=136  Identities=20%  Similarity=0.335  Sum_probs=111.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v   89 (275)
                      +..+..++|||.||...++|+-|.|+|-+-|+|..+.|...+ ..+.+ ||||.|+++-.+.-|++++ +..+.+.++.+
T Consensus         4 aaae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~   81 (267)
T KOG4454|consen    4 AAAEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQR   81 (267)
T ss_pred             CCcchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhc
Confidence            445678999999999999999999999999999999998775 45666 9999999999999999974 44555555544


Q ss_pred             cccccccCCCcceeeecC----CCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc
Q psy1314          90 KRVTKRVNPLKCKIFVGG----LTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus        90 ~~~~~~~~~~~~~l~V~~----l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      +            ++.++    |...++++.+...|+.-+++..+++.++.+ ++++.+.|+.+.-....-.++..
T Consensus        82 ~------------~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~  144 (267)
T KOG4454|consen   82 T------------LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDL  144 (267)
T ss_pred             c------------cccCCCcchhhhhcchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhh
Confidence            4            34444    777889999999999999999999998865 77888999988776666666554

>KOG1365|consensus

Probab=99.09  E-value=1.6e-10  Score=98.73  Aligned_cols=163  Identities=18%  Similarity=0.222  Sum_probs=122.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      +++..|..+.|||..++.+|..+|.-.....-...+.....++-.|.+.|.|.++|.-+-|++.+.+.+..+.|+|-.+.
T Consensus        58 ~~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~  137 (508)
T KOG1365|consen   58 DDNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKAT  137 (508)
T ss_pred             CcceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccC
Confidence            45566788899999999999999986543333333333345677899999999999999999998888888888876553


Q ss_pred             ccc-----------------CCCcceeeecCCCCCCCHHHHHHhcccCC----CeEEEEeccCCCCCCeeeEEEEEECCH
Q psy1314          94 KRV-----------------NPLKCKIFVGGLTTEISEQDVRDYFSQYG----SITEFQQPFDKSKNMKKGFCFISFDDQ  152 (275)
Q Consensus        94 ~~~-----------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G----~v~~v~i~~~~~~~~~~G~afV~f~~~  152 (275)
                      ..+                 +...-.|.+++||+++++.++.++|.+--    .++.|-+++. .+++..|-|||.|..+
T Consensus       138 ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~e  216 (508)
T KOG1365|consen  138 GEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACE  216 (508)
T ss_pred             chhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCH
Confidence            321                 11234577899999999999999996432    3344444433 3577889999999999


Q ss_pred             HHHHHHHhcCCceeCCeEEEEEEee
Q psy1314         153 NVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus       153 e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ++|+.||.++...|.-+.|++-++.
T Consensus       217 e~aq~aL~khrq~iGqRYIElFRST  241 (508)
T KOG1365|consen  217 EDAQFALRKHRQNIGQRYIELFRST  241 (508)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHHHHh
Confidence            9999999998777887777765443

>KOG0153|consensus

Probab=99.07  E-value=3.7e-10  Score=95.44  Aligned_cols=78  Identities=31%  Similarity=0.501  Sum_probs=69.6

Q ss_pred             ccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-C-ceeCCeEEE
Q psy1314          95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-K-QVICGKEVD  172 (275)
Q Consensus        95 ~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~-~~~~g~~i~  172 (275)
                      .++..-.+|||++|-..+++.+|+++|.+||+|..+.++..      +++|||+|.+.++|+.|.++. + ..|+|.+|.
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~  296 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRLK  296 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEEE
Confidence            34445688999999999999999999999999999998865      569999999999999999886 4 789999999


Q ss_pred             EEEeee
Q psy1314         173 VKRVKF  178 (275)
Q Consensus       173 v~~~~~  178 (275)
                      |.|..+
T Consensus       297 i~Wg~~  302 (377)
T KOG0153|consen  297 IKWGRP  302 (377)
T ss_pred             EEeCCC
Confidence            999887

>PF13893 RRM_5: RNA recognition motif

Probab=99.06  E-value=7.8e-10  Score=71.12  Aligned_cols=55  Identities=25%  Similarity=0.502  Sum_probs=47.9

Q ss_pred             HHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccc
Q psy1314          33 INDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRV   92 (275)
Q Consensus        33 l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~   92 (275)
                      |.++|++||+|+++.+..+.     +++|||+|.+.++|++|++ +++..+.+++|.|+++
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     5799999999999999998 4678999999998764

(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 ....

>KOG0226|consensus

Probab=99.05  E-value=1.2e-10  Score=94.43  Aligned_cols=166  Identities=17%  Similarity=0.258  Sum_probs=126.4

Q ss_pred             CCCCeEEEcCCCCCCCHHH-H--HHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          14 NDERKLFVGGLHRNTGEKE-I--NDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~-l--~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      .....+++.++-.++..+- |  ...|+.+-.+....++++. -+..++++|+.|.......++-.. ..+++.-.+|+.
T Consensus        94 P~vf~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~  172 (290)
T KOG0226|consen   94 PAVFRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRL  172 (290)
T ss_pred             cccccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceee
Confidence            4455677777766665544 3  5667777666666666663 356678999999887766666544 344555555554


Q ss_pred             ccccccc-------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314          90 KRVTKRV-------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus        90 ~~~~~~~-------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      ...+..+       ...+.+||.+.|..+++++.|...|.+|-.....++++|+-|++++||+||.|.+.+++..|+..|
T Consensus       173 a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem  252 (290)
T KOG0226|consen  173 AAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREM  252 (290)
T ss_pred             ccccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhh
Confidence            4433332       334689999999999999999999999999899999999999999999999999999999999998


Q ss_pred             C-ceeCCeEEEEEEeeeCC
Q psy1314         163 K-QVICGKEVDVKRVKFNP  180 (275)
Q Consensus       163 ~-~~~~g~~i~v~~~~~~~  180 (275)
                      + ..++.+.|.+.....+.
T Consensus       253 ~gkyVgsrpiklRkS~wke  271 (290)
T KOG0226|consen  253 NGKYVGSRPIKLRKSEWKE  271 (290)
T ss_pred             cccccccchhHhhhhhHHh
Confidence            5 88888998887766654

>KOG0153|consensus

Probab=99.05  E-value=8.8e-10  Score=93.19  Aligned_cols=81  Identities=33%  Similarity=0.497  Sum_probs=71.7

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh--CCceecCe
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA--GDHYIGNK   85 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~--~~~~~~g~   85 (275)
                      ...++.....+|||++|-..++|.+|+++|.+||+|++|.++..+      ++|||+|.+.++|+.|.+.  +...|+|.
T Consensus       220 lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~------~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  220 LEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK------GCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             cCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc------ccceeeehhhHHHHHHHHhhcceeeecce
Confidence            445667778899999999999999999999999999999998874      5999999999999998875  35588999


Q ss_pred             eeccccccc
Q psy1314          86 KIDPKRVTK   94 (275)
Q Consensus        86 ~i~v~~~~~   94 (275)
                      +|.+.|..+
T Consensus       294 Rl~i~Wg~~  302 (377)
T KOG0153|consen  294 RLKIKWGRP  302 (377)
T ss_pred             EEEEEeCCC
Confidence            999999877

>KOG0112|consensus

Probab=98.97  E-value=3.3e-10  Score=106.04  Aligned_cols=161  Identities=19%  Similarity=0.276  Sum_probs=124.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v   89 (275)
                      .+.....+||++||+..+++.+|+..|..+|.|.+|.|.+-+. +.-.-|+||.|.+...+-.|...+ ...|..-.+.+
T Consensus       367 DD~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~  445 (975)
T KOG0112|consen  367 DDFRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRI  445 (975)
T ss_pred             cchhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCcccc
Confidence            3445678999999999999999999999999999999977532 344458999999988777765543 33444334444


Q ss_pred             cccccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCC
Q psy1314          90 KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICG  168 (275)
Q Consensus        90 ~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g  168 (275)
                      ..... +......++|++|..++....|.+.|..||.|..|.+-..      .-|++|.|++...+++|++.+ ...|.+
T Consensus       446 glG~~-kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~  518 (975)
T KOG0112|consen  446 GLGQP-KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGG  518 (975)
T ss_pred             ccccc-ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCC
Confidence            43332 3445678999999999999999999999999999887533      348999999999999999987 355554


Q ss_pred             --eEEEEEEeeeC
Q psy1314         169 --KEVDVKRVKFN  179 (275)
Q Consensus       169 --~~i~v~~~~~~  179 (275)
                        +.+.|.++.+.
T Consensus       519 P~~r~rvdla~~~  531 (975)
T KOG0112|consen  519 PPRRLRVDLASPP  531 (975)
T ss_pred             CCcccccccccCC
Confidence              56777776654

>KOG0132|consensus

Probab=98.95  E-value=1.4e-09  Score=100.36  Aligned_cols=73  Identities=22%  Similarity=0.413  Sum_probs=68.1

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      ++|||+.|+.+++++||+++|+.||+|..|.++.      +++||||++....+|.+|+.+| +..+.++.|+|.|+..+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~------~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP------PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeecc------CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            7899999999999999999999999999998864      4889999999999999999999 68999999999998766

>KOG4208|consensus

Probab=98.93  E-value=3.3e-09  Score=83.76  Aligned_cols=85  Identities=22%  Similarity=0.398  Sum_probs=71.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhc-CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCe
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY-GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNK   85 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~-G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~   85 (275)
                      ...+.......++|..||.-+.+.+|..+|.++ |.|..+++-+++.||.|+|||||+|++++.|+-|-+.+ +-.|.++
T Consensus        41 ~~~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~  120 (214)
T KOG4208|consen   41 REKPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEH  120 (214)
T ss_pred             ccCCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhh
Confidence            445666777889999999999999999999998 77888899899999999999999999999999877754 4466666


Q ss_pred             eeccccc
Q psy1314          86 KIDPKRV   92 (275)
Q Consensus        86 ~i~v~~~   92 (275)
                      .|.+...
T Consensus       121 lL~c~vm  127 (214)
T KOG4208|consen  121 LLECHVM  127 (214)
T ss_pred             eeeeEEe
Confidence            6555544

>KOG0146|consensus

Probab=98.93  E-value=1.7e-09  Score=88.49  Aligned_cols=86  Identities=23%  Similarity=0.349  Sum_probs=76.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v   89 (275)
                      .+..+-+.|||-.||.+..+.||.+.|-.||.|++.++..|+.|+.||.|+||.|.+..++++||..+ +-.|.=++++|
T Consensus       280 reGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKV  359 (371)
T KOG0146|consen  280 REGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKV  359 (371)
T ss_pred             hcCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhh
Confidence            34567899999999999999999999999999999999999999999999999999999999999974 45677788888


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      +...++.
T Consensus       360 QLKRPkd  366 (371)
T KOG0146|consen  360 QLKRPKD  366 (371)
T ss_pred             hhcCccc
Confidence            7766554

>KOG4661|consensus

Probab=98.85  E-value=5.8e-09  Score=93.42  Aligned_cols=81  Identities=17%  Similarity=0.406  Sum_probs=74.7

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      +.|||.+|+..+...+|+.+|++||.|+-.+|+++.-+.-.++|+||++.+.++|.++|+.|+ +.|.|+.|.|..++..
T Consensus       406 RNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKNE  485 (940)
T KOG4661|consen  406 RNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKNE  485 (940)
T ss_pred             cceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecccC
Confidence            679999999999999999999999999999999987777789999999999999999999995 8999999999988766


Q ss_pred             CC
Q psy1314         180 PE  181 (275)
Q Consensus       180 ~~  181 (275)
                      +.
T Consensus       486 p~  487 (940)
T KOG4661|consen  486 PG  487 (940)
T ss_pred             cc
Confidence            54

>KOG4208|consensus

Probab=98.84  E-value=8.3e-09  Score=81.52  Aligned_cols=82  Identities=18%  Similarity=0.429  Sum_probs=72.7

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccC-CCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQY-GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~-G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ....-++|..+|.-+.+..|..+|.++ |.|..+++-+++.||.++|||||+|++++.|+-|-+.|| ..|.++-|.|.+
T Consensus        47 ~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   47 EIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            344568999999999999999999988 788888888999999999999999999999999999985 788889999987


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      ..+.
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7665

>KOG0116|consensus

Probab=98.81  E-value=1.1e-08  Score=90.96  Aligned_cols=79  Identities=25%  Similarity=0.447  Sum_probs=64.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ....+|||.|||+++++++|+++|..||+|+...|......++...|+||+|.+.++++.||++....+.++++.|+..
T Consensus       286 ~~~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  286 ADGLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEK  364 (419)
T ss_pred             ecccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEec
Confidence            3445599999999999999999999999999887766432344448999999999999999999877777777666644

>KOG1456|consensus

Probab=98.81  E-value=1.4e-07  Score=80.70  Aligned_cols=150  Identities=17%  Similarity=0.188  Sum_probs=114.5

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeecc
Q psy1314          12 GRNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDP   89 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v   89 (275)
                      ...+...++|-+|... +.-+.|..+|..||-|+.|++++.+     .|-|.|++.|..+.++|+..+ +..+.|.+|.+
T Consensus       283 g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  283 GGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            3456778999999876 6889999999999999999999875     378999999999999999854 55667777766


Q ss_pred             cccccc--------------------------------------cCCCcceeeecCCCCCCCHHHHHHhcccCCC-eEEE
Q psy1314          90 KRVTKR--------------------------------------VNPLKCKIFVGGLTTEISEQDVRDYFSQYGS-ITEF  130 (275)
Q Consensus        90 ~~~~~~--------------------------------------~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~-v~~v  130 (275)
                      ..+.+.                                      -..+++.|+.=|.|..+||+.|-++|..... ..+|
T Consensus       358 ~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~nek~v~~~sv  437 (494)
T KOG1456|consen  358 CVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGICNEKDVPPTSV  437 (494)
T ss_pred             eeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHhhhcCCCcceE
Confidence            544322                                      1123467888899999999999999987653 4556


Q ss_pred             EeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCc-eeCC
Q psy1314         131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ-VICG  168 (275)
Q Consensus       131 ~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~-~~~g  168 (275)
                      +|...+...  .-.+++||++.++|..||.++++ .|.+
T Consensus       438 kvFp~kser--SssGllEfe~~s~Aveal~~~NH~pi~~  474 (494)
T KOG1456|consen  438 KVFPLKSER--SSSGLLEFENKSDAVEALMKLNHYPIEG  474 (494)
T ss_pred             Eeecccccc--cccceeeeehHHHHHHHHHHhccccccC
Confidence            665444222  23479999999999999999863 3443

>KOG4661|consensus

Probab=98.78  E-value=1.7e-08  Score=90.47  Aligned_cols=81  Identities=21%  Similarity=0.399  Sum_probs=72.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~v~~~   92 (275)
                      .-.+.|||.+|+..+...+|+.+|++||+|+-.+|+++..+.-.+.|+||++.+.++|.+||+.+ .+.+.|+.|.|+.+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            34567999999999999999999999999999999999888888999999999999999999964 66899999998876


Q ss_pred             cc
Q psy1314          93 TK   94 (275)
Q Consensus        93 ~~   94 (275)
                      ..
T Consensus       483 KN  484 (940)
T KOG4661|consen  483 KN  484 (940)
T ss_pred             cc
Confidence            53

>KOG4307|consensus

Probab=98.73  E-value=2.2e-08  Score=91.70  Aligned_cols=162  Identities=11%  Similarity=0.081  Sum_probs=121.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      .+.+.+-+...++++++.+++++|... -|.+..|..+...+...|-++|+|....++.+|++.+...+-.+.+++..+.
T Consensus       309 ~d~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g  387 (944)
T KOG4307|consen  309 SDKYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPG  387 (944)
T ss_pred             chhheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCC
Confidence            556677888999999999999999754 3666666666544444789999999999999999988877777777655432


Q ss_pred             ccc----------------------------------------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE-EEe
Q psy1314          94 KRV----------------------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE-FQQ  132 (275)
Q Consensus        94 ~~~----------------------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~-v~i  132 (275)
                      ...                                        .....+|||..||..+++.++.++|...-.|++ |.|
T Consensus       388 ~~~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~l  467 (944)
T KOG4307|consen  388 NLGRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIEL  467 (944)
T ss_pred             ccccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEe
Confidence            110                                        012367999999999999999999998777777 444


Q ss_pred             ccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314         133 PFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus       133 ~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .. --+++.++.|||+|..++++.+|+.-. ++.+..+.|.|....
T Consensus       468 t~-~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si~  512 (944)
T KOG4307|consen  468 TR-LPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSIA  512 (944)
T ss_pred             cc-CCcccccchhhheeccccccchhhhcccccccCceEEEeechh
Confidence            43 345677889999999988777776554 566667777776443

>KOG0533|consensus

Probab=98.70  E-value=5.3e-08  Score=80.50  Aligned_cols=83  Identities=16%  Similarity=0.350  Sum_probs=73.1

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ....+|.|.|||..++++||+++|+.|+.++.+.+..++ .+.+.|.|-|.|...++|++|++.+ +..|+|+.+++..+
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            344789999999999999999999999999999888775 5788999999999999999999998 58899999988877


Q ss_pred             eeCCC
Q psy1314         177 KFNPE  181 (275)
Q Consensus       177 ~~~~~  181 (275)
                      .....
T Consensus       160 ~~~~~  164 (243)
T KOG0533|consen  160 SSPSQ  164 (243)
T ss_pred             cCccc
Confidence            65543

>KOG2193|consensus

Probab=98.66  E-value=2.3e-09  Score=92.82  Aligned_cols=154  Identities=14%  Similarity=0.234  Sum_probs=119.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC--ceecCeeeccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD--HYIGNKKIDPKRVTK   94 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~--~~~~g~~i~v~~~~~   94 (275)
                      +.|||+||.+.++..+|+.+|...-.-.+-.++..      .||+||.+.+..+|.+|++.+.  ..+.|+++++..+.+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k------~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVK------SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeee------cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            46899999999999999999976522112222221      3799999999999999999764  378899999988876


Q ss_pred             ccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEec-cCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEE
Q psy1314          95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP-FDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD  172 (275)
Q Consensus        95 ~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~-~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~  172 (275)
                      ++. .++++-|.|+|+...|+.|..++..||.+..|.++ .+.++-    ..-|+|.+.+.++.||.+++ ..+....++
T Consensus        76 kkq-rsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~eta----vvnvty~~~~~~~~ai~kl~g~Q~en~~~k  150 (584)
T KOG2193|consen   76 KKQ-RSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETA----VVNVTYSAQQQHRQAIHKLNGPQLENQHLK  150 (584)
T ss_pred             HHH-HhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHH----HHHHHHHHHHHHHHHHHhhcchHhhhhhhh
Confidence            644 44669999999999999999999999999998765 232221    23468889999999999984 777777777


Q ss_pred             EEEeeeCCC
Q psy1314         173 VKRVKFNPE  181 (275)
Q Consensus       173 v~~~~~~~~  181 (275)
                      +........
T Consensus       151 ~~YiPdeq~  159 (584)
T KOG2193|consen  151 VGYIPDEQN  159 (584)
T ss_pred             cccCchhhh
Confidence            776655443

>KOG4209|consensus

Probab=98.66  E-value=1.2e-07  Score=78.48  Aligned_cols=83  Identities=20%  Similarity=0.324  Sum_probs=76.5

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      .....+||+|+.+.++.++++.+|+.||.|..+.|+.|+.++.+++|+||+|.+.+.+++|+......|.++.++|....
T Consensus        99 ~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen   99 VDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             cCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeee
Confidence            34578999999999999999999999999999999999999999999999999999999999955699999999999888


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      .+.
T Consensus       179 ~~~  181 (231)
T KOG4209|consen  179 TNV  181 (231)
T ss_pred             eec
Confidence            773

>KOG4676|consensus

Probab=98.66  E-value=2.1e-08  Score=86.17  Aligned_cols=146  Identities=11%  Similarity=0.164  Sum_probs=111.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC---CCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT---GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~t---g~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ...|.|.||++.+|.++++.+|...|+|.++.|..+...   ....-.|||.|.+...+..|..+.+.++-+..|.|...
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            348999999999999999999999999999999875432   33456899999999999888887777766665554332


Q ss_pred             ccccC---------------------------------------------------------CCcceeeecCCCCCCCHH
Q psy1314          93 TKRVN---------------------------------------------------------PLKCKIFVGGLTTEISEQ  115 (275)
Q Consensus        93 ~~~~~---------------------------------------------------------~~~~~l~V~~l~~~~~~~  115 (275)
                      .....                                                         ....+|+|.+|+..+...
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            11100                                                         011568999999999999


Q ss_pred             HHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCce
Q psy1314         116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQV  165 (275)
Q Consensus       116 ~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~  165 (275)
                      ++.+.|+.+|+|....+....    ..-+|-|+|........|+..++..
T Consensus       167 e~~e~f~r~Gev~ya~~ask~----~s~~c~~sf~~qts~~halr~~gre  212 (479)
T KOG4676|consen  167 ESGESFERKGEVSYAHTASKS----RSSSCSHSFRKQTSSKHALRSHGRE  212 (479)
T ss_pred             hhhhhhhhcchhhhhhhhccC----CCcchhhhHhhhhhHHHHHHhcchh
Confidence            999999999998877665332    2346779999888888888876533

>KOG4206|consensus

Probab=98.65  E-value=8.1e-08  Score=77.16  Aligned_cols=81  Identities=19%  Similarity=0.375  Sum_probs=70.9

Q ss_pred             CcceeeecCCCCCCCHHHHHH----hcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRD----YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~----~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      ++.+|||.||+..+..++|+.    +|++||.|..|....   +.+.+|-|||.|.+.+.|..|+..+ +.-+.|+++.+
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mri   84 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRI   84 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhe
Confidence            344999999999999999998    999999999998764   3567899999999999999999998 57899999999


Q ss_pred             EEeeeCCCC
Q psy1314         174 KRVKFNPET  182 (275)
Q Consensus       174 ~~~~~~~~~  182 (275)
                      ..|+.+.+.
T Consensus        85 qyA~s~sdi   93 (221)
T KOG4206|consen   85 QYAKSDSDI   93 (221)
T ss_pred             ecccCccch
Confidence            998877553

>KOG4209|consensus

Probab=98.64  E-value=3.6e-08  Score=81.58  Aligned_cols=84  Identities=19%  Similarity=0.345  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ....+...|||+|+...+|.+++..+|+.||.|..+.|..++.++.+++|+||+|.+.+.+++++.++...|.++.+.+.
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            44567889999999999999999999999999999999999999999999999999999999999988899999988887


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      +...
T Consensus       176 ~~r~  179 (231)
T KOG4209|consen  176 LKRT  179 (231)
T ss_pred             eeee
Confidence            7643

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

Probab=98.61  E-value=2.4e-07  Score=65.81  Aligned_cols=61  Identities=16%  Similarity=0.279  Sum_probs=55.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQY--GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~--G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      +||.|+|||...|.++|.+++...  |...-+.+..|..+..+.|||||.|.++++|.+..+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~   64 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKA   64 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHH
Confidence            689999999999999999999764  6677788999988999999999999999999998886

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

>KOG0226|consensus

Probab=98.61  E-value=6e-08  Score=78.96  Aligned_cols=85  Identities=19%  Similarity=0.448  Sum_probs=74.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ...++..+||.+.|..+++++.|...|.+|-.....++++++.|++++||+||.|.+.+++..|+.. +++.++.++|..
T Consensus       185 ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpikl  264 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKL  264 (290)
T ss_pred             cCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHh
Confidence            3456678999999999999999999999998888899999999999999999999999999999985 567888888877


Q ss_pred             cccccc
Q psy1314          90 KRVTKR   95 (275)
Q Consensus        90 ~~~~~~   95 (275)
                      ..+..+
T Consensus       265 RkS~wk  270 (290)
T KOG0226|consen  265 RKSEWK  270 (290)
T ss_pred             hhhhHH
Confidence            766543

>KOG0533|consensus

Probab=98.57  E-value=2.4e-07  Score=76.60  Aligned_cols=81  Identities=16%  Similarity=0.355  Sum_probs=70.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ...+.+|.|.|||..++++||+|+|++|++++.+.|..++ ++++.|.|-|.|...++|++|++. ++..++++++.+..
T Consensus        80 ~~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~  158 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEI  158 (243)
T ss_pred             CCCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEE
Confidence            3445789999999999999999999999999999998884 699999999999999999999986 46688888877766


Q ss_pred             ccc
Q psy1314          92 VTK   94 (275)
Q Consensus        92 ~~~   94 (275)
                      ...
T Consensus       159 i~~  161 (243)
T KOG0533|consen  159 ISS  161 (243)
T ss_pred             ecC
Confidence            543

>KOG4307|consensus

Probab=98.55  E-value=2.4e-07  Score=85.08  Aligned_cols=74  Identities=15%  Similarity=0.310  Sum_probs=64.0

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      .|.+.|+|++++.+||.++|..|-.+....+++..+.+...|-|.|.|++.++|.+|.+.+ ++.|..++|.+..
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            5889999999999999999999977665555555677899999999999999999999998 4888888888764

>KOG4660|consensus

Probab=98.55  E-value=1.1e-07  Score=85.41  Aligned_cols=149  Identities=20%  Similarity=0.233  Sum_probs=98.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~   88 (275)
                      .+......+|+|-|||..+++++|+++|+.||+|..|+....     .++.+||+|-|..+|++|++.+ ...+.++.|.
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            344567889999999999999999999999999999766554     3689999999999999999875 4567776665


Q ss_pred             cccccccc-----------------------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEE
Q psy1314          89 PKRVTKRV-----------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFC  145 (275)
Q Consensus        89 v~~~~~~~-----------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~a  145 (275)
                      ......+.                       ......+++ .|++..+..-++..|+-++.+.. +.     +..-+---
T Consensus       144 ~~~~~~~~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~g-~l~P~~s~~~~~~~~~~~~~~~~-~~-----~~~~~hq~  216 (549)
T KOG4660|consen  144 RPGGARRAMGLQSGTSFLNHFGSPLANSPPGGWPRGQLFG-MLSPTRSSILLEHISSVDGSSPG-RE-----TPLLNHQR  216 (549)
T ss_pred             CCCcccccchhcccchhhhhccchhhcCCCCCCcCCccee-eeccchhhhhhhcchhccCcccc-cc-----ccchhhhh
Confidence            22211110                       001122332 37777777666666666676554 21     11112235


Q ss_pred             EEEECCHHHHHHHHhcCCceeCCeE
Q psy1314         146 FISFDDQNVAEQVLANPKQVICGKE  170 (275)
Q Consensus       146 fV~f~~~e~a~~Ai~~~~~~~~g~~  170 (275)
                      |++|.+..++..+...++..+.+..
T Consensus       217 ~~~~~~~~s~a~~~~~~G~~~s~~~  241 (549)
T KOG4660|consen  217 FVEFADNRSYAFSEPRGGFLISNSS  241 (549)
T ss_pred             hhhhccccchhhcccCCceecCCCC
Confidence            7888888887555443334444444

>KOG0106|consensus

Probab=98.54  E-value=1e-07  Score=77.16  Aligned_cols=72  Identities=25%  Similarity=0.586  Sum_probs=62.5

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      .+|||++||+.+.+.+|..+|..||.|.++.+.        .+|+||+|++..+|..||..++ ..|++.++.|.++...
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            468999999999999999999999999988764        5689999999999999999985 7788888777766654


Q ss_pred             C
Q psy1314         180 P  180 (275)
Q Consensus       180 ~  180 (275)
                      .
T Consensus        74 ~   74 (216)
T KOG0106|consen   74 R   74 (216)
T ss_pred             c
Confidence            3

>KOG1995|consensus

Probab=98.47  E-value=5.8e-07  Score=76.89  Aligned_cols=86  Identities=24%  Similarity=0.349  Sum_probs=76.8

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE--------EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE--------FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~--------v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      .....+|||.+||..+++++|.++|.+++.|..        |.|.++++|+.+|+-|.|+|++...|++||+.. ...++
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            445678999999999999999999999988754        678889999999999999999999999999998 58899


Q ss_pred             CeEEEEEEeeeCCCC
Q psy1314         168 GKEVDVKRVKFNPET  182 (275)
Q Consensus       168 g~~i~v~~~~~~~~~  182 (275)
                      +..|+|..|+.++..
T Consensus       143 gn~ikvs~a~~r~~v  157 (351)
T KOG1995|consen  143 GNTIKVSLAERRTGV  157 (351)
T ss_pred             CCCchhhhhhhccCc
Confidence            999999999888753

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

Probab=98.35  E-value=2.4e-06  Score=60.70  Aligned_cols=77  Identities=12%  Similarity=0.255  Sum_probs=62.3

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccC--CCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC----CeEEEE
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQY--GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC----GKEVDV  173 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~--G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~----g~~i~v  173 (275)
                      ++|.|+|||...|.++|.+++...  |....+-++.|-.+..+.|||||.|.+++.|.+..+.. +..+.    .+.++|
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            579999999999999999988753  67888889999889999999999999999999888775 33332    345566


Q ss_pred             EEee
Q psy1314         174 KRVK  177 (275)
Q Consensus       174 ~~~~  177 (275)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            5554

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

>KOG4454|consensus

Probab=98.34  E-value=2.5e-07  Score=73.86  Aligned_cols=77  Identities=16%  Similarity=0.261  Sum_probs=66.7

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~  176 (275)
                      +..++|||.|+...++++-|.++|-+-|+|..|.|+.+++.. .+ ||||.|+++-.+.-|++.++ ..+.+.++.+..-
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 EMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQE-QK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR   84 (267)
T ss_pred             chhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCC-Cc-eeeeecccccchhhhhhhcccchhccchhhcccc
Confidence            346789999999999999999999999999999999887654 45 99999999999999999985 7788877776543

>KOG1457|consensus

Probab=98.32  E-value=4.7e-06  Score=66.85  Aligned_cols=85  Identities=15%  Similarity=0.297  Sum_probs=64.8

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEecc-CCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeC---CeEEEEE
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPF-DKSKNMKKGFCFISFDDQNVAEQVLANPK-QVIC---GKEVDVK  174 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~-~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~---g~~i~v~  174 (275)
                      -++|||.+||.++...+|..+|..|--.+.+.+.. ++....-+-++||+|.+..+|.+|+..++ ..++   +..|++.
T Consensus        34 VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLhiE  113 (284)
T KOG1457|consen   34 VRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLHIE  113 (284)
T ss_pred             cceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeEee
Confidence            48899999999999999999999986655554432 22222335689999999999999999985 4443   5678888


Q ss_pred             EeeeCCCCCC
Q psy1314         175 RVKFNPETMG  184 (275)
Q Consensus       175 ~~~~~~~~~~  184 (275)
                      .++..+.+..
T Consensus       114 lAKSNtK~kr  123 (284)
T KOG1457|consen  114 LAKSNTKRKR  123 (284)
T ss_pred             ehhcCccccc
Confidence            8877665543

>KOG0128|consensus

Probab=98.31  E-value=6.3e-08  Score=90.72  Aligned_cols=153  Identities=17%  Similarity=0.191  Sum_probs=119.9

Q ss_pred             CCeEEEcCCCCCCCHH-HHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEK-EINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~-~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~   94 (275)
                      ...+.+.++.+...+. .++..|..++.|+.|.+......-...-+.++.+....+++.|+......+..+.+.+..+.+
T Consensus       571 ~~e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~s~~~~~esat~pa~~~~a~~~~av~~ad~  650 (881)
T KOG0128|consen  571 RREKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQSKHGSAESATVPAGGALANRSAAVGLADA  650 (881)
T ss_pred             hhhhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhhccccchhhcccccccccCCccccCCCCCc
Confidence            3456777887776555 677888899999999987633322222388899999999999998877778777777666554


Q ss_pred             ccCC-----------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC
Q psy1314          95 RVNP-----------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK  163 (275)
Q Consensus        95 ~~~~-----------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~  163 (275)
                      +...           ..+++||+||+..+.+++|+..|..++.+..+.|....++++.+|+|+++|..++++.+||....
T Consensus       651 ~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d  730 (881)
T KOG0128|consen  651 EEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRD  730 (881)
T ss_pred             hhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhh
Confidence            4322           12678999999999999999999999999888887777788899999999999999999998865


Q ss_pred             ceeCC
Q psy1314         164 QVICG  168 (275)
Q Consensus       164 ~~~~g  168 (275)
                      ..+.+
T Consensus       731 ~~~~g  735 (881)
T KOG0128|consen  731 SCFFG  735 (881)
T ss_pred             hhhhh
Confidence            44444

>KOG1548|consensus

Probab=98.30  E-value=1.7e-06  Score=73.53  Aligned_cols=80  Identities=21%  Similarity=0.363  Sum_probs=70.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEE--------EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCe
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITE--------FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGK  169 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~--------v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~  169 (275)
                      .+..|||+|||.++|.+++.++|+++|.|..        |++.++.. |..+|=|+|.|-..|+++-|++.|+ ..|.|+
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 VNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQ-GKLKGDALCCYIKRESVELAIKILDEDELRGK  211 (382)
T ss_pred             cCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCC-CCccCceEEEeecccHHHHHHHHhCcccccCc
Confidence            3467999999999999999999999998754        67777654 8889999999999999999999996 789999


Q ss_pred             EEEEEEeeeC
Q psy1314         170 EVDVKRVKFN  179 (275)
Q Consensus       170 ~i~v~~~~~~  179 (275)
                      .|+|.+|+..
T Consensus       212 ~~rVerAkfq  221 (382)
T KOG1548|consen  212 KLRVERAKFQ  221 (382)
T ss_pred             EEEEehhhhh
Confidence            9999988754

>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=98.23  E-value=1e-06  Score=64.02  Aligned_cols=71  Identities=25%  Similarity=0.452  Sum_probs=43.5

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC------ceeCCeEEEEE
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK------QVICGKEVDVK  174 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~------~~~~g~~i~v~  174 (275)
                      +.|+|.+++..++.++|+++|++|+.|..|.+.....      .|+|.|.+.+.|++|++++.      ..|.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            4688999999999999999999999999999886533      58999999999999988742      34666666655


Q ss_pred             Eee
Q psy1314         175 RVK  177 (275)
Q Consensus       175 ~~~  177 (275)
                      ...
T Consensus        76 vLe   78 (105)
T PF08777_consen   76 VLE   78 (105)
T ss_dssp             ---
T ss_pred             ECC
Confidence            443

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

>KOG1995|consensus

Probab=98.22  E-value=2.4e-06  Score=73.12  Aligned_cols=88  Identities=23%  Similarity=0.350  Sum_probs=75.7

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CC
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE--------SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GD   79 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~--------~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~   79 (275)
                      ...+.....+|||-.||..+++++|.++|.+++.|.        .|.|-+++.|+++|+-|.|+|.+...|++|+.. ..
T Consensus        59 ~~~~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~ag  138 (351)
T KOG1995|consen   59 SMADKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAG  138 (351)
T ss_pred             ccccccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcc
Confidence            344567788999999999999999999999998775        477888999999999999999999999999986 46


Q ss_pred             ceecCeeeccccccccc
Q psy1314          80 HYIGNKKIDPKRVTKRV   96 (275)
Q Consensus        80 ~~~~g~~i~v~~~~~~~   96 (275)
                      +.+.+..|.|..+..+.
T Consensus       139 kdf~gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  139 KDFCGNTIKVSLAERRT  155 (351)
T ss_pred             ccccCCCchhhhhhhcc
Confidence            78888888888776543

>KOG4660|consensus

Probab=98.19  E-value=7.5e-07  Score=80.10  Aligned_cols=71  Identities=27%  Similarity=0.442  Sum_probs=61.7

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD  172 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~  172 (275)
                      +....+|+|-|||..+++++|.++|+.||+|+.|+-     +-..++.+||+|-|..+|++|++.++ ..+.++.|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            445688999999999999999999999999998653     33458899999999999999999985 778888877

>KOG0151|consensus

Probab=98.12  E-value=4e-06  Score=77.43  Aligned_cols=83  Identities=18%  Similarity=0.338  Sum_probs=71.2

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCC---CCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK---SKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~---~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ....|||+||++.+++++|-..|..||+|..|+|+.-+   +..+.+-|+||.|.+..+|++|++.| +..+...++++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            45789999999999999999999999999999988543   33455779999999999999999998 588889999998


Q ss_pred             EeeeCCC
Q psy1314         175 RVKFNPE  181 (275)
Q Consensus       175 ~~~~~~~  181 (275)
                      |.+.-+-
T Consensus       253 Wgk~V~i  259 (877)
T KOG0151|consen  253 WGKAVPI  259 (877)
T ss_pred             ccccccc
Confidence            8865543

>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=98.02  E-value=8.9e-06  Score=55.31  Aligned_cols=68  Identities=18%  Similarity=0.301  Sum_probs=45.4

Q ss_pred             ceeeecCCCCCCCHHH----HHHhcccCC-CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314         101 CKIFVGGLTTEISEQD----VRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~----l~~~F~~~G-~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ..|+|.|||.+.+...    |++++..+| .|..|.          .+.|+|.|.+.+.|++|.+.| +..+.|.+|.|.
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            3589999999988755    557777776 565552          346999999999999999998 689999999998


Q ss_pred             Eeee
Q psy1314         175 RVKF  178 (275)
Q Consensus       175 ~~~~  178 (275)
                      +...
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            8743

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

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

Probab=97.97  E-value=2.1e-05  Score=49.61  Aligned_cols=52  Identities=19%  Similarity=0.480  Sum_probs=42.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHH
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL   75 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al   75 (275)
                      +.|-|.+.+.+..+ +|..+|.+||+|.++.+....      -..+|+|++..+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~~------~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPEST------NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCCC------cEEEEEECCHHHHHhhC
Confidence            56888899877765 455589999999998887433      28999999999999985

>KOG0151|consensus

Probab=97.97  E-value=2.9e-05  Score=71.91  Aligned_cols=81  Identities=17%  Similarity=0.265  Sum_probs=67.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC---CCCcccEEEEEEccHHHHHHHHHhC-CceecCeeec
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH---TGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKKID   88 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~---tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~i~   88 (275)
                      ....+.|||+||++.+++++|...|..||+|.+++|++-+.   ..+.+-|+||.|-+..+|++|++.+ +..+....+.
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            34566799999999999999999999999999999987542   2345679999999999999999875 5577777777


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      +-|..
T Consensus       251 ~gWgk  255 (877)
T KOG0151|consen  251 LGWGK  255 (877)
T ss_pred             ecccc
Confidence            77663

>KOG4849|consensus

Probab=97.95  E-value=2e-05  Score=67.25  Aligned_cols=76  Identities=16%  Similarity=0.280  Sum_probs=65.5

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCC--CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVK  174 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G--~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~  174 (275)
                      ...++||+||-|++|++||.+.+...|  .+.++++..++.++++||||+|...+..++++.++.+. +.|.|..-.|.
T Consensus        79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             ceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            357899999999999999999988776  56777888889999999999999999999999999984 78888765554

>KOG4210|consensus

Probab=97.91  E-value=1e-05  Score=69.27  Aligned_cols=86  Identities=23%  Similarity=0.432  Sum_probs=73.8

Q ss_pred             CCCCCCCeEE-EcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          11 PGRNDERKLF-VGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~-v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      .......+++ |.+|+.++++++|.++|..++.|..+++..++.++.++|++||.|.+...+..++....+.+.++++.+
T Consensus       179 ~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~  258 (285)
T KOG4210|consen  179 LSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRL  258 (285)
T ss_pred             cccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCccccc
Confidence            3344555666 999999999999999999999999999999999999999999999999999998887456788888888


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      .......
T Consensus       259 ~~~~~~~  265 (285)
T KOG4210|consen  259 EEDEPRP  265 (285)
T ss_pred             ccCCCCc
Confidence            7776553

>KOG0129|consensus

Probab=97.89  E-value=4e-05  Score=68.68  Aligned_cols=67  Identities=30%  Similarity=0.448  Sum_probs=62.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHh-hcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFS-QYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~-~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      ..-++.+||||+.||.-++.++|..+|+ .||.|..+-|-+|++-+-++|-+-|+|.+..+-.+||++
T Consensus       365 q~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  365 QPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             cccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            4457889999999999999999999999 699999999999988899999999999999999999987

>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=97.87  E-value=3.8e-05  Score=55.80  Aligned_cols=55  Identities=29%  Similarity=0.442  Sum_probs=36.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      ..|.|.+++..++.++|++.|++|++|..|.+...-.      .|||.|.++++|++|++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~   56 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEK   56 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHH
Confidence            3688999999999999999999999999998877532      799999999999999886

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

>KOG4849|consensus

Probab=97.84  E-value=1.8e-05  Score=67.56  Aligned_cols=76  Identities=17%  Similarity=0.275  Sum_probs=63.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC-ceecCeeec
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKID   88 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~--v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~-~~~~g~~i~   88 (275)
                      +....++||+||-|.+|++||.+.+...|.  +.++++..++.+++|||||+|...+..+.++.++.+. +.|.|....
T Consensus        77 ~Grk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~  155 (498)
T KOG4849|consen   77 EGRKYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPT  155 (498)
T ss_pred             cCceEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCe
Confidence            344567999999999999999999988775  7788888898999999999999999999999998764 466665433

>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=97.74  E-value=0.00015  Score=49.44  Aligned_cols=68  Identities=24%  Similarity=0.268  Sum_probs=43.5

Q ss_pred             CeEEEcCCCCCCCHHHHH----HHHhhcC-CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          17 RKLFVGGLHRNTGEKEIN----DYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~----~~f~~~G-~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      ..|+|.|||.+.+...|+    +++..+| +|.+|.          .+.|.|.|.+++.|++|++. .+..+.|+.|.|+
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            469999999999887655    5555675 576552          24799999999999999885 5778888888888


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      ....
T Consensus        73 ~~~~   76 (90)
T PF11608_consen   73 FSPK   76 (90)
T ss_dssp             SS--
T ss_pred             EcCC
Confidence            7643

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

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

Probab=97.63  E-value=0.00013  Score=45.97  Aligned_cols=52  Identities=23%  Similarity=0.524  Sum_probs=41.2

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHH
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL  159 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai  159 (275)
                      +.|.|.+.+....+ ++..+|.+||+|..+.+...      .-+.+|+|.++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~-~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE-EVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH-HHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            35778888877665 45558889999999987622      337999999999999985

>KOG0921|consensus

Probab=97.62  E-value=0.00033  Score=67.15  Aligned_cols=6  Identities=17%  Similarity=-0.114  Sum_probs=2.3

Q ss_pred             cccCCc
Q psy1314         264 YREAAY  269 (275)
Q Consensus       264 ~~~~~~  269 (275)
                      .++++|
T Consensus      1274 ~~Gg~~ 1279 (1282)
T KOG0921|consen 1274 GRGGNA 1279 (1282)
T ss_pred             Cccccc
Confidence            333343

>KOG1855|consensus

Probab=97.57  E-value=7.1e-05  Score=65.62  Aligned_cols=67  Identities=13%  Similarity=0.170  Sum_probs=56.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccC---CCCC--C--------eeeEEEEEECCHHHHHHHHhcCC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD---KSKN--M--------KKGFCFISFDDQNVAEQVLANPK  163 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~---~~~~--~--------~~G~afV~f~~~e~a~~Ai~~~~  163 (275)
                      +...++|.+.|||.+-.-+.|.++|..+|.|..|+|+.-   ..+.  .        .+-+|+|+|+..+.|.+|.+.++
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            346788999999999999999999999999999999865   2221  1        14579999999999999999874

>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=97.53  E-value=0.00042  Score=49.62  Aligned_cols=78  Identities=12%  Similarity=0.169  Sum_probs=51.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEE-EeeCC------CCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP------HTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~-i~~~~------~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      ..++.|.|=+.|+. ....|.++|++||.|.+.. +.++.      ..........|+|.++.+|.+||+.++..+.+.-
T Consensus         4 ~~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~   82 (100)
T PF05172_consen    4 DSETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSL   82 (100)
T ss_dssp             GGCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCE
T ss_pred             cCCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcE
Confidence            45566888899888 5667888999999987764 11100      0011234899999999999999999999998854


Q ss_pred             ec-cccc
Q psy1314          87 ID-PKRV   92 (275)
Q Consensus        87 i~-v~~~   92 (275)
                      +- |.+.
T Consensus        83 mvGV~~~   89 (100)
T PF05172_consen   83 MVGVKPC   89 (100)
T ss_dssp             EEEEEE-
T ss_pred             EEEEEEc
Confidence            43 4443

This family also includes Q05166 from SWISSPROT a suppressor of thermosensitive mutations in the DNA polymerase delta gene, Pol III []. The conserved central region appears to be distantly related to the RNA-binding region RNP-1 (RNA recognition motif, IPR000504 from INTERPRO), suggesting an RNA binding function for this protein.; PDB: 1WWH_C 3P3D_A.

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

Probab=97.51  E-value=0.00055  Score=46.62  Aligned_cols=54  Identities=19%  Similarity=0.377  Sum_probs=41.5

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      -.+..+|. +|.++...||.++|+.||.| .|..+.|.       .|||...+.+.|..++..
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~   61 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNT   61 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHH
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHH
Confidence            34445555 99999999999999999988 67777763       799999999999988875

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

>KOG1855|consensus

Probab=97.27  E-value=0.00042  Score=60.93  Aligned_cols=67  Identities=16%  Similarity=0.260  Sum_probs=56.4

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeC---CCCCC----------cccEEEEEEccHHHHHHHHHhCC
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND---PHTGQ----------SRGFAFVTFTTQKAVDDLLAAGD   79 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~---~~tg~----------~~G~afV~f~~~e~a~~al~~~~   79 (275)
                      +-++++|.+-|||.+-.-+.|.++|..+|.|..|+|+.-   +.+.+          .+-+|+|+|...+.|++|.+.++
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~  307 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLN  307 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhc
Confidence            347899999999999988999999999999999999865   33221          25679999999999999998753

>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=97.11  E-value=0.0034  Score=45.00  Aligned_cols=76  Identities=21%  Similarity=0.310  Sum_probs=50.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCC-------CCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEE-
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS-------KNMKKGFCFISFDDQNVAEQVLANPKQVICGKEV-  171 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~-------~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i-  171 (275)
                      ++-|.|=+.|+. ....|-++|++||+|.+..-.....       ......+-.|+|+++.+|.+||.+++..|.|.-+ 
T Consensus         6 ~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~mv   84 (100)
T PF05172_consen    6 ETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLMV   84 (100)
T ss_dssp             CCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEEE
T ss_pred             CeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEEE
Confidence            455778888888 4567778999999998775111100       0112458899999999999999999998988544 


Q ss_pred             EEEEe
Q psy1314         172 DVKRV  176 (275)
Q Consensus       172 ~v~~~  176 (275)
                      -|.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            45554

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.

>KOG2314|consensus

Probab=97.10  E-value=0.0013  Score=59.86  Aligned_cols=64  Identities=17%  Similarity=0.321  Sum_probs=52.9

Q ss_pred             CCCCeEEEcCCCCCCC------HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC
Q psy1314          14 NDERKLFVGGLHRNTG------EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG   78 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t------~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~   78 (275)
                      .-...|+|-|+|.--.      +.-|..+|+++|+|..+.+..+..++ ++||.|++|++..+|+.|++.+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l  125 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSL  125 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhc
Confidence            4567899999986432      23466789999999999999887655 9999999999999999999873

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.05  E-value=0.0016  Score=55.59  Aligned_cols=79  Identities=18%  Similarity=0.450  Sum_probs=59.3

Q ss_pred             CCCeEEEcCCCCCCCHHH------HHHHHhhcCCeeEEEEeeCCCC-CCcccEE--EEEEccHHHHHHHHHh-CCceecC
Q psy1314          15 DERKLFVGGLHRNTGEKE------INDYFSQYGEVESISIKNDPHT-GQSRGFA--FVTFTTQKAVDDLLAA-GDHYIGN   84 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~------l~~~f~~~G~v~~~~i~~~~~t-g~~~G~a--fV~f~~~e~a~~al~~-~~~~~~g   84 (275)
                      ..+-|||-+||+.+..++      -.++|.+||+|..|.|.+...+ ....+++  ||+|.+.|+|.+||.. .+..++|
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            345689999998876666      2479999999998888654322 2223344  9999999999999987 4678889


Q ss_pred             eeecccccc
Q psy1314          85 KKIDPKRVT   93 (275)
Q Consensus        85 ~~i~v~~~~   93 (275)
                      +.|....-.
T Consensus       193 r~lkatYGT  201 (480)
T COG5175         193 RVLKATYGT  201 (480)
T ss_pred             ceEeeecCc
Confidence            988876654

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.00  E-value=0.0038  Score=40.35  Aligned_cols=55  Identities=25%  Similarity=0.465  Sum_probs=43.6

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccC---CCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQY---GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~---G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      ..+|+|.++. +++.++|+.+|..|   .....|+++-|.       .|-|.|.+.+.|.+||..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            3579999985 47888999999988   134577777663       3899999999999999864

>KOG2314|consensus

Probab=96.94  E-value=0.0025  Score=58.01  Aligned_cols=75  Identities=17%  Similarity=0.328  Sum_probs=57.8

Q ss_pred             CcceeeecCCCCCCC------HHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeC-CeE
Q psy1314          99 LKCKIFVGGLTTEIS------EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVIC-GKE  170 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~------~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~-g~~  170 (275)
                      ....|.|.|+|.--.      ..-|.++|+++|+|..+.++.+..++ .+|+.|++|.+..+|+.|++.++ +.|+ ...
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            456788999885421      23466899999999999999887766 79999999999999999999974 4433 344


Q ss_pred             EEEE
Q psy1314         171 VDVK  174 (275)
Q Consensus       171 i~v~  174 (275)
                      +.|.
T Consensus       136 f~v~  139 (698)
T KOG2314|consen  136 FFVR  139 (698)
T ss_pred             EEee
Confidence            4444

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=96.93  E-value=0.0032  Score=53.91  Aligned_cols=79  Identities=16%  Similarity=0.370  Sum_probs=59.5

Q ss_pred             ceeeecCCCCCCCHHH----H--HHhcccCCCeEEEEeccCCCCCC-eeeE--EEEEECCHHHHHHHHhcC-CceeCCeE
Q psy1314         101 CKIFVGGLTTEISEQD----V--RDYFSQYGSITEFQQPFDKSKNM-KKGF--CFISFDDQNVAEQVLANP-KQVICGKE  170 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~----l--~~~F~~~G~v~~v~i~~~~~~~~-~~G~--afV~f~~~e~a~~Ai~~~-~~~~~g~~  170 (275)
                      .-+||-+||+.+..++    |  .++|.+||.|..|.|-+...+.. ..+.  .+|+|.+.|+|.+||... ...++|+.
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~  194 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRV  194 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCce
Confidence            5589999999886665    3  37899999999988765432111 1222  399999999999999997 48899999


Q ss_pred             EEEEEeeeC
Q psy1314         171 VDVKRVKFN  179 (275)
Q Consensus       171 i~v~~~~~~  179 (275)
                      |+...-..+
T Consensus       195 lkatYGTTK  203 (480)
T COG5175         195 LKATYGTTK  203 (480)
T ss_pred             EeeecCchH
Confidence            988766554

>KOG4676|consensus

Probab=96.83  E-value=0.0017  Score=56.50  Aligned_cols=79  Identities=14%  Similarity=0.219  Sum_probs=63.5

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCC---CCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS---KNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~---~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ..|.|.||.++++.++++.+|...|.|.++.+.....   -....-.|||.|.+...+..|....++++-++.|.|...-
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            3689999999999999999999999999998875221   1223457999999999999998888888888887776554


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      ..
T Consensus        88 ~~   89 (479)
T KOG4676|consen   88 DE   89 (479)
T ss_pred             CC
Confidence            33

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.78  E-value=0.0053  Score=46.74  Aligned_cols=73  Identities=19%  Similarity=0.258  Sum_probs=52.0

Q ss_pred             CCCCeEEEcCCC-----C-CCCH---HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecC
Q psy1314          14 NDERKLFVGGLH-----R-NTGE---KEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGN   84 (275)
Q Consensus        14 ~~~~~l~v~~Lp-----~-~~t~---~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g   84 (275)
                      ++..||.|.=+.     . ..++   .+|.+.|..||++.=++++.+        .-.|+|.+-+.|-+|+++++..+.+
T Consensus        25 PpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g   96 (146)
T PF08952_consen   25 PPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNG   96 (146)
T ss_dssp             -TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETT
T ss_pred             CCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECC
Confidence            445566666544     1 1222   367788889999888888765        4789999999999999999999999


Q ss_pred             eeeccccccc
Q psy1314          85 KKIDPKRVTK   94 (275)
Q Consensus        85 ~~i~v~~~~~   94 (275)
                      +.|.++...+
T Consensus        97 ~~l~i~LKtp  106 (146)
T PF08952_consen   97 RTLKIRLKTP  106 (146)
T ss_dssp             EEEEEEE---
T ss_pred             EEEEEEeCCc
Confidence            9998886653

; PDB: 1UFW_A 2DNR_A.

>KOG0115|consensus

Probab=96.74  E-value=0.0019  Score=53.22  Aligned_cols=95  Identities=13%  Similarity=0.220  Sum_probs=74.0

Q ss_pred             CCceecCeeecccccccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHH
Q psy1314          78 GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ  157 (275)
Q Consensus        78 ~~~~~~g~~i~v~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~  157 (275)
                      .+....++.+.|..+..      ..|+|.||..-++.+.|.+.|+.||+|....++.|. .++..+-++|+|...-.|.+
T Consensus        15 d~~~~~~~~lr~rfa~~------a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~a~~   87 (275)
T KOG0115|consen   15 DGRFPKGRSLRVRFAMH------AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPNARK   87 (275)
T ss_pred             CCCCCCCCceEEEeecc------ceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchhHHH
Confidence            46677888898888853      579999999999999999999999999887666663 46677889999999988888


Q ss_pred             HHhcCC-----ceeCCeEEEEEEeeeC
Q psy1314         158 VLANPK-----QVICGKEVDVKRVKFN  179 (275)
Q Consensus       158 Ai~~~~-----~~~~g~~i~v~~~~~~  179 (275)
                      |+....     ....++++.|......
T Consensus        88 a~rr~~~~g~~~~~~~~p~~VeP~eq~  114 (275)
T KOG0115|consen   88 AARRCREGGFGGTTGGRPVGVEPMEQP  114 (275)
T ss_pred             HHHHhccCccccCCCCCccCCChhhcc
Confidence            887752     3445566666554443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.70  E-value=0.016  Score=37.53  Aligned_cols=54  Identities=22%  Similarity=0.364  Sum_probs=45.0

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhc---CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~---G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      ...|+|.++ .+++.++|+.+|..|   .....|..+.|.       .|=|.|.+.+.|.+||.+
T Consensus         5 peavhirGv-d~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~   61 (62)
T PF10309_consen    5 PEAVHIRGV-DELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVA   61 (62)
T ss_pred             eceEEEEcC-CCCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHc
Confidence            457999998 458889999999998   235589999884       588999999999999975

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.56  E-value=0.013  Score=44.63  Aligned_cols=56  Identities=18%  Similarity=0.289  Sum_probs=45.0

Q ss_pred             HHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       116 ~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      +|-+.|..||++.-++++-+        .-.|+|.+-++|.+|+.+.+.+++|+.|+|+...+.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            66678889999998888754        269999999999999999999999999999766543

; PDB: 1UFW_A 2DNR_A.

>KOG2202|consensus

Probab=96.49  E-value=0.001  Score=54.89  Aligned_cols=61  Identities=15%  Similarity=0.396  Sum_probs=46.5

Q ss_pred             HHHHHHHh-hcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          31 KEINDYFS-QYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        31 ~~l~~~f~-~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ++|...|+ +||+|+++.|..+. --..+|-+||.|..+|+|++|++. ++.++.+++|..+.+
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            34444454 78999999776653 345678899999999999999986 466888888766654

>KOG3152|consensus

Probab=96.47  E-value=0.0022  Score=52.84  Aligned_cols=72  Identities=18%  Similarity=0.380  Sum_probs=56.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC--------CCccc----EEEEEEccHHHHHHHHHh-CCce
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT--------GQSRG----FAFVTFTTQKAVDDLLAA-GDHY   81 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~t--------g~~~G----~afV~f~~~e~a~~al~~-~~~~   81 (275)
                      ..-.||+++||+.+...-|+++|++||+|-.|.+-.+..+        +.++.    -+.|+|.+...|.++..+ ++..
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            3467999999999999999999999999999999876555        22222    367999999999887665 4566


Q ss_pred             ecCee
Q psy1314          82 IGNKK   86 (275)
Q Consensus        82 ~~g~~   86 (275)
                      |.|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            76654

>KOG2135|consensus

Probab=96.31  E-value=0.0026  Score=56.81  Aligned_cols=78  Identities=22%  Similarity=0.242  Sum_probs=64.9

Q ss_pred             CCCCCeEEEcCCCCCC-CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNT-GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~-t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ..+.+.|-+--+|..+ |.++|..+|.+||+|..|.+-....      .|.|+|.+..+|-.|.......|+++.|.+.|
T Consensus       369 ~~dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~------~a~vTF~t~aeag~a~~s~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  369 VVDHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL------HAVVTFKTRAEAGEAYASHGAVLNNRFIKLFW  442 (526)
T ss_pred             hcccchhhhhccCCCCchHhhhhhhhhhcCccccccccCchh------hheeeeeccccccchhccccceecCceeEEEE
Confidence            4456667777777776 6799999999999999999976633      79999999999988888888899999999999


Q ss_pred             ccccc
Q psy1314          92 VTKRV   96 (275)
Q Consensus        92 ~~~~~   96 (275)
                      .....
T Consensus       443 hnps~  447 (526)
T KOG2135|consen  443 HNPSP  447 (526)
T ss_pred             ecCCc
Confidence            87643

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=96.26  E-value=0.0089  Score=41.62  Aligned_cols=62  Identities=19%  Similarity=0.325  Sum_probs=44.8

Q ss_pred             EEEEEccHHHHHHHHHhCCc--eecCeeecccccccc----------cCCCcceeeecCCCCCCCHHHHHHhcc
Q psy1314          61 AFVTFTTQKAVDDLLAAGDH--YIGNKKIDPKRVTKR----------VNPLKCKIFVGGLTTEISEQDVRDYFS  122 (275)
Q Consensus        61 afV~f~~~e~a~~al~~~~~--~~~g~~i~v~~~~~~----------~~~~~~~l~V~~l~~~~~~~~l~~~F~  122 (275)
                      |.|+|.+++-|++.+++-.+  .+....+.|....-.          .....++|.|++||...++++|++.++
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            68999999999999987543  555555544332211          123457899999999999999988765

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG0115|consensus

Probab=96.11  E-value=0.0063  Score=50.26  Aligned_cols=61  Identities=18%  Similarity=0.315  Sum_probs=54.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG   78 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~   78 (275)
                      ..|+|.||+.-++-+.|.+.|+.||+|+...++.| ..++..+-.+|+|...-.|.+|+...
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~   92 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRC   92 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHh
Confidence            67999999999999999999999999998888777 55788889999999998888888764

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=96.10  E-value=0.033  Score=42.06  Aligned_cols=74  Identities=15%  Similarity=0.139  Sum_probs=56.9

Q ss_pred             CCCCCeEEEcCCCCCC----CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314          13 RNDERKLFVGGLHRNT----GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~----t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      ..+-.+|.|.=|..++    +...|...++.||+|+++.+.-.       -.|.|.|.+..+|=+|+.+......+..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGr-------qsavVvF~d~~SAC~Av~Af~s~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGR-------QSAVVVFKDITSACKAVSAFQSRAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCC-------ceEEEEehhhHHHHHHHHhhcCCCCCceEE
Confidence            3455678887766665    33456667788999999998754       279999999999999999877777777777


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      +.|..
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            77654

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

Probab=96.08  E-value=0.042  Score=37.58  Aligned_cols=54  Identities=19%  Similarity=0.283  Sum_probs=38.6

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      +...+|+ +|..+...||.++|+.||.|.-.. +.|       ..|||...+.+.|..|+..+
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~VsW-i~d-------TSAfV~l~~r~~~~~v~~~~   62 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSW-IND-------TSAFVALHNRDQAKVVMNTL   62 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEEEEE-ECT-------TEEEEEECCCHHHHHHHHHH
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEEEEE-EcC-------CcEEEEeecHHHHHHHHHHh
Confidence            3455665 999999999999999999875444 333       14999999999998887764

; 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.

>KOG2591|consensus

Probab=95.96  E-value=0.022  Score=52.05  Aligned_cols=68  Identities=13%  Similarity=0.308  Sum_probs=55.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcc--cCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFS--QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDV  173 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~--~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v  173 (275)
                      ..|.|.|+-||..+-.|+++.||.  .+-.+++|++-.+..       =||+|++.+||+.|.+.+.   +.|.|++|..
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-------WyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-------WYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-------eEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            457788899999999999999997  467888888765432       5999999999999987762   5678887643

>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=95.81  E-value=0.1  Score=38.09  Aligned_cols=60  Identities=17%  Similarity=0.189  Sum_probs=43.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~-v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      ...+.+.-.|..++.++|..+.+.+-+ |..++|+++..  .++=.+.++|.+.++|++..+.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~   73 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEE   73 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHH
Confidence            444455555555666778777777654 88899998743  2444799999999999999886

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG1996|consensus

Probab=95.69  E-value=0.032  Score=47.06  Aligned_cols=63  Identities=14%  Similarity=0.177  Sum_probs=47.7

Q ss_pred             HHHHHHhcccCCCeEEEEeccCCCCCCee-eEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEe
Q psy1314         114 EQDVRDYFSQYGSITEFQQPFDKSKNMKK-GFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV  176 (275)
Q Consensus       114 ~~~l~~~F~~~G~v~~v~i~~~~~~~~~~-G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~  176 (275)
                      ++++++..++||.|..|.|..+...-... --.||+|...++|.+|+-.++ ..+.|+.+...+-
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fy  364 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFY  364 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheec
Confidence            46788889999999998887654332211 237999999999999998885 7788888776553

>KOG3152|consensus

Probab=95.52  E-value=0.0047  Score=50.97  Aligned_cols=72  Identities=15%  Similarity=0.248  Sum_probs=56.8

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCC--------CCeee----EEEEEECCHHHHHHHHhcCC-ce
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK--------NMKKG----FCFISFDDQNVAEQVLANPK-QV  165 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~--------~~~~G----~afV~f~~~e~a~~Ai~~~~-~~  165 (275)
                      ..-.||+++||+.++..-|+++|+.||.|-.|-+.....+        +.+..    -+-|+|.+...|+.+.+.|| ..
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            4467999999999999999999999999999988765444        11111    25789999999999888874 66


Q ss_pred             eCCeE
Q psy1314         166 ICGKE  170 (275)
Q Consensus       166 ~~g~~  170 (275)
                      |.|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            77654

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.52  E-value=0.083  Score=39.96  Aligned_cols=74  Identities=16%  Similarity=0.208  Sum_probs=55.3

Q ss_pred             CCCcceeeecCCCCCC-CHHHHH---HhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEE
Q psy1314          97 NPLKCKIFVGGLTTEI-SEQDVR---DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVD  172 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~-~~~~l~---~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~  172 (275)
                      +.+-.+|.|.=|..++ ..+||+   ..++.||+|..|...-       +-.|.|.|.+..+|.+|+........|..+.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~q  155 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTMFQ  155 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCceEE
Confidence            3445677777666665 334555   4556899999998752       4469999999999999999987777888888


Q ss_pred             EEEee
Q psy1314         173 VKRVK  177 (275)
Q Consensus       173 v~~~~  177 (275)
                      +.|-.
T Consensus       156 CsWqq  160 (166)
T PF15023_consen  156 CSWQQ  160 (166)
T ss_pred             eeccc
Confidence            87754

>KOG2202|consensus

Probab=95.35  E-value=0.0056  Score=50.58  Aligned_cols=64  Identities=19%  Similarity=0.291  Sum_probs=48.4

Q ss_pred             HHHHHhcc-cCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         115 QDVRDYFS-QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       115 ~~l~~~F~-~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      ++|...|+ +||+|+++.|..+. ...-+|-++|.|..+|+|++|++.++ ..+.|++|...+....
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            34444444 89999998766442 23347789999999999999999984 8899999988766544

>KOG1996|consensus

Probab=95.24  E-value=0.07  Score=45.08  Aligned_cols=62  Identities=19%  Similarity=0.318  Sum_probs=46.9

Q ss_pred             HHHHHHHHhhcCCeeEEEEeeCCCCCCcc-cEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          30 EKEINDYFSQYGEVESISIKNDPHTGQSR-GFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        30 ~~~l~~~f~~~G~v~~~~i~~~~~tg~~~-G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ++++.+.+++||.|..|.|...+...... =-.||+|...++|.+|+-. ++..|.|+.+..-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~F  363 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACF  363 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeehee
Confidence            46788899999999999988775433322 1379999999999988764 57788888765443

>KOG2591|consensus

Probab=95.16  E-value=0.055  Score=49.57  Aligned_cols=71  Identities=11%  Similarity=0.118  Sum_probs=56.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhh--cCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecCeee
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQ--YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGNKKI   87 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~--~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g~~i   87 (275)
                      ....+.|.|+-||..+.+|+|+.+|+.  +-++++|.+-.+-       -=||+|++.+||+.|.+.+   -+.|.+++|
T Consensus       172 ~~kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpI  244 (684)
T KOG2591|consen  172 NHKRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPI  244 (684)
T ss_pred             CcceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcch
Confidence            444566888899999999999999974  6789999987763       3699999999999987754   457888877


Q ss_pred             ccc
Q psy1314          88 DPK   90 (275)
Q Consensus        88 ~v~   90 (275)
                      ..+
T Consensus       245 mAR  247 (684)
T KOG2591|consen  245 MAR  247 (684)
T ss_pred             hhh
Confidence            543

>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=94.88  E-value=0.042  Score=43.77  Aligned_cols=70  Identities=14%  Similarity=0.134  Sum_probs=41.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCe---eEEEEeeC-CCCCC-cccEEEEEEccHHHHHHHHHhC-Ccee
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQ-YGEV---ESISIKND-PHTGQ-SRGFAFVTFTTQKAVDDLLAAG-DHYI   82 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~-~G~v---~~~~i~~~-~~tg~-~~G~afV~f~~~e~a~~al~~~-~~~~   82 (275)
                      ..+..+|.|++||+.+|++++.+.++. ++..   ..+.-... ..... ..--|||.|.+.+++....... ++.|
T Consensus         4 ~~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F   80 (176)
T PF03467_consen    4 EKEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVF   80 (176)
T ss_dssp             -----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEE
T ss_pred             cccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEE
Confidence            455679999999999999999997776 5554   23331111 11111 2235999999999988888763 4343

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.

>KOG2193|consensus

Probab=94.82  E-value=0.016  Score=51.18  Aligned_cols=75  Identities=20%  Similarity=0.334  Sum_probs=57.8

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC--ceeCCeEEEEEEeee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK--QVICGKEVDVKRVKF  178 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~--~~~~g~~i~v~~~~~  178 (275)
                      .+||++||.+.++..+|..+|...-.-..-.++.      ..||+||...+..-|.+|++.++  ..+.|+++++....+
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            4689999999999999999997541111111111      25799999999999999999984  789999999987776


Q ss_pred             CCC
Q psy1314         179 NPE  181 (275)
Q Consensus       179 ~~~  181 (275)
                      +..
T Consensus        76 kkq   78 (584)
T KOG2193|consen   76 KKQ   78 (584)
T ss_pred             HHH
Confidence            644

>KOG2416|consensus

Probab=94.45  E-value=0.024  Score=52.19  Aligned_cols=62  Identities=13%  Similarity=0.247  Sum_probs=50.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~-~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      .+....++.|+|.||-.-.|.-+|++++.+ .|.|++.+|-+-      |-+|||.|.+.++|.+...+
T Consensus       438 PsR~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkI------KShCyV~yss~eEA~atr~A  500 (718)
T KOG2416|consen  438 PSRKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKI------KSHCYVSYSSVEEAAATREA  500 (718)
T ss_pred             CCCCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHh------hcceeEecccHHHHHHHHHH
Confidence            345677899999999999999999999985 566777744322      34899999999999888776

>KOG0112|consensus

Probab=94.39  E-value=0.075  Score=51.39  Aligned_cols=76  Identities=14%  Similarity=0.317  Sum_probs=60.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecC--eeec
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGN--KKID   88 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g--~~i~   88 (275)
                      .....+.|||++|..++....|...|..||.|..|.+-.-.      -|++|.+.+...++.|+..+ +..|.+  +++.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq------~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQ------PYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCC------cceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            44567889999999999999999999999999998886542      29999999999999998754 445544  4455


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      |..+.
T Consensus       525 vdla~  529 (975)
T KOG0112|consen  525 VDLAS  529 (975)
T ss_pred             ccccc
Confidence            55543

>KOG0804|consensus

Probab=94.31  E-value=0.17  Score=45.27  Aligned_cols=67  Identities=12%  Similarity=0.228  Sum_probs=54.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceec
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIG   83 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~-v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~   83 (275)
                      ....|+|--+|..+|-.||..|...+-+ |.+|+|++|..-.  +=.+.|+|.+.++|..+.+. +++.|+
T Consensus        73 ~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pn--rymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   73 SSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPN--RYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCc--eEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            3888999999999999999999987654 9999999975432  33689999999999999886 343443

>KOG2135|consensus

Probab=94.25  E-value=0.034  Score=49.92  Aligned_cols=74  Identities=15%  Similarity=0.246  Sum_probs=59.0

Q ss_pred             ceeeecCCCCCC-CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEI-SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~-~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      +.|-+.-+|+.. +.++|..+|.+||+|..|.|-..      .-.|.|+|.+..+|-+|-......|+++.|+|.|-.+.
T Consensus       373 s~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnps  446 (526)
T KOG2135|consen  373 SPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNPS  446 (526)
T ss_pred             chhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEEecCC
Confidence            445555555555 66899999999999999987543      22489999999999888877788999999999998874


Q ss_pred             C
Q psy1314         180 P  180 (275)
Q Consensus       180 ~  180 (275)
                      +
T Consensus       447 ~  447 (526)
T KOG2135|consen  447 P  447 (526)
T ss_pred             c
Confidence            3

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=93.92  E-value=0.099  Score=40.35  Aligned_cols=112  Identities=14%  Similarity=0.199  Sum_probs=77.8

Q ss_pred             EEEcCC-C-CCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccccc
Q psy1314          19 LFVGGL-H-RNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        19 l~v~~L-p-~~~t~~~l~~~f~~-~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~~   95 (275)
                      ..|+.+ . .+.+-+.|.+.+.+ ++....+.+..-     ..++..+.|.++++++++++.....+.+..+.++...+.
T Consensus        18 ~lVg~~l~~~~~~~~~l~~~l~~~W~~~~~~~i~~l-----~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~   92 (153)
T PF14111_consen   18 CLVGRVLSPKPISLSALEQELAKIWKLKGGVKIRDL-----GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPD   92 (153)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHHHhCCCCcEEEEEe-----CCCeEEEEEEeccceeEEEecccccccccchhhhhhccc
Confidence            444444 3 34677778877765 344334444332     135899999999999999998777888888887777644


Q ss_pred             cCCCc-------ceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccC
Q psy1314          96 VNPLK-------CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFD  135 (275)
Q Consensus        96 ~~~~~-------~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~  135 (275)
                      .....       .=|.|.+||.. .+++-|+.+.+.+|++..++....
T Consensus        93 ~~~~~~~~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t~  140 (153)
T PF14111_consen   93 FNPSEVKFEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENTL  140 (153)
T ss_pred             ccccccceeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCCC
Confidence            33221       22667899988 488889999999999998876543

>KOG2416|consensus

Probab=93.91  E-value=0.053  Score=50.06  Aligned_cols=75  Identities=16%  Similarity=0.255  Sum_probs=55.8

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcc-cCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ce---eCCeEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFS-QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QV---ICGKEV  171 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~-~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~---~~g~~i  171 (275)
                      ...++.|+|.||--.+|.-+|+.++. ..|.|...  +.|+.    +-.|||.|.+.++|.+.+..|+ ..   -+.+.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~--WmDkI----KShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF--WMDKI----KSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHH--HHHHh----hcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            34568899999999999999999999 55666666  33432    4469999999999998888873 32   345666


Q ss_pred             EEEEee
Q psy1314         172 DVKRVK  177 (275)
Q Consensus       172 ~v~~~~  177 (275)
                      .+.+..
T Consensus       515 ~adf~~  520 (718)
T KOG2416|consen  515 IADFVR  520 (718)
T ss_pred             Eeeecc
Confidence            666554

>KOG4285|consensus

Probab=93.88  E-value=0.32  Score=41.36  Aligned_cols=68  Identities=15%  Similarity=0.213  Sum_probs=50.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee-cccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI-DPKR   91 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i-~v~~   91 (275)
                      .=|-|=++|+... .-|..+|++||+|.+...-.+      -.+-+|.|.+.-+|++||..++..|++..+ -|+.
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~n------gNwMhirYssr~~A~KALskng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSN------GNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKP  266 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhhCeeeeeecCCC------CceEEEEecchhHHHHhhhhcCeeeccceEEeeee
Confidence            3455557776544 456788999999877666533      238899999999999999999998888544 3444

>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=93.88  E-value=1.2  Score=37.86  Aligned_cols=149  Identities=11%  Similarity=0.186  Sum_probs=93.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC-------CCCcccEEEEEEccHHHHHHHHH-------hC
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH-------TGQSRGFAFVTFTTQKAVDDLLA-------AG   78 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~-------tg~~~G~afV~f~~~e~a~~al~-------~~   78 (275)
                      +=..+.|.+.||..+++-..+...|.+||+|++|.++.+..       .....-.+.+.|-+.+.|-....       ..
T Consensus        12 ~YrTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEf   91 (309)
T PF10567_consen   12 EYRTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEF   91 (309)
T ss_pred             cceeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHH
Confidence            33456789999999999999999999999999999998751       12234578999999888766532       12


Q ss_pred             CceecCeeeccccccc---------c------------------cCCCcceeeecCCCCCC-CHHHHHHhc---ccCC--
Q psy1314          79 DHYIGNKKIDPKRVTK---------R------------------VNPLKCKIFVGGLTTEI-SEQDVRDYF---SQYG--  125 (275)
Q Consensus        79 ~~~~~g~~i~v~~~~~---------~------------------~~~~~~~l~V~~l~~~~-~~~~l~~~F---~~~G--  125 (275)
                      .+.+....+.+....-         .                  .....+.|.|. +...+ .++-|.+.+   ..-+  
T Consensus        92 K~~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL~~~~n~  170 (309)
T PF10567_consen   92 KTKLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFLKNSNNK  170 (309)
T ss_pred             HHhcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhhccCCCc
Confidence            3344444444333221         0                  01123556664 23344 333333322   1112  


Q ss_pred             --CeEEEEeccC--CCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314         126 --SITEFQQPFD--KSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       126 --~v~~v~i~~~--~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                        .++.|.|+..  +...-++-||.++|-+...|...++-+
T Consensus       171 RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYl  211 (309)
T PF10567_consen  171 RYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYL  211 (309)
T ss_pred             eEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHH
Confidence              3556666633  233456789999999999988887764

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.

>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=93.09  E-value=0.19  Score=40.08  Aligned_cols=64  Identities=14%  Similarity=0.108  Sum_probs=39.5

Q ss_pred             CcceeeecCCCCCCCHHHHHHhccc-CCCe---EEEE--eccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQ-YGSI---TEFQ--QPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~-~G~v---~~v~--i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      ...+|.|++||+.+|++++.+.++. ++..   ..+.  +.........-.-|+|.|.+.+++...+...
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~   75 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRF   75 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHC
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhc
Confidence            4568999999999999999987776 5544   2333  1111111111234899999999998888876

Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast, human to plants []. Exon junction complexes (EJCs) are deposited ~24 nucleotides upstream of exon-exon junctions after splicing. Translation causes displacement of the EJCs, however, premature translation termination upstream of one or more EJCs triggers the recruitment of UPF1, UPF2 and UPF3 and activates the NMD pathway [, ]. This family contains UPF3. The crystal structure of the complex between human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain) has been determined to 1.95A. The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b ribonucleoprotein (RNP) domain, which is generally used by these domains to bind nucleic acids. In UPF3b the RNP domain does not bind RNA, whereas the UPF2 construct and the complex do. It is clear that some RNP domains have evolved for specific protein-protein interactions rather than as nucleic acid binding modules [].; PDB: 1UW4_A 2L08_A.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=92.27  E-value=2.1  Score=41.33  Aligned_cols=62  Identities=11%  Similarity=0.143  Sum_probs=40.7

Q ss_pred             CCCCCHHHHHHhcccCCCe-----EEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         109 TTEISEQDVRDYFSQYGSI-----TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       109 ~~~~~~~~l~~~F~~~G~v-----~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      ...++..+|..++..-+.|     -.|+|..        .|.||+... +.|...+..+ +..+.+++|.|..+...
T Consensus       496 ~~~~~~~~~~~~i~~~~~~~~~~ig~i~i~~--------~~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~  563 (629)
T PRK11634        496 DDGVEVRHIVGAIANEGDISSRYIGNIKLFA--------SHSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGDA  563 (629)
T ss_pred             ccCCCHHHHHHHHHhhcCCChhhCCcEEEeC--------CceEEEcCh-hhHHHHHHHhccccccCCceEEEECCCC
Confidence            3556777777777654433     3355542        267888754 3466677777 57899999999887543

>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=90.53  E-value=1  Score=36.11  Aligned_cols=61  Identities=15%  Similarity=0.142  Sum_probs=42.6

Q ss_pred             CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEEEEeeeC
Q psy1314         113 SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDVKRVKFN  179 (275)
Q Consensus       113 ~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v~~~~~~  179 (275)
                      ..+.|+++|..+..+..+.+++.      -.-..|.|.+.++|.+|...+.   ..+.+..++|.++...
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            45889999999998877766643      2238999999999999999875   6799999999888544

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=90.18  E-value=2.5  Score=30.88  Aligned_cols=59  Identities=12%  Similarity=0.091  Sum_probs=43.1

Q ss_pred             eeecCCCCCCCHHHHHHhcccCC-CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK  163 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G-~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~  163 (275)
                      +.+-..|..++-++|..+.+.+- .|..++|++|..  .++=.++++|.+.++|++-.+..|
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~--pnrymVLikF~~~~~Ad~Fy~~fN   75 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGT--PNRYMVLIKFRDQESADEFYEEFN   75 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCC--CceEEEEEEECCHHHHHHHHHHhC
Confidence            33444566667777877777664 577788888754  346689999999999999988753

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG4285|consensus

Probab=90.05  E-value=1.3  Score=37.86  Aligned_cols=72  Identities=19%  Similarity=0.301  Sum_probs=50.6

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeE-EEEEEeeeCCC
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKE-VDVKRVKFNPE  181 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~-i~v~~~~~~~~  181 (275)
                      |.|=++|+. .-..|-.+|++||+|.+.....      .-.+-+|.|.++.+|+|||.+....|++.. |-|+...++..
T Consensus       200 VTVfGFppg-~~s~vL~~F~~cG~Vvkhv~~~------ngNwMhirYssr~~A~KALskng~ii~g~vmiGVkpCtDksv  272 (350)
T KOG4285|consen  200 VTVFGFPPG-QVSIVLNLFSRCGEVVKHVTPS------NGNWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKPCTDKSV  272 (350)
T ss_pred             EEEeccCcc-chhHHHHHHHhhCeeeeeecCC------CCceEEEEecchhHHHHhhhhcCeeeccceEEeeeecCCHHH
Confidence            444455544 3356789999999987765431      234889999999999999999888887754 44555455433

>KOG2068|consensus

Probab=89.92  E-value=0.2  Score=43.32  Aligned_cols=80  Identities=18%  Similarity=0.373  Sum_probs=55.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEeeCCCCC-C--cccEEEEEEccHHHHHHHHHhC-CceecCee
Q psy1314          14 NDERKLFVGGLHRNTGEKEIN---DYFSQYGEVESISIKNDPHTG-Q--SRGFAFVTFTTQKAVDDLLAAG-DHYIGNKK   86 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~---~~f~~~G~v~~~~i~~~~~tg-~--~~G~afV~f~~~e~a~~al~~~-~~~~~g~~   86 (275)
                      -..+-+||-+|+..+..+.+.   +.|.+||.|..|.+..++.+- .  .--.++|+|...|+|..||..- +..+.++.
T Consensus        75 Vqknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~  154 (327)
T KOG2068|consen   75 VQKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRA  154 (327)
T ss_pred             hhhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhh
Confidence            345678899999887555544   478888999999988876311 1  1123899999999999999863 44666666


Q ss_pred             ecccccc
Q psy1314          87 IDPKRVT   93 (275)
Q Consensus        87 i~v~~~~   93 (275)
                      ++.....
T Consensus       155 lka~~gt  161 (327)
T KOG2068|consen  155 LKASLGT  161 (327)
T ss_pred             hHHhhCC
Confidence            5544443

>KOG2068|consensus

Probab=89.56  E-value=0.1  Score=45.01  Aligned_cols=79  Identities=19%  Similarity=0.365  Sum_probs=53.4

Q ss_pred             ceeeecCCCCCCCH-HHHH--HhcccCCCeEEEEeccCCC--CC-CeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314         101 CKIFVGGLTTEISE-QDVR--DYFSQYGSITEFQQPFDKS--KN-MKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus       101 ~~l~V~~l~~~~~~-~~l~--~~F~~~G~v~~v~i~~~~~--~~-~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      ..+||-+|+..+.. ..|+  +.|.+||.|..|.+..+..  .. ....-++|+|...|+|..||... +..++++.++.
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            45788888877644 4444  6788899999998877652  11 11223799999999999999876 35566666555


Q ss_pred             EEeeeC
Q psy1314         174 KRVKFN  179 (275)
Q Consensus       174 ~~~~~~  179 (275)
                      .....+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            444433

>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=88.53  E-value=2.7  Score=28.18  Aligned_cols=58  Identities=21%  Similarity=0.348  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHhhcCC-----eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          26 RNTGEKEINDYFSQYGE-----VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        26 ~~~t~~~l~~~f~~~G~-----v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ..++..+|..++.....     |-.|.|..+        |+||+-... .|+.+++. .+..+.++++.++.+
T Consensus        11 dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   11 DGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             cCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            45788999999987643     557888765        899988665 45666665 567899998887653

; 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=87.85  E-value=2.3  Score=34.16  Aligned_cols=60  Identities=13%  Similarity=0.066  Sum_probs=42.0

Q ss_pred             CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC---ceecCeeecccccc
Q psy1314          28 TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD---HYIGNKKIDPKRVT   93 (275)
Q Consensus        28 ~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~---~~~~g~~i~v~~~~   93 (275)
                      ...+.|+++|..++.+.++.++..-      +-..|.|.+.++|.+|...+.   ..+.+..+.+-...
T Consensus         7 ~~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~   69 (184)
T PF04847_consen    7 DNLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQ   69 (184)
T ss_dssp             --HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE---
T ss_pred             hhHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcc
Confidence            3568999999999998888887652      368899999999999988754   57888887776553

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.

>KOG4410|consensus

Probab=87.85  E-value=2.9  Score=35.48  Aligned_cols=61  Identities=20%  Similarity=0.273  Sum_probs=42.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEEeeCCCCCCcccEEEEEEccH-------HHHHHHHHh
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQ-------KAVDDLLAA   77 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v-~~~~i~~~~~tg~~~G~afV~f~~~-------e~a~~al~~   77 (275)
                      .+......|+++|||.++.-.||+..+.+.+.+ .+|.+.-      ..|-||+.|.+.       +++++++..
T Consensus       325 ~~a~~~~di~~~nl~rd~rv~dlk~~lr~~~~~pm~iswkg------~~~k~flh~~~~~~~~~~~~~~~~~~~s  393 (396)
T KOG4410|consen  325 VEAGAKTDIKLTNLSRDIRVKDLKSELRKRECTPMSISWKG------HFGKCFLHFGNRKGVPSTQDDMDKVLKS  393 (396)
T ss_pred             ccCccccceeeccCccccchHHHHHHHHhcCCCceeEeeec------CCcceeEecCCccCCCCCchHHHHHhcc
Confidence            334445669999999999999999999887643 2333322      356899999653       455555543

>KOG4574|consensus

Probab=87.69  E-value=0.31  Score=47.03  Aligned_cols=76  Identities=18%  Similarity=0.172  Sum_probs=61.1

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-C--ceeCCeEEEEEEeee
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-K--QVICGKEVDVKRVKF  178 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~--~~~~g~~i~v~~~~~  178 (275)
                      +..+.|.+-..+-..|..+|.+||.|...+.+++-      -.|.|+|.+.+.|..|++.+ +  ..+.|.+.+|.+++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            34555666667788899999999999999887763      36999999999999999987 3  457788889999887


Q ss_pred             CCCCC
Q psy1314         179 NPETM  183 (275)
Q Consensus       179 ~~~~~  183 (275)
                      .+--.
T Consensus       374 ~~~~e  378 (1007)
T KOG4574|consen  374 LPMYE  378 (1007)
T ss_pred             ccccc
Confidence            76543

>KOG4483|consensus

Probab=87.52  E-value=1.9  Score=38.32  Aligned_cols=66  Identities=12%  Similarity=0.178  Sum_probs=51.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCe
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNK   85 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~-v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~   85 (275)
                      .+=.+.|-|-++|.....+||...|+.|+. --+|.++.+.       ++|-.|.+...|..||.+...++.-+
T Consensus       388 ~dlpHVlEIydfp~efkteDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~kh~~lKiR  454 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKTEDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTLKHDWLKIR  454 (528)
T ss_pred             ccccceeEeccCchhhccHHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhccCceEEee
Confidence            344678999999999999999999999965 4467777664       79999999999999998633344333

>KOG2253|consensus

Probab=86.48  E-value=0.37  Score=45.23  Aligned_cols=70  Identities=14%  Similarity=0.162  Sum_probs=58.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      .....++||+++...+..+-++.+...+|.|..+....         |+|++|..+.....|+..+. ..+++..+.+..
T Consensus        37 ~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~  107 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENV  107 (668)
T ss_pred             CCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhhccc
Confidence            34567899999999999999999999999988776542         89999999999999988874 567777766544

>KOG2253|consensus

Probab=86.10  E-value=0.64  Score=43.75  Aligned_cols=69  Identities=16%  Similarity=0.145  Sum_probs=54.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCc-eecCeeec
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDH-YIGNKKID   88 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~-~~~g~~i~   88 (275)
                      ....+..+|||+||...+..+-+..++..+|-|.++..+.         |+|..|........|+..+.. .+++..+.
T Consensus        35 ~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~  104 (668)
T KOG2253|consen   35 QPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLI  104 (668)
T ss_pred             cCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhh
Confidence            3446678999999999999999999999999987776654         899999999888887775433 44454443

>KOG4574|consensus

Probab=84.47  E-value=0.38  Score=46.48  Aligned_cols=55  Identities=24%  Similarity=0.201  Sum_probs=46.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG   78 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~   78 (275)
                      +..+-|.+..++-..|..+|++||.|.+++.+++-.      .|.|+|.+.|.|..|+.++
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl  354 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDAL  354 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhh
Confidence            344555666778888999999999999999988854      8999999999999999873

>KOG2318|consensus

Probab=83.88  E-value=3.3  Score=38.60  Aligned_cols=119  Identities=13%  Similarity=0.214  Sum_probs=68.0

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHhhc----CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314          13 RNDERKLFVGGLHRN-TGEKEINDYFSQY----GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~----G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      ....++|-|.|+.|+ +...+|.-+|+.|    |.|.+|.|....            |-...-++.       .+.|.++
T Consensus       171 ~~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSe------------FGkeRM~eE-------eV~GP~~  231 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSE------------FGKERMKEE-------EVHGPPK  231 (650)
T ss_pred             ccccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhh------------hhHHHhhhh-------cccCChh
Confidence            466789999999998 7889999999988    578888887652            222221111       2334333


Q ss_pred             cccccccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-Ccee
Q psy1314          88 DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVI  166 (275)
Q Consensus        88 ~v~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~  166 (275)
                      .+...........       ..+..-++-.+..+.+|+ +..+..          =||.|+|.+.+.|.+.-+.. +..+
T Consensus       232 el~~~~e~~~~s~-------sD~ee~~~~~~~kLR~Yq-~~rLkY----------YyAVvecDsi~tA~~vYe~CDG~Ef  293 (650)
T KOG2318|consen  232 ELFKPVEEYKESE-------SDDEEEEDVDREKLRQYQ-LNRLKY----------YYAVVECDSIETAKAVYEECDGIEF  293 (650)
T ss_pred             hhccccccCcccc-------cchhhhhhHHHHHHHHHH-hhhhee----------EEEEEEecCchHHHHHHHhcCccee
Confidence            3322211111110       111111122344444443 222221          27999999999999998887 4555


Q ss_pred             CC
Q psy1314         167 CG  168 (275)
Q Consensus       167 ~g  168 (275)
                      ..
T Consensus       294 Es  295 (650)
T KOG2318|consen  294 ES  295 (650)
T ss_pred             cc
Confidence            54

>KOG4213|consensus

Probab=83.85  E-value=0.86  Score=35.89  Aligned_cols=67  Identities=15%  Similarity=0.206  Sum_probs=42.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC-CCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT-GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~t-g~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      .++++..  |.+...++|.++-+  +++..+.+.+.... -..+|..||+|.+.+.|.++++.......-..
T Consensus       111 ~r~v~~K--~td~ql~~l~qw~~--~k~~nv~mr~~~~k~~~fkGsvkv~f~tk~qa~a~~~~~e~~~~e~e  178 (205)
T KOG4213|consen  111 ERTVYKK--ITDDQLDDLNQWAS--GKGHNVKMRRHGNKAHPFKGSVKVTFQTKEQAFANDDTHEEKGAETE  178 (205)
T ss_pred             Hhhhhcc--CCHHHHHHHHHHhc--ccceEeeccccCCCCCCCCCceEEEeecHHHHHhhhhhhhhhccchH
Confidence            3455555  33334444555444  78888888664221 25789999999999999998876544444333

>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=81.26  E-value=4.6  Score=26.99  Aligned_cols=59  Identities=25%  Similarity=0.374  Sum_probs=32.1

Q ss_pred             CCCCCHHHHHHhcccCC-----CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314         109 TTEISEQDVRDYFSQYG-----SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus       109 ~~~~~~~~l~~~F~~~G-----~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      -..++..+|..++....     .|-.|+|..+        |+||+-... .|++++..+ +..+.|+++.|..|
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~-~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            34577888888887653     4566777533        789888654 566677776 47899999999865

; PDB: 2G0C_A 3MOJ_B.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	275
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		8e-26
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		9e-26
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		9e-26
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-25
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-25
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-25
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-25
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		1e-08
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		2e-14
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		5e-07
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-14
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		1e-08
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		5e-14
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		3e-07
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		6e-14
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		2e-08
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		1e-13
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		8e-07
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-13
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-09
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-11
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-11
3nnc_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		2e-11
2dhs_A	187	Solution Structure Of Nucleic Acid Binding Protein		3e-11
3nmr_A	175	Crystal Structure Of Cugbp1 Rrm12-Rna Complex Lengt		1e-10
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		4e-10
1wtb_A	79	Complex Structure Of The C-Terminal Rna-Binding Dom		6e-09
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		1e-09
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		1e-09
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-09
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-09
1iqt_A	75	Solution Structure Of The C-Terminal Rna-Binding Do		2e-08
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		8e-09
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		7e-06
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		9e-09
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		2e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		3e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		2e-07
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		4e-07
2cqg_A	103	Solution Structure Of The Rna Binding Domain Of Tar		7e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		6e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		8e-07
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		7e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		9e-07
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		8e-05
3vaf_A	174	Structure Of U2af65 Variant With Bru3 Dna Length =		2e-06
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		2e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		2e-06
2g4b_A	172	Structure Of U2af65 Variant With Polyuridine Tract		2e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		3e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		9e-04
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		3e-06
2yh0_A	198	Solution Structure Of The Closed Conformation Of Hu		6e-06
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		6e-06
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		6e-06
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		7e-06
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		7e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		8e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		9e-06
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		9e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		1e-05
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		1e-05
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		1e-05
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		1e-05
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		2e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		2e-05
2xsf_A	89	Crystal Structure Of The Rrm Domain Of Mouse Delete		3e-04
2cq0_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		2e-05
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-05
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		3e-05
3nnh_A	88	Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuug		7e-05
1x5t_A	96	Solution Structure Of The Second Rrm Domain In Spli		3e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-05
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		6e-05
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		7e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-05
2xs5_A	87	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		8e-05
2xs2_A	102	Crystal Structure Of The Rrm Domain Of Mouse Delete		4e-04
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		1e-04
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		2e-04
1d9a_A	85	Solution Structure Of The Second Rna-Binding Domain		2e-04
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		2e-04
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		2e-04
1u6f_A	139	Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit		3e-04
2u2f_A	85	Solution Structure Of The Second Rna-Binding Domain		3e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		4e-04
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		4e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		4e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		4e-04
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		9e-04
1x4a_A	109	Solution Structure Of Rrm Domain In Splicing Factor		5e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		5e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		5e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		6e-04
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		7e-04
2dnk_A	105	Solution Structure Of Rna Binding Domain In Bruno-L		7e-04
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		8e-04
2dno_A	102	Solution Structure Of Rna Binding Domain In Trinucl		8e-04
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		8e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		9e-04

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score =  114 bits (284), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  + 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
           A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG I  
Sbjct: 74  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            +   D+    K+GF F++FDD +  ++++      + G   +V++
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179

>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 =  114 bits (284), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  + 
Sbjct: 15  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
           A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG I  
Sbjct: 75  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 134
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            +   D+    K+GF F++FDD +  ++++      + G   +V++
Sbjct: 135 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 180

>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 =  113 bits (283), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  + 
Sbjct: 13  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
           A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG I  
Sbjct: 73  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 132
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            +   D+    K+GF F++FDD +  ++++      + G   +V++
Sbjct: 133 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 178

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score =  113 bits (283), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  + 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
           A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG I  
Sbjct: 67  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 126
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            +   D+    K+GF F++FDD +  ++++      + G   +V++
Sbjct: 127 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 172

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score =  113 bits (283), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  + 
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
           A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG I  
Sbjct: 74  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 133
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            +   D+    K+GF F++FDD +  ++++      + G   +V++
Sbjct: 134 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 179

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score =  113 bits (282), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 55/166 (33%), Positives = 91/166 (54%), Gaps = 7/166 (4%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  + 
Sbjct: 12  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 77  AGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
           A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG I  
Sbjct: 72  ARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEV 131
Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            +   D+    K+GF F++FDD +  ++++      + G   +V++
Sbjct: 132 IEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 177

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score =  110 bits (276), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 56/161 (34%), Positives = 95/161 (59%), Gaps = 2/161 (1%)
Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           K+F+GGL+ +T E  + +YF +YG V  + I  DP TG+SRGF F++F    +VD+++  
Sbjct: 5   KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT 64
Query: 78  GDHYIGNKKIDPKRVTKRVNPLKC-KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
             H +  K IDPKR   R    K  KIFVGG+  ++  ++  ++FSQ+G+I + Q   DK
Sbjct: 65  -QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK 123
Query: 137 SKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK 177
                +GF F+++D  +  ++V  N       +++++KR +
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE 164

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 49/75 (65%), Gaps = 1/75 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+F+GGL  + +E ++R+YF +YG++T+ +   D +    +GF F+SF+  +  ++V+ 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Query: 161 NPKQVICGKEVDVKR 175
             + ++ GK +D KR
Sbjct: 64  T-QHILDGKVIDPKR 77

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 76.3 bits (186), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +F+GGL  +T +K++ DYFS++GEV   ++K DP TG+SRGF FV F   ++VD ++   
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 79 DHYIGNKKIDPKR 91
          +H +  K IDPKR
Sbjct: 62 EHKLNGKVIDPKR 74

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 21/73 (28%), Positives = 43/73 (58%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +F+GGL+ + +++D++DYFS++G + +     D      +GF F+ F +    ++V+   
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 163 KQVICGKEVDVKR 175
           +  + GK +D KR
Sbjct: 62  EHKLNGKVIDPKR 74

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 34/73 (46%), Positives = 47/73 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD +LA 
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 86
Query: 78 GDHYIGNKKIDPK 90
            H + +K IDPK
Sbjct: 87 SRHELDSKTIDPK 99

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+F+GGL+ + +++ +R+YF Q+G + E     D      +GF F++F DQ   ++VLA
Sbjct: 26  CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 85
Query: 161 NPKQVICGKEVDVK 174
             +  +  K +D K
Sbjct: 86  QSRHELDSKTIDPK 99

>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 = 74.7 bits (182), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 35/83 (42%), Positives = 53/83 (63%)
Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          A     D  K FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   
Sbjct: 4  ASKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDA 63
Query: 69 KAVDDLLAAGDHYIGNKKIDPKR 91
           +V+ +L   +H +  + IDPK+
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKK 86

>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 = 52.0 bits (123), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K FVGGL+ + S++D++DYF+++G + +     D +    +GF FI F D    E+VL  
Sbjct: 13  KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 162 PKQVICGKEVDVKR 175
            +  + G+ +D K+
Sbjct: 73  KEHRLDGRVIDPKK 86

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 74.7 bits (182), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 34/73 (46%), Positives = 47/73 (64%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD +LA 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61
Query: 78 GDHYIGNKKIDPK 90
            H + +K IDPK
Sbjct: 62 SRHELDSKTIDPK 74

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/74 (33%), Positives = 44/74 (59%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+F+GGL+ + +++ +R+YF Q+G + E     D      +GF F++F DQ   ++VLA
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60
Query: 161 NPKQVICGKEVDVK 174
             +  +  K +D K
Sbjct: 61  QSRHELDSKTIDPK 74

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 49/79 (62%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           RKLF+GGL   T E+ + +Y+ Q+G++    +  DP + +SRGF FVTF++   VD  +A
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 77  AGDHYIGNKKIDPKRVTKR 95
           A  H I  + ++PKR   R
Sbjct: 88  ARPHSIDGRVVEPKRAVAR 106

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 24/81 (29%), Positives = 44/81 (54%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ E +E+ +R+Y+ Q+G +T+     D +    +GF F++F      +  +A 
Sbjct: 29  KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 162 PKQVICGKEVDVKRVKFNPET 182
               I G+ V+ KR     E+
Sbjct: 89  RPHSIDGRVVEPKRAVAREES 109

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 72.4 bits (176), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 37/78 (47%), Positives = 45/78 (57%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KLFVGGL  +T ++ +  YFSQYGEV    I  D  T QSRGF FV F     V  +LA+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 78 GDHYIGNKKIDPKRVTKR 95
            H +  + IDPK  T R
Sbjct: 78 RPHTLDGRNIDPKPCTPR 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 = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 42/73 (57%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL    +++ +R YFSQYG + +     DK+ N  +GF F+ F D N    VLA+
Sbjct: 18  KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS 77
Query: 162 PKQVICGKEVDVK 174
               + G+ +D K
Sbjct: 78  RPHTLDGRNIDPK 90

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 40/145 (27%), Positives = 71/145 (48%), Gaps = 2/145 (1%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
           L V  L +N  + E+   FS  GEVES  +  D   G S G+ FV + T K  +  +   
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 79  DHY-IGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
           +   + +K I           +K   +++ GL   ++++DV D FS++G I   +   D+
Sbjct: 65  NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 137 SKNMKKGFCFISFDDQNVAEQVLAN 161
           +  + +G  FI FD ++ AE+ + +
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAITS 149

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 40/145 (27%), Positives = 71/145 (48%), Gaps = 2/145 (1%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
           L V  L +N  + E+   FS  GEVES  +  D   G S G+ FV + T K  +  +   
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 79  DHY-IGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK 136
           +   + +K I           +K   +++ GL   ++++DV D FS++G I   +   D+
Sbjct: 65  NGLRLQSKTIKVSYARPSSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQ 124
Query: 137 SKNMKKGFCFISFDDQNVAEQVLAN 161
           +  + +G  FI FD ++ AE+ + +
Sbjct: 125 TTGLSRGVAFIRFDKRSEAEEAITS 149

>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 47/160 (29%), Positives = 78/160 (48%), Gaps = 21/160 (13%)
Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKAV 71
           +D  K+FVG + R   EK++ + F QYG V  I++  D      QS+G  FVTF T+KA 
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 72  DD---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRD 119
            +         +L    H I  K  D ++   V  R      K+F+G ++ + +E D+R 
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR------KLFIGMISKKCTENDIRV 114
Query: 120 YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
            FS +G I E  +       + +G  F++F  + +A+  +
Sbjct: 115 MFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAI 153

>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 = 65.5 bits (158), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 47/159 (29%), Positives = 78/159 (49%), Gaps = 21/159 (13%)
Query: 15  DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND--PHTGQSRGFAFVTFTTQKAVD 72
           D  K+FVG + R   EK++ + F QYG V  I++  D   +  QS+G  FVTF T+KA  
Sbjct: 14  DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAAL 73
Query: 73  D---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRDY 120
           +         +L    H I  K  D ++   V  R      K+F+G ++ + +E D+R  
Sbjct: 74  EAQNALHNMKVLPGMHHPIQMKPADSEKNNAVEDR------KLFIGMISKKCTENDIRVM 127
Query: 121 FSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           FS +G I E  +       + +G  F++F  + +A+  +
Sbjct: 128 FSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAMAQTAI 165

>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex Length = 175

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 47/160 (29%), Positives = 76/160 (47%), Gaps = 21/160 (13%)
Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKAV 71
           +D  K FVG + R   EK++ + F QYG V  I++  D      QS+G  FVTF T+KA 
Sbjct: 1   SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 72  DD---------LLAAGDHYIGNKKIDPKR---VTKRVNPLKCKIFVGGLTTEISEQDVRD 119
            +         +L    H I  K  D ++   V  R      K+F+G ++ + +E D+R 
Sbjct: 61  LEAQNALHNXKVLPGXHHPIQXKPADSEKNNAVEDR------KLFIGXISKKCTENDIRV 114
Query: 120 YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
            FS +G I E  +       + +G  F++F  +  A+  +
Sbjct: 115 XFSSFGQIEEC-RILRGPDGLSRGCAFVTFTTRAXAQTAI 153

>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 = 62.0 bits (149), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 30/74 (40%), Positives = 46/74 (62%)
Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGGL  +T E++I +YF  +GEVESI +  D  T + RGF F+TF  ++ V  ++ 
Sbjct: 2  KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Query: 77 AGDHYIGNKKIDPK 90
             H +G  K + K
Sbjct: 62 KKYHNVGLSKCEIK 75

>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 = 57.8 bits (138), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 21/58 (36%), Positives = 38/58 (65%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           KIFVGGL+ +  E+ +R+YF  +G +   + P D   N ++GFCFI+F ++   ++++
Sbjct: 3   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 60

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 46/76 (60%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGG+     E ++R+YF ++G +TE    +D  K   +GF FI+F+D+   +Q +  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
Query: 162 PKQVICGKEVDVKRVK 177
               I GK+V+VKR +
Sbjct: 72  HFHDIMGKKVEVKRAE 87

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 10/147 (6%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
           L V  L +N  ++E    F   GE+ES  +  D  TGQS G+ FV +      +KA++ L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 75  --LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
             L      I      P   + R       ++V GL   ++++++   FSQYG I   + 
Sbjct: 65  NGLRLQTKTIKVSYARPSSASIR----DANLYVSGLPKTMTQKELEQLFSQYGRIITSRI 120
Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQVL 159
             D+   + +G  FI FD +  AE+ +
Sbjct: 121 LVDQVTGVSRGVGFIRFDKRIEAEEAI 147

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 68/147 (46%), Gaps = 10/147 (6%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
           L V  L +N  + E    F   G++ES  +  D  TGQS G+ FV ++      KA++ L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 75  --LAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
             L      I      P   + R       ++V GL   +S++++   FSQYG I   + 
Sbjct: 67  NGLKLQTKTIKVSYARPSSASIR----DANLYVSGLPKTMSQKEMEQLFSQYGRIITSRI 122
Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQVL 159
             D++  + +G  FI FD +  AE+ +
Sbjct: 123 LLDQATGVSRGVGFIRFDKRIEAEEAI 149

>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 = 59.3 bits (142), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/72 (40%), Positives = 44/72 (61%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +FVGGL  +T E++I +YF  +GEVESI +  D  T + RGF F+TF  ++ V  ++   
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61
Query: 79 DHYIGNKKIDPK 90
           H +G  K + K
Sbjct: 62 YHNVGLSKCEIK 73

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 37/57 (64%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           IFVGGL+ +  E+ +R+YF  +G +   + P D   N ++GFCFI+F ++   ++++
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 57.4 bits (137), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 45/79 (56%), Gaps = 4/79 (5%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          +DE KLFVGGL  +T E+ +   FS+YG++  + +  D  T +SRGF FVTF       D
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 74 LLAAGDHYIGNKKIDPKRV 92
           + A    +  K +D +++
Sbjct: 70 AMMA----MNGKSVDGRQI 84

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 46/78 (58%), Gaps = 4/78 (5%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+FVGGL+ + +EQ +   FS+YG I+E     D+     +GF F++F++ + A+  +  
Sbjct: 14  KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM-- 71
Query: 162 PKQVICGKEVDVKRVKFN 179
               + GK VD ++++ +
Sbjct: 72  --MAMNGKSVDGRQIRVD 87

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 44/73 (60%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           IFVGGL+   + +DV+ YF Q+G + +    FDK+ N  +GF F++F+ +++ E+V    
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 163 KQVICGKEVDVKR 175
              I  K V+ K+
Sbjct: 62  FHEINNKMVECKK 74

>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 = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/166 (28%), Positives = 77/166 (46%), Gaps = 21/166 (12%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVD-- 72
           L+VG LH +  E  + + FS  G + SI +  D  T +S G+A+V F      ++A+D  
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 73  --DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
             D++      I   + DP      V      IF+  L   I  + + D FS +G+I   
Sbjct: 78  NFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAFGNILSC 133
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQ-------VLANPKQVICGK 169
           +   D  +N  KG+ F+ F+ Q  AE+       +L N ++V  G+
Sbjct: 134 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177

>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 = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 47/166 (28%), Positives = 77/166 (46%), Gaps = 21/166 (12%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVD-- 72
           L+VG LH +  E  + + FS  G + SI +  D  T +S G+A+V F      ++A+D  
Sbjct: 13  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 73  --DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
             D++      I   + DP      V      IF+  L   I  + + D FS +G+I   
Sbjct: 73  NFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAFGNILSC 128
Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQ-------VLANPKQVICGK 169
           +   D  +N  KG+ F+ F+ Q  AE+       +L N ++V  G+
Sbjct: 129 KVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G+AGP R     L+VG LH N  E  +   F  +G +ESI +  D  TG+S+G+ F+TF+
Sbjct: 22 GSAGPMR-----LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFS 76
Query: 67 ----TQKAVDDL 74
               +KA++ L
Sbjct: 77 DSECAKKALEQL 88

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 40/64 (62%), Gaps = 2/64 (3%)
Query: 5  ANGTAGPGRNDERK--LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G  R  ++   L V GL   T E+++ +YFS +GEV  + +K D  TG S+GF F
Sbjct: 2  SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 63 VTFT 66
          V FT
Sbjct: 62 VRFT 65

>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna- Binding Protein-43 Length = 103

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           + V GL  + +EQD+++YFS +G +   Q   D      KGF F+ F +     +V++  
Sbjct: 18  LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ- 76
Query: 163 KQVICGKEVDVK 174
           + +I G+  D K
Sbjct: 77  RHMIDGRWCDCK 88

>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 = 51.2 bits (121), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 34/157 (21%), Positives = 72/157 (45%), Gaps = 13/157 (8%)
Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           +++VG ++   GE  I   F+ +G ++SI +  D  T + +GFAFV +   +A    L  
Sbjct: 30  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 78  GDH-YIGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEISEQDVRDYFSQY 124
            +   +G + I   R +   +  P+            +I+V  +  ++S+ D++  F  +
Sbjct: 90  MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 149
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           G I       D +    KG+ FI ++    ++  +++
Sbjct: 150 GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 186

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 50.8 bits (120), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 34/157 (21%), Positives = 72/157 (45%), Gaps = 13/157 (8%)
Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           +++VG ++   GE  I   F+ +G ++SI +  D  T + +GFAFV +   +A    L  
Sbjct: 15  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 78  GDH-YIGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEISEQDVRDYFSQY 124
            +   +G + I   R +   +  P+            +I+V  +  ++S+ D++  F  +
Sbjct: 75  MNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 134
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           G I       D +    KG+ FI ++    ++  +++
Sbjct: 135 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 171

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 94  KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           +R   + C+++VG +  E+ E  +R  F+ +G I      +D      KGF F+ ++   
Sbjct: 7   QRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 66
Query: 154 VAEQVLANPKQVIC-GKEVDVKR 175
            A+  L     V+  G+ + V R
Sbjct: 67  AAQLALEQMNSVMLGGRNIKVGR 89

>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 = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 34/157 (21%), Positives = 71/157 (45%), Gaps = 13/157 (8%)
Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           +++VG ++   GE  I   F+ +G ++SI    D  T + +GFAFV +   +A    L  
Sbjct: 14  RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 78  GDHY-IGNKKIDPKRVTK--RVNPLK----------CKIFVGGLTTEISEQDVRDYFSQY 124
            +   +G + I   R +   +  P+            +I+V  +  ++S+ D++  F  +
Sbjct: 74  XNSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF 133
Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           G I       D +    KG+ FI ++    ++  +++
Sbjct: 134 GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSS 170

>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 = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 1/83 (1%)
Query: 94  KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           +R   + C+++VG +  E+ E  +R  F+ +G I      +D      KGF F+ ++   
Sbjct: 6   QRALAIXCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPE 65
Query: 154 VAEQVLANPKQV-ICGKEVDVKR 175
            A+  L     V + G+ + V R
Sbjct: 66  AAQLALEQXNSVXLGGRNIKVGR 88

>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna Length = 174

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 17/171 (9%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP----HTGQSRGFAFVTF-----T 66
           R+L+VG +     E+ + D+F+    +  ++    +P       Q + FAF+ F     T
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66
Query: 67  TQ-KAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYG 125
           TQ  A D ++  G      +  D + +     P   K+F+GGL   +++  V++  + +G
Sbjct: 67  TQAMAFDGIIFQGQSLKIRRPHDYQPL-----PGAHKLFIGGLPNYLNDDQVKELLTSFG 121
Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-KEVDVKR 175
            +  F    D +  + KG+ F  + D NV +Q +A    +  G K++ V+R
Sbjct: 122 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 172

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 39/72 (54%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL    ++  +R YF  +G I E     D+     +G+ F++  D+  AE+   +
Sbjct: 19  KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 162 PKQVICGKEVDV 173
           P  +I G++ +V
Sbjct: 79  PNPIIDGRKANV 90

>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 = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/91 (29%), Positives = 51/91 (56%), Gaps = 5/91 (5%)
Query: 90  KRVTKRVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
           + V  R NP   C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ 
Sbjct: 35  RHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVY 94
Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKRVKFN 179
           F++ + A++     K+   G E+D +R++ +
Sbjct: 95  FENVDDAKEA----KERANGMELDGRRIRVD 121

>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract Length = 172

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 42/171 (24%), Positives = 80/171 (46%), Gaps = 17/171 (9%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP----HTGQSRGFAFVTF-----T 66
           R+L+VG +     E+ + D+F+    +  ++    +P       Q + FAF+ F     T
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 67  TQ-KAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYG 125
           TQ  A D ++  G      +  D + +     P   K+F+GGL   +++  V++  + +G
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPL-----PGAHKLFIGGLPNYLNDDQVKELLTSFG 119
Query: 126 SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-KEVDVKR 175
            +  F    D +  + KG+ F  + D NV +Q +A    +  G K++ V+R
Sbjct: 120 PLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          KLF+GGL+R T EK +   F ++G +  + +  D  T +SRGFAF+TF
Sbjct: 9  KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITF 55

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 8/80 (10%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAEQ 157
           K+F+GGL  E +E+ ++  F ++G I+E     D++ +  +GF FI+F    D +N A+ 
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKNAAKD 67
Query: 158 VLANPKQVICGKEVDVKRVK 177
           +     + + GK + V++ K
Sbjct: 68  MNG---KSLHGKAIKVEQAK 84

>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 = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 42/66 (63%)
Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          ++G++G   +D  KLF+G + RN  EK++   F ++G++  +++  D  TG  +G AF+T
Sbjct: 2  SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61
Query: 65 FTTQKA 70
          +  +++
Sbjct: 62 YCERES 67

>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human U2af65 Tandem Rrm1 And Rrm2 Domains Length = 198

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 44/186 (23%), Positives = 81/186 (43%), Gaps = 27/186 (14%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDP----HTGQSRGFAFVTF-----T 66
           R+L+VG +     E+ + D+F+    +  ++    +P       Q + FAF+ F     T
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64
Query: 67  TQ-KAVDDLLAAGDHYIGNKKID---------------PKRVTKRVNPLKCKIFVGGLTT 110
           TQ  A D ++  G      +  D               P  V+  V     K+F+GGL  
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124
Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-K 169
            +++  V++  + +G +  F    D +  + KG+ F  + D NV +Q +A    +  G K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184
Query: 170 EVDVKR 175
           ++ V+R
Sbjct: 185 KLLVQR 190

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 95  RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           R NP   C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ +
Sbjct: 9   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 154 VAEQVLANPKQVICGKEVDVKRVK 177
            A++     K+   G E+D +R++
Sbjct: 69  DAKEA----KERANGMELDGRRIR 88

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          GP R+ E   LFV  +H    E EI + F  YGE+++I +  D  TG S+G+A V + T 
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 69 K 69
          K
Sbjct: 79 K 79

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          GP R+ E   LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  V + T 
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 69 K 69
          K
Sbjct: 75 K 75

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDER-KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          GP R+ E   LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  V + T 
Sbjct: 2  GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 69 K 69
          K
Sbjct: 62 K 62

>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 = 47.8 bits (112), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 95  RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           R NP   C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ +
Sbjct: 9   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 68
Query: 154 VAEQVLANPKQVICGKEVDVKRVKFN 179
            A++     K+   G E+D +R++ +
Sbjct: 69  DAKEA----KERANGMELDGRRIRVD 90

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 5/86 (5%)
Query: 95  RVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           R NP   C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ +
Sbjct: 6   RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 65
Query: 154 VAEQVLANPKQVICGKEVDVKRVKFN 179
            A++     K+   G E+D +R++ +
Sbjct: 66  DAKEA----KERANGMELDGRRIRVD 87

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          GP R+ E   LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  V + T 
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 69 K 69
          K
Sbjct: 76 K 76

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 8/153 (5%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
           L V  L ++  ++E+   F   G + +  I  D  TG S G+AFV FT    +Q+A+  L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 75  LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
                  + NK++           +K   ++V  L   I++  +   F +YGSI +    
Sbjct: 66  ---NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 122
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
            DK     +G  F+ ++ +  A++ ++    VI
Sbjct: 123 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  V + T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  V + T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 10  GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
           GP R+ E   LFV  +H    E EI + F  YGE+++I +  D  TG S+G+A V + T 
Sbjct: 65  GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 69  K 69
           K
Sbjct: 125 K 125

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 33/51 (64%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  V + T K
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G  G G+     +FVGG+     E EI  +F++YG V+ + I  D  TG S+G+ FV+F 
Sbjct: 1  GPLGSGKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFY 59
Query: 67 TQKAVDDLLAAGDHYIGNK-KIDP 89
              V  ++ +  ++ G K K+ P
Sbjct: 60 NDVDVQKIVESQINFHGKKLKLGP 83

>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In Azoospermia-Like Length = 89

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAE 156
           +FVGG+   + E ++R +F++YGS+ E +   D++  + KG+ F+SF    D Q + E
Sbjct: 13  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 69

>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 = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/63 (34%), Positives = 38/63 (60%), Gaps = 2/63 (3%)
Query: 5  ANGTAGPGR--NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++GP R  +D   + V  L  +T E ++ + F  +G +  I +  D  TGQS+GFAF
Sbjct: 2  SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 63 VTF 65
          ++F
Sbjct: 62 ISF 64

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 38/153 (24%), Positives = 69/153 (45%), Gaps = 8/153 (5%)
Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT----TQKAVDDL 74
           L V  L ++  ++E+   F   G + +  I  D  TG S G+AFV FT    +Q+A+  L
Sbjct: 17  LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 75  LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
                  + NK++           +K   ++V  L   I++  +   F +YGSI +    
Sbjct: 77  NGIT---VRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNIL 133
Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVI 166
            DK     +G  F+ ++ +  A++ ++    VI
Sbjct: 134 RDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 45.8 bits (107), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND--PHTGQSRGFAFVTFTTQKA 70
          +D  K+FVG + R   EK++ + F QYG V  I++  D   +  QS+G  FVTF T+KA
Sbjct: 1  SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA 59

>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna Length = 88

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/56 (39%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN--MKKGFCFISFDDQNVA 155
           K+FVG +    SE+D+R+ F QYG++ E     D+S+N    KG CF++F  +  A
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing Factor 3b Length = 96

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 2/78 (2%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKA 70
          G +    +F+G L     EK + D FS +G + ++  I  DP TG S+G+AF+ F +  A
Sbjct: 1  GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 71 VDDLLAAGD-HYIGNKKI 87
           D  + A +  Y+ N+ I
Sbjct: 61 SDAAIEAMNGQYLCNRPI 78

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G +    L+VG LH N  E  +   F  +G++++I +  D  TG+S+G+ F+TF+  +  
Sbjct: 1  GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 72 DDLLAAGDHY-IGNKKIDPKRVTKRVN 97
             L   + + +  + +    VT+R++
Sbjct: 61 RRALEQLNGFELAGRPMRVGHVTERLD 87

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 34/57 (59%), Gaps = 6/57 (10%)
Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +C++FVG L T+I+E+D +  F +YG      +P +   N  +GF FI  + + +AE
Sbjct: 22  RCRLFVGNLPTDITEEDFKRLFERYG------EPSEVFINRDRGFGFIRLESRTLAE 72

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 37/75 (49%)
Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          ++G++GP  +    L V  L   T    +   F +YG V  + I  +PHT   RGFAFV 
Sbjct: 2  SSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVR 61
Query: 65 FTTQKAVDDLLAAGD 79
          F  ++   D  AA D
Sbjct: 62 FHDRRDAQDAEAAMD 76

>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 = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +FVGG+     E EI  +F++YG V+ + I  D  TG S+G+ FV+F     V  ++ + 
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 79 DHYIGNK-KIDP 89
           ++ G K K+ P
Sbjct: 71 INFHGKKLKLGP 82

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAE 156
           +FVGG+   + E ++R +F++YGS+ E +   D++  + KG+ F+SF    D Q + E
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68

>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 = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          +FVGG+     E EI  +F++YG V+ + I  D  TG S+G+ FV+F     V  ++ + 
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 79 DHYIGNK-KIDP 89
           ++ G K K+ P
Sbjct: 71 INFHGKKLKLGP 82

>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 = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 36/58 (62%), Gaps = 5/58 (8%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF----DDQNVAE 156
           +FVGG+   + E ++R +F++YGS+ E +   D++  + KG+ F+SF    D Q + E
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVE 68

>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 = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 32/59 (54%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +FVG +  E +E+ ++D FS+ G +  F+  +D+     KG+ F  + DQ  A   + N
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 15  DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           D+R ++VG +   +  +++  +FS  G +  I+I  D  +G  +G+A++ F  + +VD  
Sbjct: 35  DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94
Query: 75  LAAGDHYIGNKKIDPKRVTKRVN 97
           +A  +     + I  K + KR N
Sbjct: 95  VAMDETVFRGRTI--KVLPKRTN 115

>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2) Of Hu Antigen C (Huc) Length = 85

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F
Sbjct: 4  LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 50

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 43/77 (55%), Gaps = 17/77 (22%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           +FVG  T +++E ++R++FSQYG + +    +PF       + F F++F D  +A     
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-------RAFAFVTFADDQIA----- 55
Query: 161 NPKQVICGKEVDVKRVK 177
              Q +CG+++ +K + 
Sbjct: 56  ---QSLCGEDLIIKGIS 69

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
           ++FV  L+   SE+D+   FS YG ++E   P D      KGF F++F
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTF 57

>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From Trypanosoma Cruzi Length = 139

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           R L V  +     E ++   F +YG +ES+ I  D  T QSRG+ FV F +  +    +A
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 77  AGDHY-IGNKKI 87
             + + I NK++
Sbjct: 103 GLNGFNILNKRL 114

>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of Hu2af65 Length = 85

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 33/59 (55%)
Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           K+F+GGL   +++  V++  + +G +  F    D +  + KG+ F  + D NV +Q +A
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D R ++VG +      +E+  +F   G V  ++I  D  +G  +GFA++ F+ +++V   
Sbjct: 4  DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
          LA  +     ++I  K + KR N
Sbjct: 64 LALDESLFRGRQI--KVIPKRTN 84

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 2/83 (2%)
Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D R ++VG +      +E+  +F   G V  ++I  D  +G  +GFA++ F+ +++V   
Sbjct: 5  DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
          LA  +     ++I  K + KR N
Sbjct: 65 LALDESLFRGRQI--KVIPKRTN 85

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 93  TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
           TKRV      ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+  
Sbjct: 11  TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELA 64
Query: 153 NVAEQVLANPKQV-ICGKEVDVKRVK 177
             A   + N  +  + G+ + V   K
Sbjct: 65  EDAAAAIDNMNESELFGRTIRVNLAK 90

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G   +R L+VGGL     +K ++  F  +G++  I I  D  T + RGFAFV F   +  
Sbjct: 1  GSTTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF---ELA 57
Query: 72 DDLLAAGDH 80
          +D  AA D+
Sbjct: 58 EDAAAAIDN 66

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93  TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           TKRV      ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+
Sbjct: 4   TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 55

>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2 Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 7/61 (11%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG--FCFISFDDQNVAEQV 158
           C+I+VG L  +I  +D+ D F +YG+I +        KN + G  F F+ F+D   AE  
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-----KNRRGGPPFAFVEFEDPRDAEDA 77
Query: 159 L 159
           +
Sbjct: 78  V 78

>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc) In Complex With A Cap Analogue M7gpppg Length = 156

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 80  HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN 139
           H+ G+ +   K + K      C ++VG L+   +E+ + + FS+ G I +     DK K 
Sbjct: 24  HFRGDNEEQEKLLKK-----SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKK 78
Query: 140 MKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK 177
              GFCF+ +  +  AE    N  + I G  +D + ++
Sbjct: 79  TACGFCFVEYYSRADAE----NAMRYINGTRLDDRIIR 112

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          RN +  ++VGGL     E  + + F Q G V +  +  D  TGQ +G+ FV F +++  D
Sbjct: 12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDAD 71

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN- 161
           +FVG L+ EI+ +D++  F+ +G I++ +   D +    KG+ F+SF ++  AE  + + 
Sbjct: 18  VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 162 PKQVICGKEV 171
             Q + G+++
Sbjct: 78  GGQWLGGRQI 87

>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 = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/80 (27%), Positives = 46/80 (57%), Gaps = 4/80 (5%)
Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +FVG L+ EI+ +D++  F+ +G I++ +   D +    KG+ F+SF ++  AE  +   
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAI--- 74
Query: 163 KQVICGKEVDVKRVKFNPET 182
            Q + G+ +  ++++ N  T
Sbjct: 75  -QQMGGQWLGGRQIRTNWAT 93

>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4 Rna Binding Protein Length = 105

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 7/76 (9%)
Query: 5  ANGTAGPGRN--DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G  R     RKLFVG L++   E ++   F  +G +E  +I   P  G S+G AF
Sbjct: 2  SSGSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAF 60
Query: 63 VTFTT----QKAVDDL 74
          V +++    Q A++ L
Sbjct: 61 VKYSSHAEAQAAINAL 76

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93  TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           TKRV      ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+
Sbjct: 62  TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 113

>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide Repeat Containing 4 Variant Length = 102

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 5/66 (7%)
Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----Q 68
          R ++RKLFVG L +   ++++   F  +G ++  ++   P  G S+G AFV F T    Q
Sbjct: 9  RGEDRKLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPD-GTSKGCAFVKFQTHAEAQ 67
Query: 69 KAVDDL 74
           A++ L
Sbjct: 68 AAINTL 73

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 6/58 (10%)
Query: 93  TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           TKRV      ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+
Sbjct: 6   TKRV------LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 57

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 40.8 bits (94), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL- 159
             + V  LT   S   +R  F +YG + +   P D+     +GF F+ F D+  AE  + 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 160 ANPKQVICGKEVDVKRVKF 178
           A    V+ G+E+ V+  ++
Sbjct: 108 AMDGAVLDGRELRVQMARY 126

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	275
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-67
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-27
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-66
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-26
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	8e-20
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-43
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-19
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	7e-39
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	6e-13
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-38
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-34
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-15
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	5e-33
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-20
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	5e-33
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-13
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	9e-33
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-20
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	2e-32
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-32
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-16
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	3e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-32
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-14
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	2e-32
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-26
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	2e-31
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	1e-26
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	3e-31
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-21
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	5e-31
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	7e-28
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-31
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-21
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	9e-31
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	1e-18
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-30
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	4e-23
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-30
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-28
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-28
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-13
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	4e-28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-25
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-08
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-26
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-13
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-26
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-25
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-22
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-24
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-23
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-22
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-18
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	7e-22
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-20
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	8e-21
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-13
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-20
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	4e-15
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-20
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	1e-11
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-19
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	3e-14
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-19
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	1e-11
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	2e-19
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-10
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-19
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	2e-12
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	7e-19
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	5e-11
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-19
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-12
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-10
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	2e-18
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-18
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-13
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-18
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-12
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-18
1x4e_A	85	RNA binding motif, single-stranded interacting pro	1e-10
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-18
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-11
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-18
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	1e-11
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	4e-18
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	7e-11
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-12
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	7e-11
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	5e-18
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-11
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	6e-18
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	7e-11
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	7e-18
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-12
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	8e-18
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-11
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-17
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-17
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-10
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-17
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-11
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-17
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-11
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-17
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	4e-10
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-17
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-11
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-17
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-10
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	6e-17
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-10
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	9e-17
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-09
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-16
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	1e-09
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-16
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-09
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-16
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-11
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-16
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-09
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-16
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-10
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	7e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-08
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	9e-16
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-14
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	1e-15
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-11
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	2e-15
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-09
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	1e-04
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-15
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-06
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-15
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-15
2dis_A	109	Unnamed protein product; structural genomics, RRM	1e-13
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	5e-15
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-08
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-15
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-07
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-15
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	6e-09
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	8e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	1e-08
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	8e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-09
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-15
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-09
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	9e-15
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-06
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	1e-14
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-06
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	1e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	4e-09
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	8e-08
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	3e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	5e-08
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	3e-14
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	9e-05
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-14
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-10
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	5e-14
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	6e-09
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-14
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	7e-14
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-07
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-13
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-10
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	2e-13
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	1e-07
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	2e-13
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	7e-12
1x5o_A	114	RNA binding motif, single-stranded interacting pro	2e-13
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-07
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-13
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	7e-10
2div_A	99	TRNA selenocysteine associated protein; structural	2e-13
2div_A	99	TRNA selenocysteine associated protein; structural	3e-09
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-13
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	2e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	3e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-09
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-13
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-13
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-09
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-12
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	1e-11
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-12
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-12
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-10
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-12
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	4e-09
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-12
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-10
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-12
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-06
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-12
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-08
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	5e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-12
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	9e-07
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-11
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-10
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	4e-12
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	5e-07
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-12
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	4e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	4e-12
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	6e-12
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-11
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	6e-12
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	9e-10
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	7e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	1e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	6e-08
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-11
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	1e-08
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	1e-11
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-11
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-07
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-11
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	9e-06
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-11
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-11
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	3e-10
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-09
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	2e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-07
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-11
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	2e-07
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	3e-11
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	5e-09
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	3e-09
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-11
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	5e-07
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-11
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-10
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	6e-08
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	2e-06
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-10
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	3e-08
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	1e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-09
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-10
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	5e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	7e-10
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	1e-06
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-08
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	1e-06
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	1e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-06
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	3e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	7e-07
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-09
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	3e-06
1x5p_A	97	Negative elongation factor E; structure genomics,	4e-09
1x5p_A	97	Negative elongation factor E; structure genomics,	8e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	4e-09
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	7e-06
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-09
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-05
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	5e-09
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	1e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-09
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	7e-09
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-05
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	3e-07
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	2e-08
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	1e-06
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-05
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-08
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	7e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	4e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-08
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	9e-05
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-08
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-07
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	5e-06
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	1e-07
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-05
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-05
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	3e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-07
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-05
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	3e-07
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-07
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	4e-04
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-07
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-05
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	9e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	3e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-06
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-06
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	1e-04

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score =  205 bits (525), Expect = 2e-67
 Identities = 56/162 (34%), Positives = 95/162 (58%), Gaps = 2/162 (1%)

Query: 15  DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           +  K+F+GGL+ +T E  + +YF +YG V  + I  DP TG+SRGF F++F    +VD++
Sbjct: 2   ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61

Query: 75  LAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP 133
           +    H +  K IDPKR   R    K  KIFVGG+  ++  ++  ++FSQ+G+I + Q  
Sbjct: 62  VKT-QHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLM 120

Query: 134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            DK     +GF F+++D  +  ++V  N       +++++KR
Sbjct: 121 LDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKR 162

>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 =  101 bits (255), Expect = 7e-27
 Identities = 30/83 (36%), Positives = 46/83 (55%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
           ++   K+FVGG+  +   KE  ++FSQ+G +    +  D  TGQSRGF FVT+ +  AVD
Sbjct: 84  QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVD 143

Query: 73  DLLAAGDHYIGNKKIDPKRVTKR 95
            +         ++KI+ KR   R
Sbjct: 144 RVCQNKFIDFKDRKIEIKRAEPR 166

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score =  204 bits (520), Expect = 3e-66
 Identities = 61/186 (32%), Positives = 98/186 (52%), Gaps = 8/186 (4%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
              RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD 
Sbjct: 11  EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 70

Query: 74  LLAAGDHYIGNKKIDPKRVTKRVNPLK-------CKIFVGGLTTEISEQDVRDYFSQYGS 126
            + A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG 
Sbjct: 71  AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 130

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSV 186
           I   +   D+    K+GF F++FDD +  ++++      + G   +V++     E M S 
Sbjct: 131 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE-MASA 189

Query: 187 SGAVRG 192
           S + RG
Sbjct: 190 SSSQRG 195

>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 =  101 bits (253), Expect = 2e-26
 Identities = 30/92 (32%), Positives = 48/92 (52%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
           R +          +K+FVGG+  +T E  + DYF QYG++E I I  D  +G+ RGFAFV
Sbjct: 92  REDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFV 151

Query: 64  TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           TF    +VD ++    H +     + ++   +
Sbjct: 152 TFDDHDSVDKIVIQKYHTVNGHNCEVRKALSK 183

>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 = 83.9 bits (208), Expect = 8e-20
 Identities = 20/87 (22%), Positives = 44/87 (50%)

Query: 89  PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
            K  + +      K+F+GGL+ E +++ +R +F Q+G++T+     D +    +GF F++
Sbjct: 2   SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61

Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKR 175
           +      +  +      + G+ V+ KR
Sbjct: 62  YATVEEVDAAMNARPHKVDGRVVEPKR 88

>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 =  144 bits (366), Expect = 2e-43
 Identities = 34/166 (20%), Positives = 71/166 (42%), Gaps = 7/166 (4%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTTQKAV 71
           R+L+VG +     E+ + D+F+    +  ++             Q + FAF+ F +    
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 72  DDLLAAGDHYIGNKKIDPKRVTKRVNPLKC-KIFVGGLTTEISEQDVRDYFSQYGSITEF 130
              +A        + +  +R           K+F+GGL   +++  V++  + +G +  F
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAF 124

Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR 175
               D +  + KG+ F  + D NV +Q +A      +  K++ V+R
Sbjct: 125 NLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR 170

>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 = 81.9 bits (203), Expect = 2e-19
 Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 1/77 (1%)

Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           KLF+GGL     + ++ +  + +G +++ ++  D  TG S+G+AF  +      D  +A 
Sbjct: 96  KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155

Query: 78  GD-HYIGNKKIDPKRVT 93
            +   +G+KK+  +R +
Sbjct: 156 LNGMQLGDKKLLVQRAS 172

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  134 bits (339), Expect = 7e-39
 Identities = 37/194 (19%), Positives = 77/194 (39%), Gaps = 16/194 (8%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
                  +++VG ++   GE  I   F+ +G ++SI +  D  T + +GFAFV +   +A
Sbjct: 23  GALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA 82

Query: 71  VDDLLAA-GDHYIGNKKIDPKRVTKRVNPLKC------------KIFVGGLTTEISEQDV 117
               L       +G + I   R +                    +I+V  +  ++S+ D+
Sbjct: 83  AQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142

Query: 118 RDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRV 176
           +  F  +G I       D +    KG+ FI ++    ++  +++     + G+ + V + 
Sbjct: 143 KSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA 202

Query: 177 --KFNPETMGSVSG 188
                P    +  G
Sbjct: 203 VTPPMPLLTPATPG 216

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.4 bits (160), Expect = 6e-13
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 1/89 (1%)

Query: 88  DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
                 +    +  +++VG +  E+ E  +R  F+ +G I      +D      KGF F+
Sbjct: 16  GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFV 75

Query: 148 SFDDQNVAEQVLANPKQV-ICGKEVDVKR 175
            ++    A+  L     V + G+ + V R
Sbjct: 76  EYEVPEAAQLALEQMNSVMLGGRNIKVGR 104

>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 =  130 bits (328), Expect = 9e-38
 Identities = 45/176 (25%), Positives = 80/176 (45%), Gaps = 19/176 (10%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTT---- 67
           +D  K+FVG + R   EK++ + F QYG V  I++  D      QS+G  FVTF T    
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 68  QKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK-----CKIFVGGLTTEISEQDVRDYFS 122
            +A + L    +  +      P ++    +         K+F+G ++ + +E D+R  FS
Sbjct: 61  LEAQNAL---HNMKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFS 117

Query: 123 QYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA--NPKQVI--CGKEVDVK 174
            +G I E +          +G  F++F  + +A+  +   +  Q +  C   + VK
Sbjct: 118 SFGQIEECRILRGPDGLS-RGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK 172

>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 =  121 bits (306), Expect = 2e-34
 Identities = 40/151 (26%), Positives = 69/151 (45%), Gaps = 8/151 (5%)

Query: 16  ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAV 71
           +  L V  L +N  ++E    F   GE+ES  +  D  TGQS G+ FV +      +KA+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 72  DDLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEF 130
           + L       +  K I           ++   ++V GL   ++++++   FSQYG I   
Sbjct: 62  NTL---NGLRLQTKTIKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITS 118

Query: 131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +   D+   + +G  FI FD +  AE+ +  
Sbjct: 119 RILVDQVTGVSRGVGFIRFDKRIEAEEAIKG 149

>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 = 71.5 bits (176), Expect = 2e-15
 Identities = 20/61 (32%), Positives = 31/61 (50%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
              +  L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F  +   +
Sbjct: 85  SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 144

Query: 73  D 73
           +
Sbjct: 145 E 145

>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 =  115 bits (291), Expect = 5e-33
 Identities = 39/90 (43%), Positives = 50/90 (55%)

Query: 6  NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +G    G ++  KLFVGGL  +T ++ +  YFSQYGEV    I  D  T QSRGF FV F
Sbjct: 6  SGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65

Query: 66 TTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
               V  +LA+  H +  + IDPK  T R
Sbjct: 66 KDPNCVGTVLASRPHTLDGRNIDPKPCTPR 95

>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 = 83.1 bits (206), Expect = 1e-20
 Identities = 28/75 (37%), Positives = 42/75 (56%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+FVGGL    +++ +R YFSQYG + +     DK+ N  +GF F+ F D N    VLA
Sbjct: 17  GKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA 76

Query: 161 NPKQVICGKEVDVKR 175
           +    + G+ +D K 
Sbjct: 77  SRPHTLDGRNIDPKP 91

>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 =  117 bits (296), Expect = 5e-33
 Identities = 32/169 (18%), Positives = 63/169 (37%), Gaps = 10/169 (5%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
                 LF+G L+ N    E+    S+      +++  D  TG +R F +V F + + ++
Sbjct: 10  STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFESAEDLE 68

Query: 73  DLLAAGDHYIGNKKIDPKRVTKRVNPLK---CKIFVGGLTTEISEQDVRDYFSQYGSITE 129
             L      +   +I  ++   R +        +    L+  I+E ++++ F     I  
Sbjct: 69  KALELTGLKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR- 127

Query: 130 FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK 177
                       KG  +I F  +  AE+ L   +   I G+ V +    
Sbjct: 128 ----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG 172

>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 = 65.7 bits (161), Expect = 2e-13
 Identities = 16/93 (17%), Positives = 31/93 (33%), Gaps = 6/93 (6%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
           +  G         R L    L  N  E E+ + F    E+           G+S+G A++
Sbjct: 87  KPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRL-----VSQDGKSKGIAYI 141

Query: 64  TFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
            F ++   +  L       I  + +      ++
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 =  114 bits (288), Expect = 9e-33
 Identities = 35/83 (42%), Positives = 54/83 (65%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          A     D  K+FVGGL  +T +K++ DYF+++GEV   +IK DP+TG+SRGF F+ F   
Sbjct: 4  ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDA 63

Query: 69 KAVDDLLAAGDHYIGNKKIDPKR 91
           +V+ +L   +H +  + IDPK+
Sbjct: 64 ASVEKVLDQKEHRLDGRVIDPKK 86

>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 = 82.2 bits (204), Expect = 2e-20
 Identities = 25/75 (33%), Positives = 45/75 (60%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+FVGGL+ + S++D++DYF+++G + +     D +    +GF FI F D    E+VL 
Sbjct: 12  GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLD 71

Query: 161 NPKQVICGKEVDVKR 175
             +  + G+ +D K+
Sbjct: 72  QKEHRLDGRVIDPKK 86

>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 =  114 bits (287), Expect = 2e-32
 Identities = 31/89 (34%), Positives = 50/89 (56%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++G   +   K+FVGG+  N GE E+ +YF ++G V  + +  D    + RGF F+TF 
Sbjct: 1  GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFE 60

Query: 67 TQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           +++VD  +    H I  KK++ KR   R
Sbjct: 61 DEQSVDQAVNMHFHDIMGKKVEVKRAEPR 89

>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 = 95.3 bits (238), Expect = 3e-25
 Identities = 29/74 (39%), Positives = 45/74 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGG+     E ++R+YF ++G +TE    +D  K   +GF FI+F+D+   +Q +  
Sbjct: 12  KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71

Query: 162 PKQVICGKEVDVKR 175
               I GK+V+VKR
Sbjct: 72  HFHDIMGKKVEVKR 85

>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 =  117 bits (295), Expect = 2e-32
 Identities = 34/186 (18%), Positives = 71/186 (38%), Gaps = 27/186 (14%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTTQKAV 71
           R+L+VG +     E+ + D+F+    +  ++             Q + FAF+ F +    
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 72  DDLLAAGDHYIGNKKIDPKRVTKRVNPLKC---------------------KIFVGGLTT 110
              +A        + +  +R                               K+F+GGL  
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 111 EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGK 169
            +++  V++  + +G +  F    D +  + KG+ F  + D NV +Q +A      +  K
Sbjct: 125 YLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDK 184

Query: 170 EVDVKR 175
           ++ V+R
Sbjct: 185 KLLVQR 190

>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 = 73.9 bits (182), Expect = 3e-16
 Identities = 21/95 (22%), Positives = 45/95 (47%), Gaps = 1/95 (1%)

Query: 2   AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
            Y     +    +   KLF+GGL     + ++ +  + +G +++ ++  D  TG S+G+A
Sbjct: 100 VYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYA 159

Query: 62  FVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
           F  +      D  +A  +   +G+KK+  +R +  
Sbjct: 160 FCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 194

>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 = 57.7 bits (140), Expect = 3e-10
 Identities = 18/105 (17%), Positives = 38/105 (36%), Gaps = 5/105 (4%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVA 155
            +++VG +   I+E+ + D+F+    +    Q           N  K F F+ F   +  
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 156 EQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASA 200
            Q +A    +  G+ + ++R        G            V++ 
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTV 109

>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 =  116 bits (292), Expect = 2e-32
 Identities = 36/150 (24%), Positives = 67/150 (44%), Gaps = 8/150 (5%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
             L V  L ++  ++E+   F   G + +  I  D  TG S G+AFV FT+    Q+A+ 
Sbjct: 4   TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63

Query: 73  DLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
            L       + NK++           +K   ++V  L   I++  +   F +YGSI +  
Sbjct: 64  VL---NGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN 120

Query: 132 QPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
              DK     +G  F+ ++ +  A++ ++ 
Sbjct: 121 ILRDKLTGRPRGVAFVRYNKREEAQEAISA 150

>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 = 68.0 bits (167), Expect = 3e-14
 Identities = 16/61 (26%), Positives = 30/61 (49%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
              +  L+V  L R   + +++  F +YG +   +I  D  TG+ RG AFV +  ++   
Sbjct: 86  SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ 145

Query: 73  D 73
           +
Sbjct: 146 E 146

>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 =  114 bits (287), Expect = 2e-32
 Identities = 35/85 (41%), Positives = 49/85 (57%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
              +   K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  
Sbjct: 20  HMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG 79

Query: 71  VDDLLAAGDHYIGNKKIDPKRVTKR 95
           VD +LA   H + +K IDPK    R
Sbjct: 80  VDKVLAQSRHELDSKTIDPKVAFPR 104

>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 = 99.3 bits (248), Expect = 1e-26
 Identities = 27/100 (27%), Positives = 53/100 (53%), Gaps = 2/100 (2%)

Query: 76  AAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD 135
           ++  H+  +  + P+      +   CK+F+GGL+ + +++ +R+YF Q+G + E     D
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGSSG--CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60

Query: 136 KSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
                 +GF F++F DQ   ++VLA  +  +  K +D K 
Sbjct: 61  PLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV 100

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

 Score =  110 bits (278), Expect = 2e-31
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  NT  +++  YF Q+G+V+   +  D  T + RGF FVTF ++  V+ +   
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 78 GDHYIGNKKIDPKR 91
            H I NK ++ K+
Sbjct: 61 HFHEINNKMVECKK 74

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

 Score = 97.9 bits (245), Expect = 1e-26
 Identities = 27/74 (36%), Positives = 45/74 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+   + +DV+ YF Q+G + +    FDK+ N  +GF F++F+ +++ E+V   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 162 PKQVICGKEVDVKR 175
               I  K V+ K+
Sbjct: 61  HFHEINNKMVECKK 74

>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 =  111 bits (279), Expect = 3e-31
 Identities = 32/85 (37%), Positives = 50/85 (58%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
             +   RKLF+GGL   T E+ + +Y+ Q+G++    +  DP + +SRGF FVTF++   
Sbjct: 22  REKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE 81

Query: 71  VDDLLAAGDHYIGNKKIDPKRVTKR 95
           VD  +AA  H I  + ++PKR   R
Sbjct: 82  VDAAMAARPHSIDGRVVEPKRAVAR 106

>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 = 85.8 bits (213), Expect = 2e-21
 Identities = 26/91 (28%), Positives = 46/91 (50%)

Query: 85  KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
            +  P    KR      K+F+GGL+ E +E+ +R+Y+ Q+G +T+     D +    +GF
Sbjct: 12  LETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGF 71

Query: 145 CFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            F++F      +  +A     I G+ V+ KR
Sbjct: 72  GFVTFSSMAEVDAAMAARPHSIDGRVVEPKR 102

>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 =  109 bits (275), Expect = 5e-31
 Identities = 30/74 (40%), Positives = 45/74 (60%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  +T E++I +YF  +GEVESI +  D  T + RGF F+TF  ++ V  ++  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 78 GDHYIGNKKIDPKR 91
            H +G  K + K 
Sbjct: 61 KYHNVGLSKCEIKV 74

>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 =  101 bits (254), Expect = 7e-28
 Identities = 22/74 (29%), Positives = 43/74 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+ +  E+ +R+YF  +G +   + P D   N ++GFCFI+F ++   ++++  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 162 PKQVICGKEVDVKR 175
               +   + ++K 
Sbjct: 61  KYHNVGLSKCEIKV 74

>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 =  110 bits (276), Expect = 7e-31
 Identities = 27/91 (29%), Positives = 42/91 (46%), Gaps = 1/91 (1%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
           +            L V GL   T E+++ +YFS +GEV  + +K D  TG S+GF FV 
Sbjct: 4  GSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVR 63

Query: 65 FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
          FT  +    +++   H I  +  D K    +
Sbjct: 64 FTEYETQVKVMSQ-RHMIDGRWCDCKLPNSK 93

>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 = 83.4 bits (207), Expect = 9e-21
 Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + V GL  + +EQD+++YFS +G +   Q   D      KGF F+ F +     +V++
Sbjct: 16  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 75

Query: 161 NPKQVICGKEVDVKR 175
               +I G+  D K 
Sbjct: 76  QR-HMIDGRWCDCKL 89

>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 =  110 bits (276), Expect = 9e-31
 Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 4/111 (3%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
            +            K+FVGGL  +T +  +  YF  +G++E   +  D  TG+SRG+ FV
Sbjct: 5   SSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFV 64

Query: 64  TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKC----KIFVGGLTT 110
           T   + A +      +  I  +K +         P        I V G ++
Sbjct: 65  TMADRAAAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSGPSS 115

>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 = 78.5 bits (194), Expect = 1e-18
 Identities = 24/95 (25%), Positives = 44/95 (46%), Gaps = 2/95 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            KIFVGGL    ++  +R YF  +G I E     D+     +G+ F++  D+  AE+   
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77

Query: 161 NPKQVICGKEVDVKR--VKFNPETMGSVSGAVRGA 193
           +P  +I G++ +V    +   P ++ +        
Sbjct: 78  DPNPIIDGRKANVNLAYLGAKPRSLQTGFAIGVSG 112

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

 Score =  108 bits (273), Expect = 1e-30
 Identities = 34/74 (45%), Positives = 47/74 (63%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD +LA 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 78 GDHYIGNKKIDPKR 91
            H + +K IDPK 
Sbjct: 62 SRHELDSKTIDPKV 75

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

 Score = 89.1 bits (222), Expect = 4e-23
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+F+GGL+ + +++ +R+YF Q+G + E     D      +GF F++F DQ   ++VLA
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 161 NPKQVICGKEVDVKR 175
             +  +  K +D K 
Sbjct: 61  QSRHELDSKTIDPKV 75

>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 =  112 bits (283), Expect = 4e-30
 Identities = 33/169 (19%), Positives = 61/169 (36%), Gaps = 15/169 (8%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
                +LFVG L  +  E++    F +YGE   + I  D      RGF F+   ++   +
Sbjct: 19  YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAE 72

Query: 73  DLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
              A  D   + ++ +  +  T         + V  L+  +S + +   FSQ+G + +  
Sbjct: 73  IAKAELDGTILKSRPLRIRFATHGAA-----LTVKNLSPVVSNELLEQAFSQFGPVEKAV 127

Query: 132 QPFDKSKNMKKGFCFISFDDQNVAEQVLA--NPKQVICGKEVDVKRVKF 178
              D       G  F+ F  +  A + L        +         V+ 
Sbjct: 128 VVVDDR-GRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVEP 175

>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 =  108 bits (273), Expect = 2e-28
 Identities = 34/176 (19%), Positives = 70/176 (39%), Gaps = 17/176 (9%)

Query: 12  GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
               E  L++     +  ++ I D       V             SR FA++  T+    
Sbjct: 113 SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDA 172

Query: 68  QKAVDDLLAAGDHYIGNKKI-----DPKRVTKRVNPLKC---KIFVGGLTTEIS-EQDVR 118
           +  V+ L       I    +     +P   +KR +       +I +  L+TE+  E  +R
Sbjct: 173 RYCVEKL---NGLKIEGYTLVTKVSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLR 229

Query: 119 DYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLANPKQVICGKEVDV 173
           + F  +GSI +   P  + ++       F+ F++++ AE+ L   + ++  +E+ V
Sbjct: 230 ESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISV 285

>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 =  107 bits (270), Expect = 7e-28
 Identities = 19/146 (13%), Positives = 50/146 (34%), Gaps = 10/146 (6%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
             +   + V  L ++  + ++  YF   G +  + + +     ++  FA + F       
Sbjct: 38  NRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGAL 95

Query: 73  DLLAAGDHYIGNKKIDPKRVTKRVNPLK-CKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
             +      +G  +I        V+ L  C +++       +++++RD       +    
Sbjct: 96  AAITKTHKVVGQNEI-------IVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSI 148

Query: 132 QPFDKSKNMKKGFCFISFDDQNVAEQ 157
           +      N  + F +I    +  A  
Sbjct: 149 RLPSLRFNTSRRFAYIDVTSKEDARY 174

>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 = 66.9 bits (164), Expect = 4e-13
 Identities = 22/124 (17%), Positives = 37/124 (29%), Gaps = 7/124 (5%)

Query: 57  SRGFAFVTFT-TQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQ 115
           S  +       +++ +D+   A     G           R N     + V  L    ++ 
Sbjct: 1   SMEYGHHARPDSKRPLDEGSPAA---AGLTSKKANEALTR-NRELTTVLVKNLPKSYNQN 56

Query: 116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR 175
            V  YF   G I          KN    F  I F   + A   +    +V+   E+ V  
Sbjct: 57  KVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAITKTHKVVGQNEIIVSH 114

Query: 176 VKFN 179
           +   
Sbjct: 115 LTEC 118

>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 =  108 bits (271), Expect = 4e-28
 Identities = 33/175 (18%), Positives = 64/175 (36%), Gaps = 16/175 (9%)

Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
            L V  L  +  +++  +    +G +E   +     TGQS+G+ F  +       +A  D
Sbjct: 97  LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156

Query: 74  LLAAGDHYIGNKKI-----DPKRVTKRVNPLKCKIFVGGLTTEISEQD-VRDYFSQYGSI 127
           L       +G + +     D  ++T  +   +C + V  L    ++ D +    S   S 
Sbjct: 157 L---LGKPLGPRTLYVHWTDAGQLTPALLHSRC-LCVDRLPPGFNDVDALCRALSAVHSP 212

Query: 128 TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNPE 181
           T  Q    +     KGF  + ++   +AE+         + G  + V      P 
Sbjct: 213 TFCQLACGQD-GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>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 =  101 bits (254), Expect = 1e-25
 Identities = 25/164 (15%), Positives = 65/164 (39%), Gaps = 20/164 (12%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
           RK+ + GL  +   +E++D  S Y  ++           + +G AFVT       + A++
Sbjct: 23  RKILIRGLPGDVTNQEVHDLLSDYE-LKYC------FVDKYKGTAFVTLLNGEQAEAAIN 75

Query: 73  DLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ 132
                        ++  + ++ ++ P    + V  L   +++Q   +    +GS+     
Sbjct: 76  AF--------HQSRLRERELSVQLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFL 127

Query: 133 PFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDVKR 175
            + +     KG+ F  +  ++ A +  ++   + +  + + V  
Sbjct: 128 VYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW 171

>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 = 53.1 bits (128), Expect = 2e-08
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 11/99 (11%)

Query: 80  HYIGNKKIDPKR-VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK 138
           H +  ++I  +   T+R    + KI + GL  +++ Q+V D  S Y     F        
Sbjct: 1   HMLDPEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYELKYCF-------V 53

Query: 139 NMKKGFCFISFDDQNVAEQVLA--NPKQVICGKEVDVKR 175
           +  KG  F++  +   AE  +   + +  +  +E+ V+ 
Sbjct: 54  DKYKGTAFVTLLNGEQAEAAINAFH-QSRLRERELSVQL 91

>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 =  102 bits (256), Expect = 1e-26
 Identities = 47/185 (25%), Positives = 76/185 (41%), Gaps = 15/185 (8%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
                 L+VG LH +  E  + + FS  G + SI +  D  T +S G+A+V F      +
Sbjct: 12  SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAE 71

Query: 73  DLLAAGDHY-IGNKKI-------DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQY 124
             L   +   I  K +       DP      V      IF+  L   I  + + D FS +
Sbjct: 72  RALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVG----NIFIKNLDKSIDNKALYDTFSAF 127

Query: 125 GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDVKRVKFNPETM 183
           G+I   +   D  +N  KG+ F+ F+ Q  AE+ +      ++  ++V V R K   E  
Sbjct: 128 GNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKERE 185

Query: 184 GSVSG 188
             +  
Sbjct: 186 AELGA 190

>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 = 66.1 bits (162), Expect = 3e-13
 Identities = 27/117 (23%), Positives = 52/117 (44%), Gaps = 6/117 (5%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
           ++    +F+  L ++   K + D FS +G + S  +  D     S+G+ FV F TQ+A +
Sbjct: 100 KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAE 157

Query: 73  DLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT 128
             +   +   + ++K+    V +  +  + +  +G    E    DV DY    G I 
Sbjct: 158 RAIEKMNGMLLNDRKV---FVGRFKSRKEREAELGARAKEFYPYDVPDYAGSSGRIV 211

>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 = 98.8 bits (247), Expect = 9e-26
 Identities = 34/166 (20%), Positives = 67/166 (40%), Gaps = 14/166 (8%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           R L+VG L +   E  +  YF   G + +I I  D    ++  +AFV +      +  L 
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQ 59

Query: 77  AGDHY-IGNKKI-------DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT 128
             +   I N  +         +  +         +FVG L   + ++ +R+ F  + S  
Sbjct: 60  TLNGKQIENNIVKINWAFQSQQSSSDDTF----NLFVGDLNVNVDDETLRNAFKDFPSYL 115

Query: 129 EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN-PKQVICGKEVDV 173
                +D      +G+ F+SF  Q+ A+  + +   Q + G+ + +
Sbjct: 116 SGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>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 = 65.2 bits (160), Expect = 3e-13
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 1/85 (1%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
            A  +     +D   LFVG L+ N  ++ + + F  +    S  +  D  TG SRG+ FV
Sbjct: 75  WAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFV 134

Query: 64  TFTTQKAVDDLLAAGD-HYIGNKKI 87
           +FT+Q    + + +     +  + +
Sbjct: 135 SFTSQDDAQNAMDSMQGQDLNGRPL 159

>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 = 95.0 bits (237), Expect = 3e-25
 Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 6/84 (7%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G +    +FVG    +  E E+ ++FSQYG+V  + I         R FAFVTF   +  
Sbjct: 1  GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIA 55

Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
            L    D  I    +       +
Sbjct: 56 QSLCGE-DLIIKGISVHISNAEPK 78

>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 = 87.7 bits (218), Expect = 2e-22
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FVG  T +++E ++R++FSQYG + +   P        + F F++F D  +A+ +   
Sbjct: 7   GVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE 61

Query: 162 PKQVICGKEVDVKR 175
              +I G  V +  
Sbjct: 62  D-LIIKGISVHISN 74

>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 = 93.1 bits (232), Expect = 1e-24
 Identities = 23/88 (26%), Positives = 33/88 (37%), Gaps = 6/88 (6%)

Query: 8  TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
           +    +   K+FVG    +   +E+  +F QYGEV  + I         R FAFVTF  
Sbjct: 3  GSHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFAD 57

Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           K    L    D  I    +       +
Sbjct: 58 DKVAQSLC-GEDLIIKGISVHISNAEPK 84

>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 = 91.1 bits (227), Expect = 1e-23
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 6/75 (8%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+FVG  T +++ ++++ +F QYG + +   P        + F F++F D  VA+ +  
Sbjct: 12  SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG 66

Query: 161 NPKQVICGKEVDVKR 175
               +I G  V +  
Sbjct: 67  ED-LIIKGISVHISN 80

>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 = 88.4 bits (220), Expect = 1e-22
 Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 2/84 (2%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G+     +FVGG+     E EI  +F++YG V+ + I  D  TG S+G+ FV+F     V
Sbjct: 5  GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDV 63

Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
            ++ +       KK+      ++
Sbjct: 64 QKIVESQ-INFHGKKLKLGPAIRK 86

>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 = 76.9 bits (190), Expect = 3e-18
 Identities = 19/74 (25%), Positives = 43/74 (58%), Gaps = 2/74 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FVGG+   + E ++R +F++YGS+ E +   D++  + KG+ F+SF +    ++++ +
Sbjct: 11  TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRT-GVSKGYGFVSFYNDVDVQKIVES 69

Query: 162 PKQVICGKEVDVKR 175
                 GK++ +  
Sbjct: 70  QIN-FHGKKLKLGP 82

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

 Score = 86.2 bits (214), Expect = 7e-22
 Identities = 19/87 (21%), Positives = 37/87 (42%), Gaps = 5/87 (5%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
             G +  R +FV G  R     ++++YF  +G V S+ +  D        FA V     
Sbjct: 1  GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDV 55

Query: 69 KAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           A + +L+   H +G  ++  +   ++
Sbjct: 56 GAREAVLSQSQHSLGGHRLRVRPREQK 82

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

 Score = 81.6 bits (202), Expect = 5e-20
 Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 6/91 (6%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FV G    +    + +YF  +G +       D     K  F  +   D    E VL+ 
Sbjct: 10  SVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKD-----KGVFAIVEMGDVGAREAVLSQ 64

Query: 162 PKQVICGKEVDVKRVKFNPETMGSVSGAVRG 192
            +  + G  + V+  +   E     S + +G
Sbjct: 65  SQHSLGGHRLRVRP-REQKEFQSPASKSPKG 94

>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 = 83.9 bits (208), Expect = 8e-21
 Identities = 25/103 (24%), Positives = 50/103 (48%), Gaps = 3/103 (2%)

Query: 5   ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
           ++G++G   +D  KLF+G + RN  EK++   F ++G++  +++  D  TG  +G AF+T
Sbjct: 2   SSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLT 61

Query: 65  FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGG 107
           +  +++      A       K +       +V P   +   G 
Sbjct: 62  YCERESAL---KAQSALHEQKTLPGMNRPIQVKPADSESRGGS 101

>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 = 64.3 bits (157), Expect = 1e-13
 Identities = 17/82 (20%), Positives = 41/82 (50%), Gaps = 4/82 (4%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +    K+F+G +   + E+D++  F ++G I E     D+   M KG  F+++ ++  A 
Sbjct: 10  DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESAL 69

Query: 157 QVLA--NPKQVI--CGKEVDVK 174
           +  +  + ++ +    + + VK
Sbjct: 70  KAQSALHEQKTLPGMNRPIQVK 91

>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 = 83.1 bits (206), Expect = 2e-20
 Identities = 19/84 (22%), Positives = 37/84 (44%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
            D R +F   L      +++ D+FS  G+V  + I +D ++ +S+G A+V F   ++V  
Sbjct: 23  RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82

Query: 74  LLAAGDHYIGNKKIDPKRVTKRVN 97
            +      +    I  +      N
Sbjct: 83  AIGLTGQRLLGVPIIVQASQAEKN 106

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 68.9 bits (169), Expect = 4e-15
 Identities = 17/106 (16%), Positives = 37/106 (34%)

Query: 84  NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
           +   +P             +F   L   I  +D+ D+FS  G + + +   D++    KG
Sbjct: 9   SPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKG 68

Query: 144 FCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGA 189
             ++ F +       +    Q + G  + V+  +     +   S  
Sbjct: 69  IAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEKNRLSGPSSG 114

>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 = 82.3 bits (204), Expect = 3e-20
 Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 1/92 (1%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
           +  +    +DE KLFVGGL  +T E+ +   FS+YG++  + +  D  T +SRGF FVT
Sbjct: 1  GSSGSSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVT 60

Query: 65 FTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
          F       D + A +   +  ++I   +  K 
Sbjct: 61 FENIDDAKDAMMAMNGKSVDGRQIRVDQAGKS 92

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 22/76 (28%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+FVGGL+ + +EQ +   FS+YG I+E     D+     +GF F++F++ + A+  + 
Sbjct: 13  GKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMM 72

Query: 161 NP-KQVICGKEVDVKR 175
               + + G+++ V +
Sbjct: 73  AMNGKSVDGRQIRVDQ 88

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

 Score = 80.8 bits (199), Expect = 1e-19
 Identities = 24/93 (25%), Positives = 37/93 (39%), Gaps = 9/93 (9%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEV--ESISIKNDPHTGQSRGFAFVTFT 66
             G +  RK+FVGGL  +  E EI   F ++G +  +             +G+AF+ F 
Sbjct: 1  GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ 60

Query: 67 TQKAVDDLLAAGDHYIGN-------KKIDPKRV 92
           + +V  L+ A     G          I  K V
Sbjct: 61 EESSVQALIDACLEEDGKLYLCVSSPTIKDKPV 93

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

 Score = 66.5 bits (162), Expect = 3e-14
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK--KGFCFISFDDQNVAEQV 158
            K+FVGGL  +I E ++   F ++G +        +SK+    KG+ F+ F +++  + +
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 159 LANPKQV-------ICGKEVDVKRVKFNP 180
           +    +        +    +  K V+  P
Sbjct: 69  IDACLEEDGKLYLCVSSPTIKDKPVQIRP 97

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

 Score = 81.7 bits (202), Expect = 1e-19
 Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 4/77 (5%)

Query: 2   AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
               +G +G     +R L+VGGL     +K ++  F  +G++  I I  D  T + RGFA
Sbjct: 49  GSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFA 108

Query: 62  FVTFTT----QKAVDDL 74
           FV F        A+D++
Sbjct: 109 FVEFELAEDAAAAIDNM 125

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

 Score = 59.8 bits (145), Expect = 1e-11
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+    A   +
Sbjct: 63  KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 122

Query: 160 AN 161
            N
Sbjct: 123 DN 124

>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 = 80.3 bits (199), Expect = 2e-19
 Identities = 24/72 (33%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++GP  +    L V  L   T    +   F +YG V  + I  +PHT   RGFAFV F 
Sbjct: 4  GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 67 T----QKAVDDL 74
               Q A   +
Sbjct: 64 DRRDAQDAEAAM 75

>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 = 56.1 bits (136), Expect = 1e-10
 Identities = 15/56 (26%), Positives = 25/56 (44%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
             + V  LT   S   +R  F +YG + +   P +      +GF F+ F D+  A+
Sbjct: 14  ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQ 69

>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 = 78.7 bits (195), Expect = 4e-19
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 4/69 (5%)

Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-- 67
          G     +R L+VGGL     +K ++  F  +G++  I I  D  T + RGFAFV F    
Sbjct: 1  GSMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 60

Query: 68 --QKAVDDL 74
              A+D++
Sbjct: 61 DAAAAIDNM 69

>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 = 60.6 bits (148), Expect = 2e-12
 Identities = 19/64 (29%), Positives = 31/64 (48%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             K  ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+    A  
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 64

Query: 158 VLAN 161
            + N
Sbjct: 65  AIDN 68

>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 = 78.4 bits (194), Expect = 7e-19
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 4  RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
            +       +    L V GL   T E+++ + FS+YG +  +SI  D  + +SRGFAFV
Sbjct: 3  SGSSGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 62

Query: 64 TFTT----QKAVDDL 74
           F      ++A +  
Sbjct: 63 YFENVDDAKEAKERA 77

>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 = 57.2 bits (139), Expect = 5e-11
 Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ + A++   
Sbjct: 16  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75

Query: 161 NPKQVICGKEVDVKRVKFN 179
                  G E+D +R++ +
Sbjct: 76  R----ANGMELDGRRIRVS 90

>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 = 78.4 bits (194), Expect = 7e-19
 Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 4/73 (5%)

Query: 6  NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +G +G     +  ++V  L  +    ++   FS+YG+V  ++I  D  T +S+G AF+ F
Sbjct: 6  SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILF 65

Query: 66 TT----QKAVDDL 74
                Q     +
Sbjct: 66 LDKDSAQNCTRAI 78

>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 = 59.9 bits (146), Expect = 4e-12
 Identities = 18/64 (28%), Positives = 29/64 (45%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P K  ++V  L   ++  D+   FS+YG + +     DK     KG  FI F D++ A+ 
Sbjct: 14  PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQN 73

Query: 158 VLAN 161
               
Sbjct: 74  CTRA 77

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

 Score = 78.2 bits (193), Expect = 2e-18
 Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
            + G   P       L V  L   T    +   F +YG V  + I  D +T +SRGFAFV
Sbjct: 35  MSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94

Query: 64  TFTT----QKAVDDL 74
            F      + A+D +
Sbjct: 95  RFHDKRDAEDAMDAM 109

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

 Score = 55.5 bits (134), Expect = 4e-10
 Identities = 17/57 (29%), Positives = 26/57 (45%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             + V  LT   S   +R  F +YG + +   P D+     +GF F+ F D+  AE 
Sbjct: 48  TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAED 104

>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 = 78.2 bits (193), Expect = 2e-18
 Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
             +       +    L V GL   T E+++ + FS+YG +  +SI  D  + +SRGFAFV
Sbjct: 34  SRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93

Query: 64  TFTT----QKAVDDL 74
            F      ++A +  
Sbjct: 94  YFENVDDAKEAKERA 108

>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 = 57.4 bits (139), Expect = 1e-10
 Identities = 22/79 (27%), Positives = 44/79 (55%), Gaps = 4/79 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ + A++   
Sbjct: 47  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106

Query: 161 NPKQVICGKEVDVKRVKFN 179
                  G E+D +R++ +
Sbjct: 107 R----ANGMELDGRRIRVD 121

>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 = 76.5 bits (189), Expect = 3e-18
 Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 4/62 (6%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQKAVD 72
          R +++G +  +  E++I D  S  G V ++ +  DP TG+S+G+AF+ F    ++  AV 
Sbjct: 3  RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 73 DL 74
          +L
Sbjct: 63 NL 64

>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 = 63.0 bits (154), Expect = 4e-13
 Identities = 14/61 (22%), Positives = 27/61 (44%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +++G +  + +E+ + D  S  G +   +  FD      KG+ FI F D   +   + 
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62

Query: 161 N 161
           N
Sbjct: 63  N 63

>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 = 76.9 bits (190), Expect = 3e-18
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 6/74 (8%)

Query: 7  GTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          G++G       +R L+VGGL     +K ++  F  +G++  I I  D  T + RGFAFV 
Sbjct: 1  GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60

Query: 65 FTT----QKAVDDL 74
          F        A+D++
Sbjct: 61 FELAEDAAAAIDNM 74

>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 = 59.2 bits (144), Expect = 9e-12
 Identities = 19/62 (30%), Positives = 31/62 (50%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+    A   +
Sbjct: 12  KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 71

Query: 160 AN 161
            N
Sbjct: 72  DN 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 = 76.0 bits (188), Expect = 4e-18
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 4/67 (5%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
          G +    L++ GL   T ++++      YG++ S     D  T + +G+ FV F +    
Sbjct: 1  GSSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAA 60

Query: 68 QKAVDDL 74
          QKAV  L
Sbjct: 61 QKAVTAL 67

>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 = 56.0 bits (136), Expect = 1e-10
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
            +++ GL    ++QD+      YG I   +   DK+ N  KG+ F+ FD  + A++ +  
Sbjct: 7   GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA 66

Query: 161 -NPKQVICGKEVDVKRVK 177
                      V  +  K
Sbjct: 67  LK------ASGVQAQMAK 78

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

 Score = 77.1 bits (190), Expect = 4e-18
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
          +++    L+ N  E  + D   +YGEVE + I   P T +  G A V FT+    ++ V 
Sbjct: 7  KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 73 DL 74
          +L
Sbjct: 67 NL 68

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

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 11/74 (14%), Positives = 26/74 (35%), Gaps = 1/74 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++    L   + E  ++D   +YG + E +           G   + F     A++ + N
Sbjct: 8   EVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKN 67

Query: 162 P-KQVICGKEVDVK 174
                + G  +  +
Sbjct: 68  LHLTSVMGNIIHAQ 81

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

 Score = 76.9 bits (190), Expect = 4e-18
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 4  RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          +     GP R+ E   LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  
Sbjct: 10 QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 69

Query: 63 VTFTT----QKAVDDL 74
          V + T    Q A++ L
Sbjct: 70 VEYETYKEAQAAMEGL 85

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

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 15/56 (26%), Positives = 28/56 (50%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
             +FV G+  E +E+D+ D F++YG I       D+     KG+  + ++    A+
Sbjct: 24  WILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 76.4 bits (189), Expect = 4e-18
 Identities = 21/67 (31%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
          G +    L+VG LH N  E  +   F  +G++++I +  D  TG+S+G+ F+TF+     
Sbjct: 1  GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60

Query: 68 QKAVDDL 74
          ++A++ L
Sbjct: 61 RRALEQL 67

>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 = 56.8 bits (138), Expect = 7e-11
 Identities = 18/60 (30%), Positives = 26/60 (43%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++VG L   I+E  +R  F  +G I       D      KG+ FI+F D   A + L  
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

>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 = 76.6 bits (189), Expect = 4e-18
 Identities = 18/68 (26%), Positives = 35/68 (51%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
            + + +F+  L  ++ E+ + +   Q+G+++ + +   P T  S+G AF  F TQ+A  
Sbjct: 12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQ 71

Query: 73 DLLAAGDH 80
            LAA   
Sbjct: 72 KCLAAASL 79

>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 = 60.4 bits (147), Expect = 5e-12
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL- 159
             +F+  L+ +  E+ + +   Q+G +   +          KG  F  F  Q  A++ L 
Sbjct: 16  KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 75

Query: 160 -ANPKQVICGKEVDVKRVKFNP 180
            A+ +    G ++D +++K + 
Sbjct: 76  AASLEAEGGGLKLDGRQLKVDL 97

>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 = 76.5 bits (189), Expect = 5e-18
 Identities = 22/76 (28%), Positives = 41/76 (53%), Gaps = 6/76 (7%)

Query: 5  ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++GP    +D   + V  L  +T E ++ + F  +G +  I +  D  TGQS+GFAF
Sbjct: 2  SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 63 VTFTT----QKAVDDL 74
          ++F       +A+  +
Sbjct: 62 ISFHRREDAARAIAGV 77

>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 = 56.8 bits (138), Expect = 7e-11
 Identities = 19/57 (33%), Positives = 29/57 (50%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             I V  L+ +  E D+++ F  +GSI+      DK+    KGF FISF  +  A +
Sbjct: 16  ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72

>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 = 77.0 bits (190), Expect = 5e-18
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 5/76 (6%)

Query: 4  RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          +     GP R+ E   LFV G+H    E++I+D F++YGE+++I +  D  TG  +G+  
Sbjct: 9  QDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTL 68

Query: 63 VTFTT----QKAVDDL 74
          V + T    Q A++ L
Sbjct: 69 VEYETYKEAQAAMEGL 84

>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 = 57.8 bits (140), Expect = 6e-11
 Identities = 15/55 (27%), Positives = 28/55 (50%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
            +FV G+  E +E+D+ D F++YG I       D+     KG+  + ++    A+
Sbjct: 24  ILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78

>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 = 75.6 bits (187), Expect = 6e-18
 Identities = 18/62 (29%), Positives = 34/62 (54%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D R ++VG +      +E+  +F   G V  ++I  D  +G  +GFA++ F+ +++V   
Sbjct: 5  DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64

Query: 75 LA 76
          LA
Sbjct: 65 LA 66

>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 = 56.4 bits (137), Expect = 7e-11
 Identities = 16/59 (27%), Positives = 26/59 (44%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            I+VG +    + +++  +F   GS+       DK     KGF +I F D+      LA
Sbjct: 8   SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66

>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 = 76.2 bits (188), Expect = 7e-18
 Identities = 25/83 (30%), Positives = 41/83 (49%), Gaps = 2/83 (2%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
          +   KLF+GGL+R T EK +   F ++G +  + +  D  T +SRGFAF+TF       +
Sbjct: 5  DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKN 63

Query: 74 LLAAGD-HYIGNKKIDPKRVTKR 95
               +   +  K I  ++  K 
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAKKP 86

>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 = 62.3 bits (152), Expect = 1e-12
 Identities = 25/105 (23%), Positives = 50/105 (47%), Gaps = 2/105 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+F+GGL  E +E+ ++  F ++G I+E     D++ +  +GF FI+F++   A+    
Sbjct: 8   GKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRT-SKSRGFAFITFENPADAKNAAK 66

Query: 161 NP-KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAY 204
           +   + + GK + V++ K      G        +  R  S    +
Sbjct: 67  DMNGKSLHGKAIKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLEH 111

>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 = 76.3 bits (188), Expect = 8e-18
 Identities = 21/79 (26%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 15  DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           D+R ++VG +   +  +++  +FS  G +  I+I  D  +G  +G+A++ F  + +VD  
Sbjct: 35  DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAA 94

Query: 75  LAAGDHYIGNK--KIDPKR 91
           +A  +     +  K+ PKR
Sbjct: 95  VAMDETVFRGRTIKVLPKR 113

>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 = 59.7 bits (145), Expect = 1e-11
 Identities = 23/86 (26%), Positives = 40/86 (46%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  ++VG +    + QD+  +FS  GSI       DK     KG+ +I F ++N  +  +
Sbjct: 36  KRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV 95

Query: 160 ANPKQVICGKEVDVKRVKFNPETMGS 185
           A  + V  G+ + V   + N   + S
Sbjct: 96  AMDETVFRGRTIKVLPKRTNMPGISS 121

>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 = 75.8 bits (187), Expect = 1e-17
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 5  ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++GP   RN +  ++VGGL     E  + + F Q G V +  +  D  TGQ +G+ F
Sbjct: 2  SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 63 VTFTT----QKAVDDL 74
          V F +      A+  +
Sbjct: 62 VEFLSEEDADYAIKIM 77

>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 = 53.4 bits (129), Expect = 1e-09
 Identities = 15/62 (24%), Positives = 29/62 (46%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
              ++VGGL  ++SE  + + F Q G +     P D+     +G+ F+ F  +  A+  +
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAI 74

Query: 160 AN 161
             
Sbjct: 75  KI 76

>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 = 77.2 bits (190), Expect = 1e-17
 Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
             +            L V  L   T    +   F +YG V  + I  D +T +SRGFAFV
Sbjct: 58  SHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 117

Query: 64  TFTT----QKAVDDL 74
            F      + A+D +
Sbjct: 118 RFHDKRDAEDAMDAM 132

>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 = 57.2 bits (138), Expect = 2e-10
 Identities = 26/119 (21%), Positives = 39/119 (32%), Gaps = 20/119 (16%)

Query: 58  RGFAFVTFTTQKAVDDLLA--AGDHYIGNKKIDPKRVTKRVNPLK--------------- 100
            G      TT +AVD   A      Y  +  +D +                         
Sbjct: 8   NGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV 67

Query: 101 ---CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
                + V  LT   S   +R  F +YG + +   P D+     +GF F+ F D+  AE
Sbjct: 68  EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126

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

 Score = 75.1 bits (185), Expect = 1e-17
 Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 4/83 (4%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
            + +  +  +T    I    S Y    V +I +  D  T Q+RGFAFV  ++      L
Sbjct: 10 DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 75 LAAGDHYIGNKKIDPKRVTKRVN 97
          L          KID K +   V+
Sbjct: 70 LQILQSLHPPLKIDGKTI--GVD 90

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

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 16/79 (20%), Positives = 26/79 (32%), Gaps = 7/79 (8%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
            I +  +        +    S Y   ++   +   DK     +GF F+       A Q+L
Sbjct: 11  TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70

Query: 160 AN-----PKQVICGKEVDV 173
                  P   I GK + V
Sbjct: 71  QILQSLHPPLKIDGKTIGV 89

>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 = 74.5 bits (184), Expect = 2e-17
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 5/62 (8%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKND-PHTGQSRGFAFVTFTT----QKAVD 72
          K+ +G L RN  +  I + FS YG+++ I +  +  H   S+G+A+V F      +KA+ 
Sbjct: 6  KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 73 DL 74
           +
Sbjct: 66 HM 67

>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 = 57.9 bits (141), Expect = 2e-11
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 4/80 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVL 159
            K+ +G LT  +++  + + FS YG I     P ++      KG+ ++ F++ + AE+ L
Sbjct: 5   TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64

Query: 160 A--NPKQVICGKEVDVKRVK 177
              +  Q I G+E+    V 
Sbjct: 65  KHMDGGQ-IDGQEITATAVL 83

>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 = 74.6 bits (184), Expect = 3e-17
 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 4/78 (5%)

Query: 1  MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF 60
          MA         G     +L+VG LH N  E  +   F  +G +ESI +  D  TG+S+G+
Sbjct: 11 MAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGY 70

Query: 61 AFVTFTT----QKAVDDL 74
           F+TF+     +KA++ L
Sbjct: 71 GFITFSDSECAKKALEQL 88

>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 = 55.0 bits (133), Expect = 4e-10
 Identities = 19/61 (31%), Positives = 29/61 (47%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            +++VG L   I+E  +R  F  +G I   Q   D      KG+ FI+F D   A++ L 
Sbjct: 27  MRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86

Query: 161 N 161
            
Sbjct: 87  Q 87

>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 = 74.6 bits (184), Expect = 3e-17
 Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 10 GPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
          GP R+ E   LFV  +H    E EI + F  YGE+++I +  D  TG S+G+A V + T 
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78

Query: 68 ---QKAVDDL 74
               A + L
Sbjct: 79 KQALAAKEAL 88

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 12/60 (20%), Positives = 23/60 (38%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FV  +  E  E ++++ F  YG I       D+     KG+  + ++    A      
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

>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 = 75.3 bits (185), Expect = 6e-17
 Identities = 26/76 (34%), Positives = 37/76 (48%), Gaps = 5/76 (6%)

Query: 4   RANGTAGPGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
                 GP R+ E   LFV  +H    E EI + F  YGE+++I +  D  TG S+G+A 
Sbjct: 59  DDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 118

Query: 63  VTFTT----QKAVDDL 74
           V + T      A + L
Sbjct: 119 VEYETHKQALAAKEAL 134

>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 = 57.9 bits (140), Expect = 1e-10
 Identities = 12/56 (21%), Positives = 23/56 (41%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
             +FV  +  E  E ++++ F  YG I       D+     KG+  + ++    A 
Sbjct: 73  WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128

>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 = 73.4 bits (181), Expect = 6e-17
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT--- 67
           G +   +LFV  L   + E+++   FS YG +  +    D  T + +GFAFVTF     
Sbjct: 3  SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH 62

Query: 68 -QKAVDDL 74
            KA  ++
Sbjct: 63 AVKAYAEV 70

>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 = 55.7 bits (135), Expect = 2e-10
 Identities = 19/56 (33%), Positives = 29/56 (51%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           ++FV  L+   SE+D+   FS YG ++E   P D      KGF F++F     A +
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

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

 Score = 74.6 bits (183), Expect = 9e-17
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 3/98 (3%)

Query: 1   MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIK--NDPHTGQSR 58
                  T    RN    ++VG     T ++++       G  + + +K   +   GQS+
Sbjct: 40  KTPAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSK 99

Query: 59  GFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
           G+A V   ++ +V  LL       +  +K+D +  T++
Sbjct: 100 GYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ 137

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

 Score = 54.9 bits (132), Expect = 1e-09
 Identities = 15/76 (19%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGS--ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
            ++VG  +   ++Q +       G   + E +   +++    KG+  +    +N   ++L
Sbjct: 57  AVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLL 116

Query: 160 AN-PKQVICGKEVDVK 174
              P +V+ G++VDV+
Sbjct: 117 ELLPGKVLNGEKVDVR 132

>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 = 73.6 bits (181), Expect = 1e-16
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 4/78 (5%)

Query: 1   MAYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF 60
             +       P  +  R L V  +     E ++   F +YG +ES+ I  D  T QSRG+
Sbjct: 27  QQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGY 86

Query: 61  AFVTFTT----QKAVDDL 74
            FV F +    Q+A+  L
Sbjct: 87  GFVKFQSGSSAQQAIAGL 104

>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 = 54.8 bits (132), Expect = 1e-09
 Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 8/98 (8%)

Query: 84  NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
            ++  P         +   + V  + T + E  +R  F +YG I   +   D+     +G
Sbjct: 26  QQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRG 85

Query: 144 FCFISFDDQNVAEQVLA--NPKQVICGKEVDVKRVKFN 179
           + F+ F   + A+Q +A  N      G  +  KR+K  
Sbjct: 86  YGFVKFQSGSSAQQAIAGLN------GFNILNKRLKVA 117

>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 = 72.3 bits (178), Expect = 2e-16
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 4  RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH-TGQSRGFAF 62
            +    P +    K+ V  +     ++EI + FS +GE++++ +      TG  RGF F
Sbjct: 3  SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62

Query: 63 VTFTT----QKAVDDL 74
          V F T    +KA + L
Sbjct: 63 VDFITKQDAKKAFNAL 78

>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 = 53.8 bits (130), Expect = 1e-09
 Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 4/81 (4%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQV 158
             KI V  +  + +++++R+ FS +G +   + P   +     +GF F+ F  +  A++ 
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74

Query: 159 LANPKQVICGKEVDVKRVKFN 179
                       +  +R+   
Sbjct: 75  FNALCH---STHLYGRRLVLE 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 = 71.9 bits (177), Expect = 2e-16
 Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF----TTQK 69
             R +FVG +     E+++ D FS+ G V S  +  D  TG+ +G+ F  +    T   
Sbjct: 6  RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65

Query: 70 AVDDL 74
          A+ +L
Sbjct: 66 AMRNL 70

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 18/60 (30%), Positives = 32/60 (53%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FVG +  E +E+ ++D FS+ G +  F+  +D+     KG+ F  + DQ  A   + N
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

>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 = 71.4 bits (176), Expect = 3e-16
 Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 3/61 (4%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---QKAVDD 73
          R ++VG L  +   +++ + FSQ+G+V ++ +  D  T + +GF FV        +A+  
Sbjct: 2  RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 74 L 74
          L
Sbjct: 62 L 62

>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 = 52.6 bits (127), Expect = 2e-09
 Identities = 14/51 (27%), Positives = 27/51 (52%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
            I+VG L    + + V++ FSQ+G +   +  +D+     KGF F+   ++
Sbjct: 3   NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE 53

>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 = 71.5 bits (176), Expect = 3e-16
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKA 70
           +RKLFVG L++   E+++   F  +G ++  ++   P  G S+G AFV F++    Q A
Sbjct: 14 RDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAA 72

Query: 71 VDDL 74
          +  L
Sbjct: 73 IHAL 76

>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 = 55.4 bits (134), Expect = 3e-10
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 93  TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
           ++       K+FVG L  + SE+DV   F  +G I E         +  KG  F+ F   
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSH 66

Query: 153 NVAEQVLA--NPKQVI--CGKEVDVK 174
             A+  +   +  Q +      + VK
Sbjct: 67  TEAQAAIHALHGSQTMPGASSSLVVK 92

>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 = 70.4 bits (173), Expect = 7e-16
 Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 1/88 (1%)

Query: 8  TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
            G        LF+G L+ N    E+    S+      +++  D  TG +R F +V F +
Sbjct: 9  VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVV-DVRTGTNRKFGYVDFES 67

Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           + ++  L      +   +I  ++   R
Sbjct: 68 AEDLEKALELTGLKVFGNEIKLEKPKGR 95

>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 = 49.6 bits (119), Expect = 3e-08
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 1/77 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +F+G L    S  +++   S+  +  +     D      + F ++ F+     E+ L 
Sbjct: 18  FNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE 76

Query: 161 NPKQVICGKEVDVKRVK 177
                + G E+ +++ K
Sbjct: 77  LTGLKVFGNEIKLEKPK 93

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

 Score = 70.2 bits (172), Expect = 9e-16
 Identities = 11/73 (15%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
            R +++ G   +    +I ++    G+V +I ++   H    +G  FV F + ++    
Sbjct: 10 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKF 68

Query: 75 LAAGDHYIGNKKI 87
          +           +
Sbjct: 69 VETPGQKYKETDL 81

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

 Score = 66.7 bits (163), Expect = 2e-14
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +++ G  T+ +  D++++    G +   Q      K   KG  F+ FD    A++ +  
Sbjct: 13  SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAF-KGSIFVVFDSIESAKKFVET 71

Query: 162 PKQVICGKEVDVKR 175
           P Q     ++ +  
Sbjct: 72  PGQKYKETDLLILF 85

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

 Score = 69.6 bits (171), Expect = 1e-15
 Identities = 14/75 (18%), Positives = 34/75 (45%), Gaps = 5/75 (6%)

Query: 4  RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
           +         ++ KLF+ GL  +  ++E+ +    +G V+ + +  +   G+ +G A+V
Sbjct: 5  SSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYV 63

Query: 64 TFTT----QKAVDDL 74
           +       +AV  +
Sbjct: 64 EYENESQASQAVMKM 78

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

 Score = 56.9 bits (138), Expect = 6e-11
 Identities = 10/62 (16%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K K+F+ GL    +++++ +    +G++ + +   +++    KG  ++ +++++ A Q +
Sbjct: 17  KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQASQAV 75

Query: 160 AN 161
             
Sbjct: 76  MK 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 = 72.0 bits (176), Expect = 2e-15
 Identities = 25/186 (13%), Positives = 51/186 (27%), Gaps = 45/186 (24%)

Query: 15  DERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           D   L V GL         + + F  YG VE +            G A V      AVD 
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDR 57

Query: 74  LLAAGDHY-IGNKKID--------------------------------------PKRVTK 94
            +   ++  +  +K++                                       +    
Sbjct: 58  AITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKN 117

Query: 95  RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
           R+      +       E++E++  +   + G            K+ +     + +D ++ 
Sbjct: 118 RIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD 177

Query: 155 AEQVLA 160
           A + L 
Sbjct: 178 ALETLG 183

>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 = 55.9 bits (134), Expect = 1e-09
 Identities = 9/77 (11%), Positives = 22/77 (28%), Gaps = 1/77 (1%)

Query: 19  LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK-AVDDLLAA 77
           L          E+   +   + G     S+K      +      + + ++  A++ L   
Sbjct: 126 LHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFL 185

Query: 78  GDHYIGNKKIDPKRVTK 94
             + + N         K
Sbjct: 186 NHYQMKNPNGPYPYTLK 202

>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 = 41.2 bits (96), Expect = 1e-04
 Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 6/62 (9%)

Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
             + V GL    ++   V + F  YG++ + +    K      G   +   D    ++ +
Sbjct: 5   PVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAI 59

Query: 160 AN 161
            +
Sbjct: 60  TH 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 = 69.2 bits (170), Expect = 2e-15
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 3  YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          + +    G G     KL V  L     + +I + F+++G ++  ++  D  +G+S G A 
Sbjct: 16 FDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTAD 74

Query: 63 VTFTT----QKAVDDL 74
          V F       KA+   
Sbjct: 75 VHFERKADALKAMKQY 90

>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 = 45.0 bits (107), Expect = 1e-06
 Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           K+ V  L   +S+ D+++ F+++G++ +    +D+S     G   + F+ +  A +
Sbjct: 31  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRS-GRSLGTADVHFERKADALK 85

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

 Score = 68.5 bits (168), Expect = 5e-15
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 4  RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
          R +      ++  ++L V  +     + ++   F Q+G++  + I  +     S+GF FV
Sbjct: 17 RGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFV 74

Query: 64 TFTT----QKAVDDL 74
          TF       +A + L
Sbjct: 75 TFENSADADRAREKL 89

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

 Score = 51.2 bits (123), Expect = 1e-08
 Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++ V  +     + D+R  F Q+G I + +  F++     KGF F++F++   A++    
Sbjct: 31  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREK 88

Query: 162 PKQVICGKEVDVKRVKFN 179
               + G  V+ ++++ N
Sbjct: 89  ----LHGTVVEGRKIEVN 102

>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 = 68.7 bits (168), Expect = 5e-15
 Identities = 17/102 (16%), Positives = 40/102 (39%), Gaps = 9/102 (8%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--PFDKSKNMKKGFCFISFDDQNVAE- 156
            C++F+GG+      +++ +  ++                K   +GF F+ ++    A  
Sbjct: 8   NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAM 67

Query: 157 --QVLANPKQVICGKEVDVK----RVKFNPETMGSVSGAVRG 192
             + L   +  + G ++ V      +  + + M +VSG   G
Sbjct: 68  ARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETVSGPSSG 109

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 64.8 bits (158), Expect = 1e-13
 Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 10/87 (11%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDP-HTGQSRGFAFVTFTTQKAVD 72
             +LF+GG+ +    +EI +  ++  E V  + +        ++RGFAFV + + +A  
Sbjct: 7  GNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 73 D---LLAAGDHYIGNKKI-----DPKR 91
               L  G   +   +I     +P+ 
Sbjct: 67 MARRKLMPGRIQLWGHQIAVDWAEPEI 93

>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 = 68.0 bits (167), Expect = 5e-15
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 2/62 (3%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
           L++G L   T ++++ +     G  ++  I    +   GQS+GFA V   ++ +   L+
Sbjct: 3  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 76 AA 77
            
Sbjct: 63 DL 64

>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 = 49.5 bits (119), Expect = 2e-08
 Identities = 10/61 (16%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
            +++G LT   +++D+ +     G   I E +   +++    KGF  +    +  +++++
Sbjct: 3   ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 62

Query: 160 A 160
            
Sbjct: 63  D 63

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

 Score = 68.0 bits (167), Expect = 5e-15
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
             G +   ++FV  L  +   K + D F++ G V    IK +   G+S+G   V F + 
Sbjct: 1  GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58

Query: 68 ---QKAVDDL 74
             ++A   +
Sbjct: 59 EVAERACRMM 68

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

 Score = 46.8 bits (112), Expect = 2e-07
 Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           C+IFV  L  + + + ++D F++ G +       +  K+  KG   + F+   VAE+
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKS--KGCGVVKFESPEVAER 63

>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 = 67.6 bits (166), Expect = 6e-15
 Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 8/81 (9%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           +FVG L        I   F+ +G +    +  D  TG+S+G+ FV+F  +   ++ +  
Sbjct: 8  HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67

Query: 78 -GDHYIGNKKIDPKRVTKRVN 97
           G  ++G ++I       R N
Sbjct: 68 MGGQWLGGRQI-------RTN 81

>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 = 51.0 bits (123), Expect = 6e-09
 Identities = 17/59 (28%), Positives = 32/59 (54%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            +FVG L+ EI+   +   F+ +G I++ +   D +    KG+ F+SF ++  AE  + 
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66

>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 = 67.7 bits (166), Expect = 8e-15
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 5/74 (6%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          ++G        +R +FVG L     E+ + + F Q G +  ++I  D   G+ + F FV 
Sbjct: 5  SSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVC 63

Query: 65 FTT----QKAVDDL 74
          F        A+  L
Sbjct: 64 FKHPESVSYAIALL 77

>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 = 50.3 bits (121), Expect = 1e-08
 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             +FVG L   + E+ + + F Q G +T+     D+     K F F+ F        
Sbjct: 17  RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSY 72

>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 = 67.7 bits (166), Expect = 8e-15
 Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 6/68 (8%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT--- 67
            ++  ++L V  +     + ++   F Q+G++  + I  +     S+GF FVTF     
Sbjct: 10 ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSAD 67

Query: 68 -QKAVDDL 74
            +A + L
Sbjct: 68 ADRAREKL 75

>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 = 52.7 bits (127), Expect = 2e-09
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
            ++ V  +     + D+R  F Q+G I + +  F++  +  KGF F++F++   A+
Sbjct: 16  KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS--KGFGFVTFENSADAD 69

>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 = 67.1 bits (165), Expect = 9e-15
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 8/81 (9%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           LFVG L+ N  ++ + + F  +    S  +  D  TG SRG+ FV+FT+Q    + + +
Sbjct: 3  NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62

Query: 78 GD-HYIGNKKIDPKRVTKRVN 97
               +  + +       R+N
Sbjct: 63 MQGQDLNGRPL-------RIN 76

>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 = 52.9 bits (128), Expect = 1e-09
 Identities = 14/56 (25%), Positives = 27/56 (48%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
            +FVG L   + ++ +R+ F  + S       +D      +G+ F+SF  Q+ A+ 
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 58

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

 Score = 69.5 bits (170), Expect = 9e-15
 Identities = 18/77 (23%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 2   AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
            + +    G G     KL V  L     + +I + F+++G ++  ++  D  +G+S G A
Sbjct: 74  LFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTA 132

Query: 62  FVTFTT----QKAVDDL 74
            V F       KA+   
Sbjct: 133 DVHFERRADALKAMKQY 149

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

 Score = 45.6 bits (108), Expect = 2e-06
 Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           K+ V  L   +S+ D+++ F+++G++ +    +D+S     G   + F+ +  A +
Sbjct: 90  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGR-SLGTADVHFERRADALK 144

>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 = 68.2 bits (167), Expect = 1e-14
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 5/76 (6%)

Query: 3  YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          + +    G G     KL V  L     + +I + F+++G ++  ++  D  +G+S G A 
Sbjct: 22 FDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTAD 80

Query: 63 VTFTT----QKAVDDL 74
          V F       KA+   
Sbjct: 81 VHFERRADALKAMKQY 96

>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 = 45.1 bits (107), Expect = 2e-06
 Identities = 12/56 (21%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           K+ V  L   +S+ D+++ F+++G++ +    +D+S     G   + F+ +  A +
Sbjct: 37  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRS-LGTADVHFERRADALK 91

>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 = 66.8 bits (164), Expect = 1e-14
 Identities = 27/89 (30%), Positives = 44/89 (49%), Gaps = 9/89 (10%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKA 70
          G +    +F+G L     EK + D FS +G + ++  I  DP TG S+G+AF+ F +  A
Sbjct: 1  GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60

Query: 71 VDDLLAAGD-HYIGNKKIDPKRVTKRVNP 98
           D  + A +  Y+ N+ I        V+ 
Sbjct: 61 SDAAIEAMNGQYLCNRPI-------TVSY 82

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 51.8 bits (125), Expect = 4e-09
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ-PFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            IF+G L  EI E+ + D FS +G I +  +   D      KG+ FI+F   + ++  + 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 161 NPK-QVICGKEVDV 173
               Q +C + + V
Sbjct: 67  AMNGQYLCNRPITV 80

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 7/70 (10%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQ---SRGFAFVTFTT- 67
          G +    LF+  L+ +T E+ +   FS+ G ++S +I    +      S GF FV +   
Sbjct: 1  GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60

Query: 68 ---QKAVDDL 74
             QKA+  L
Sbjct: 61 EQAQKALKQL 70

>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 = 48.4 bits (116), Expect = 8e-08
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK---KGFCFISFDDQNVAEQ 157
             +F+  L    +E+ ++  FS+ G+I        K+K       GF F+ +     A++
Sbjct: 6   SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65

Query: 158 VLAN-PKQVICGKEVDVKR 175
            L       + G +++V+ 
Sbjct: 66  ALKQLQGHTVDGHKLEVRI 84

>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 = 3e-14
 Identities = 11/77 (14%), Positives = 31/77 (40%), Gaps = 8/77 (10%)

Query: 2  AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
              +        + + L +  L  +  E+ + + F +   ++          G+S+G+A
Sbjct: 1  GSSGSSGNSTWSGESKTLVLSNLSYSATEETLQEVFEKATFIKVP----QNQNGKSKGYA 56

Query: 62 FVTFTT----QKAVDDL 74
          F+ F +    ++A++  
Sbjct: 57 FIEFASFEDAKEALNSC 73

>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 = 48.8 bits (117), Expect = 5e-08
 Identities = 15/82 (18%), Positives = 35/82 (42%), Gaps = 8/82 (9%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + +  L+   +E+ +++ F +   I   Q    KS    KG+ FI F     A++ L 
Sbjct: 16  KTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKS----KGYAFIEFASFEDAKEALN 71

Query: 161 NPKQVICGKEVDVKRVKFNPET 182
           +       +E++ + ++   + 
Sbjct: 72  S----CNKREIEGRAIRLELQG 89

>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 = 68.8 bits (168), Expect = 3e-14
 Identities = 31/200 (15%), Positives = 59/200 (29%), Gaps = 52/200 (26%)

Query: 19  LFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
           L V  L+      + +   F  YG+V+ + I  +      +  A V        Q A+  
Sbjct: 6   LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSH 60

Query: 74  L---------------------------------LAAGDHYIGNKKIDPKRVTKRVNPLK 100
           L                                    G+  +   K    +  + + P  
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + +  +   +SE+D++  FS  G + +  + F K     +    I       A Q L 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALI 176

Query: 161 --NPKQVICGKEVDVKRVKF 178
             +   +     +   RV F
Sbjct: 177 DLHNHDLGENHHL---RVSF 193

>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 = 41.4 bits (97), Expect = 9e-05
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
             + V  L  E ++ Q +   F  YG +   +  F+K     K    +   D N A+  +
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAM 58

Query: 160 ANPK-QVICGKEVDVKRVK 177
           ++     + GK + +   K
Sbjct: 59  SHLNGHKLHGKPIRITLSK 77

>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 = 66.2 bits (162), Expect = 3e-14
 Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 7/75 (9%)

Query: 4  RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
                GP  N++ +++VG L  +   K+I D F +YG +  I +KN         FAFV
Sbjct: 10 GGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR---GGPPFAFV 66

Query: 64 TFTT----QKAVDDL 74
           F      + AV   
Sbjct: 67 EFEDPRDAEDAVYGR 81

>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 = 56.6 bits (137), Expect = 1e-10
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 3/56 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           C+I+VG L  +I  +D+ D F +YG+I +      +       F F+ F+D   AE
Sbjct: 23  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAE 75

>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 = 65.8 bits (161), Expect = 5e-14
 Identities = 18/77 (23%), Positives = 35/77 (45%), Gaps = 9/77 (11%)

Query: 7  GTAGPGRN-----DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
          G++G         +   +FVG L      ++I   F+ +G +    +  D  TG+S+G+ 
Sbjct: 1  GSSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYG 60

Query: 62 FVTFTT----QKAVDDL 74
          FV+F      + A+  +
Sbjct: 61 FVSFFNKWDAENAIQQM 77

>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 = 52.0 bits (125), Expect = 6e-09
 Identities = 18/56 (32%), Positives = 34/56 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
            +FVG L+ EI+ +D++  F+ +G I++ +   D +    KG+ F+SF ++  AE 
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAEN 72

>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 = 65.4 bits (160), Expect = 7e-14
 Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 4/62 (6%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
          + L++  L     E+++   F+++ E +   I+    TG+ RG AF+TF       +A+ 
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85

Query: 73 DL 74
           +
Sbjct: 86 LV 87

>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 = 53.1 bits (128), Expect = 2e-09
 Identities = 11/57 (19%), Positives = 27/57 (47%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             +++  L+  ++E+D+   F+++         F       +G  FI+F ++ +A Q
Sbjct: 26  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82

>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 = 65.0 bits (159), Expect = 7e-14
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 9/64 (14%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKA 70
            R L    L  N  E E+ + F    E+     +     G+S+G A++ F +    +K 
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKN 69

Query: 71 VDDL 74
          +++ 
Sbjct: 70 LEEK 73

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 5/60 (8%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +    L+  I+E ++++ F     I              KG  +I F  +  AE+ L  
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEE 72

>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 = 65.6 bits (160), Expect = 1e-13
 Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 4/65 (6%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QK 69
                L+VG L   T E++I + FS+ G+++ I +  D     + GF FV + +    + 
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96

Query: 70  AVDDL 74
           A+  +
Sbjct: 97  AMRYI 101

>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 = 57.1 bits (138), Expect = 2e-10
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 4/72 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C ++VG L+   +E+ + + FS+ G I +     DK K    GFCF+ +  +  AE  + 
Sbjct: 40  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99

Query: 161 NPKQVICGKEVD 172
                I G  +D
Sbjct: 100 Y----INGTRLD 107

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 7/74 (9%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
           LF+  L +  G++++   F  +G V S  +  D  T  S+ F FV++      Q A+  
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86

Query: 74 LLAAGDHYIGNKKI 87
          +       IG K++
Sbjct: 87 M---NGFQIGMKRL 97

>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 = 48.5 bits (116), Expect = 1e-07
 Identities = 22/88 (25%), Positives = 42/88 (47%), Gaps = 8/88 (9%)

Query: 94  KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           ++  P    +F+  L  E  +QD+   F  +G++   +   DK  N+ K F F+S+D+  
Sbjct: 19  QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78

Query: 154 VAEQVLA--NPKQVICGKEVDVKRVKFN 179
            A+  +   N      G ++ +KR+K  
Sbjct: 79  SAQAAIQSMN------GFQIGMKRLKVQ 100

>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 = 67.1 bits (163), Expect = 2e-13
 Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 3/95 (3%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFA 61
            A             L++G L   T ++++ +     G  ++  I    +   GQS+GFA
Sbjct: 56  AAPNVVYTYTGKRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFA 115

Query: 62  FVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
            V   ++ +   L+       +  +      V K+
Sbjct: 116 LVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNKQ 150

>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 = 62.4 bits (151), Expect = 7e-12
 Identities = 25/162 (15%), Positives = 53/162 (32%), Gaps = 8/162 (4%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
            +++G LT   +++D+ +     G   I E +   +++    KGF  +    +  +++++
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 160 AN-PKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPSTY 218
              PK+ + G+   V     N + +       R        +G   A  PG         
Sbjct: 130 DLLPKRELHGQNPVVT--PVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGG---SSRAA 184

Query: 219 AGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYG 260
                   G   G+                   +PA  T + 
Sbjct: 185 FPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTHHH 226

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 5/70 (7%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
          A     D   L++  L  +  E+E+ +    +G+V S  I  D  +G SRG  F    + 
Sbjct: 18 AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMEST 76

Query: 68 ---QKAVDDL 74
             +  +   
Sbjct: 77 EKCEAVIGHF 86

>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 = 48.0 bits (115), Expect = 1e-07
 Identities = 16/101 (15%), Positives = 32/101 (31%), Gaps = 9/101 (8%)

Query: 85  KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
                 ++ K+       +++  L   + EQ++ +    +G +   +   D S    +G 
Sbjct: 10  ASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSS-GTSRGV 68

Query: 145 CFISFDDQNVAEQVLA--NPKQVICGKEVDV-----KRVKF 178
            F   +     E V+   N K  I               KF
Sbjct: 69  GFARMESTEKCEAVIGHFNGKF-IKTPPGVSAPTEPLLCKF 108

>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 = 63.5 bits (155), Expect = 2e-13
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQ 56
           +       +D   +FV GL  N   + + DYF Q G +++        I++  D  TG+
Sbjct: 2  GHHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGK 61

Query: 57 SRGFAFVTFTTQKAVD 72
           +G A V+F    +  
Sbjct: 62 LKGEATVSFDDPPSAK 77

>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 = 54.2 bits (131), Expect = 7e-10
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 8/63 (12%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
            IFV GL   ++ + V DYF Q G I   ++          D+     KG   +SFDD  
Sbjct: 15  TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 74

Query: 154 VAE 156
            A+
Sbjct: 75  SAK 77

>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 = 63.5 bits (155), Expect = 2e-13
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 5/74 (6%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFV 63
          ++G++G   +    L++G L     E  I+  F+  GE V S+ I  +  TG   G+ FV
Sbjct: 2  SSGSSGMAAS----LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFV 57

Query: 64 TFTTQKAVDDLLAA 77
           F      +  L  
Sbjct: 58 EFADLATAEKCLHK 71

>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 = 52.3 bits (126), Expect = 3e-09
 Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 3/85 (3%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
           + +   +++G L   + E  +   F+  G ++   +   ++   +  G+CF+ F D   A
Sbjct: 6   SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATA 65

Query: 156 EQVLANPK-QVICGKEVDVKRVKFN 179
           E+ L     + + G     KR K N
Sbjct: 66  EKCLHKINGKPLPGATP-AKRFKLN 89

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

 Score = 63.9 bits (156), Expect = 3e-13
 Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 7/74 (9%)

Query: 18  KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
            LF+  L +   + ++   F  +G V S  +  D  T  S+ F FV+F      Q A+  
Sbjct: 42  NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKA 101

Query: 74  LLAAGDHYIGNKKI 87
           +       +G K++
Sbjct: 102 M---NGFQVGTKRL 112

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

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P  C +F+  L  E ++ D+   F  +G++   +   DK  ++ K F F+SFD+ + A+ 
Sbjct: 38  PEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQV 97

Query: 158 VLA--NPKQVICGKEVDVKRVK 177
            +   N      G +V  KR+K
Sbjct: 98  AIKAMN------GFQVGTKRLK 113

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 21/118 (17%), Positives = 45/118 (38%), Gaps = 17/118 (14%)

Query: 7   GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
           G  G G      +F+  L ++   K + D FS +G + S  +  D     S+G+ FV F 
Sbjct: 1   GPLGSG-----NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFE 53

Query: 67  TQKAVDDLLAAGD-HYIGNKKI---------DPKRVTKRVNPLKCKIFVGGLTTEISE 114
           TQ+A +  +   +   + ++K+         + +            +++       + 
Sbjct: 54  TQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGPGSTR 111

>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 = 53.4 bits (129), Expect = 2e-09
 Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 5/90 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             IF+  L   I  + + D FS +G+I   +   D++ +  KG+ F+ F+ Q  AE+ + 
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS--KGYGFVHFETQEAAERAIE 63

Query: 161 --NPKQVICGKEVDVKRVKFNPETMGSVSG 188
             N   ++  ++V V R K   E    +  
Sbjct: 64  KMN-GMLLNDRKVFVGRFKSRKEREAELGA 92

>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 = 63.0 bits (154), Expect = 4e-13
 Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 15/77 (19%)

Query: 7  GTAGPGRNDER-----KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
          G++G    ++      +LFVG L  +  E+E+   F +YG+   + I  D      +GF 
Sbjct: 1  GSSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 54

Query: 62 FVTFTT----QKAVDDL 74
          F+   T    + A  +L
Sbjct: 55 FIRLETRTLAEIAKVEL 71

>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 = 57.3 bits (139), Expect = 4e-11
 Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
            ++FVG L  +I+E+++R  F +YG   E     D      KGF FI  + + +AE 
Sbjct: 16  SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEI 66

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 62.4 bits (152), Expect = 9e-13
 Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 7/62 (11%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
          R L++  L      +E+ D F +YG +  I + N   T ++RG A+V +      + AVD
Sbjct: 9  RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNAVD 65

Query: 73 DL 74
           L
Sbjct: 66 HL 67

>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 = 52.0 bits (125), Expect = 6e-09
 Identities = 10/55 (18%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           +++  L  +I+ +++ D F +YG I + +          +G  ++ ++D   A+ 
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE---TRGTAYVVYEDIFDAKN 62

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 19/105 (18%), Positives = 35/105 (33%), Gaps = 16/105 (15%)

Query: 9   AGPGRNDERKLFVGGLHRNTGEKEINDYF-----SQYGEVESISIKNDPHTGQSRGFAFV 63
              G +    + V GL     ++ +  YF     S  G V S          +      +
Sbjct: 1   GSSGSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQ--------RLGCGGVL 52

Query: 64  TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGL 108
           TF      + +LA  DH +   ++  +    R      ++ + GL
Sbjct: 53  TFREPADAERVLAQADHELHGAQLSLRPAPPRAP---ARLLLQGL 94

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 59.2 bits (143), Expect = 1e-11
 Identities = 15/82 (18%), Positives = 32/82 (39%), Gaps = 13/82 (15%)

Query: 101 CKIFVGGLTTEISEQDVRDYF-----SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
             + V GL   + ++ +  YF     S  G +  +Q+              ++F +   A
Sbjct: 9   VAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRL--------GCGGVLTFREPADA 60

Query: 156 EQVLANPKQVICGKEVDVKRVK 177
           E+VLA     + G ++ ++   
Sbjct: 61  ERVLAQADHELHGAQLSLRPAP 82

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

 Score = 61.6 bits (150), Expect = 2e-12
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFT 66
          D   +FV GL  N   + + DYF Q G +++        I++  D  TG+ +G A V+F 
Sbjct: 6  DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 65

Query: 67 TQKAVD 72
             +  
Sbjct: 66 DPPSAK 71

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

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 8/63 (12%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
            IFV GL   ++ + V DYF Q G I   ++          D+     KG   +SFDD  
Sbjct: 9   TIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPP 68

Query: 154 VAE 156
            A+
Sbjct: 69  SAK 71

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

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 26/80 (32%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K++VG L    G+ E+   FS YG + ++ I  +P      GFAFV F   +  +D +  
Sbjct: 2  KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNP-----PGFAFVEFEDPRDAEDAVRG 56

Query: 78 GDHYIGNKKIDPKRVTKRVN 97
           D     K I   RV  RV 
Sbjct: 57 LD----GKVICGSRV--RVE 70

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

 Score = 55.0 bits (133), Expect = 3e-10
 Identities = 26/101 (25%), Positives = 38/101 (37%), Gaps = 6/101 (5%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K++VG L T   + ++   FS YG +       +       GF F+ F+D   AE  +  
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56

Query: 162 P-KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
              +VICG  V V+     P          R     V   G
Sbjct: 57  LDGKVICGSRVRVELSTGMPRRSRFDRPPARRKLLEVLFNG 97

>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 = 61.5 bits (150), Expect = 2e-12
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 8/76 (10%)

Query: 5  ANGTAGPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G        R L+VG L R+  E  I   FSQ G  +S  +  +  +     + F
Sbjct: 2  SSGSSGMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCF 59

Query: 63 VTFTT----QKAVDDL 74
          V F        A+  +
Sbjct: 60 VEFYEHRDAAAALAAM 75

>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 = 52.3 bits (126), Expect = 4e-09
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 2/60 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++VG L+ +++E  +   FSQ G     +   + + N    +CF+ F +   A   LA 
Sbjct: 17  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAA 74

>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 = 61.1 bits (149), Expect = 2e-12
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 8/67 (11%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++G       KL VG +      +E+   F +YG V    I         + +AFV   
Sbjct: 1  GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHME 52

Query: 67 TQKAVDD 73
            +   +
Sbjct: 53 RAEDAVE 59

>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 = 55.3 bits (134), Expect = 2e-10
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 9/74 (12%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+ VG ++   + Q++R  F +YG + E          + K + F+  +    A + + 
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECD--------IVKDYAFVHMERAEDAVEAIR 62

Query: 161 N-PKQVICGKEVDV 173
                   GK + V
Sbjct: 63  GLDNTEFQGKRMHV 76

>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 = 61.6 bits (150), Expect = 2e-12
 Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 7/76 (9%)

Query: 5  ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G  +       +FV  L    G K++ + FS  G V    I  D   G+SRG   
Sbjct: 2  SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGT 60

Query: 63 VTFTT----QKAVDDL 74
          VTF       +A+   
Sbjct: 61 VTFEQSIEAVQAISMF 76

>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 = 45.8 bits (109), Expect = 1e-06
 Identities = 17/87 (19%), Positives = 36/87 (41%), Gaps = 4/87 (4%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
             L   +FV  L  ++  + +++ FS  G +       DK     +G   ++F+    A 
Sbjct: 12  GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAV 70

Query: 157 QVLA--NPKQVICGKEVDVKRVKFNPE 181
           Q ++  N  Q++  + + VK  +    
Sbjct: 71  QAISMFN-GQLLFDRPMHVKMDERALP 96

>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 = 65.6 bits (159), Expect = 2e-12
 Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 4/95 (4%)

Query: 3   YRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
           +  +       +  + LFV  ++ +T E ++   F  YG ++ I +     +G+ RG+AF
Sbjct: 89  WDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAF 148

Query: 63  VTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
           + +  ++   D+ +A  H    KKID +RV   V 
Sbjct: 149 IEYEHER---DMHSAYKH-ADGKKIDGRRVLVDVE 179

>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 = 53.7 bits (128), Expect = 2e-08
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 85  KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
           K  DP             +FV  +  + +E  +R  F  YG I      + K     +G+
Sbjct: 87  KMWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGY 146

Query: 145 CFISFDDQNVAEQVLANPKQV-ICGKEV 171
            FI ++ +        +     I G+ V
Sbjct: 147 AFIEYEHERDMHSAYKHADGKKIDGRRV 174

>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 = 60.4 bits (147), Expect = 2e-12
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 14/87 (16%)

Query: 7  GTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          G++G    D+    L+VGGL     E ++ ++F Q+GE+ +I++         +  AF+ 
Sbjct: 1  GSSGSSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQ 54

Query: 65 FTT----QKAVDDLLAAGDHYIGNKKI 87
          F T    + A +         +  +++
Sbjct: 55 FATRQAAEVAAEKSF--NKLIVNGRRL 79

>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 = 59.6 bits (145), Expect = 5e-12
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +     ++VGGL   I+E D+R++F Q+G I              +   FI F  +  AE
Sbjct: 9   DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAE 62

Query: 157 QVLANP--KQVICGKEVDVK 174
                   K ++ G+ ++VK
Sbjct: 63  VAAEKSFNKLIVNGRRLNVK 82

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

 Score = 60.5 bits (147), Expect = 3e-12
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 10/82 (12%)

Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-- 67
           P R   RKL +  +  +   + ++    QYG VES    N            VT+++  
Sbjct: 9  VPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKD 65

Query: 68 --QKAVDDLLAAGDHYIGNKKI 87
            ++A+D L       + N  +
Sbjct: 66 QARQALDKL---NGFQLENFTL 84

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

 Score = 45.5 bits (108), Expect = 9e-07
 Identities = 8/58 (13%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
             K+ +  +   +  + +     QYG +   +Q    S   +     +++  ++ A Q
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDS---ETAVVNVTYSSKDQARQ 69

>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 = 62.2 bits (151), Expect = 3e-12
 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)

Query: 12  GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
               + K++VG L  N  + E+   F  YG + S+ +  +P      GFAFV F   +  
Sbjct: 69  SCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNP-----PGFAFVEFEDPRDA 123

Query: 72  DD 73
            D
Sbjct: 124 AD 125

>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 = 58.0 bits (140), Expect = 8e-11
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           PL CK++VG L    ++ ++   F  YG +       +       GF F+ F+D   A 
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAA 124

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

 Score = 60.4 bits (147), Expect = 3e-12
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 6/66 (9%)

Query: 92  VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD 151
           + +   P     ++G +    +E D+   F  +G I +F+   +      KG CFI +D 
Sbjct: 19  IIRSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDT 72

Query: 152 QNVAEQ 157
              A  
Sbjct: 73  HEQAAV 78

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

 Score = 55.8 bits (135), Expect = 2e-10
 Identities = 7/49 (14%), Positives = 18/49 (36%), Gaps = 6/49 (12%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
           ++G +     E ++   F  +G +       +      +G  F+ + T
Sbjct: 30 AYIGNIPHFATEADLIPLFQNFGFILDFKHYPE------KGCCFIKYDT 72

>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 = 60.4 bits (147), Expect = 4e-12
 Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 9/88 (10%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFV 63
           +  A  G+     + V  +       EI D+F  Y  +  S+ +K +   G   G A V
Sbjct: 4  GSSGASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMV 62

Query: 64 TFTT----QKAVDDLLAAGDHYIGNKKI 87
           F +      AV DL    D  IG++K+
Sbjct: 63 AFESRDEATAAVIDL---NDRPIGSRKV 87

>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 = 46.1 bits (110), Expect = 5e-07
 Identities = 15/81 (18%), Positives = 31/81 (38%), Gaps = 1/81 (1%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P    I V  +   +S  ++ D+F  Y  I          K M  G   ++F+ ++ A  
Sbjct: 13  PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 158 VLAN-PKQVICGKEVDVKRVK 177
            + +   + I  ++V +    
Sbjct: 73  AVIDLNDRPIGSRKVKLVLGS 93

>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 = 60.5 bits (147), Expect = 4e-12
 Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 8/66 (12%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFT 66
          D   ++V GL+ +    ++ D+F Q G V+         I I  D  TG+ +G A V++ 
Sbjct: 14 DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 73

Query: 67 TQKAVD 72
                
Sbjct: 74 DPPTAK 79

>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 = 52.4 bits (126), Expect = 4e-09
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 8/63 (12%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQ--------PFDKSKNMKKGFCFISFDDQN 153
            I+V GL   ++  D+ D+F Q G +   ++          DK     KG   +S++D  
Sbjct: 17  AIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPP 76

Query: 154 VAE 156
            A+
Sbjct: 77  TAK 79

>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 = 60.0 bits (146), Expect = 4e-12
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 10/85 (11%)

Query: 91  RVTKRVNPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISF 149
            +  R + +K ++F+G L  + +S++D+   FS YG I +         N+K  F FI F
Sbjct: 13  GLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQF 64

Query: 150 DDQNVAEQVLANP-KQVICGKEVDV 173
           D+       +    +++  GK++ +
Sbjct: 65  DNPQSVRDAIEXESQEMNFGKKLIL 89

>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 = 55.8 bits (135), Expect = 2e-10
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 9/72 (12%)

Query: 3  YRANGTAGPGRNDERKLFVGGL-HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
          + ++G    G + + +LF+G L  +N  ++++   FS YG +  I+IK          F 
Sbjct: 9  HHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFG 60

Query: 62 FVTFTTQKAVDD 73
          F+ F   ++V D
Sbjct: 61 FIQFDNPQSVRD 72

>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 = 63.1 bits (153), Expect = 5e-12
 Identities = 32/213 (15%), Positives = 59/213 (27%), Gaps = 52/213 (24%)

Query: 6   NGTAGPGRNDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
               G        L V  L+      + +   F  YG+V+ + I  +      +  A V 
Sbjct: 24  IAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQ 78

Query: 65  FTT----QKAVDDL-----------------------------LAAGDHYIGNK----KI 87
                  Q A+  L                                   Y  +     K 
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

Query: 88  DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
              +  + + P    + +  +   +SE+D++  FS  G + +  + F K     +    I
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALI 194

Query: 148 SFDDQNVAEQVLA--NPKQVICGKEVDVKRVKF 178
                  A Q L   +   +     +   RV F
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHL---RVSF 224

>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 = 59.6 bits (145), Expect = 6e-12
 Identities = 13/72 (18%), Positives = 24/72 (33%), Gaps = 12/72 (16%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++G       KL++G L       ++   F                     G+AFV + 
Sbjct: 1  GSSGSSGM--NKLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYP 52

Query: 67 T----QKAVDDL 74
                +A++ L
Sbjct: 53 DQNWAIRAIETL 64

>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 = 58.8 bits (143), Expect = 1e-11
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 8/78 (10%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
           K+++G L+  ++  D+R  F           P      +K G+ F+ + DQN A + +  
Sbjct: 10  KLYIGNLSPAVTADDLRQLFGDRK------LPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63

Query: 161 -NPKQVICGKEVDVKRVK 177
            + K  + GK ++V    
Sbjct: 64  LSGKVELHGKIMEVDYSV 81

>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 = 60.0 bits (146), Expect = 6e-12
 Identities = 23/99 (23%), Positives = 45/99 (45%), Gaps = 7/99 (7%)

Query: 85  KKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
           K++  + V  + +P  C ++ GG+ + +++Q +R  FS +G I E +   +      KG+
Sbjct: 10  KQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGY 63

Query: 145 CFISFDDQNVAEQVLAN-PKQVICGKEVDVKRVKFNPET 182
            F+ F     A   + +     I G  V     K +P+ 
Sbjct: 64  SFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPDM 102

>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 = 54.3 bits (131), Expect = 9e-10
 Identities = 12/60 (20%), Positives = 29/60 (48%), Gaps = 10/60 (16%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
          ++ GG+     ++ +   FS +G++  I +  +      +G++FV F+T      A+  +
Sbjct: 28 VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSV 81

>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 = 59.5 bits (145), Expect = 7e-12
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 8/71 (11%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
           G +   KLF+G L R   E+EI   F QYG+V    I         + + FV    + A
Sbjct: 3  SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTA 54

Query: 71 VDDLLAAGDHY 81
           +D +    HY
Sbjct: 55 AEDAIRNLHHY 65

>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 = 58.0 bits (141), Expect = 2e-11
 Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 9/74 (12%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            K+F+G L  E +EQ++R  F QYG + E          + K + F+  +D+  AE  + 
Sbjct: 9   VKLFIGNLPREATEQEIRSLFEQYGKVLECD--------IIKNYGFVHIEDKTAAEDAIR 60

Query: 161 N-PKQVICGKEVDV 173
           N     + G  ++V
Sbjct: 61  NLHHYKLHGVNINV 74

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 15/77 (19%)

Query: 7  GTAGPGRNDE-----RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
          G++G   +++     + L+V  L  +T E+ I   F+         +K      + R +A
Sbjct: 1  GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYA 54

Query: 62 FVTFTT----QKAVDDL 74
          FV F+      +A+  L
Sbjct: 55 FVHFSNREDAVEAMKAL 71

>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 = 48.4 bits (116), Expect = 6e-08
 Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 10/76 (13%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++V  L    SE+ +   F+        +          + + F+ F ++  A + +  
Sbjct: 17  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKA 70

Query: 162 PKQVICGKEVDVKRVK 177
               + GK +D   ++
Sbjct: 71  ----LNGKVLDGSPIE 82

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

 Score = 59.2 bits (144), Expect = 1e-11
 Identities = 18/81 (22%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
             +VG L  NT + +I+  F     + S+ +  D  T + +GF +V F    ++ + L 
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 77 AGDHYIGNKKIDPKRVTKRVN 97
               +G++ +       RV+
Sbjct: 75 YDGALLGDRSL-------RVD 88

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
             +VG L     + D+   F     I   +   DK  +  KGFC++ FD+ +  ++ L  
Sbjct: 17  TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75

Query: 162 PKQVICGKEVDV 173
              ++  + + V
Sbjct: 76  DGALLGDRSLRV 87

>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 = 59.9 bits (145), Expect = 1e-11
 Identities = 19/92 (20%), Positives = 38/92 (41%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
              G+      ++  + + GL     ++EI  +FS    V +         G+  G AFV
Sbjct: 30  MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89

Query: 64  TFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
            F +Q+  +  L      IG++ I+  + ++ 
Sbjct: 90  QFASQELAEKALGKHKERIGHRYIEVFKSSQE 121

>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 = 52.2 bits (125), Expect = 6e-09
 Identities = 14/75 (18%), Positives = 32/75 (42%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + + GL    +++++  +FS    +          +    G  F+ F  Q +AE+ L 
Sbjct: 43  GFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG 102

Query: 161 NPKQVICGKEVDVKR 175
             K+ I  + ++V +
Sbjct: 103 KHKERIGHRYIEVFK 117

>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 = 1e-11
 Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 9/88 (10%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFV 63
           +  +  G+     + V  +       EI D+F  Y  +  S+ +K +   G   G A V
Sbjct: 4  GSSGSSSGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNE-KGMPTGEAMV 62

Query: 64 TFTT----QKAVDDLLAAGDHYIGNKKI 87
           F +      AV DL    D  IG++K+
Sbjct: 63 AFESRDEATAAVIDL---NDRPIGSRKV 87

>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 = 45.8 bits (109), Expect = 6e-07
 Identities = 13/64 (20%), Positives = 25/64 (39%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P    I V  +   +S  ++ D+F  Y  I          K M  G   ++F+ ++ A  
Sbjct: 13  PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72

Query: 158 VLAN 161
            + +
Sbjct: 73  AVID 76

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 9/96 (9%)

Query: 2  AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
              +          + LFV GL  +T E+ + + F          I  D  TG S+GF 
Sbjct: 1  GSSGSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFG 57

Query: 62 FVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKRVN 97
          FV F +++       A +    + +ID  +V   ++
Sbjct: 58 FVDFNSEEDAKAAKEAME----DGEIDGNKV--TLD 87

>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 = 42.6 bits (101), Expect = 9e-06
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +FV GL+ + +E+ +++ F         +   D+     KGF F+ F+ +  A+    
Sbjct: 16  KTLFVKGLSEDTTEETLKESFDGSVRA---RIVTDRETGSSKGFGFVDFNSEEDAKAAKE 72

Query: 161 NPKQVICGKEVDVKRVKFN 179
                +   E+D  +V  +
Sbjct: 73  A----MEDGEIDGNKVTLD 87

>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 = 58.4 bits (142), Expect = 1e-11
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 9/67 (13%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++G   N   K+FVG +      +E+   F + G V    +         + +AFV   
Sbjct: 1  GSSGSSGN-TWKIFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHME 51

Query: 67 TQKAVDD 73
           +     
Sbjct: 52 KEADAKA 58

>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 = 57.6 bits (140), Expect = 3e-11
 Identities = 20/89 (22%), Positives = 40/89 (44%), Gaps = 9/89 (10%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            KIFVG ++   + Q++R  F + G + E          + K + F+  + +  A+  +A
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECD--------VVKDYAFVHMEKEADAKAAIA 61

Query: 161 N-PKQVICGKEVDVKRVKFNPETMGSVSG 188
               + + GK ++V+      +  G  SG
Sbjct: 62  QLNGKEVKGKRINVELSTKGQKKSGPSSG 90

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 20/90 (22%), Positives = 39/90 (43%)

Query: 6  NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +    P   ++  + + GL     ++EI  +FS    V +         G+S G AFV F
Sbjct: 5  SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 66 TTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           +Q+  +  L      IG++ I+  + ++ 
Sbjct: 65 ASQEIAEKALKKHKERIGHRYIEIFKSSRA 94

>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 = 55.1 bits (133), Expect = 3e-10
 Identities = 14/75 (18%), Positives = 32/75 (42%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           + + GL    S++++  +FS    +          +    G  F+ F  Q +AE+ L   
Sbjct: 18  VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77

Query: 163 KQVICGKEVDVKRVK 177
           K+ I  + +++ +  
Sbjct: 78  KERIGHRYIEIFKSS 92

>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 = 59.0 bits (143), Expect = 2e-11
 Identities = 11/88 (12%), Positives = 28/88 (31%), Gaps = 2/88 (2%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTT 67
           G   + +    +  +  +  + ++  +       E ++ +  D + GQ  G A V F  
Sbjct: 8  EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNN-GQGLGQALVQFKN 66

Query: 68 QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
          +             +  ++     VT  
Sbjct: 67 EDDARKSERLHRKKLNGREAFVHVVTLE 94

>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 = 53.2 bits (128), Expect = 2e-09
 Identities = 18/113 (15%), Positives = 35/113 (30%), Gaps = 2/113 (1%)

Query: 89  PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
                  VN  K    +  +   I++ DV  +                +     G   + 
Sbjct: 4   GSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQ 63

Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
           F +++ A +     ++ + G+E  V  V    E M  +       G    S+G
Sbjct: 64  FKNEDDARKSERLHRKKLNGREAFVHVV--TLEDMREIEKNPPAQGKSGPSSG 114

>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 = 58.4 bits (142), Expect = 2e-11
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 9/74 (12%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDD 73
           L+V  L     ++ +   FS +G + S  +  +   G+S+GF FV F++     KAV +
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTE 74

Query: 74 LLAAGDHYIGNKKI 87
          +       +  K +
Sbjct: 75 M---NGRIVATKPL 85

>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 = 45.7 bits (109), Expect = 7e-07
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 5/75 (6%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             ++V  L   I ++ +R  FS +G+IT  +   +  ++  KGF F+ F     A + + 
Sbjct: 16  VNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRS--KGFGFVCFSSPEEATKAVT 73

Query: 161 --NPKQVICGKEVDV 173
             N  +++  K + V
Sbjct: 74  EMN-GRIVATKPLYV 87

>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 = 58.2 bits (141), Expect = 3e-11
 Identities = 17/94 (18%), Positives = 41/94 (43%), Gaps = 2/94 (2%)

Query: 2  AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
          +  ++G   P   D+  + V G+  +  E ++ D+F     V+++ +  D   G++ G  
Sbjct: 2  SSGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNG 59

Query: 62 FVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           V F + +   + L      +  + ++    T+R
Sbjct: 60 LVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER 93

>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 = 47.4 bits (113), Expect = 2e-07
 Identities = 17/98 (17%), Positives = 31/98 (31%), Gaps = 4/98 (4%)

Query: 96  VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
           +NP    + V G+     E DVRD+F     +       D       G   + F      
Sbjct: 12  INPDDLYVSVHGMPFSAMENDVRDFFHGLR-VDAVHLLKDHVGR-NNGNGLVKFLSPQDT 69

Query: 156 EQVLANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGA 193
            + L   + ++  + V+V           +  G +   
Sbjct: 70  FEALKRNRMLMIQRYVEVSPA--TERQWVAAGGHITSG 105

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

 Score = 58.1 bits (141), Expect = 3e-11
 Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 12/67 (17%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT---- 67
          G     +LFV     +  E E+N+ F  +G ++ + I          GFAFV F      
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESA 78

Query: 68 QKAVDDL 74
           KA++++
Sbjct: 79 AKAIEEV 85

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

 Score = 51.9 bits (125), Expect = 5e-09
 Identities = 13/90 (14%), Positives = 34/90 (37%), Gaps = 11/90 (12%)

Query: 88  DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
                 +       ++FV     ++ E ++ + F  +G + E +        +  GF F+
Sbjct: 19  SHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK--------ILNGFAFV 70

Query: 148 SFDDQNVAEQVLA--NPKQVICGKEVDVKR 175
            F++   A + +   + K     + ++V  
Sbjct: 71  EFEEAESAAKAIEEVHGKS-FANQPLEVVY 99

>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 = 58.7 bits (142), Expect = 3e-11
 Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 9   AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTT 67
           +         +++ GL      K + D+F +   VE SI I   P+ G++ G  FV F  
Sbjct: 18  SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPN-GKATGEGFVEFRN 76

Query: 68  QKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
           +      L     Y+GN+ I    +TK+
Sbjct: 77  EADYKAALCRHKQYMGNRFIQVHPITKK 104

>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 = 53.3 bits (128), Expect = 3e-09
 Identities = 17/99 (17%), Positives = 36/99 (36%), Gaps = 2/99 (2%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +++ GL  E   + V D+F +   + +             G  F+ F ++   +  L   
Sbjct: 28  VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87

Query: 163 KQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
           KQ +  + + V  +    + M      +R       S+G
Sbjct: 88  KQYMGNRFIQVHPI--TKKGMLEKIDMIRKRLQSGPSSG 124

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 57.8 bits (140), Expect = 3e-11
 Identities = 15/81 (18%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 20  FVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD 79
            +        +K +   FS+ G+V ++    D  TG+++GF FV   +      ++ +  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 80  HYIGNKKIDPKRVTKRVNPLK 100
                K++D  +    +  +K
Sbjct: 76  ----GKRLD-LKHRLFLYTMK 91

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 45.9 bits (109), Expect = 5e-07
 Identities = 11/58 (18%), Positives = 27/58 (46%)

Query: 104 FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +      + ++ +   FS+ G +   + P D++    KGF F+     N A++++ +
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKS 73

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

 Score = 57.2 bits (139), Expect = 4e-11
 Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 10/78 (12%)

Query: 98  PLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           P K ++F+G L  + +S++D+   FS YG I +         N+K  F FI FD+     
Sbjct: 8   PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQI--------NIKNAFGFIQFDNPQSVR 59

Query: 157 QVLANP-KQVICGKEVDV 173
             +    +++  GK++ +
Sbjct: 60  DAIECESQEMNFGKKLIL 77

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

 Score = 53.8 bits (130), Expect = 8e-10
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 9/60 (15%)

Query: 15 DERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           + +LF+G L  +N  ++++   FS YG +  I+IK          F F+ F   ++V D
Sbjct: 9  PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRD 60

>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 = 56.9 bits (138), Expect = 8e-11
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 7/81 (8%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
             F+G L  +  E+ I ++F           +   +  + +GF +  F    ++   L+
Sbjct: 20 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 77 AGDHYIGNKKIDPKRVTKRVN 97
            +  +GN++I       RV+
Sbjct: 80 LNEESLGNRRI-------RVD 93

>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 = 48.8 bits (117), Expect = 6e-08
 Identities = 15/73 (20%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLA 160
             F+G L  +++E+ ++++F     I+  + P + S   + KGF +  F+D +     L+
Sbjct: 21  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79

Query: 161 NPKQVICGKEVDV 173
             ++ +  + + V
Sbjct: 80  LNEESLGNRRIRV 92

>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 = 56.2 bits (136), Expect = 1e-10
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++G        + + G   N  EK + ++ +    V +I I  + H G   G+ FV F+
Sbjct: 1  GSSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPV-AIRIVRNAH-GNKTGYIFVDFS 58

Query: 67 TQKAVDDLLAAGDHYIGNKKI 87
           ++ V   L     Y+G + I
Sbjct: 59 NEEEVKQALKCNREYMGGRYI 79

>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 = 44.2 bits (105), Expect = 2e-06
 Identities = 14/83 (16%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            + + G    ++E++V ++ +        +   +     K G+ F+ F ++   +Q L  
Sbjct: 12  TVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALKC 69

Query: 162 PKQVICGKEVDVKRVKFNPETMG 184
            ++ + G+ ++V R K +  + G
Sbjct: 70  NREYMGGRYIEVFREK-SGPSSG 91

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 56.1 bits (136), Expect = 1e-10
 Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 11/70 (15%)

Query: 10 GPGRND-ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
          G G+ +   +L+VGGL  NT    +   F ++G + +I             FA++ + + 
Sbjct: 10 GYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESL 63

Query: 68 ---QKAVDDL 74
             Q A   +
Sbjct: 64 DAAQAACAKM 73

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 7/63 (11%)

Query: 95  RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
           + NP    ++VGGL    S   +   F ++GSI                F +I ++  + 
Sbjct: 13  KANPTTR-LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDA 65

Query: 155 AEQ 157
           A+ 
Sbjct: 66  AQA 68

>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 = 56.6 bits (137), Expect = 1e-10
 Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 10/79 (12%)

Query: 97  NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
             +  ++F+G L T  + + DV   FS+YG +           ++ KG+ F+ + ++  A
Sbjct: 24  KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGC--------SVHKGYAFVQYSNERHA 75

Query: 156 EQVLANP-KQVICGKEVDV 173
              +     +V+ G+ +D+
Sbjct: 76  RAAVLGENGRVLAGQTLDI 94

>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 = 52.4 bits (126), Expect = 3e-09
 Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 10/78 (12%)

Query: 13 RNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          ++   ++F+G L+     + ++   FS+YG V   S+         +G+AFV ++ ++  
Sbjct: 24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHA 75

Query: 72 DDLLAAGDHY-IGNKKID 88
             +   +   +  + +D
Sbjct: 76 RAAVLGENGRVLAGQTLD 93

>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 = 56.1 bits (136), Expect = 1e-10
 Identities = 14/71 (19%), Positives = 30/71 (42%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
             F+G L  +  E+ I ++F           +   +  + +GF +  F    ++   L+
Sbjct: 16 YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 77 AGDHYIGNKKI 87
            +  +GNK+I
Sbjct: 76 LNEESLGNKRI 86

>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 = 48.8 bits (117), Expect = 5e-08
 Identities = 16/73 (21%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQVLA 160
             F+G L  +++E+ ++++F     I+  + P + S   + KGF +  F+D +     L+
Sbjct: 17  TAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 161 NPKQVICGKEVDV 173
             ++ +  K + V
Sbjct: 76  LNEESLGNKRIRV 88

>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 = 55.4 bits (134), Expect = 3e-10
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 12/62 (19%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVD 72
          + LFV  L     E+ +   FSQ+G++E +           + +AF+ F       KA++
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKK--------LKDYAFIHFDERDGAVKAME 63

Query: 73 DL 74
          ++
Sbjct: 64 EM 65

>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 = 53.1 bits (128), Expect = 2e-09
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 9/77 (11%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FV  L   ++E+ +   FSQ+G +   +          K + FI FD+++ A + +  
Sbjct: 13  VLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEE 64

Query: 162 -PKQVICGKEVDVKRVK 177
              + + G+ +++   K
Sbjct: 65  MNGKDLEGENIEIVFAK 81

>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 = 54.2 bits (131), Expect = 7e-10
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 11/74 (14%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKE----INDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          A P       +++  L+    + E    ++  FS++G++  I +     + + RG AFV 
Sbjct: 1  AVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVI 57

Query: 65 FTT----QKAVDDL 74
          F        A+  +
Sbjct: 58 FKEVSSATNALRSM 71

>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 = 45.3 bits (108), Expect = 1e-06
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 8/79 (10%)

Query: 100 KCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
              I++  L  +I + +++      FS++G I +      +S  M+ G  F+ F + + A
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVS--RSLKMR-GQAFVIFKEVSSA 64

Query: 156 EQVLANPK-QVICGKEVDV 173
              L + +      K + +
Sbjct: 65  TNALRSMQGFPFYDKPMRI 83

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 53.3 bits (128), Expect = 1e-09
 Identities = 15/91 (16%), Positives = 34/91 (37%), Gaps = 6/91 (6%)

Query: 88  DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFI 147
            P        PL   ++VG L  +    D++    + GS+     P   +    +   F+
Sbjct: 7   GPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSV-----PLRLTWQGPRRRAFL 61

Query: 148 SFDDQNVAEQVLANPKQV-ICGKEVDVKRVK 177
            + D   A+Q ++  + + +    + V   +
Sbjct: 62  HYPDSAAAQQAVSCLQGLRLGTDTLRVALAR 92

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 7/78 (8%)

Query: 2  AYRANGTAGPGRND--ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRG 59
          +  +   + PG        ++VG L R+    ++     + G V        P     R 
Sbjct: 3  SGSSGPGSPPGEGAPLAADVYVGNLPRDARVSDLKRALRELGSVPLRLTWQGP-----RR 57

Query: 60 FAFVTFTTQKAVDDLLAA 77
           AF+ +    A    ++ 
Sbjct: 58 RAFLHYPDSAAAQQAVSC 75

>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 = 53.3 bits (128), Expect = 1e-09
 Identities = 14/85 (16%), Positives = 33/85 (38%), Gaps = 4/85 (4%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          +D   +   GL  +   +++ ++FS          I    +   G+ RG A +   +++ 
Sbjct: 9  DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQD 67

Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKR 95
          V   L     Y+G + ++   +   
Sbjct: 68 VQKALEKHRMYMGQRYVEVYEINNE 92

>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 = 43.7 bits (103), Expect = 5e-06
 Identities = 12/79 (15%), Positives = 27/79 (34%), Gaps = 2/79 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFCFISFDDQNVAEQV 158
             I   GL    + +DV ++FS                    ++G   I  + +   ++ 
Sbjct: 12  FLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKA 71

Query: 159 LANPKQVICGKEVDVKRVK 177
           L   +  +  + V+V  + 
Sbjct: 72  LEKHRMYMGQRYVEVYEIN 90

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 53.4 bits (128), Expect = 3e-09
 Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 15/105 (14%)

Query: 5   ANGTAGPGRNDERK----------LFVGGLHRNTGEKEINDYFSQYGEV----ESISIKN 50
           ++G++G G ++E            + + GL      +E+  +F Q+  +    E I    
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 51  DPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
            P  G+  G AFV F  ++   + L      +G + I+  R T  
Sbjct: 62  YPD-GRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA 105

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQP---FDKSKNMKKGFCFISFDDQNVAEQVL 159
           + + GL    + ++V  +F Q+  IT  ++             G  F+ F  +  A+  L
Sbjct: 26  VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85

Query: 160 ANPKQVICGKEVDVKRVK 177
              K ++  + +++ R  
Sbjct: 86  RKHKDLLGKRYIELFRST 103

>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 = 53.0 bits (127), Expect = 3e-09
 Identities = 15/94 (15%), Positives = 35/94 (37%), Gaps = 4/94 (4%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGFA 61
          +    GP   +   + + GL  +   +++ ++ S       V  +        G+  G A
Sbjct: 6  SGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEA 64

Query: 62 FVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
          FV   ++  V   L      +G++ I+  +  + 
Sbjct: 65 FVELESEDDVKLALKKDRESMGHRYIEVFKSHRT 98

>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 = 46.1 bits (109), Expect = 7e-07
 Identities = 15/102 (14%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQY---GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           + + GL    S +DV+++ S       +      + + +  + G  F+  + ++  +  L
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78

Query: 160 ANPKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAG 201
              ++ +  + ++V +   +   M  V        A   S+G
Sbjct: 79  KKDRESMGHRYIEVFKS--HRTEMDWVLKHSGPNSASGPSSG 118

>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 = 52.5 bits (126), Expect = 3e-09
 Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 11/77 (14%)

Query: 2  AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
              +    P R  E ++ V GL  +   +++ D+  + G+V    +  D       G  
Sbjct: 1  GSSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTG 53

Query: 62 FVTFTT----QKAVDDL 74
           V F        AV  L
Sbjct: 54 VVEFVRKEDMTYAVRKL 70

>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 = 44.0 bits (104), Expect = 3e-06
 Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 8/83 (9%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           + ++ V GL    S QD++D+  + G +         +   + G   + F  +      +
Sbjct: 15  ENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAV 67

Query: 160 AN-PKQVICGKEVDVKRVKFNPE 181
                      E +   ++   +
Sbjct: 68  RKLDNTKFRSHEGETAYIRVKVD 90

>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 = 51.9 bits (125), Expect = 4e-09
 Identities = 13/85 (15%), Positives = 33/85 (38%), Gaps = 9/85 (10%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
                ++V G   +++   +R  FS +G+I +            +   F++++    A+Q
Sbjct: 13  RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQ 64

Query: 158 VLAN-PKQVICGKEVDVKRVKFNPE 181
            +A      +   ++ V   +  P 
Sbjct: 65  AVAELNGTQVESVQLKVNIARKQPM 89

>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 = 51.1 bits (123), Expect = 8e-09
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 12/68 (17%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT--- 67
                  L+V G   +     +   FS +G +  +S+         R  AFVT+     
Sbjct: 10 RAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMES 61

Query: 68 -QKAVDDL 74
            +AV +L
Sbjct: 62 ADQAVAEL 69

>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 = 52.9 bits (127), Expect = 4e-09
 Identities = 16/84 (19%), Positives = 31/84 (36%), Gaps = 2/84 (2%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFV 63
             +            + + GL     E +I ++FS    V  + I+  P  G+  G A V
Sbjct: 34  SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPV-RVHIEIGPD-GRVTGEADV 91

Query: 64  TFTTQKAVDDLLAAGDHYIGNKKI 87
            F T +     ++     + ++ I
Sbjct: 92  EFATHEEAVAAMSKDRANMQHRYI 115

>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 = 43.7 bits (103), Expect = 7e-06
 Identities = 12/92 (13%), Positives = 30/92 (32%), Gaps = 2/92 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + + GL  + +E D+ ++FS                    G   + F     A   ++
Sbjct: 47  HCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADVEFATHEEAVAAMS 104

Query: 161 NPKQVICGKEVDVKRVKFNPETMGSVSGAVRG 192
             +  +  + +++        + G+ S  V  
Sbjct: 105 KDRANMQHRYIELFLNSTTGASNGAYSSQVMQ 136

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 52.0 bits (125), Expect = 4e-09
 Identities = 17/91 (18%), Positives = 38/91 (41%), Gaps = 13/91 (14%)

Query: 16  ERKLFVGGL------HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
           +  + V  +           +  I+  FS++G++ +     +   G+++G+ F+ + +  
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72

Query: 70  AVDDLLAAGDHYIGNKKIDPKRVTKRVNPLK 100
              D +   D      K+D K+ T RVN   
Sbjct: 73  HAVDAVKNAD----GYKLD-KQHTFRVNLFT 98

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 8/67 (11%)

Query: 101 CKIFVGGL------TTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNV 154
             I V  +        E  +  +   FS++G IT    P +  K   KG+ F+ +     
Sbjct: 16  SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYIFLEYASPAH 73

Query: 155 AEQVLAN 161
           A   + N
Sbjct: 74  AVDAVKN 80

>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 = 51.3 bits (123), Expect = 5e-09
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 6/72 (8%)

Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVT 64
          GP  +  R+L+VG +     E+ + D+F+    +  ++             Q + FAF+ 
Sbjct: 1  GPLGSA-RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLE 59

Query: 65 FTTQKAVDDLLA 76
          F +       +A
Sbjct: 60 FRSVDETTQAMA 71

>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 = 50.1 bits (120), Expect = 1e-08
 Identities = 16/79 (20%), Positives = 34/79 (43%), Gaps = 5/79 (6%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVAE 156
           +++VG +   I+E+ + D+F+    +    Q           N  K F F+ F   +   
Sbjct: 8   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67

Query: 157 QVLANPKQVICGKEVDVKR 175
           Q +A    +  G+ + ++R
Sbjct: 68  QAMAFDGIIFQGQSLKIRR 86

>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 = 51.3 bits (123), Expect = 6e-09
 Identities = 10/62 (16%), Positives = 20/62 (32%), Gaps = 7/62 (11%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
              I V  L  + + Q+V D    Y     +        +  K   F++  +   A+  +
Sbjct: 5   SSGILVKNLPQDSNCQEVHDLLKDYDLKYCY-------VDRNKRTAFVTLLNGEQAQNAI 57

Query: 160 AN 161
             
Sbjct: 58  QM 59

>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 = 49.3 bits (118), Expect = 3e-08
 Identities = 11/70 (15%), Positives = 26/70 (37%), Gaps = 7/70 (10%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G +    + V  L +++  +E++D    Y            +  +++  AFVT    +  
Sbjct: 1  GSSGSSGILVKNLPQDSNCQEVHDLLKDYDLKYC-------YVDRNKRTAFVTLLNGEQA 53

Query: 72 DDLLAAGDHY 81
           + +     Y
Sbjct: 54 QNAIQMFHQY 63

>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 = 51.2 bits (123), Expect = 7e-09
 Identities = 15/82 (18%), Positives = 31/82 (37%), Gaps = 2/82 (2%)

Query: 6  NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTF 65
          +  +         + + GL     E +I ++FS       + I+  P  G+  G A V F
Sbjct: 5  SSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEF 62

Query: 66 TTQKAVDDLLAAGDHYIGNKKI 87
           T +     +A     + ++ +
Sbjct: 63 ATHEDAVAAMAKDKANMQHRYV 84

>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 = 41.2 bits (97), Expect = 3e-05
 Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 2/73 (2%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           + + GL    +E D+ ++FS                    G   + F     A   +A  
Sbjct: 18  VHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPD-GRVTGEADVEFATHEDAVAAMAKD 75

Query: 163 KQVICGKEVDVKR 175
           K  +  + V++  
Sbjct: 76  KANMQHRYVELFL 88

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 22/94 (23%), Positives = 42/94 (44%), Gaps = 9/94 (9%)

Query: 103 IFVGGLTTEISEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
           +FVG LT ++ +  + ++F + Y S    +   D++  + KG+ F+ F D+   ++ L  
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQT-GVSKGYGFVKFTDELEQKRALTE 70

Query: 161 -NPKQVICGKEVDV-----KRVKFNPETMGSVSG 188
                 +  K V +     K  +  P   G  SG
Sbjct: 71  CQGAVGLGSKPVRLSVAIPKASRVKPVESGPSSG 104

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

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 4/80 (5%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
               E  LFVG L  +  +  + ++F + Y       +  D  TG S+G+ FV FT + 
Sbjct: 4  GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDEL 62

Query: 70 AVDDLLAA--GDHYIGNKKI 87
               L    G   +G+K +
Sbjct: 63 EQKRALTECQGAVGLGSKPV 82

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 50.7 bits (121), Expect = 2e-08
 Identities = 12/82 (14%), Positives = 30/82 (36%), Gaps = 11/82 (13%)

Query: 1  MAYRANGTAGPGRNDERKLFVGGLHRNTGEKE----INDYFSQYGEVESISIKNDPHTGQ 56
          M     G+  P     + + +  ++    +++    +    S  G++  I +     +  
Sbjct: 14 MDSPDLGSTPPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDD 70

Query: 57 SRGFAFVTFTT----QKAVDDL 74
          + G A++ F T    Q  V+  
Sbjct: 71 NSGKAYIVFATQESAQAFVEAF 92

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 45.7 bits (108), Expect = 1e-06
 Identities = 10/78 (12%), Positives = 25/78 (32%), Gaps = 8/78 (10%)

Query: 101 CKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
             + +  +  E+ ++ ++       S  G I +             G  +I F  Q  A+
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDN---SGKAYIVFATQESAQ 86

Query: 157 QVLANPK-QVICGKEVDV 173
             +   +     G  + +
Sbjct: 87  AFVEAFQGYPFQGNPLVI 104

>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 = 50.4 bits (120), Expect = 3e-08
 Identities = 18/106 (16%), Positives = 36/106 (33%), Gaps = 12/106 (11%)

Query: 4   RANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQY---GEVESISIKNDPHTGQSRGF 60
           R +   GP   +   + + GL  +   +++ ++ S          +        G+  G 
Sbjct: 32  RGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGE 90

Query: 61  AFVTFTTQKAVDDLLAAGDHYIGNKKI--------DPKRVTKRVNP 98
           AFV   ++  V   L      +G++ I        +   V K   P
Sbjct: 91  AFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHSGP 136

>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 = 41.9 bits (98), Expect = 4e-05
 Identities = 10/80 (12%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ--QPFDKSKNMKKGFCFISFDDQNVAEQ 157
              + + GL    S +DV+++ S                 +  + G  F+    ++  + 
Sbjct: 44  GFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKM 103

Query: 158 VLANPKQVICGKEVDVKRVK 177
            L   ++ +  + ++V +  
Sbjct: 104 ALKKDRESMGHRYIEVFKSH 123

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 17/85 (20%), Positives = 37/85 (43%), Gaps = 13/85 (15%)

Query: 19 LFVGGL------HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          + V  +           +  I+  FS++G++ +     +   G+++G+ F+ + +     
Sbjct: 4  IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAV 61

Query: 73 DLLAAGDHYIGNKKIDPKRVTKRVN 97
          D +   D      K+D K+ T RVN
Sbjct: 62 DAVKNAD----GYKLD-KQHTFRVN 81

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 42.4 bits (100), Expect = 7e-06
 Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 8/65 (12%)

Query: 103 IFVGGL------TTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
           I V  +        E  +  +   FS++G IT    P +  K   KG+ F+ +     A 
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKT--KGYIFLEYASPAHAV 61

Query: 157 QVLAN 161
             + N
Sbjct: 62  DAVKN 66

>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 = 52.2 bits (124), Expect = 4e-08
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 11/74 (14%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          A P       +++  L+    + E+       FSQ+G++  I +     + + RG AFV 
Sbjct: 2  AVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVS---RSLKMRGQAFVI 58

Query: 65 FTT----QKAVDDL 74
          F        A+  +
Sbjct: 59 FKEVSSATNALRSM 72

>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 = 52.2 bits (124), Expect = 5e-08
 Identities = 27/177 (15%), Positives = 52/177 (29%), Gaps = 11/177 (6%)

Query: 103 IFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQV 158
           I++  L  +I + +++      FSQ+G I +      +S  M+ G  F+ F + + A   
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILV--SRSLKMR-GQAFVIFKEVSSATNA 68

Query: 159 LAN-PKQVICGKEVDVKRVKFNPETMGSVSGAVRGAGARVASAGTAYAAAPGRVVAYPST 217
           L +        K + ++  K + + +  + G       R          +        + 
Sbjct: 69  LRSMQGFPFYDKPMRIQYAKTDSDIIAKMKG---TFVERDRKREKRKPKSQETPATKKAV 125

Query: 218 YAGYAATDYGYTAGSYDAYATAYPGYDYSAMGYAYPAAATSYGGGKYREAAYTRHAP 274
             G A    G   G                     P      G       A  +  P
Sbjct: 126 QGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPP 182

>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 = 42.2 bits (98), Expect = 9e-05
 Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 5/61 (8%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +F+  L  E +E  +   F+Q+    E      +    +    F+ FD++  A     
Sbjct: 208 HILFLTNLPEETNELMLSMLFNQFPGFKEV-----RLVPGRHDIAFVEFDNEVQAGAARD 262

Query: 161 N 161
            
Sbjct: 263 A 263

>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 = 48.8 bits (116), Expect = 8e-08
 Identities = 14/105 (13%), Positives = 36/105 (34%), Gaps = 13/105 (12%)

Query: 76  AAGDHYIGNKKIDPKRV----TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ 131
           ++  H+  +  + P+      ++        I +  L  +++E +V      +G +T   
Sbjct: 3   SSHHHHHHSSGLVPRGSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLL 62

Query: 132 QPFDKSKNMKKGFCFISFDDQNVAE---QVLANPKQVICGKEVDV 173
                     K   FI  + +  A        +   V+ G+ + +
Sbjct: 63  ------MLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI 101

>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 = 39.9 bits (93), Expect = 1e-04
 Identities = 10/54 (18%), Positives = 24/54 (44%), Gaps = 6/54 (11%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          R + +  L  +  E E+      +G+V ++ +       + +  AF+   T++A
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLM------LKGKNQAFIEMNTEEA 79

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 51.8 bits (123), Expect = 1e-07
 Identities = 25/147 (17%), Positives = 44/147 (29%), Gaps = 39/147 (26%)

Query: 28  TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI 87
           T  K++ D+ S       IS+ +      S         T   V  LL     Y+  +  
Sbjct: 272 TRFKQVTDFLSAATTTH-ISLDH-----HSMTL------TPDEVKSLLLK---YLDCRPQ 316

Query: 88  DPKRVTKRVNPLKCKIFVGGLTTEISEQDVR-DYFSQYG----------SITEFQQPFDK 136
           D  R     NP +  I        I +     D +              S+    +P + 
Sbjct: 317 DLPREVLTTNPRRLSIIA----ESIRDGLATWDNWKHVNCDKLTTIIESSL-NVLEPAE- 370

Query: 137 SKNMKKGF--CFISF-DDQNVAEQVLA 160
               +K F    + F    ++   +L+
Sbjct: 371 ---YRKMFDRLSV-FPPSAHIPTILLS 393

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 49.1 bits (117), Expect = 1e-07
 Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 9/67 (13%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTT---- 67
            +++V  L ++  EK++   F +Y +  S + +          G+ +G AF+        
Sbjct: 46  CRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAA 105

Query: 68  QKAVDDL 74
            KA+ + 
Sbjct: 106 AKALKEA 112

>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 = 44.4 bits (105), Expect = 5e-06
 Identities = 19/111 (17%), Positives = 41/111 (36%), Gaps = 20/111 (18%)

Query: 66  TTQKAVDDLLAAGDHYIGNKKIDPKRVTK---RVNPLK---------CKIFVGGLTTEIS 113
                 D++       I  ++++  R+++       +          C+I+V  L   + 
Sbjct: 2   PLGSDSDEM---PSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQ 58

Query: 114 EQDVRDYFSQYGSITEFQQP----FDKSKNMK-KGFCFISFDDQNVAEQVL 159
           E+D++  F +Y   +   Q         K  + KG  FI   ++  A + L
Sbjct: 59  EKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKAL 109

>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 = 48.3 bits (115), Expect = 1e-07
 Identities = 16/70 (22%), Positives = 26/70 (37%), Gaps = 11/70 (15%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT- 67
            P R  E ++ V GL  +   +++ D+  + G+V    +  D       G   V F   
Sbjct: 9  GPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRK 61

Query: 68 ---QKAVDDL 74
               AV  L
Sbjct: 62 EDMTYAVRKL 71

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 8/83 (9%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           + ++ V GL    S QD++D+  + G +         +   + G   + F  +      +
Sbjct: 16  ENRVVVSGLPPSGSWQDLKDHMREAGDVCY-------ADVYRDGTGVVEFVRKEDMTYAV 68

Query: 160 AN-PKQVICGKEVDVKRVKFNPE 181
                      E +   ++   +
Sbjct: 69  RKLDNTKFRSHEGETAYIRVKVD 91

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

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 9/74 (12%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
           I +  L  +++E +V      +G +T             K   FI  + +  A  ++   
Sbjct: 19  IHIRKLPIDVTEGEVISLGLPFGKVTNLL------MLKGKNQAFIEMNTEEAANTMVNYY 72

Query: 161 -NPKQVICGKEVDV 173
            +   V+ G+ + +
Sbjct: 73  TSVTPVLRGQPIYI 86

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 11/77 (14%), Positives = 30/77 (38%), Gaps = 10/77 (12%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          R + +  L  +  E E+      +G+V ++ +         +  AF+   T++A +    
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAAN---T 67

Query: 77 AGDHYIGNKK-IDPKRV 92
            ++Y      +  + +
Sbjct: 68 MVNYYTSVTPVLRGQPI 84

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.4 bits (117), Expect = 2e-07
 Identities = 14/74 (18%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +++ G  T+ +  D++++    G +   Q      K  K G  F+ FD    A++ + 
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFK-GSIFVVFDSIESAKKFVE 168

Query: 161 NPKQVICGKEVDVK 174
            P Q     ++ + 
Sbjct: 169 TPGQKYKETDLLIL 182

>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 = 48.7 bits (115), Expect = 3e-07
 Identities = 10/75 (13%), Positives = 27/75 (36%), Gaps = 1/75 (1%)

Query: 13  RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
               R +++ G   +    +I ++    G+V +I ++        +G  FV F + ++  
Sbjct: 106 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAK 164

Query: 73  DLLAAGDHYIGNKKI 87
             +           +
Sbjct: 165 KFVETPGQKYKETDL 179

>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 = 47.1 bits (112), Expect = 3e-07
 Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 10/72 (13%)

Query: 7  GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G++G     +  +    L   T   EI + FS++G +  + +            A V F 
Sbjct: 1  GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFL 54

Query: 67 T----QKAVDDL 74
               +KA   L
Sbjct: 55 EPLEARKAFRHL 66

>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 = 42.1 bits (99), Expect = 1e-05
 Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 6/58 (10%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           K  I    L       ++++ FS++GS+     P             + F +   A +
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARK 61

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 46.8 bits (111), Expect = 3e-07
 Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 10/66 (15%)

Query: 19 LFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPHTGQSR---GFAFVTFTT----Q 68
          +FV GL +   + E+    +YF ++G++  + I N      S+     A+VT+       
Sbjct: 18 VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 69 KAVDDL 74
          +A+  +
Sbjct: 78 RAIQCV 83

>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 = 41.8 bits (98), Expect = 2e-05
 Identities = 11/64 (17%), Positives = 26/64 (40%), Gaps = 6/64 (9%)

Query: 100 KCKIFVGGLTTEISEQDV---RDYFSQYGSITE---FQQPFDKSKNMKKGFCFISFDDQN 153
           K  +FV GL+  +++ +V    +YF ++G I +                   ++++    
Sbjct: 15  KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74

Query: 154 VAEQ 157
            A +
Sbjct: 75  DALR 78

>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 = 46.4 bits (110), Expect = 4e-07
 Identities = 9/74 (12%), Positives = 25/74 (33%), Gaps = 9/74 (12%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--- 159
           + +  L  E++E +V      +G +T             K   F+    +  A  ++   
Sbjct: 18  LHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYY 71

Query: 160 ANPKQVICGKEVDV 173
           +     +  + + +
Sbjct: 72  SAVTPHLRNQPIYI 85

>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 = 37.9 bits (88), Expect = 4e-04
 Identities = 13/77 (16%), Positives = 29/77 (37%), Gaps = 10/77 (12%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          R L +  L     E E+      +G+V +I +       + +  AF+   T++A      
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAI---T 66

Query: 77 AGDHYIGNKK-IDPKRV 92
            ++Y      +  + +
Sbjct: 67 MVNYYSAVTPHLRNQPI 83

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 46.0 bits (109), Expect = 7e-07
 Identities = 8/77 (10%), Positives = 22/77 (28%), Gaps = 7/77 (9%)

Query: 2  AYRANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
                          ++ +  L      +++ D   +     + S     +T    G  
Sbjct: 14 LVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFS---SVNTRDFDGTG 70

Query: 62 FVTFTT----QKAVDDL 74
           + F +     +A++ L
Sbjct: 71 ALEFPSEEILVEALERL 87

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 41.7 bits (98), Expect = 2e-05
 Identities = 12/82 (14%), Positives = 28/82 (34%), Gaps = 3/82 (3%)

Query: 78  GDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS 137
             H+  +  +       ++   + +I +  L    S QD++D   +    T F     + 
Sbjct: 6   HHHHHSSGLVPRGSHMSKLPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRD 65

Query: 138 KNMKKGFCFISFDDQNVAEQVL 159
                G   + F  + +  + L
Sbjct: 66  ---FDGTGALEFPSEEILVEAL 84

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

 Score = 45.5 bits (108), Expect = 9e-07
 Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 9/74 (12%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL--- 159
           + + GL   + E D+ +   ++G I+             K    + F+D   A   +   
Sbjct: 24  VHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYA 77

Query: 160 ANPKQVICGKEVDV 173
           A+ +  I G    V
Sbjct: 78  ADNQIYIAGHPAFV 91

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

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 11/77 (14%), Positives = 25/77 (32%), Gaps = 10/77 (12%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            + + GL     E ++ +   ++G +  + +         +  A V F     V     
Sbjct: 22 PVVHIRGLIDGVVEADLVEALQEFGPISYVVV------MPKKRQALVEFED---VLGACN 72

Query: 77 AGDHYIGNK-KIDPKRV 92
          A ++   N+  I     
Sbjct: 73 AVNYAADNQIYIAGHPA 89

>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 = 44.8 bits (106), Expect = 2e-06
 Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 15/94 (15%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           + V GL   + E D+ +   ++G+I              K    + F++ + A++ +   
Sbjct: 18  VHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFA 71

Query: 163 KQV---ICGKEVDV-----KRVKFNPETMGSVSG 188
             V   I G++        KR+   P   G  SG
Sbjct: 72  ADVPVYIAGQQAFFNYSTSKRIT-RPGNSGPSSG 104

>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 = 42.5 bits (100), Expect = 1e-05
 Identities = 13/89 (14%), Positives = 32/89 (35%), Gaps = 13/89 (14%)

Query: 5  ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G          + V GL  +  E ++ +   ++G +  + +         +  A 
Sbjct: 2  SSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQAL 55

Query: 63 VTFTT----QKAVDDLLAAGDHYIGNKKI 87
          V F      ++ V         YI  ++ 
Sbjct: 56 VEFENIDSAKECVTFAADVP-VYIAGQQA 83

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 8/57 (14%), Positives = 19/57 (33%), Gaps = 6/57 (10%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           +  GGL   +S   +     + G +     P +      K + F  +     +++  
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAY 80

>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 = 44.5 bits (105), Expect = 2e-06
 Identities = 9/60 (15%), Positives = 24/60 (40%), Gaps = 10/60 (16%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKAVDDL 74
          +  GGL       ++     + G V+++ +  +      + ++F  + T    ++A   L
Sbjct: 30 VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTL 83

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

 Score = 45.9 bits (108), Expect = 3e-06
 Identities = 18/74 (24%), Positives = 27/74 (36%), Gaps = 15/74 (20%)

Query: 6   NGTAGPGRNDERKLFVGGLHRN---------TGEKEINDYFSQYGEVESISIKNDPHTGQ 56
            G  G  R   + L+VGG+              E  I   FS+ G+++ I         +
Sbjct: 124 MGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYV------E 177

Query: 57  SRGFAFVTFTTQKA 70
           S+   FV F  Q  
Sbjct: 178 SKNCGFVKFKYQAN 191

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 112

 Score = 39.9 bits (93), Expect = 1e-04
 Identities = 19/94 (20%), Positives = 30/94 (31%), Gaps = 16/94 (17%)

Query: 84  NKKIDPKRVTKRVNPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKK 142
           ++K D K+   RV      I +  L     S+  V      YG I  +           K
Sbjct: 15  DQKFDQKQELGRV------IHLSNLPHSGYSDSAVLKLAEPYGKIKNYIL------MRMK 62

Query: 143 GFCFISFDDQNVAEQVL---ANPKQVICGKEVDV 173
              FI  + +  A  ++           G+ V V
Sbjct: 63  SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV 96

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	275
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
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
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.97
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.97
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.91
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.87
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.85
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.83
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.83
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.83
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.83
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.82
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.82
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.82
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.81
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.81
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.81
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.81
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.8
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.8
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.8
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.8
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.8
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.8
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.8
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.8
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.8
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.8
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.8
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.8
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.8
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.8
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.79
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.79
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.79
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.79
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.79
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.79
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.79
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.79
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.79
2div_A	99	TRNA selenocysteine associated protein; structural	99.79
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.79
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.79
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.79
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.79
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.79
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.79
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.79
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.79
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.79
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.79
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.78
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.78
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.78
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.78
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.78
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.78
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.78
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.78
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.78
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.78
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.78
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.78
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.78
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.78
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.77
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.77
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.77
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.77
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.77
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.77
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.77
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.77
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.77
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.77
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.77
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.77
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.77
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.77
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.77
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.77
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.76
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.76
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.76
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.76
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.76
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.76
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.76
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.76
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.76
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.76
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.76
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.76
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.76
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.76
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.75
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.75
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.75
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.75
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.75
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.75
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.75
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.75
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.75
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.75
2div_A	99	TRNA selenocysteine associated protein; structural	99.75
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.75
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.75
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.75
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.74
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.74
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.74
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.74
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.74
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.74
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.74
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.74
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.74
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.74
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.74
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.74
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.74
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.74
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.74
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.74
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.74
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.74
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.74
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.74
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.74
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.74
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.74
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.73
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.73
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.73
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.73
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.73
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.73
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.73
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.72
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.72
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.72
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.72
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.72
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.72
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.72
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.72
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.56
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.72
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.72
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.72
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.71
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.71
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.71
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.71
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.71
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.71
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.7
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.7
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.7
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.7
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.7
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.7
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.7
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.7
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.7
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.7
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.7
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.69
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.69
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.69
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.69
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.69
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.69
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.69
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.69
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.51
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.69
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.68
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.68
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.68
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.68
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.68
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.68
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.68
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.68
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.68
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.68
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.68
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.67
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.67
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.67
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.67
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.67
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.67
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.67
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.67
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.66
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.66
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.66
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.66
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.65
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.65
1x5p_A	97	Negative elongation factor E; structure genomics,	99.65
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.65
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.64
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.64
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.64
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.64
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.64
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.64
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.64
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.63
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.63
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.63
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.63
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.63
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.62
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.62
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.62
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.62
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.62
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.61
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.61
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.61
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.61
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.58
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.58
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.58
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.57
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.54
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.53
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.53
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.53
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.53
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.52
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.52
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.52
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.51
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.5
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.49
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.48
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.47
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.46
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.43
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.43
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.42
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.4
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.4
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.38
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.37
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.37
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.34
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.27
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.23
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.17
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.16
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.09
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.06
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.0
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.96
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.85
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.83
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.73
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.7
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.66
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.39
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.33
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.22
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	98.07
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.75
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.68
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.54
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.44
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.3
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.25
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.22
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.94
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.61
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.55
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.49
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.19
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.11
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.56
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.49
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.26
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	85.38
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	83.75

>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=2.2e-38  Score=256.90  Aligned_cols=178  Identities=31%  Similarity=0.615  Sum_probs=155.6

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      ....++.+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+.++..+.++.|
T Consensus         5 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l   84 (196)
T 1l3k_A            5 ESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVV   84 (196)
T ss_dssp             ---CCCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEEC
T ss_pred             cCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEe
Confidence            34456678899999999999999999999999999999999999999999999999999999999999998899999999


Q ss_pred             cccccccccCC-------CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHh
Q psy1314          88 DPKRVTKRVNP-------LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA  160 (275)
Q Consensus        88 ~v~~~~~~~~~-------~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~  160 (275)
                      .+.++......       ..++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|.+||+
T Consensus        85 ~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  164 (196)
T 1l3k_A           85 EPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI  164 (196)
T ss_dssp             EEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             eeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHH
Confidence            99987654322       34789999999999999999999999999999999999899999999999999999999999


Q ss_pred             cCCceeCCeEEEEEEeeeCCCCCCC
Q psy1314         161 NPKQVICGKEVDVKRVKFNPETMGS  185 (275)
Q Consensus       161 ~~~~~~~g~~i~v~~~~~~~~~~~~  185 (275)
                      .++..|+|+.|.|.++.++.+....
T Consensus       165 ~~~~~~~G~~i~v~~a~~k~~~~~~  189 (196)
T 1l3k_A          165 QKYHTVNGHNCEVRKALSKQEMASA  189 (196)
T ss_dssp             CSCCEETTEECEEEECC--------
T ss_pred             hCCcEECCEEEEEEecCChhHhccc
Confidence            8889999999999999998776543

>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=2.8e-36  Score=248.23  Aligned_cols=167  Identities=26%  Similarity=0.383  Sum_probs=149.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ..+.++|||+|||+++|+++|+++|++||+|++|+|++++.|++++|||||+|.+.++|++||+. +...+.++.|.+.+
T Consensus        12 ~~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~   91 (213)
T 4f02_A           12 SYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMW   91 (213)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccc
Confidence            45678999999999999999999999999999999999999999999999999999999999975 57789999998887


Q ss_pred             cccccC---CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          92 VTKRVN---PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        92 ~~~~~~---~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      +.....   ....+|||+|||+.+++++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++|++||+.| +..|+
T Consensus        92 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~  169 (213)
T 4f02_A           92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLN  169 (213)
T ss_dssp             CCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             ccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            754432   234789999999999999999999999999999999885  347999999999999999999987 58999


Q ss_pred             CeEEEEEEeeeCCC
Q psy1314         168 GKEVDVKRVKFNPE  181 (275)
Q Consensus       168 g~~i~v~~~~~~~~  181 (275)
                      |++|.|.++.++.+
T Consensus       170 g~~i~V~~a~~~~~  183 (213)
T 4f02_A          170 DRKVFVGRFKSRKE  183 (213)
T ss_dssp             TEECEEEECCCHHH
T ss_pred             CEEEEEEEcCCCcc
Confidence            99999999987654

>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=1.1e-36  Score=240.79  Aligned_cols=166  Identities=33%  Similarity=0.683  Sum_probs=152.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      .++++|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+. .+.+.++.|.+.++.
T Consensus         1 k~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            1 KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT-QHILDGKVIDPKRAI   79 (167)
T ss_dssp             CGGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS-CCEETTEECCCEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc-ccccCCeEccccccc
Confidence            3678999999999999999999999999999999999999999999999999999999999995 578999999998876


Q ss_pred             cccC-CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEE
Q psy1314          94 KRVN-PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVD  172 (275)
Q Consensus        94 ~~~~-~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~  172 (275)
                      ++.. ....+|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++..+..+.|++|.
T Consensus        80 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~  159 (167)
T 2cjk_A           80 PRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIE  159 (167)
T ss_dssp             CHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEE
T ss_pred             chhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEE
Confidence            5433 345789999999999999999999999999999999998899999999999999999999999545889999999


Q ss_pred             EEEeeeCC
Q psy1314         173 VKRVKFNP  180 (275)
Q Consensus       173 v~~~~~~~  180 (275)
                      |.++.+++
T Consensus       160 V~~a~pk~  167 (167)
T 2cjk_A          160 IKRAEPRH  167 (167)
T ss_dssp             EEECCCCC
T ss_pred             EeecCCCC
Confidence            99998763

>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=4.1e-35  Score=241.13  Aligned_cols=170  Identities=21%  Similarity=0.408  Sum_probs=152.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~   92 (275)
                      .+.++|||+|||.++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+ +++..+.++.|.|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            346799999999999999999999999999999999998899999999999999999999999 5788999999999877


Q ss_pred             ccccC------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHh
Q psy1314          93 TKRVN------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA  160 (275)
Q Consensus        93 ~~~~~------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~  160 (275)
                      .....            ...++|||+|||..+++++|+++|++||.|..|.|+.+..++.++|||||+|.+.++|.+|++
T Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~  185 (216)
T 2qfj_A          106 SNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS  185 (216)
T ss_dssp             SCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH
T ss_pred             CCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHH
Confidence            55432            334799999999999999999999999999999999999899999999999999999999999


Q ss_pred             cC-CceeCCeEEEEEEeeeCCCCC
Q psy1314         161 NP-KQVICGKEVDVKRVKFNPETM  183 (275)
Q Consensus       161 ~~-~~~~~g~~i~v~~~~~~~~~~  183 (275)
                      .+ +..|.|++|.|.++..++...
T Consensus       186 ~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          186 SMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             HHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             HccCCEeCCcEEEEEEecCCCCCC
Confidence            87 588999999999999876543

>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=5.2e-35  Score=231.14  Aligned_cols=162  Identities=21%  Similarity=0.383  Sum_probs=150.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~   93 (275)
                      +.++|||+|||+++|+++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|++ +++..+.+++|.+.++.
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            56899999999999999999999999999999999998899999999999999999999997 57889999999999887


Q ss_pred             cccCC-CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCC--e
Q psy1314          94 KRVNP-LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICG--K  169 (275)
Q Consensus        94 ~~~~~-~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g--~  169 (275)
                      +.... ..++|+|+|||..+++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|.+|++.+ +..+.|  +
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~  161 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQ  161 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCe
Confidence            65443 4688999999999999999999999999999999999888999999999999999999999987 578877  9


Q ss_pred             EEEEEEe
Q psy1314         170 EVDVKRV  176 (275)
Q Consensus       170 ~i~v~~~  176 (275)
                      +|.|.+|
T Consensus       162 ~l~V~~A  168 (168)
T 1b7f_A          162 PLSVRLA  168 (168)
T ss_dssp             CCEEEEC
T ss_pred             EEEEEeC
Confidence            9999875

>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=1.4e-34  Score=228.01  Aligned_cols=160  Identities=21%  Similarity=0.393  Sum_probs=147.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHH-HhCCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL-AAGDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al-~~~~~~~~g~~i~v~~~~~~   95 (275)
                      ++|||+|||.++|+++|+++|++||+|.+|.++.++ +++++|||||+|.+.++|++|+ .+++..+.++.|.+.++...
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            589999999999999999999999999999999986 4779999999999999999999 56788999999999887655


Q ss_pred             c---CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          96 V---NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        96 ~---~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      .   ....++|+|+|||..+++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|.+|++.+ +..+.|++|
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i  159 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL  159 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Confidence            3   334688999999999999999999999999999999999999999999999999999999999977 589999999


Q ss_pred             EEEEee
Q psy1314         172 DVKRVK  177 (275)
Q Consensus       172 ~v~~~~  177 (275)
                      .|.+++
T Consensus       160 ~v~~a~  165 (166)
T 3md3_A          160 RINWAA  165 (166)
T ss_dssp             EEEESC
T ss_pred             EEEecC
Confidence            999885

>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=1.5e-34  Score=228.10  Aligned_cols=162  Identities=26%  Similarity=0.426  Sum_probs=148.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~   93 (275)
                      ++++|||+|||+++|+++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|++ +++..+.+++|.+.++.
T Consensus         1 s~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   80 (167)
T 1fxl_A            1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (167)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CcceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecC
Confidence            36899999999999999999999999999999999998899999999999999999999998 57889999999999887


Q ss_pred             cccC-CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeE-
Q psy1314          94 KRVN-PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKE-  170 (275)
Q Consensus        94 ~~~~-~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~-  170 (275)
                      +... ...++|+|+|||..+++++|+++|++||.|..+.++.+..++.++|+|||+|.+.++|.+|++.+ +..+.|+. 
T Consensus        81 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~  160 (167)
T 1fxl_A           81 PSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATE  160 (167)
T ss_dssp             CCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSS
T ss_pred             CCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCcc
Confidence            5543 34578999999999999999999999999999999999889999999999999999999999987 58888865 


Q ss_pred             -EEEEEe
Q psy1314         171 -VDVKRV  176 (275)
Q Consensus       171 -i~v~~~  176 (275)
                       |.|.+|
T Consensus       161 ~i~v~~A  167 (167)
T 1fxl_A          161 PITVKFA  167 (167)
T ss_dssp             CCEEEEC
T ss_pred             ceEEEeC
Confidence             777664

>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=1.3e-33  Score=224.49  Aligned_cols=163  Identities=28%  Similarity=0.442  Sum_probs=140.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCC--CcccEEEEEEccHHHHHHHHHh-CCceec---Ceee
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKAVDDLLAA-GDHYIG---NKKI   87 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg--~~~G~afV~f~~~e~a~~al~~-~~~~~~---g~~i   87 (275)
                      +++++|||+|||+++|+++|+++|++||+|.+|.|++++.++  +++|||||+|.+.++|++|++. ++..+.   .+.+
T Consensus         1 s~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~   80 (175)
T 3nmr_A            1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPI   80 (175)
T ss_dssp             CCCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccce
Confidence            367899999999999999999999999999999999998887  8999999999999999999985 444444   4555


Q ss_pred             cccccccccC--CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c
Q psy1314          88 DPKRVTKRVN--PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q  164 (275)
Q Consensus        88 ~v~~~~~~~~--~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~  164 (275)
                      .+.++.....  ...++|||+|||..+++++|+++|++||.|..+.++.+. ++.++|||||+|.+.++|++|++.++ .
T Consensus        81 ~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~  159 (175)
T 3nmr_A           81 QMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQA  159 (175)
T ss_dssp             EEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTS
T ss_pred             EEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCC
Confidence            5555544332  256889999999999999999999999999999999885 58899999999999999999999875 5


Q ss_pred             eeC---CeEEEEEEee
Q psy1314         165 VIC---GKEVDVKRVK  177 (275)
Q Consensus       165 ~~~---g~~i~v~~~~  177 (275)
                      .+.   +++|.|.+++
T Consensus       160 ~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          160 QTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             CCCTTCSSCCEEEECC
T ss_pred             cccCCCCCCeEEEecC
Confidence            555   4999999874

>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=5.7e-34  Score=226.95  Aligned_cols=165  Identities=20%  Similarity=0.291  Sum_probs=145.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      ..++.+.++|||+|||.++|+++|+++|++||.+.. .++.+..+++++|||||+|.+.++|++||++++..+.+++|.|
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v   85 (175)
T 1fje_B            7 GSESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKL   85 (175)
T ss_dssp             SSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEE
Confidence            356788999999999999999999999999998766 3444556788999999999999999999988889999999999


Q ss_pred             cccccccC---CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ce
Q psy1314          90 KRVTKRVN---PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QV  165 (275)
Q Consensus        90 ~~~~~~~~---~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~  165 (275)
                      .++..+..   ...++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|.+|++.++ ..
T Consensus        86 ~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~  160 (175)
T 1fje_B           86 EKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAE  160 (175)
T ss_dssp             ECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEE
T ss_pred             ecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCE
Confidence            99876533   346899999999999999999999999988766     4567889999999999999999999874 89


Q ss_pred             eCCeEEEEEEeeeCC
Q psy1314         166 ICGKEVDVKRVKFNP  180 (275)
Q Consensus       166 ~~g~~i~v~~~~~~~  180 (275)
                      |.|++|.|.++.+++
T Consensus       161 ~~g~~i~v~~a~~k~  175 (175)
T 1fje_B          161 IDGRSVSLYYTGEKG  175 (175)
T ss_dssp             ETTEEEEEEECSSCC
T ss_pred             ECCeEEEEEecCCCC
Confidence            999999999998764

>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=8.3e-33  Score=219.40  Aligned_cols=157  Identities=24%  Similarity=0.491  Sum_probs=142.4

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCcee
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQY----G-------EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYI   82 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~----G-------~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~   82 (275)
                      .+.++|||+|||+++|+++|+++|++|    |       .|.++.+..+      +|||||+|.++++|++|+++++..+
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~------~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT------TTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCC------CCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            367899999999999999999999999    6       6777777543      7899999999999999997788899


Q ss_pred             cCeeecccccccccC-CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc
Q psy1314          83 GNKKIDPKRVTKRVN-PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus        83 ~g~~i~v~~~~~~~~-~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      .+++|.+.++..... ...++|+|+|||..+++++|+++|++||.|..+.++.++.++.++|+|||+|.+.++|++|++.
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~  155 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG  155 (172)
T ss_dssp             TTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHH
T ss_pred             cCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            999999998765533 3358899999999999999999999999999999999988999999999999999999999998


Q ss_pred             C-CceeCCeEEEEEEe
Q psy1314         162 P-KQVICGKEVDVKRV  176 (275)
Q Consensus       162 ~-~~~~~g~~i~v~~~  176 (275)
                      + +..+.|++|.|.+|
T Consensus       156 l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          156 LNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             HTTCEETTEECEEEEC
T ss_pred             cCCCEECCeEEEEEeC
Confidence            6 58999999999986

>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=2.6e-32  Score=221.36  Aligned_cols=162  Identities=23%  Similarity=0.455  Sum_probs=143.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCcee
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQY----G-------EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYI   82 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~----G-------~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~   82 (275)
                      ..+++|||+|||+++|+++|+++|++|    |       .|.++.+.      +++|||||+|.+.++|++||++++..+
T Consensus         2 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al~l~g~~~   75 (198)
T 2yh0_A            2 AMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIF   75 (198)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHGGGTTEEE
T ss_pred             CceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHHHhcCCEE
Confidence            357899999999999999999999999    5       55566554      457999999999999999997788899


Q ss_pred             cCeeecccccccccC---------------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCe
Q psy1314          83 GNKKIDPKRVTKRVN---------------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK  141 (275)
Q Consensus        83 ~g~~i~v~~~~~~~~---------------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~  141 (275)
                      .+++|.|.++.....                     ...++|||+|||..+++++|+++|++||.|..|.++.++.++.+
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~  155 (198)
T 2yh0_A           76 QGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLS  155 (198)
T ss_dssp             TTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSE
T ss_pred             cCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCc
Confidence            999999998765421                     34589999999999999999999999999999999999889999


Q ss_pred             eeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeCCC
Q psy1314         142 KGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       142 ~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~~~  181 (275)
                      +|||||+|.+.++|++|++.+ +..|.|++|.|.++.++..
T Consensus       156 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          156 KGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             ceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999999986 5899999999999987653

>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=99.98  E-value=2e-31  Score=228.37  Aligned_cols=167  Identities=16%  Similarity=0.216  Sum_probs=153.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~   92 (275)
                      ...++|||+|||+++|+++|+++|++||+|.++.++.++.+++++|||||+|.+.++|.+|++ +++..+.++.|.|.++
T Consensus        93 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a  172 (284)
T 3smz_A           93 PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWT  172 (284)
T ss_dssp             CCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            356799999999999999999999999999999999999999999999999999999999995 5788999999999988


Q ss_pred             ccccC----CCcceeeecCCCCCC-CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-Ccee
Q psy1314          93 TKRVN----PLKCKIFVGGLTTEI-SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVI  166 (275)
Q Consensus        93 ~~~~~----~~~~~l~V~~l~~~~-~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~  166 (275)
                      .....    ...++|||+|||..+ ++++|+++|++||.|..|.|+.+. ++.++|+|||+|.+.++|.+|++.+ +..|
T Consensus       173 ~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~  251 (284)
T 3smz_A          173 DAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSL  251 (284)
T ss_dssp             CGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCcc
Confidence            76543    245789999999995 999999999999999999999886 6889999999999999999999987 5899


Q ss_pred             CCeEEEEEEeeeCCC
Q psy1314         167 CGKEVDVKRVKFNPE  181 (275)
Q Consensus       167 ~g~~i~v~~~~~~~~  181 (275)
                      .|++|.|.++.+++.
T Consensus       252 ~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          252 GGSHLRVSFCAPGPP  266 (284)
T ss_dssp             TTEECEEEECCSSSC
T ss_pred             CCeEEEEEEecCCCc
Confidence            999999999988765

>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=99.97  E-value=6.7e-31  Score=224.85  Aligned_cols=159  Identities=19%  Similarity=0.324  Sum_probs=140.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~----~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      .+..++++|||+|||.++|+++|+    ++|++||.|.+|.|++   +++++|||||+|.+.++|++||+ +++..+.++
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   80 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   80 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCc
Confidence            456779999999999999999976    8999999999999886   67899999999999999999996 467799999


Q ss_pred             eecccccccccC--------------------------------------------------------------------
Q psy1314          86 KIDPKRVTKRVN--------------------------------------------------------------------   97 (275)
Q Consensus        86 ~i~v~~~~~~~~--------------------------------------------------------------------   97 (275)
                      .|.|.++.....                                                                    
T Consensus        81 ~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~  160 (282)
T 3pgw_A           81 PMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQ  160 (282)
T ss_pred             EEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCC
Confidence            999887654321                                                                    


Q ss_pred             --------------------------------------------CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEec
Q psy1314          98 --------------------------------------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP  133 (275)
Q Consensus        98 --------------------------------------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~  133 (275)
                                                                  ...++|||+|||..+++++|+++|++||.|..|.|+
T Consensus       161 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~  240 (282)
T 3pgw_A          161 PPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV  240 (282)
T ss_pred             CCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEe
Confidence                                                        134679999999999999999999999999999998


Q ss_pred             cCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeC-CeEEEEEEee
Q psy1314         134 FDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVIC-GKEVDVKRVK  177 (275)
Q Consensus       134 ~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~-g~~i~v~~~~  177 (275)
                      .++     +|||||+|.+.++|.+|++.++ ..|. |+.|.|.+++
T Consensus       241 ~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          241 PGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             cCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            653     5899999999999999999884 8888 9999999875

>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=99.97  E-value=2.2e-31  Score=217.37  Aligned_cols=156  Identities=17%  Similarity=0.201  Sum_probs=133.6

Q ss_pred             CCCCeEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          14 NDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp-~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      .+.++|||+||| .++|+++|+++|++||.|.+|+|+.++     +|||||+|.+.++|++||+ +++..+.+++|.|.+
T Consensus         2 ~~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~   76 (205)
T 3tyt_A            2 ADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCV   76 (205)
T ss_dssp             CCCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEE
Confidence            357899999999 899999999999999999999998763     7999999999999999998 578899999999987


Q ss_pred             cccccC--------------------------------------CCcceeeecCCCCCCCHHHHHHhcccCCCe--EEEE
Q psy1314          92 VTKRVN--------------------------------------PLKCKIFVGGLTTEISEQDVRDYFSQYGSI--TEFQ  131 (275)
Q Consensus        92 ~~~~~~--------------------------------------~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v--~~v~  131 (275)
                      +.....                                      .+.++|||+|||+++|+++|+++|++||.|  ..++
T Consensus        77 s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~  156 (205)
T 3tyt_A           77 SKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVK  156 (205)
T ss_dssp             CSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEE
T ss_pred             ccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEE
Confidence            642110                                      123479999999999999999999999998  8899


Q ss_pred             eccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCe----EEEEEEe
Q psy1314         132 QPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGK----EVDVKRV  176 (275)
Q Consensus       132 i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~----~i~v~~~  176 (275)
                      ++.++  +.++|+|||+|.+.++|.+||+.|+ ..|.++    ++.|+++
T Consensus       157 ~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          157 VFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             ECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            88775  4457999999999999999999985 778876    5666654

>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=2.9e-31  Score=228.18  Aligned_cols=165  Identities=19%  Similarity=0.318  Sum_probs=142.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G-~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      .+.++|||+|||+++|+++|+++|++|| +|.+|.|+.++. +.++|||||+|.+.++|++|++ +++..+.++.|.|.+
T Consensus       115 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  193 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKV  193 (292)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3578999999999999999999999999 999999998865 7899999999999999999999 678899999999998


Q ss_pred             cccccC--------CCcceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccCCC-CCCeeeEEEEEECCHHHHHHHHhc
Q psy1314          92 VTKRVN--------PLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKS-KNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus        92 ~~~~~~--------~~~~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~~~-~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      +.+...        ...++|||+|||.. +++++|+++|++||.|..|.|+.+.. |+.++|||||+|.+.++|.+|+ .
T Consensus       194 a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~  272 (292)
T 2ghp_A          194 SNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-Q  272 (292)
T ss_dssp             CCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-G
T ss_pred             CCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-H
Confidence            765432        23478999999999 99999999999999999999999876 5889999999999999999999 7


Q ss_pred             C-CceeCCeEEEEEEeeeCC
Q psy1314         162 P-KQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       162 ~-~~~~~g~~i~v~~~~~~~  180 (275)
                      + +..|.|++|.|.++.++|
T Consensus       273 l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          273 MNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             GTTEEETTEEEEEEECCCCC
T ss_pred             hcCCEECCcEEEEEEecCCC
Confidence            6 589999999999998874

>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=1.5e-30  Score=220.44  Aligned_cols=160  Identities=21%  Similarity=0.352  Sum_probs=143.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||+++|+++|+++|++||+|.+|.|.++      +|||||+|.+.++|++|++ +++..+.++.|.
T Consensus        16 ~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           16 EKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             CCSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            344466789999999999999999999999999999999754      6899999999999999998 578899999999


Q ss_pred             ccccccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-C-cee
Q psy1314          89 PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-K-QVI  166 (275)
Q Consensus        89 v~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~-~~~  166 (275)
                      |.++.+     ..+|||+|||..+|+++|+++|++||.|..|.|+.+ .++.++|||||+|.+.++|.+||..+ + ..+
T Consensus        90 v~~a~~-----~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~  163 (261)
T 3sde_A           90 IRFATH-----GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFL  163 (261)
T ss_dssp             EEECCC-----SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEE
T ss_pred             eeeccc-----CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEE
Confidence            998853     568999999999999999999999999999999998 57899999999999999999999997 3 444


Q ss_pred             C---CeEEEEEEeeeCCC
Q psy1314         167 C---GKEVDVKRVKFNPE  181 (275)
Q Consensus       167 ~---g~~i~v~~~~~~~~  181 (275)
                      .   +++|.|.++....+
T Consensus       164 ~~~~~r~i~v~~~~~~~~  181 (261)
T 3sde_A          164 LTTTPRPVIVEPMEQFDD  181 (261)
T ss_dssp             SSSSCCBCEEEECCCEES
T ss_pred             ecCCCceEEEeeccccCc
Confidence            4   89999999887644

>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=9.9e-31  Score=217.38  Aligned_cols=160  Identities=18%  Similarity=0.257  Sum_probs=140.5

Q ss_pred             CCCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314          10 GPGRNDERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      .....++++|||+|||+ ++|+++|+++|++||+|.+|.|+.++     +|||||+|.+.++|++||+ +++..+.++.|
T Consensus        28 ~~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l  102 (229)
T 2adc_A           28 GLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPI  102 (229)
T ss_dssp             GGGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBC
T ss_pred             CCCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34456789999999999 99999999999999999999999875     6899999999999999997 67889999999


Q ss_pred             ccccccccc------------------------------------CCCcceeeecCCCCCCCHHHHHHhcccCC-CeEEE
Q psy1314          88 DPKRVTKRV------------------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYG-SITEF  130 (275)
Q Consensus        88 ~v~~~~~~~------------------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G-~v~~v  130 (275)
                      .|.++....                                    ....++|||+|||..+++++|+++|++|| .|..|
T Consensus       103 ~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v  182 (229)
T 2adc_A          103 RITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGF  182 (229)
T ss_dssp             EEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEE
T ss_pred             EEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEE
Confidence            998775331                                    11247899999999999999999999999 99999


Q ss_pred             EeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC-CeEEEEEEeeeC
Q psy1314         131 QQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC-GKEVDVKRVKFN  179 (275)
Q Consensus       131 ~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~-g~~i~v~~~~~~  179 (275)
                      .++.+     .+|+|||+|.+.++|.+|++.+ +..+. +++|.|.+++++
T Consensus       183 ~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          183 KFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             EECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             EEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99653     3689999999999999999987 58888 999999998753

>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=9.7e-31  Score=224.93  Aligned_cols=163  Identities=13%  Similarity=0.255  Sum_probs=138.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      .....+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.+  ++|||||+|.+.++|++||++++..+.++.|.+
T Consensus        35 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v  112 (292)
T 2ghp_A           35 LTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIV  112 (292)
T ss_dssp             -------CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEE
Confidence            344567889999999999999999999999999999999998643  579999999999999999988888999999999


Q ss_pred             cccccccCCCcceeeecCCCCCCCHHHHHHhcccCC-CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          90 KRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        90 ~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G-~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      .++      ..++|||+|||..+++++|+++|++|| .|..|.++.+.. +.++|||||+|.+.++|.+|++.+ +..|.
T Consensus       113 ~~~------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~  185 (292)
T 2ghp_A          113 SHL------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIE  185 (292)
T ss_dssp             EEC------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             EEC------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            876      467899999999999999999999999 999999998865 678999999999999999999976 58999


Q ss_pred             CeEEEEEEeeeCCC
Q psy1314         168 GKEVDVKRVKFNPE  181 (275)
Q Consensus       168 g~~i~v~~~~~~~~  181 (275)
                      |++|.|.++.+...
T Consensus       186 g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          186 GYTLVTKVSNPLEK  199 (292)
T ss_dssp             TEECEEEECCCC--
T ss_pred             CcEEEEEECCCCcc
Confidence            99999999886543

>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=9.4e-30  Score=217.93  Aligned_cols=156  Identities=15%  Similarity=0.322  Sum_probs=142.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      .++++|||+|||.++|+++|+++|++|| |.+|.+      ++++|||||+|.+.++|++|++. ++..+.+++|.+.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~------~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~   92 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQ   92 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE------ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEec
Confidence            4578999999999999999999999999 989888      34578999999999999999975 778999999999875


Q ss_pred             ccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          93 TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        93 ~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      .     ..++|||+|||.++++++|+++|++||.|..+.++.+..++.++|||||+|.+.++|.+|++.+ +..+.|++|
T Consensus        93 ~-----~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i  167 (284)
T 3smz_A           93 P-----TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTL  167 (284)
T ss_dssp             C-----CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             C-----CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            4     4578999999999999999999999999999999999999999999999999999999999776 589999999


Q ss_pred             EEEEeeeCCC
Q psy1314         172 DVKRVKFNPE  181 (275)
Q Consensus       172 ~v~~~~~~~~  181 (275)
                      .|.++.++..
T Consensus       168 ~v~~a~~~~~  177 (284)
T 3smz_A          168 YVHWTDAGQL  177 (284)
T ss_dssp             EEEECCGGGC
T ss_pred             EEEECCCCCC
Confidence            9999987654

>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=2.3e-30  Score=210.26  Aligned_cols=155  Identities=17%  Similarity=0.257  Sum_probs=137.3

Q ss_pred             CCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccc
Q psy1314          15 DERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRV   92 (275)
Q Consensus        15 ~~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~   92 (275)
                      ++++|||+|||+ ++|+++|+++|++||.|.+|.|+.++     +|||||+|.+.++|++|++ +++..+.++.|.|.++
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     6899999999999999998 6788999999999876


Q ss_pred             cccc------------------------------------CCCcceeeecCCCCCCCHHHHHHhcccCC-CeEEEEeccC
Q psy1314          93 TKRV------------------------------------NPLKCKIFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFD  135 (275)
Q Consensus        93 ~~~~------------------------------------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G-~v~~v~i~~~  135 (275)
                      ....                                    ..+.++|+|+|||..+++++|+++|++|| .|..|.++.+
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            5331                                    12257899999999999999999999999 9999999764


Q ss_pred             CCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC-CeEEEEEEeeeC
Q psy1314         136 KSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC-GKEVDVKRVKFN  179 (275)
Q Consensus       136 ~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~-g~~i~v~~~~~~  179 (275)
                      .     +|+|||+|.+.++|.+|++.+ +..+. +++|.|.+++++
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     789999999999999999987 58888 999999998754

>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=9.5e-24  Score=165.19  Aligned_cols=136  Identities=16%  Similarity=0.238  Sum_probs=108.4

Q ss_pred             EEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC--ceecCeee------cccc-------cccccCCCcceeeecCCC
Q psy1314          45 SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD--HYIGNKKI------DPKR-------VTKRVNPLKCKIFVGGLT  109 (275)
Q Consensus        45 ~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~--~~~~g~~i------~v~~-------~~~~~~~~~~~l~V~~l~  109 (275)
                      ++.|+.+..  +++||+||+|.+.++|++|++.+.  ..+.+...      ....       .........++|||+|||
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            566777654  689999999999999999997532  12222111      1110       111122346899999999


Q ss_pred             CCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeCCCC
Q psy1314         110 TEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNPET  182 (275)
Q Consensus       110 ~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~~~~  182 (275)
                      +++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++.++...
T Consensus        80 ~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  153 (158)
T 2kn4_A           80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  153 (158)
T ss_dssp             TTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSCC
T ss_pred             CCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCCC
Confidence            99999999999999999999999999989999999999999999999999987 58899999999999876543

>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=99.87  E-value=2.3e-22  Score=148.93  Aligned_cols=100  Identities=20%  Similarity=0.400  Sum_probs=72.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~   93 (275)
                      ...+|||+|||+++|+++|+++|++||+|++|+|+.++  +.++|||||+|.+.++|++||+ +++..+.++.|.|.++.
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            46789999999999999999999999999999999985  4589999999999999999997 47889999999999876


Q ss_pred             cccCC---------CcceeeecCCCCCCCHHH
Q psy1314          94 KRVNP---------LKCKIFVGGLTTEISEQD  116 (275)
Q Consensus        94 ~~~~~---------~~~~l~V~~l~~~~~~~~  116 (275)
                      ++...         ...+|||+|||+++|++.
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            54322         235799999999999864

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=99.85  E-value=1.6e-21  Score=175.78  Aligned_cols=83  Identities=19%  Similarity=0.361  Sum_probs=78.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+.+|+++|+++|++||.|+.|.|+.+..++.++|||||+|.+.++|++||+.|+ ..|.|++|.|.++.
T Consensus       101 ~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~  180 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVER  180 (437)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45799999999999999999999999999999999999999999999999999999999998874 89999999999998


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      .+..
T Consensus       181 ~~~~  184 (437)
T 3pgw_S          181 GRTV  184 (437)
T ss_pred             CCCC
Confidence            7655

>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=99.84  E-value=9.4e-21  Score=136.36  Aligned_cols=80  Identities=18%  Similarity=0.289  Sum_probs=75.6

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+++|+++|+++|++||+|..|.|++++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.+++
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            4578999999999999999999999999999999999999999999999999999999999987 589999999999986


Q ss_pred             e
Q psy1314         178 F  178 (275)
Q Consensus       178 ~  178 (275)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            5

>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=99.84  E-value=1.6e-20  Score=135.19  Aligned_cols=81  Identities=27%  Similarity=0.397  Sum_probs=75.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~   92 (275)
                      .+.++|||+|||+++|+++|+++|++||+|.+|.|++++.+++++|||||+|.+.++|++|++ +++..+.+++|.|+++
T Consensus        17 ~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~A   96 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYA   96 (99)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            345789999999999999999999999999999999999999999999999999999999997 4788999999999988


Q ss_pred             cc
Q psy1314          93 TK   94 (275)
Q Consensus        93 ~~   94 (275)
                      .+
T Consensus        97 kP   98 (99)
T 4fxv_A           97 RP   98 (99)
T ss_dssp             CB
T ss_pred             eC
Confidence            54

>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=99.83  E-value=2.3e-20  Score=145.65  Aligned_cols=85  Identities=22%  Similarity=0.376  Sum_probs=79.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45689999999999999999999999999999999999999999999999999999999999987 58999999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      ......
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.83  E-value=3.3e-20  Score=133.49  Aligned_cols=90  Identities=33%  Similarity=0.640  Sum_probs=83.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      ....+..+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+++++.+.++.|
T Consensus         2 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l   81 (99)
T 2dgs_A            2 SSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKV   81 (99)
T ss_dssp             CCCCCCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEE
Confidence            34566778899999999999999999999999999999999999999999999999999999999999988899999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++.++..
T Consensus        82 ~V~~a~~~~~   91 (99)
T 2dgs_A           82 EVKRAEPRDS   91 (99)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEECCCCcc
Confidence            9999876644

>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=99.83  E-value=7.5e-21  Score=147.43  Aligned_cols=120  Identities=20%  Similarity=0.377  Sum_probs=103.3

Q ss_pred             CCcccEEEEEEccHHHHHHHHHh--CCceecCeeecccccccc-----------------cCCCcceeeecCCCCCCCHH
Q psy1314          55 GQSRGFAFVTFTTQKAVDDLLAA--GDHYIGNKKIDPKRVTKR-----------------VNPLKCKIFVGGLTTEISEQ  115 (275)
Q Consensus        55 g~~~G~afV~f~~~e~a~~al~~--~~~~~~g~~i~v~~~~~~-----------------~~~~~~~l~V~~l~~~~~~~  115 (275)
                      ...+|+++|+|.+.++|++|++.  ++..+.+ .+.+..+...                 .....++|||+|||++++++
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            35689999999999999999975  4567888 8887776542                 12345899999999999999


Q ss_pred             HHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeCC
Q psy1314         116 DVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       116 ~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~~  180 (275)
                      +|+++|++||.|..|.|+.+     ++|||||+|.+.++|++||+.+ +..|.|++|.|.++.+++
T Consensus        89 ~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           89 ELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             HHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             HHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            99999999999999999876     5899999999999999999976 588999999999988653

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

Probab=99.83  E-value=3.7e-20  Score=129.98  Aligned_cols=84  Identities=42%  Similarity=0.818  Sum_probs=77.0

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      ...+..+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+++++.+.++.|.
T Consensus         4 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~   83 (87)
T 3s7r_A            4 ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVID   83 (87)
T ss_dssp             ---CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEE
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEE
Confidence            34556788999999999999999999999999999999999999999999999999999999999999989999999999


Q ss_pred             cccc
Q psy1314          89 PKRV   92 (275)
Q Consensus        89 v~~~   92 (275)
                      |+++
T Consensus        84 v~~A   87 (87)
T 3s7r_A           84 PKKA   87 (87)
T ss_dssp             EEEC
T ss_pred             EEeC
Confidence            8764

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.82  E-value=1.4e-19  Score=134.12  Aligned_cols=86  Identities=27%  Similarity=0.536  Sum_probs=79.8

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR  175 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~  175 (275)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.++..|.+++|.|.+
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~   92 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNL   92 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999999999999997799999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +..+..
T Consensus        93 a~~~~~   98 (116)
T 2cqd_A           93 AYLGAK   98 (116)
T ss_dssp             STTTCC
T ss_pred             cccCCC
Confidence            976543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.82  E-value=9.7e-21  Score=134.17  Aligned_cols=83  Identities=20%  Similarity=0.336  Sum_probs=75.8

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC--CceecCeeeccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG--DHYIGNKKIDPKRV   92 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G-~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~--~~~~~g~~i~v~~~   92 (275)
                      +++|||+|||+++|+++|+++|++|| +|++|+|++++.|++++|||||+|.+.++|++||+.+  ...+.|++|.|+++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            57899999999999999999999999 7999999999999999999999999999999999864  34799999999998


Q ss_pred             ccccCC
Q psy1314          93 TKRVNP   98 (275)
Q Consensus        93 ~~~~~~   98 (275)
                      .++...
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            776543

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1e-19  Score=132.34  Aligned_cols=91  Identities=43%  Similarity=0.688  Sum_probs=83.8

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      .....+..+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+.++..|.++.
T Consensus         7 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~   86 (105)
T 2dh8_A            7 GMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRN   86 (105)
T ss_dssp             CCCCCCSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEE
T ss_pred             CCCcCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEE
Confidence            34456678889999999999999999999999999999999999999999999999999999999999999888999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.++..
T Consensus        87 l~V~~a~~~~~   97 (105)
T 2dh8_A           87 IDPKPCTPRGM   97 (105)
T ss_dssp             EBCCCSCCSSC
T ss_pred             EEEEEccCCCC
Confidence            99999876654

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

Probab=99.82  E-value=8.5e-20  Score=133.83  Aligned_cols=83  Identities=23%  Similarity=0.287  Sum_probs=77.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      +.+.++|||+|||+++|+++|+++|++||+|++|.|+.++.|++++|||||+|.+.++|++||+ +++..+.++.|.|++
T Consensus         3 ~~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            3 QIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999998 578899999999998


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +...
T Consensus        83 a~~~   86 (110)
T 3s8s_A           83 DIKG   86 (110)
T ss_dssp             CSTT
T ss_pred             CCCC
Confidence            8543

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

Probab=99.82  E-value=1.9e-20  Score=142.44  Aligned_cols=123  Identities=18%  Similarity=0.221  Sum_probs=81.4

Q ss_pred             EEEEEEccHHHHHHHHHhCC-ceecCeeecccccccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCC
Q psy1314          60 FAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK  138 (275)
Q Consensus        60 ~afV~f~~~e~a~~al~~~~-~~~~g~~i~v~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~  138 (275)
                      +.|+++++...+..|++.+. ....++...-....+......++|||+|||+++++++|+++|++||.|..|.|+.++.+
T Consensus         6 ~~~~~~~~~~~~~~a~~~~~g~~~~g~~~~~~~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~   85 (135)
T 2lea_A            6 HHHHHSSGLVPRGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT   85 (135)
T ss_dssp             -----------------------------CCSCCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSS
T ss_pred             cccccccCCCchhhhhhhccCCCCCCCCCCCcCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCC
Confidence            46677777777777777642 22233222212222333445688999999999999999999999999999999999989


Q ss_pred             CCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeCCCC
Q psy1314         139 NMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNPET  182 (275)
Q Consensus       139 ~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~~~~  182 (275)
                      +.++|||||+|.+.++|++||+.+ +..|.|++|.|.+++++...
T Consensus        86 g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~  130 (135)
T 2lea_A           86 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPP  130 (135)
T ss_dssp             SSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCC
T ss_pred             CccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCC
Confidence            999999999999999999999987 48899999999999876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.81  E-value=3.2e-20  Score=131.48  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=76.2

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCC-CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-C-ceeCCeEEEEEEee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-K-QVICGKEVDVKRVK  177 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G-~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~-~~~~g~~i~v~~~~  177 (275)
                      .+|||+|||+++|+++|+++|++|| +|.+|+|++++.++.++|||||+|.+.++|++||+.+ + ..+.|++|.|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            5799999999999999999999999 8999999999999999999999999999999999986 4 57999999999998


Q ss_pred             eCCCC
Q psy1314         178 FNPET  182 (275)
Q Consensus       178 ~~~~~  182 (275)
                      +++..
T Consensus        82 ~~~~~   86 (91)
T 2lxi_A           82 PKPKI   86 (91)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            77653

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=2.4e-19  Score=132.76  Aligned_cols=89  Identities=26%  Similarity=0.468  Sum_probs=81.5

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      .......+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+.++..|.++.|
T Consensus         9 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l   88 (116)
T 2cqd_A            9 HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKA   88 (116)
T ss_dssp             CCCCCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEEC
T ss_pred             CCCcCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEE
Confidence            34555677899999999999999999999999999999999999999999999999999999999999987779999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++....
T Consensus        89 ~V~~a~~~~   97 (116)
T 2cqd_A           89 NVNLAYLGA   97 (116)
T ss_dssp             EEEESTTTC
T ss_pred             EEEEcccCC
Confidence            999986543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=1.3e-19  Score=132.75  Aligned_cols=90  Identities=39%  Similarity=0.639  Sum_probs=77.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      +...+..+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+.++..+.++.|
T Consensus        17 ~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l   96 (109)
T 2rs2_A           17 RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTI   96 (109)
T ss_dssp             ---------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEE
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEE
Confidence            33456677899999999999999999999999999999999999999999999999999999999999998899999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++..+..
T Consensus        97 ~V~~a~~~~~  106 (109)
T 2rs2_A           97 DPKVAFPRRA  106 (109)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEccCCCC
Confidence            9999876543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.9e-19  Score=130.41  Aligned_cols=90  Identities=22%  Similarity=0.422  Sum_probs=82.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      ....+..+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..|.++.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   86 (103)
T 2cq0_A            7 GPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI   86 (103)
T ss_dssp             CSCCCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            334567788999999999999999999999999999999999999999999999999999999999999 4678999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.++..
T Consensus        87 l~v~~a~~~~~   97 (103)
T 2cq0_A           87 LNVEWAKPSTN   97 (103)
T ss_dssp             CEEEESSCCCC
T ss_pred             EEEEECCCCCC
Confidence            99999876644

>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=99.81  E-value=2.1e-19  Score=130.63  Aligned_cols=91  Identities=24%  Similarity=0.381  Sum_probs=82.7

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCe
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNK   85 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~   85 (275)
                      .....+..+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.++
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   85 (105)
T 1x5u_A            6 SGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGK   85 (105)
T ss_dssp             SCCCCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSC
T ss_pred             CCCcccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            34456678889999999999999999999999999999999999998999999999999999999999995 67899999


Q ss_pred             eecccccccccC
Q psy1314          86 KIDPKRVTKRVN   97 (275)
Q Consensus        86 ~i~v~~~~~~~~   97 (275)
                      .|.|+++.++..
T Consensus        86 ~l~v~~a~~~~~   97 (105)
T 1x5u_A           86 PIRVNKASAHNK   97 (105)
T ss_dssp             BCEEEETTTTSC
T ss_pred             EEEEEECCCCCc
Confidence            999999876544

>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=2.5e-19  Score=128.84  Aligned_cols=87  Identities=24%  Similarity=0.409  Sum_probs=79.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..+.+++|.|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (99)
T 1whw_A            3 SGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV   82 (99)
T ss_dssp             CCCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            346778999999999999999999999999999999999998899999999999999999999995 5678999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      +++.++..
T Consensus        83 ~~a~~~~~   90 (99)
T 1whw_A           83 LPSTIKKE   90 (99)
T ss_dssp             EECCCCST
T ss_pred             EEcCCCcc
Confidence            99877654

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=2.9e-19  Score=128.50  Aligned_cols=87  Identities=33%  Similarity=0.604  Sum_probs=79.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+..+..|.|++|.|.++
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            44568999999999999999999999999999999999999999999999999999999999994468999999999999


Q ss_pred             eeCCCCC
Q psy1314         177 KFNPETM  183 (275)
Q Consensus       177 ~~~~~~~  183 (275)
                      .++....
T Consensus        87 ~~~~~~~   93 (99)
T 2dgs_A           87 EPRDSKS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccC
Confidence            9876644

>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=99.80  E-value=3.2e-19  Score=131.91  Aligned_cols=88  Identities=19%  Similarity=0.354  Sum_probs=80.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..|.++.|.
T Consensus        19 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   98 (115)
T 2cpz_A           19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   98 (115)
T ss_dssp             CCCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CcCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34455678999999999999999999999999999999999998999999999999999999999964 78899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.++..
T Consensus        99 V~~a~~~~~  107 (115)
T 2cpz_A           99 VQLKRSKND  107 (115)
T ss_dssp             EECCCCSCC
T ss_pred             EEEcCCCCc
Confidence            999876644

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.5e-19  Score=130.92  Aligned_cols=90  Identities=26%  Similarity=0.438  Sum_probs=82.2

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      ...++..+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..+.++.
T Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   84 (103)
T 2dnm_A            5 SSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRE   84 (103)
T ss_dssp             CCSSCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBC
T ss_pred             CCCCCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            445667788999999999999999999999999999999999999999999999999999999999999 5788999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.....
T Consensus        85 l~V~~a~~~~~   95 (103)
T 2dnm_A           85 LRVQVARYGRR   95 (103)
T ss_dssp             CEEEECSSCCS
T ss_pred             EEEEECCcCCC
Confidence            99999876543

>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=3.8e-19  Score=126.82  Aligned_cols=87  Identities=25%  Similarity=0.381  Sum_probs=80.1

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCe
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNK   85 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~   85 (275)
                      ......+.+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.++
T Consensus         6 ~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   85 (95)
T 2cqc_A            6 SGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGR   85 (95)
T ss_dssp             CCCCCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            44456677889999999999999999999999999999999999999999999999999999999999994 78899999


Q ss_pred             eecccccc
Q psy1314          86 KIDPKRVT   93 (275)
Q Consensus        86 ~i~v~~~~   93 (275)
                      +|.|+++.
T Consensus        86 ~l~v~~a~   93 (95)
T 2cqc_A           86 RIRVSGPS   93 (95)
T ss_dssp             EEEEECCS
T ss_pred             EEEEEecC
Confidence            99999875

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

Probab=99.80  E-value=3.9e-20  Score=131.82  Aligned_cols=84  Identities=24%  Similarity=0.312  Sum_probs=75.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC--eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-C----ceec
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGE--VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-D----HYIG   83 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~--v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~----~~~~   83 (275)
                      .....-.+|||+|||+++|+++|+++|++||.  |.+|+|++|+.|++++|||||+|.+.++|++||+.+ +    ..++
T Consensus         4 ~~~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~   83 (95)
T 2lkz_A            4 HHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKID   83 (95)
T ss_dssp             CSSCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEET
T ss_pred             ccCCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceEC
Confidence            44567789999999999999999999999995  679999999999999999999999999999999864 2    2689


Q ss_pred             Ceeeccccccc
Q psy1314          84 NKKIDPKRVTK   94 (275)
Q Consensus        84 g~~i~v~~~~~   94 (275)
                      |++|.|+++..
T Consensus        84 Gr~i~V~~Aks   94 (95)
T 2lkz_A           84 GKTIGVDFAKS   94 (95)
T ss_dssp             TEEEEEEECCC
T ss_pred             CEEEEEEEccC
Confidence            99999998853

>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=99.80  E-value=5.5e-19  Score=127.97  Aligned_cols=88  Identities=31%  Similarity=0.506  Sum_probs=80.7

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      ......+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. .+.+.++.|.
T Consensus         8 ~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~l~   86 (103)
T 2cqg_A            8 VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCD   86 (103)
T ss_dssp             CSCCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEE
T ss_pred             CCCccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEE
Confidence            345567788999999999999999999999999999999999999999999999999999999999994 7799999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.++..
T Consensus        87 v~~a~~~~~   95 (103)
T 2cqg_A           87 CKLPNSKQS   95 (103)
T ss_dssp             EECCCTTCC
T ss_pred             EEecCCCCc
Confidence            999877654

>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=5.5e-19  Score=130.61  Aligned_cols=93  Identities=20%  Similarity=0.489  Sum_probs=83.7

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC
Q psy1314           6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN   84 (275)
Q Consensus         6 ~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g   84 (275)
                      ......+..+.++|||+|||.++|+++|+++|++||.|++|.|+.++.+++++|||||+|.+.++|++||+. ++..|.+
T Consensus         5 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g   84 (115)
T 2dgo_A            5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGG   84 (115)
T ss_dssp             CCSSCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETT
T ss_pred             CCcCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            344456677889999999999999999999999999999999999988999999999999999999999985 6789999


Q ss_pred             eeecccccccccCC
Q psy1314          85 KKIDPKRVTKRVNP   98 (275)
Q Consensus        85 ~~i~v~~~~~~~~~   98 (275)
                      +.|.|+++..+...
T Consensus        85 ~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           85 RQIRTNWATRKPPA   98 (115)
T ss_dssp             EECEEEESSCCCCC
T ss_pred             EEEEEEEccCCCCC
Confidence            99999998766543

>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=4.9e-19  Score=128.25  Aligned_cols=87  Identities=25%  Similarity=0.336  Sum_probs=80.4

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      .....++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.
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            3456789999999999999999999999999999999999989999999999999999999999987 589999999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (103)
T 2cq0_A           91 WAKPSTNS   98 (103)
T ss_dssp             ESSCCCCS
T ss_pred             ECCCCCCC
Confidence            99887654

>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=4.8e-19  Score=127.33  Aligned_cols=86  Identities=29%  Similarity=0.453  Sum_probs=79.8

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.++
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            45689999999999999999999999999999999999989999999999999999999999887 48899999999999


Q ss_pred             eeCCCCC
Q psy1314         177 KFNPETM  183 (275)
Q Consensus       177 ~~~~~~~  183 (275)
                      .+++...
T Consensus        86 ~~~~~~~   92 (99)
T 1whw_A           86 TIKKEAS   92 (99)
T ss_dssp             CCCSTTC
T ss_pred             CCCcccc
Confidence            9887653

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

Probab=99.80  E-value=2.2e-19  Score=131.61  Aligned_cols=82  Identities=13%  Similarity=0.185  Sum_probs=76.8

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      .+.++|||+|||+++++++|+++|++||.|.+|.|+.|+.+++++|||||+|.+.++|++||+.+ +..|.|+.|.|.++
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            34678999999999999999999999999999999999999999999999999999999999987 48999999999998


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      ...
T Consensus        84 ~~~   86 (110)
T 3s8s_A           84 IKG   86 (110)
T ss_dssp             STT
T ss_pred             CCC
Confidence            654

>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=99.80  E-value=1.2e-19  Score=134.22  Aligned_cols=105  Identities=18%  Similarity=0.301  Sum_probs=93.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      .++..++|||+|||.++|+++|+++|++||.|.+|.|+.+   +.++|||||+|.+.++|++|++ +++..+.++.|.|.
T Consensus         4 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   80 (115)
T 3lqv_A            4 PPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVL   80 (115)
T ss_dssp             CTTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            3567789999999999999999999999999999999876   4558999999999999999999 57889999999999


Q ss_pred             ccccccCCCcceeeecCCCCCCCHHHHHHhcccCCC
Q psy1314          91 RVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS  126 (275)
Q Consensus        91 ~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~  126 (275)
                      ++.+....       .+++...++++|+++|++||.
T Consensus        81 ~a~~~~~~-------~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           81 YYNANRAF-------QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             ECCHHHHT-------TTSCHHHHHHHHHHHHHHHCC
T ss_pred             EecCChhh-------hhhhHhHhHHHHHHHHHHhCC
Confidence            98765443       577888899999999999984

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=2.6e-19  Score=129.46  Aligned_cols=89  Identities=31%  Similarity=0.564  Sum_probs=81.1

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      ......+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..+.++.|
T Consensus         5 ~~~~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 1x5s_A            5 SSGMASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQI   84 (102)
T ss_dssp             CCCCCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            34556788999999999999999999999999999999999999999999999999999999999996 57789999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++.++..
T Consensus        85 ~v~~a~~~~~   94 (102)
T 1x5s_A           85 RVDQAGKSSD   94 (102)
T ss_dssp             EEEEEECCCC
T ss_pred             EEEECCCCCC
Confidence            9999876554

>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=2.5e-19  Score=127.78  Aligned_cols=84  Identities=25%  Similarity=0.413  Sum_probs=78.3

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++.
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            4679999999999999999999999999999999999999999999999999999999999976 588999999999998


Q ss_pred             eCCCC
Q psy1314         178 FNPET  182 (275)
Q Consensus       178 ~~~~~  182 (275)
                      .+...
T Consensus        84 ~~~~~   88 (95)
T 2dnz_A           84 ERLDG   88 (95)
T ss_dssp             CCCCC
T ss_pred             cccCC
Confidence            77653

>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=3.5e-19  Score=127.01  Aligned_cols=85  Identities=26%  Similarity=0.554  Sum_probs=79.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      +.+.++|||+|||.++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+ +++..+.+++|.|++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            4578899999999999999999999999999999999999999999999999999999999998 578899999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.++..
T Consensus        82 a~~~~~   87 (95)
T 2dnz_A           82 VTERLD   87 (95)
T ss_dssp             SSCCCC
T ss_pred             cccccC
Confidence            876644

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

Probab=99.80  E-value=1.5e-19  Score=130.92  Aligned_cols=83  Identities=13%  Similarity=0.287  Sum_probs=76.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ....+.++|||+|||+++|+++|+++|++||+|.+|.|++++. ++++|||||+|.+.++|++||+++++.+.++.|.|.
T Consensus         6 ~~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~   84 (103)
T 1s79_A            6 KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLIL   84 (103)
T ss_dssp             SSCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEE
T ss_pred             cccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEE
Confidence            4456779999999999999999999999999999999999977 999999999999999999999987889999999998


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      ++..
T Consensus        85 ~~~~   88 (103)
T 1s79_A           85 FKDD   88 (103)
T ss_dssp             EHHH
T ss_pred             EchH
Confidence            7654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=4.9e-19  Score=126.02  Aligned_cols=87  Identities=21%  Similarity=0.384  Sum_probs=79.0

Q ss_pred             CCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecC
Q psy1314           6 NGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGN   84 (275)
Q Consensus         6 ~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g   84 (275)
                      .+.+.....+.++|||+|||.++++++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++|++ +++..+.+
T Consensus         6 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g   85 (94)
T 2e5h_A            6 SGMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFG   85 (94)
T ss_dssp             CCCCCSCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETT
T ss_pred             CCCCCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCC
Confidence            34445666788999999999999999999999999999999999999999999999999999999999997 56789999


Q ss_pred             eeeccccc
Q psy1314          85 KKIDPKRV   92 (275)
Q Consensus        85 ~~i~v~~~   92 (275)
                      ++|.|+++
T Consensus        86 ~~l~v~~a   93 (94)
T 2e5h_A           86 RVIKASIA   93 (94)
T ss_dssp             EEEEEEEC
T ss_pred             cEEEEEec
Confidence            99999876

>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=99.80  E-value=4.7e-19  Score=130.07  Aligned_cols=90  Identities=21%  Similarity=0.402  Sum_probs=81.6

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-C------Cc
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-G------DH   80 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~------~~   80 (275)
                      ....+..+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+. +      +.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A            7 GLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CCCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            3445667789999999999999999999999999999999999999999999999999999999999985 4      68


Q ss_pred             eecCeeecccccccccC
Q psy1314          81 YIGNKKIDPKRVTKRVN   97 (275)
Q Consensus        81 ~~~g~~i~v~~~~~~~~   97 (275)
                      .+.++.|.|+++.++..
T Consensus        87 ~~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           87 KLDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             ESSSCEEEEECCCCCCC
T ss_pred             EEcCEEEEEEECCCCcc
Confidence            99999999999876644

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

Probab=99.80  E-value=6e-19  Score=123.75  Aligned_cols=80  Identities=31%  Similarity=0.624  Sum_probs=75.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.++..|+|++|.|.+|
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            45678999999999999999999999999999999999999999999999999999999999998888999999999875

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

Probab=99.80  E-value=4.6e-19  Score=128.40  Aligned_cols=87  Identities=20%  Similarity=0.371  Sum_probs=79.4

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      .....+.++|||+|||.++|+++|+++|++|+ |++|.|+.++.+++++|||||+|.+.++|++||++++..|.++.|.|
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V   87 (103)
T 2dng_A            9 ELPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRV   87 (103)
T ss_dssp             CCCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEE
T ss_pred             CCCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEE
Confidence            34456788999999999999999999999996 99999999999999999999999999999999977888999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      +++.++..
T Consensus        88 ~~a~~~~~   95 (103)
T 2dng_A           88 DIAEGRKQ   95 (103)
T ss_dssp             EECCCCCC
T ss_pred             EEecCCCC
Confidence            99876544

>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=99.79  E-value=3.8e-19  Score=124.72  Aligned_cols=83  Identities=23%  Similarity=0.525  Sum_probs=74.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ..+.++|||+|||.++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++|++. ++..+.++.|.|++
T Consensus         3 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            3 LGSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             ---CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            35678999999999999999999999999999999999998999999999999999999999984 78899999999998


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +.++
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            8654

>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=3.9e-19  Score=129.96  Aligned_cols=91  Identities=27%  Similarity=0.525  Sum_probs=82.3

Q ss_pred             CCCCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceec
Q psy1314           5 ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIG   83 (275)
Q Consensus         5 ~~~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~   83 (275)
                      ...+......+.++|||+|||.++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++|++ +++..+.
T Consensus        15 ~~~~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~   94 (108)
T 2jrs_A           15 MANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELA   94 (108)
T ss_dssp             SCCSSCCSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSS
T ss_pred             cccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEEC
Confidence            344455667788999999999999999999999999999999999999999999999999999999999997 5788999


Q ss_pred             Ceeecccccccc
Q psy1314          84 NKKIDPKRVTKR   95 (275)
Q Consensus        84 g~~i~v~~~~~~   95 (275)
                      ++.|.|+++.++
T Consensus        95 g~~l~V~~a~~k  106 (108)
T 2jrs_A           95 GRPMKVGHVTER  106 (108)
T ss_dssp             SSCCEEECSCSS
T ss_pred             CEEEEEEEcccC
Confidence            999999998765

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.79  E-value=4.8e-19  Score=135.38  Aligned_cols=85  Identities=21%  Similarity=0.372  Sum_probs=78.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++
T Consensus        40 ~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  119 (139)
T 1u6f_A           40 DVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALA  119 (139)
T ss_dssp             TTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34589999999999999999999999999999999999999999999999999999999999987 58899999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      ..+..+
T Consensus       120 ~~~~~~  125 (139)
T 1u6f_A          120 ASGHQR  125 (139)
T ss_dssp             SCCCCC
T ss_pred             CCCCCC
Confidence            887654

>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=99.79  E-value=2.3e-20  Score=142.22  Aligned_cols=121  Identities=9%  Similarity=0.091  Sum_probs=73.1

Q ss_pred             cEEEEEEccHHHHHHHHHhCCceecCeeeccc---ccccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccC
Q psy1314          59 GFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK---RVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD  135 (275)
Q Consensus        59 G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~---~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~  135 (275)
                      ++||.+|..++.+..++........+...--.   ..........++|||+|||+++|+++|+++|++|| |+.|.|+.+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~~~g~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d   80 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIG   80 (139)
T ss_dssp             -------------------------------------------CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCS
T ss_pred             CcccccccCccccchhcccchhccCCCCCCCCCCCcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEEC
Confidence            57888888877766666543333333322111   11112234567899999999999999999999999 679999999


Q ss_pred             CCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeCCC
Q psy1314         136 KSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE  181 (275)
Q Consensus       136 ~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~~~  181 (275)
                      +. ++++|||||+|.+.++|++||+..+..|.++.|+|..+..++.
T Consensus        81 ~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~~  125 (139)
T 2hgn_A           81 PD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGA  125 (139)
T ss_dssp             SS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSCC
T ss_pred             CC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCCC
Confidence            76 8999999999999999999995556899999999988876543

>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=3.1e-19  Score=129.05  Aligned_cols=90  Identities=23%  Similarity=0.371  Sum_probs=81.8

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      .......+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..+.++.
T Consensus         4 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2cqb_A            4 GSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRT   83 (102)
T ss_dssp             CSSCSCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEE
T ss_pred             CcCCcCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            344556788999999999999999999999999999999999999999999999999999999999997 5788999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.++..
T Consensus        84 l~V~~a~~~~~   94 (102)
T 2cqb_A           84 IRVNLAKPMRI   94 (102)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEeCCCCCC
Confidence            99999876644

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=1.6e-19  Score=130.63  Aligned_cols=87  Identities=17%  Similarity=0.238  Sum_probs=77.9

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      .....+.+.++|||+|||+++|+++|+++|++||.+ +|.|+.++ +++++|||||+|.++++|++||+++.+.|.++.|
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i   84 (102)
T 1wez_A            7 GSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYV   84 (102)
T ss_dssp             CSSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEE
Confidence            334566788999999999999999999999999955 99999997 8999999999999999999999888889999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|..+.+..
T Consensus        85 ~V~~~~~~~   93 (102)
T 1wez_A           85 ELFLNSTAG   93 (102)
T ss_dssp             EEEEECCCC
T ss_pred             EEEECCCCC
Confidence            998876543

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.2e-19  Score=129.52  Aligned_cols=88  Identities=24%  Similarity=0.384  Sum_probs=79.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES-ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~-~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      ...+...+.++|||+|||+++|+++|+++|++||.|.+ |.|+.+ .+++++|||||+|.++++|++||+.+++.+.++.
T Consensus         7 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~   85 (104)
T 1wg5_A            7 GNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRY   85 (104)
T ss_dssp             CCCSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcE
Confidence            34455677899999999999999999999999999987 888888 7899999999999999999999999888999999


Q ss_pred             eccccccccc
Q psy1314          87 IDPKRVTKRV   96 (275)
Q Consensus        87 i~v~~~~~~~   96 (275)
                      |.|..+..++
T Consensus        86 i~v~~~~~~~   95 (104)
T 1wg5_A           86 IEIFKSSRAE   95 (104)
T ss_dssp             CEEEEECTTT
T ss_pred             EEEEECCHHH
Confidence            9998876543

>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=99.79  E-value=4.2e-19  Score=131.28  Aligned_cols=88  Identities=23%  Similarity=0.376  Sum_probs=80.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  101 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQL  101 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999999989999999999999999999999887 5899999999999


Q ss_pred             eeeCCCCCC
Q psy1314         176 VKFNPETMG  184 (275)
Q Consensus       176 ~~~~~~~~~  184 (275)
                      ++++.....
T Consensus       102 a~~~~~~~~  110 (115)
T 2cpz_A          102 KRSKNDSKS  110 (115)
T ss_dssp             CCCSCCCCC
T ss_pred             cCCCCcCCC
Confidence            988766543

>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=1.2e-18  Score=126.27  Aligned_cols=86  Identities=26%  Similarity=0.414  Sum_probs=79.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+. .+.|+|++|.|.++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEECC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc-CCeeCCeEEEEEec
Confidence            44568899999999999999999999999999999999999999999999999999999999995 57899999999999


Q ss_pred             eeCCCCC
Q psy1314         177 KFNPETM  183 (275)
Q Consensus       177 ~~~~~~~  183 (275)
                      .+++...
T Consensus        91 ~~~~~~~   97 (103)
T 2cqg_A           91 NSKQSQD   97 (103)
T ss_dssp             CTTCCCC
T ss_pred             CCCCcCC
Confidence            9876654

>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=99.79  E-value=6.3e-19  Score=122.43  Aligned_cols=81  Identities=25%  Similarity=0.411  Sum_probs=75.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~~   94 (275)
                      ..+|||+|||.++++++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|++ +++..+.+++|.|+++.+
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            3689999999999999999999999999999999999999999999999999999999998 478899999999999876


Q ss_pred             cc
Q psy1314          95 RV   96 (275)
Q Consensus        95 ~~   96 (275)
                      ++
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=4.6e-19  Score=126.65  Aligned_cols=84  Identities=25%  Similarity=0.417  Sum_probs=78.3

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEE-EeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEF-QQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v-~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ..++|||+|||.++++++|+++|++||.|..| .|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++
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            46899999999999999999999999999999 99999889999999999999999999999987 58899999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      .+++..
T Consensus        84 ~~~~~~   89 (96)
T 1x5t_A           84 FKKDSK   89 (96)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            877653

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=6.4e-19  Score=126.66  Aligned_cols=86  Identities=21%  Similarity=0.288  Sum_probs=78.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee-EEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCee--
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE-SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKK--   86 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~-~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~--   86 (275)
                      ....+.++|||+|||+++|+++|+++|++||+|. +|.|+.++.+++++|||||+|.+.++|++|++. ++..+.++.  
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~   83 (99)
T 2div_A            4 GSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPA   83 (99)
T ss_dssp             CCCSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSC
T ss_pred             CCCCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcc
Confidence            4466789999999999999999999999999999 999999999999999999999999999999995 677999998  


Q ss_pred             --eccccccccc
Q psy1314          87 --IDPKRVTKRV   96 (275)
Q Consensus        87 --i~v~~~~~~~   96 (275)
                        |.|.++....
T Consensus        84 ~~l~v~~a~~~~   95 (99)
T 2div_A           84 KRFKLNYATYSG   95 (99)
T ss_dssp             EECCEEETTCCS
T ss_pred             eeEEEeecCCCC
Confidence              8888876543

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=3.9e-19  Score=127.07  Aligned_cols=85  Identities=29%  Similarity=0.541  Sum_probs=78.8

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESI-SIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~-~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      +.+.++|||+|||.++|+++|+++|++||+|.+| .|+.++.+++++|||||+|.+.++|++||+ +++..+.+++|.|+
T Consensus         2 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             CSCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4578999999999999999999999999999999 999998999999999999999999999999 56789999999999


Q ss_pred             ccccccC
Q psy1314          91 RVTKRVN   97 (275)
Q Consensus        91 ~~~~~~~   97 (275)
                      ++.++..
T Consensus        82 ~a~~~~~   88 (96)
T 1x5t_A           82 YAFKKDS   88 (96)
T ss_dssp             ESCCCCC
T ss_pred             EecccCC
Confidence            9876654

>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=5.1e-19  Score=128.59  Aligned_cols=87  Identities=21%  Similarity=0.389  Sum_probs=80.1

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      .....++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.
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            3456789999999999999999999999999999999999989999999999999999999999987 588999999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (105)
T 1x5u_A           91 KASAHNKN   98 (105)
T ss_dssp             ETTTTSCC
T ss_pred             ECCCCCcC
Confidence            99877654

>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=99.79  E-value=4.6e-19  Score=123.71  Aligned_cols=81  Identities=26%  Similarity=0.445  Sum_probs=75.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      ...+.++|||+|||+++++++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++|++ +++..+.+++|.|+
T Consensus         3 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   82 (85)
T 3mdf_A            3 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   82 (85)
T ss_dssp             CCCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            45678999999999999999999999999999999999998999999999999999999999996 57889999999998


Q ss_pred             cc
Q psy1314          91 RV   92 (275)
Q Consensus        91 ~~   92 (275)
                      ++
T Consensus        83 ~a   84 (85)
T 3mdf_A           83 LA   84 (85)
T ss_dssp             EC
T ss_pred             Ec
Confidence            76

>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=99.79  E-value=4.6e-19  Score=129.08  Aligned_cols=90  Identities=24%  Similarity=0.464  Sum_probs=80.3

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCcee---c
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYI---G   83 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~---~   83 (275)
                      .......+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..+   .
T Consensus         5 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   84 (106)
T 2dgp_A            5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGM   84 (106)
T ss_dssp             CCSCCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTC
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCC
Confidence            345566788999999999999999999999999999999999999999999999999999999999998 456666   8


Q ss_pred             CeeecccccccccC
Q psy1314          84 NKKIDPKRVTKRVN   97 (275)
Q Consensus        84 g~~i~v~~~~~~~~   97 (275)
                      +++|.|+++..+..
T Consensus        85 g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           85 NRPIQVKPADSESR   98 (106)
T ss_dssp             SSCCEEEECCCCSC
T ss_pred             CceEEEEECCcccc
Confidence            89999999876543

>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=99.79  E-value=5.4e-19  Score=123.91  Aligned_cols=82  Identities=24%  Similarity=0.437  Sum_probs=74.9

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||.++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.+ +..+.|++|.|.+++
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            4678999999999999999999999999999999999889999999999999999999999986 589999999999998


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ++|
T Consensus        85 ~kp   87 (87)
T 3bs9_A           85 RKP   87 (87)
T ss_dssp             ---
T ss_pred             CCC
Confidence            764

>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=5.3e-19  Score=128.34  Aligned_cols=87  Identities=17%  Similarity=0.415  Sum_probs=79.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC-CCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT-GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~t-g~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||+++|+++|+++|++|| |++|.|+.++.+ ++++|||||+|.+.++|++||.+++..+.++.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~   87 (104)
T 1wi8_A            9 RLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIR   87 (104)
T ss_dssp             CCCSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEE
Confidence            34456778999999999999999999999999 999999999888 9999999999999999999996678899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.++..
T Consensus        88 V~~a~~~~~   96 (104)
T 1wi8_A           88 VDVADQAQD   96 (104)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCCCC
Confidence            999877654

>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=1.1e-18  Score=126.58  Aligned_cols=85  Identities=19%  Similarity=0.397  Sum_probs=77.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCC-CCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK-NMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~-~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ....++|||+|||+++++++|+++|++|| |..|.|+.++.+ +.++|||||+|.+.++|++|| .+ +..|.+++|.|.
T Consensus        12 ~~~~~~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           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVD   89 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEE
Confidence            34568999999999999999999999999 999999999887 899999999999999999999 65 689999999999


Q ss_pred             EeeeCCCCC
Q psy1314         175 RVKFNPETM  183 (275)
Q Consensus       175 ~~~~~~~~~  183 (275)
                      ++.++....
T Consensus        90 ~a~~~~~~~   98 (104)
T 1wi8_A           90 VADQAQDKD   98 (104)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCCCCCC
Confidence            998876643

>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=1.3e-18  Score=125.31  Aligned_cols=86  Identities=16%  Similarity=0.316  Sum_probs=78.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++||+. ++..+.++.|.
T Consensus        11 ~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   89 (100)
T 2do4_A           11 YSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIK   89 (100)
T ss_dssp             CSSCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3455678899999999999999999999999999999999997 899999999999999999999965 77899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |+++.++.
T Consensus        90 v~~a~~~~   97 (100)
T 2do4_A           90 VAISNSGP   97 (100)
T ss_dssp             EEECCCCS
T ss_pred             EEECCCCC
Confidence            99987654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.79  E-value=2.5e-18  Score=127.04  Aligned_cols=87  Identities=24%  Similarity=0.442  Sum_probs=80.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   91 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445789999999999999999999999999999999999889999999999999999999999987 5899999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +..++...
T Consensus        92 a~~~~~~~   99 (115)
T 2dgo_A           92 ATRKPPAP   99 (115)
T ss_dssp             SSCCCCCS
T ss_pred             ccCCCCCC
Confidence            99887654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.79  E-value=6.7e-19  Score=128.93  Aligned_cols=86  Identities=29%  Similarity=0.533  Sum_probs=78.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.++..|+|+.|.|.++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a  101 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA  101 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      .+++.+
T Consensus       102 ~~~~~~  107 (109)
T 2rs2_A          102 FPRRAQ  107 (109)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            877653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=9.1e-19  Score=123.90  Aligned_cols=86  Identities=21%  Similarity=0.399  Sum_probs=78.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      +.....+.++|||+|||+++|+++|+++|++| .|.+|.|+.+ .+++++|||||+|.+.++|++||++++..+.++.|.
T Consensus         3 ~~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~   80 (91)
T 2dgw_A            3 SGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIE   80 (91)
T ss_dssp             CCCCCCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEE
T ss_pred             CCCCCCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEE
Confidence            34566788999999999999999999999999 9999999999 789999999999999999999999778899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |.++.++.
T Consensus        81 v~~a~~~~   88 (91)
T 2dgw_A           81 VFREKSGP   88 (91)
T ss_dssp             EEEESSCC
T ss_pred             EEECCcCC
Confidence            99987653

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

Probab=99.79  E-value=6.2e-19  Score=128.36  Aligned_cols=86  Identities=26%  Similarity=0.445  Sum_probs=78.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||.++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+ +++..+.++.|.|
T Consensus        18 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   97 (106)
T 1p27_B           18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV   97 (106)
T ss_dssp             CCBTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEE
Confidence            344567889999999999999999999999999999999999999999999999999999999998 5788999999999


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      +++.++.
T Consensus        98 ~~a~~~~  104 (106)
T 1p27_B           98 DWCFVRG  104 (106)
T ss_dssp             EESEESS
T ss_pred             EeecCCC
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=4.5e-19  Score=128.19  Aligned_cols=87  Identities=25%  Similarity=0.461  Sum_probs=80.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.+
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            345689999999999999999999999999999999999999999999999999999999999886 5899999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +.++....
T Consensus        89 a~~~~~~~   96 (102)
T 2cqb_A           89 AKPMRIKE   96 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98876544

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=4.3e-19  Score=131.43  Aligned_cols=84  Identities=29%  Similarity=0.527  Sum_probs=78.8

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF  178 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~  178 (275)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+..+..|.|++|.|.++.+
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCC
Confidence            35899999999999999999999999999999999999999999999999999999999999966899999999999988


Q ss_pred             CCCC
Q psy1314         179 NPET  182 (275)
Q Consensus       179 ~~~~  182 (275)
                      +...
T Consensus       106 ~~~~  109 (116)
T 1x4b_A          106 REES  109 (116)
T ss_dssp             CCCC
T ss_pred             CccC
Confidence            7654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=3.1e-19  Score=132.16  Aligned_cols=84  Identities=38%  Similarity=0.710  Sum_probs=78.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      .+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+.++..|.++.|.|+++.
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~  104 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAV  104 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECC
Confidence            44589999999999999999999999999999999999999999999999999999999999998889999999999987


Q ss_pred             cccC
Q psy1314          94 KRVN   97 (275)
Q Consensus        94 ~~~~   97 (275)
                      ++..
T Consensus       105 ~~~~  108 (116)
T 1x4b_A          105 AREE  108 (116)
T ss_dssp             SCCC
T ss_pred             CCcc
Confidence            7654

>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=9.9e-19  Score=127.47  Aligned_cols=90  Identities=22%  Similarity=0.451  Sum_probs=81.4

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeC-CCCCCcccEEEEEEccHHHHHHHHHh--CCceecC
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKND-PHTGQSRGFAFVTFTTQKAVDDLLAA--GDHYIGN   84 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~-~~tg~~~G~afV~f~~~e~a~~al~~--~~~~~~g   84 (275)
                      .......+.++|||+|||.++|+++|+++|++||+|++|.|+.+ +.+++++|||||+|.+.++|++||+.  ++..+.+
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g   86 (107)
T 2cph_A            7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   86 (107)
T ss_dssp             CSSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             cccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC
Confidence            34456677899999999999999999999999999999999998 78999999999999999999999986  5789999


Q ss_pred             eeecccccccccC
Q psy1314          85 KKIDPKRVTKRVN   97 (275)
Q Consensus        85 ~~i~v~~~~~~~~   97 (275)
                      +.|.|+++.++..
T Consensus        87 ~~l~v~~a~~~~~   99 (107)
T 2cph_A           87 RRLVLEWADSEVT   99 (107)
T ss_dssp             CBCEEEECCCCCC
T ss_pred             CEEEEEeCCCCCC
Confidence            9999999876544

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=5.1e-19  Score=128.63  Aligned_cols=87  Identities=32%  Similarity=0.518  Sum_probs=80.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+..+..|+|++|.|.++
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEc
Confidence            45568999999999999999999999999999999999999999999999999999999999999558999999999999


Q ss_pred             eeCCCCC
Q psy1314         177 KFNPETM  183 (275)
Q Consensus       177 ~~~~~~~  183 (275)
                      .++....
T Consensus        93 ~~~~~~~   99 (105)
T 2dh8_A           93 TPRGMQP   99 (105)
T ss_dssp             CCSSCCT
T ss_pred             cCCCCCC
Confidence            8876543

>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=99.78  E-value=2.4e-19  Score=132.40  Aligned_cols=85  Identities=11%  Similarity=0.090  Sum_probs=78.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCe-eEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v-~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      ..+.+.++|||+|||+++|+++|+++|++||.| .+|.|+.++ +++++|||||+|.+.++|++||++++..|.++.|.|
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            345678899999999999999999999999999 899999997 999999999999999999999999888999999999


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      .++..+.
T Consensus        89 ~~a~~~~   95 (114)
T 2cpy_A           89 HVVTLED   95 (114)
T ss_dssp             EEECHHH
T ss_pred             EECCHHH
Confidence            9886543

>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=7.6e-19  Score=132.49  Aligned_cols=88  Identities=26%  Similarity=0.382  Sum_probs=80.7

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      ....+++.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..|.+++|
T Consensus        39 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           39 NRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             CSSCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34556778999999999999999999999999999999999999999999999999999999999999 57789999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++.++.
T Consensus       119 ~V~~a~~~~  127 (129)
T 2kxn_B          119 RVDFSITKR  127 (129)
T ss_dssp             EESCCSSSS
T ss_pred             EEEEecCCC
Confidence            999987653

>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=3.8e-19  Score=128.57  Aligned_cols=87  Identities=25%  Similarity=0.497  Sum_probs=79.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.+
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            345689999999999999999999999999999999999999999999999999999999999887 5889999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +..+....
T Consensus        89 a~~~~~~~   96 (102)
T 1x5s_A           89 AGKSSDNR   96 (102)
T ss_dssp             EECCCCCC
T ss_pred             CCCCCCCC
Confidence            99876543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=6.8e-19  Score=126.29  Aligned_cols=85  Identities=21%  Similarity=0.389  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCC---CCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPH---TGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~---tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      ..+.++|||+|||+++|+++|+++|++||+|++|.|+.++.   |++++|||||+|.+.++|++||+. ++..+.++.|.
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            46789999999999999999999999999999999999876   668999999999999999999995 67899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++..+..
T Consensus        82 V~~a~~~~~   90 (98)
T 2cpf_A           82 VRISERATK   90 (98)
T ss_dssp             EECSSCSSC
T ss_pred             EEEccCCCC
Confidence            999876544

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

Probab=99.78  E-value=1.3e-18  Score=126.14  Aligned_cols=86  Identities=23%  Similarity=0.412  Sum_probs=78.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhh-cCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCce-ecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQ-YGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHY-IGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~-~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~-~~g~~i   87 (275)
                      .++.+.++|||+|||+++|+++|+++|++ ||+|.+|.|+.++ +++++|||||+|.+.++|++||+. ++.. +.++.|
T Consensus         4 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l   82 (104)
T 2dhg_A            4 GSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV   82 (104)
T ss_dssp             CCSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeE
Confidence            45677899999999999999999999999 9999999999998 999999999999999999999995 5667 999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++.++..
T Consensus        83 ~v~~a~~~~~   92 (104)
T 2dhg_A           83 RLSVAIPKAS   92 (104)
T ss_dssp             CCCBCCCCCS
T ss_pred             EEEEccCCCc
Confidence            9999876543

>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=99.78  E-value=4.5e-19  Score=133.23  Aligned_cols=87  Identities=21%  Similarity=0.410  Sum_probs=80.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|+.|.|.+
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   98 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW   98 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            445689999999999999999999999999999999999989999999999999999999999876 5889999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +..+....
T Consensus        99 a~~~~~~~  106 (126)
T 3ex7_B           99 CFVRGPPK  106 (126)
T ss_dssp             SEESSSCC
T ss_pred             ecCCCCCC
Confidence            99887654

>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=99.78  E-value=2.9e-19  Score=131.89  Aligned_cols=82  Identities=22%  Similarity=0.366  Sum_probs=76.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      .+.++|||+|||.++|+++|+++|++||.|++|.|+.++.+++++|||||+|.+.++|++||.++++.|.++.|.|+++.
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            45679999999999999999999999999999999999999999999999999999999999778899999999999886


Q ss_pred             cc
Q psy1314          94 KR   95 (275)
Q Consensus        94 ~~   95 (275)
                      .+
T Consensus       103 ~~  104 (114)
T 2cq4_A          103 AE  104 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=3.3e-19  Score=130.25  Aligned_cols=83  Identities=18%  Similarity=0.311  Sum_probs=75.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      .+...+..+|||+|||+++|+++|+++|++| .|.+|.|+.++. ++++|||||+|.++++|++||+++++.|.++.|.|
T Consensus        10 ~~~~~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   87 (109)
T 2dnn_A           10 LPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEV   87 (109)
T ss_dssp             CCCCHHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            3445556799999999999999999999999 899999999965 99999999999999999999988899999999999


Q ss_pred             ccccc
Q psy1314          90 KRVTK   94 (275)
Q Consensus        90 ~~~~~   94 (275)
                      ..+..
T Consensus        88 ~~a~~   92 (109)
T 2dnn_A           88 SPATE   92 (109)
T ss_dssp             EECCH
T ss_pred             EECCc
Confidence            87754

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

Probab=99.78  E-value=2.4e-18  Score=124.59  Aligned_cols=85  Identities=19%  Similarity=0.366  Sum_probs=77.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||+++++++|+++|++|+ |..|.|+.++.+++++|||||+|.+.++|++||+..+..|.|++|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEe
Confidence            34568999999999999999999999996 99999999999999999999999999999999943469999999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      .++...
T Consensus        91 ~~~~~~   96 (103)
T 2dng_A           91 EGRKQD   96 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            877654

>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=99.78  E-value=5.6e-19  Score=124.37  Aligned_cols=81  Identities=23%  Similarity=0.492  Sum_probs=76.0

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~   94 (275)
                      +.++|||+|||.++|+++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|+.+++..+.++.|.|+++.+
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            46899999999999999999999999999999999999899999999999999999999997788899999999998865


Q ss_pred             c
Q psy1314          95 R   95 (275)
Q Consensus        95 ~   95 (275)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.78  E-value=1.7e-19  Score=149.22  Aligned_cols=81  Identities=16%  Similarity=0.313  Sum_probs=75.4

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCC--CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G--~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ..++|||+|||+++|+++|+++|++||  .|+.|+|++++.+++++|||||+|.+.++|++||+.|+ +.|.+++|.|.+
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            457899999999999999999999999  99999999999999999999999999999999999885 899999999999


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +...
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8754

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=4.2e-19  Score=128.59  Aligned_cols=86  Identities=22%  Similarity=0.379  Sum_probs=79.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            445689999999999999999999999999999999999999999999999999999999999976 5889999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      +..+...
T Consensus        90 a~~~~~~   96 (103)
T 2dnm_A           90 ARYGRRD   96 (103)
T ss_dssp             CSSCCSC
T ss_pred             CCcCCCC
Confidence            9876544

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=9.1e-19  Score=125.63  Aligned_cols=85  Identities=18%  Similarity=0.336  Sum_probs=77.6

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCC---CCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS---KNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~---~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ..++|||+|||+++++++|+++|++||.|..|.|+.++.   ++.++|||||+|.+.++|++||+.+ +..|.+++|.|.
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            467899999999999999999999999999999998876   6689999999999999999999987 589999999999


Q ss_pred             EeeeCCCCC
Q psy1314         175 RVKFNPETM  183 (275)
Q Consensus       175 ~~~~~~~~~  183 (275)
                      ++..+....
T Consensus        84 ~a~~~~~~~   92 (98)
T 2cpf_A           84 ISERATKPA   92 (98)
T ss_dssp             CSSCSSCCC
T ss_pred             EccCCCCCC
Confidence            998776543

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

Probab=99.78  E-value=2e-19  Score=128.11  Aligned_cols=80  Identities=21%  Similarity=0.282  Sum_probs=73.1

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCC--eEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c----eeCCeEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGS--ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q----VICGKEV  171 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~--v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~----~~~g~~i  171 (275)
                      .-.+|||+|||+++|+++|+++|++||.  |.+|+|++|+.+++++|||||+|.+.++|++||+.++ .    .|+|++|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            4578999999999999999999999995  6789999999999999999999999999999999863 2    5999999


Q ss_pred             EEEEeee
Q psy1314         172 DVKRVKF  178 (275)
Q Consensus       172 ~v~~~~~  178 (275)
                      .|.+++.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999874

>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=1.2e-18  Score=124.29  Aligned_cols=84  Identities=23%  Similarity=0.395  Sum_probs=75.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      ......+.++|||+|||+++++++|+++|++||+|++|.|+.++. ++++|||||+|.+.++|++||+ +++..+.+++|
T Consensus         9 ~~~~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (95)
T 2ywk_A            9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPI   87 (95)
T ss_dssp             ---CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEE
Confidence            345567789999999999999999999999999999999999975 8999999999999999999999 57889999999


Q ss_pred             cccccc
Q psy1314          88 DPKRVT   93 (275)
Q Consensus        88 ~v~~~~   93 (275)
                      .|+++.
T Consensus        88 ~V~~a~   93 (95)
T 2ywk_A           88 NVSGPS   93 (95)
T ss_dssp             EEECCC
T ss_pred             EEEEcC
Confidence            998875

>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=99.78  E-value=1.4e-18  Score=128.68  Aligned_cols=84  Identities=26%  Similarity=0.457  Sum_probs=77.5

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++
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            456799999999999999999999999999999999998 8899999999999999999999987 58899999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      +.+...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876654

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

Probab=99.78  E-value=1.3e-18  Score=125.44  Aligned_cols=82  Identities=13%  Similarity=0.177  Sum_probs=72.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-C--CceecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-G--DHYIGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~--~~~~~g~~i   87 (275)
                      ..+.+.++|||+|||+++|+++|+++|++||+|++|.|+++      ||||||+|.+.++|++|++. +  +..+.|++|
T Consensus        11 ~~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l   84 (105)
T 1sjq_A           11 GSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPI   84 (105)
T ss_dssp             -CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            34677899999999999999999999999999999999975      68999999999999999984 3  368999999


Q ss_pred             cccccccccCC
Q psy1314          88 DPKRVTKRVNP   98 (275)
Q Consensus        88 ~v~~~~~~~~~   98 (275)
                      .|.++..+...
T Consensus        85 ~V~~A~~~~~~   95 (105)
T 1sjq_A           85 YIQFSNHKELK   95 (105)
T ss_dssp             CBCCCSSSSCC
T ss_pred             EEEEcCCCCCC
Confidence            99999766443

>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=1.4e-18  Score=125.86  Aligned_cols=89  Identities=18%  Similarity=0.369  Sum_probs=80.1

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      .......+.++|||+|||+++|+++|+++|++||+|.+|.|+.+  +++++|||||+|.+.++|++||+ +++..+.++.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   84 (103)
T 2d9p_A            7 GDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKP   84 (103)
T ss_dssp             CCCCCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSB
T ss_pred             CCccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcE
Confidence            34455678899999999999999999999999999999999998  88999999999999999999998 5788999999


Q ss_pred             ecccccccccCC
Q psy1314          87 IDPKRVTKRVNP   98 (275)
Q Consensus        87 i~v~~~~~~~~~   98 (275)
                      |.|+++.++...
T Consensus        85 l~V~~a~~~~~~   96 (103)
T 2d9p_A           85 LYVALAQRKEER   96 (103)
T ss_dssp             CEEEECSSCCCC
T ss_pred             EEEEEecccccC
Confidence            999998776543

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

Probab=99.78  E-value=2.7e-19  Score=121.94  Aligned_cols=75  Identities=37%  Similarity=0.658  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      +|||+|||+++|+++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|+++++..+.+++|.|+++
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            599999999999999999999999999999999988999999999999999999999998888999999988764

>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=9.8e-19  Score=127.50  Aligned_cols=88  Identities=16%  Similarity=0.366  Sum_probs=80.5

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccC-CCCCCeeeEEEEEECCHHHHHHHHhcC--CceeCCeEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFD-KSKNMKKGFCFISFDDQNVAEQVLANP--KQVICGKEVD  172 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~-~~~~~~~G~afV~f~~~e~a~~Ai~~~--~~~~~g~~i~  172 (275)
                      .....++|||+|||..+++++|+++|++||.|..|.|+.+ +.++.++|||||+|.+.++|++||+.+  +..|.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3456789999999999999999999999999999999998 788999999999999999999999987  4889999999


Q ss_pred             EEEeeeCCCCC
Q psy1314         173 VKRVKFNPETM  183 (275)
Q Consensus       173 v~~~~~~~~~~  183 (275)
                      |.++.+++...
T Consensus        91 v~~a~~~~~~~  101 (107)
T 2cph_A           91 LEWADSEVTVQ  101 (107)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEeCCCCCCCC
Confidence            99999876643

>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=99.78  E-value=1.3e-18  Score=127.66  Aligned_cols=87  Identities=18%  Similarity=0.302  Sum_probs=79.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-------CceeCCe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-------KQVICGK  169 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-------~~~~~g~  169 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+       +..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~   91 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   91 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCE
Confidence            445689999999999999999999999999999999999999999999999999999999999976       5789999


Q ss_pred             EEEEEEeeeCCCCC
Q psy1314         170 EVDVKRVKFNPETM  183 (275)
Q Consensus       170 ~i~v~~~~~~~~~~  183 (275)
                      +|.|.++.++....
T Consensus        92 ~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           92 QLKVDLAVTRDEAA  105 (111)
T ss_dssp             EEEEECCCCCCCCC
T ss_pred             EEEEEECCCCccCC
Confidence            99999998876544

>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=2.8e-18  Score=124.26  Aligned_cols=88  Identities=24%  Similarity=0.330  Sum_probs=78.1

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      ....+..+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+  ++|||||+|.+.++|++||+ +++..+.++.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   84 (103)
T 2cqi_A            7 GMMEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKE   84 (103)
T ss_dssp             CCCCCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCe
Confidence            34456678899999999999999999999999999999999998543  68999999999999999998 6788999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++..+..
T Consensus        85 l~V~~a~~~~~   95 (103)
T 2cqi_A           85 VKVNWATTPSS   95 (103)
T ss_dssp             EEEEECCCTTC
T ss_pred             EEEEECCCCcc
Confidence            99999876543

>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=99.78  E-value=1.5e-18  Score=120.59  Aligned_cols=80  Identities=20%  Similarity=0.399  Sum_probs=75.8

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      ++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.+ +..+.|++|.|.++.++
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            58999999999999999999999999999999999999999999999999999999999986 58999999999999876


Q ss_pred             C
Q psy1314         180 P  180 (275)
Q Consensus       180 ~  180 (275)
                      +
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.77  E-value=1.4e-18  Score=127.39  Aligned_cols=87  Identities=26%  Similarity=0.385  Sum_probs=79.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus        20 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   99 (110)
T 1oo0_B           20 PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQ   99 (110)
T ss_dssp             BCCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            3445667889999999999999999999999999999999999999999999999999999999998 578899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |+++.++.
T Consensus       100 V~~a~~~~  107 (110)
T 1oo0_B          100 VDWCFVKG  107 (110)
T ss_dssp             EEESEESS
T ss_pred             EEEcccCC
Confidence            99987654

>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=99.77  E-value=4.7e-19  Score=132.46  Aligned_cols=84  Identities=25%  Similarity=0.426  Sum_probs=76.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--EEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE--SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~--~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      .....+.++|||+|||+++|+++|+++|++| .|+  +|.|+.++. ++++|||||+|.++++|++||++++..|.++.|
T Consensus        36 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I  113 (126)
T 2hgm_A           36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYI  113 (126)
T ss_dssp             TTCSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEE
Confidence            3455678899999999999999999999999 677  899999976 999999999999999999999998899999999


Q ss_pred             cccccccc
Q psy1314          88 DPKRVTKR   95 (275)
Q Consensus        88 ~v~~~~~~   95 (275)
                      .|..+..+
T Consensus       114 ~V~~a~~~  121 (126)
T 2hgm_A          114 EVFKSSQE  121 (126)
T ss_dssp             CCEEECHH
T ss_pred             EEEECCHH
Confidence            99887654

>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=99.77  E-value=2.8e-19  Score=126.30  Aligned_cols=81  Identities=19%  Similarity=0.313  Sum_probs=70.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G--~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~   93 (275)
                      .+|||+|||+++|+++|+++|++||  .|.+|.|+.++.+++++|||||+|.+.++|++||+ +++..+.|+.|.|+++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  99999999999999999999999999999999997 56779999999999987


Q ss_pred             cccC
Q psy1314          94 KRVN   97 (275)
Q Consensus        94 ~~~~   97 (275)
                      +...
T Consensus        82 ~~~~   85 (90)
T 3p5t_L           82 KLEH   85 (90)
T ss_dssp             ----
T ss_pred             CCcc
Confidence            6543

>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=99.77  E-value=2.1e-18  Score=125.29  Aligned_cols=87  Identities=23%  Similarity=0.424  Sum_probs=77.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC---ee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN---KK   86 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g---~~   86 (275)
                      ....+.++|||+|||.++|+++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++||+. ++..+.+   +.
T Consensus        10 ~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~   88 (105)
T 2dnh_A           10 SRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSS   88 (105)
T ss_dssp             CSCCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCcc
Confidence            444668999999999999999999999999999999999997 799999999999999999999984 6777887   99


Q ss_pred             ecccccccccCC
Q psy1314          87 IDPKRVTKRVNP   98 (275)
Q Consensus        87 i~v~~~~~~~~~   98 (275)
                      |.|+++..+...
T Consensus        89 l~V~~a~~~~~~  100 (105)
T 2dnh_A           89 LVVKFADTDKES  100 (105)
T ss_dssp             CEEEESCSSCCC
T ss_pred             EEEEECccCccc
Confidence            999998766543

>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=99.77  E-value=9.8e-19  Score=126.44  Aligned_cols=82  Identities=15%  Similarity=0.183  Sum_probs=73.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||+++|+++|+++|++||.+ .|.|+.++ +++++|||||+|.+.++|++||+..++.|.++.|+|..+
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            3456899999999999999999999999954 99999997 899999999999999999999976568999999999887


Q ss_pred             eeCC
Q psy1314         177 KFNP  180 (275)
Q Consensus       177 ~~~~  180 (275)
                      ....
T Consensus        90 ~~~~   93 (102)
T 1wez_A           90 STAG   93 (102)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7554

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

Probab=99.77  E-value=1.4e-18  Score=128.92  Aligned_cols=82  Identities=21%  Similarity=0.336  Sum_probs=75.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      .+..+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.++.|.|
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            3456678999999999999999999999999999999999999999999999999999999999985 678999999999


Q ss_pred             ccc
Q psy1314          90 KRV   92 (275)
Q Consensus        90 ~~~   92 (275)
                      +++
T Consensus       115 ~~a  117 (118)
T 2khc_A          115 QLK  117 (118)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            876

>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=7.3e-19  Score=127.97  Aligned_cols=87  Identities=21%  Similarity=0.396  Sum_probs=79.0

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee---CCeEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI---CGKEV  171 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~---~g~~i  171 (275)
                      .....++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.++ ..+   .+++|
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            34567899999999999999999999999999999999999999999999999999999999999874 566   88999


Q ss_pred             EEEEeeeCCCC
Q psy1314         172 DVKRVKFNPET  182 (275)
Q Consensus       172 ~v~~~~~~~~~  182 (275)
                      .|.++..+...
T Consensus        89 ~v~~a~~~~~~   99 (106)
T 2dgp_A           89 QVKPADSESRG   99 (106)
T ss_dssp             EEEECCCCSCC
T ss_pred             EEEECCccccc
Confidence            99999887654

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.5e-18  Score=125.66  Aligned_cols=86  Identities=21%  Similarity=0.368  Sum_probs=78.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.+  ++.+++||||+|.+.++|++||+.+ +..|.+++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL   89 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            345689999999999999999999999999999999988  7889999999999999999999986 5889999999999


Q ss_pred             eeeCCCCCC
Q psy1314         176 VKFNPETMG  184 (275)
Q Consensus       176 ~~~~~~~~~  184 (275)
                      +.++..+..
T Consensus        90 a~~~~~~~~   98 (103)
T 2d9p_A           90 AQRKEERQS   98 (103)
T ss_dssp             CSSCCCCCC
T ss_pred             ecccccCCC
Confidence            998776543

>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=99.77  E-value=1.6e-18  Score=123.87  Aligned_cols=82  Identities=22%  Similarity=0.413  Sum_probs=76.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~   93 (275)
                      ++++|||+|||.++++++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++|++ +++..+.++.|.|+++.
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            46899999999999999999999999999999999999999999999999999999999997 57889999999999987


Q ss_pred             ccc
Q psy1314          94 KRV   96 (275)
Q Consensus        94 ~~~   96 (275)
                      ++.
T Consensus        81 ~~~   83 (96)
T 2x1f_A           81 NSD   83 (96)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            654

>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=9.8e-19  Score=128.83  Aligned_cols=86  Identities=22%  Similarity=0.369  Sum_probs=79.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeE--------EEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT--------EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~--------~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      ....++|||+|||.++++++|+++|++||.|.        .|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   91 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   91 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccC
Confidence            45678999999999999999999999999999        6999999899999999999999999999999986 58999


Q ss_pred             CeEEEEEEeeeCCCC
Q psy1314         168 GKEVDVKRVKFNPET  182 (275)
Q Consensus       168 g~~i~v~~~~~~~~~  182 (275)
                      |++|.|.++..++..
T Consensus        92 g~~l~V~~a~~~~~~  106 (113)
T 2cpe_A           92 GSKLKVSLARKKPPM  106 (113)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CCEEEEEECCCCCCC
Confidence            999999999887654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.77  E-value=2e-18  Score=131.92  Aligned_cols=89  Identities=27%  Similarity=0.437  Sum_probs=81.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      ..+..+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.++.|.
T Consensus        36 ~~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  115 (139)
T 1u6f_A           36 NPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLK  115 (139)
T ss_dssp             SCCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            44566788999999999999999999999999999999999999999999999999999999999995 67899999999


Q ss_pred             ccccccccCC
Q psy1314          89 PKRVTKRVNP   98 (275)
Q Consensus        89 v~~~~~~~~~   98 (275)
                      |+++..+...
T Consensus       116 v~~a~~~~~~  125 (139)
T 1u6f_A          116 VALAASGHQR  125 (139)
T ss_dssp             EEESSCCCCC
T ss_pred             EEECCCCCCC
Confidence            9998766543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=124.11  Aligned_cols=85  Identities=24%  Similarity=0.383  Sum_probs=78.1

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hC
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AG   78 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~--------~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~   78 (275)
                      +....+...++|||+|||.++|+++|+++|++||.|.+        |.|+.++.+++++|||||+|.+.++|++|++ ++
T Consensus         5 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~   84 (99)
T 2la6_A            5 HHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD   84 (99)
T ss_dssp             CSCCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC
Confidence            34556778899999999999999999999999999999        9999999999999999999999999999997 57


Q ss_pred             CceecCeeeccccc
Q psy1314          79 DHYIGNKKIDPKRV   92 (275)
Q Consensus        79 ~~~~~g~~i~v~~~   92 (275)
                      +..+.++.|.|+++
T Consensus        85 g~~~~g~~l~V~~A   98 (99)
T 2la6_A           85 GKEFSGNPIKVSFA   98 (99)
T ss_dssp             TCBSSSSBCEEEEC
T ss_pred             CCEeCCcEEEEEec
Confidence            88999999998876

>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=99.77  E-value=1.5e-18  Score=136.59  Aligned_cols=86  Identities=17%  Similarity=0.353  Sum_probs=77.3

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  150 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  150 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            4578999999999999999999999999999999999999999999999999999999999987 588999999999999


Q ss_pred             eCCCCCC
Q psy1314         178 FNPETMG  184 (275)
Q Consensus       178 ~~~~~~~  184 (275)
                      .++....
T Consensus       151 ~~~~~~~  157 (165)
T 1rk8_A          151 VKGPKRV  157 (165)
T ss_dssp             ECC----
T ss_pred             CCCCCCC
Confidence            8876543

>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=1.9e-18  Score=127.28  Aligned_cols=88  Identities=22%  Similarity=0.341  Sum_probs=80.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE--------SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDH   80 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~--------~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~   80 (275)
                      ..+..+.++|||+|||.++|+++|+++|++||.|.        .|.|+.++.+++++|||||+|.+.++|++||+ +++.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~   88 (113)
T 2cpe_A            9 PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGK   88 (113)
T ss_dssp             CCCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             cccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCC
Confidence            34567889999999999999999999999999999        69999999999999999999999999999998 5788


Q ss_pred             eecCeeecccccccccC
Q psy1314          81 YIGNKKIDPKRVTKRVN   97 (275)
Q Consensus        81 ~~~g~~i~v~~~~~~~~   97 (275)
                      .|.++.|.|+++..+..
T Consensus        89 ~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           89 DFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             EETTEECEEECSSCCCC
T ss_pred             ccCCCEEEEEECCCCCC
Confidence            99999999999876644

>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=5.3e-18  Score=122.75  Aligned_cols=89  Identities=21%  Similarity=0.398  Sum_probs=78.6

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      ........+.++|||+|||.++|+++|+++|++||+|++|.|+.++.  .++|||||+|.+.++|++||+ +++..|.++
T Consensus         6 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   83 (103)
T 2cq3_A            6 SGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGR   83 (103)
T ss_dssp             CCCSCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCE
Confidence            33445567789999999999999999999999999999999999864  389999999999999999998 478899999


Q ss_pred             eecccccccccC
Q psy1314          86 KIDPKRVTKRVN   97 (275)
Q Consensus        86 ~i~v~~~~~~~~   97 (275)
                      .|.|+++.++..
T Consensus        84 ~l~v~~a~~~~~   95 (103)
T 2cq3_A           84 KIEVNNATARVM   95 (103)
T ss_dssp             ECEEEECCSSCC
T ss_pred             EEEEEEcccCCC
Confidence            999999876544

>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=3.9e-19  Score=121.11  Aligned_cols=75  Identities=40%  Similarity=0.721  Sum_probs=71.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      +|||+|||+++|+++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|++++++.+.++.|.|+++
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            699999999999999999999999999999999999999999999999999999999999888999999988753

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

Probab=99.77  E-value=2.4e-18  Score=123.90  Aligned_cols=84  Identities=15%  Similarity=0.348  Sum_probs=77.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456889999999999999999999999999999999988 8899999999999999999999886 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +.+++.
T Consensus        93 a~~~~~   98 (100)
T 2do4_A           93 SNSGPS   98 (100)
T ss_dssp             CCCCSC
T ss_pred             CCCCCC
Confidence            987764

>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=2.7e-18  Score=125.13  Aligned_cols=83  Identities=22%  Similarity=0.385  Sum_probs=76.3

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      ....++.++|||+|||+++|+++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus        23 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  101 (107)
T 3ulh_A           23 GAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN  101 (107)
T ss_dssp             -CCCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            4556778999999999999999999999999999999999997 99999999999999999999999 478899999999


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      |+++.
T Consensus       102 V~~a~  106 (107)
T 3ulh_A          102 IQLVT  106 (107)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            98764

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.77  E-value=6.8e-19  Score=130.76  Aligned_cols=84  Identities=17%  Similarity=0.298  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGE---VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~---v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      ....+.++|||+|||+++|+++|+++|++||.   |.+|+|+.++. ++++|||||+|.+.++|++||+++++.|.++.|
T Consensus        12 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i   90 (118)
T 2db1_A           12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYI   90 (118)
T ss_dssp             SCBCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEE
Confidence            44567889999999999999999999999999   89999999976 999999999999999999999988899999999


Q ss_pred             cccccccc
Q psy1314          88 DPKRVTKR   95 (275)
Q Consensus        88 ~v~~~~~~   95 (275)
                      .|.++..+
T Consensus        91 ~V~~a~~~   98 (118)
T 2db1_A           91 EVFKSHRT   98 (118)
T ss_dssp             EEEEECHH
T ss_pred             EEEECCHH
Confidence            99887543

>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=2e-18  Score=127.85  Aligned_cols=84  Identities=30%  Similarity=0.518  Sum_probs=77.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      +.++.++|||+|||.++|+++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++||+. ++..+.++.|.|+
T Consensus         3 e~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~   81 (116)
T 2fy1_A            3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVE   81 (116)
T ss_dssp             TTCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45778999999999999999999999999999999999997 899999999999999999999985 5779999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++..+.
T Consensus        82 ~a~~~~   87 (116)
T 2fy1_A           82 QAKKPS   87 (116)
T ss_dssp             ECCCSS
T ss_pred             ECCCCC
Confidence            987654

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

Probab=99.77  E-value=4.7e-19  Score=121.26  Aligned_cols=76  Identities=45%  Similarity=0.777  Sum_probs=72.3

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ++|||+|||+++|+++|+++|++||+|.+|.++.++.+++++|||||+|.+.++|++|++.++..+.|++|.|+++
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            4799999999999999999999999999999999999999999999999999999999998779999999988875

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

Probab=99.77  E-value=2e-18  Score=125.63  Aligned_cols=85  Identities=21%  Similarity=0.425  Sum_probs=79.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..|.|++|.|.+
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            345688999999999999999999999999999999999999999999999999999999999976 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +.+++.
T Consensus       100 a~~~~~  105 (106)
T 1p27_B          100 CFVRGP  105 (106)
T ss_dssp             SEESSC
T ss_pred             ecCCCC
Confidence            998764

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.77  E-value=3.3e-19  Score=128.51  Aligned_cols=83  Identities=17%  Similarity=0.284  Sum_probs=76.7

Q ss_pred             CCCCCeEEEcCCCC------CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecC-
Q psy1314          13 RNDERKLFVGGLHR------NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGN-   84 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~------~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g-   84 (275)
                      ...+++|||+|||.      ++++++|+++|++||+|.+|.|+.++.|++++|||||+|.+.++|++||+ +++..+.+ 
T Consensus         3 ~~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            3 LGSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             SCGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            34578999999999      99999999999999999999999999999999999999999999999997 57889998 


Q ss_pred             eeecccccccc
Q psy1314          85 KKIDPKRVTKR   95 (275)
Q Consensus        85 ~~i~v~~~~~~   95 (275)
                      +.|.|.++.++
T Consensus        83 r~l~V~~a~~~   93 (100)
T 3ns6_A           83 HRLFLYTMKDV   93 (100)
T ss_dssp             CBCEEEESHHH
T ss_pred             eEEEEEECchh
Confidence            99999988654

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2.8e-18  Score=122.02  Aligned_cols=81  Identities=23%  Similarity=0.419  Sum_probs=75.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..|.+++|.|.+
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            445689999999999999999999999999999999999999999999999999999999999887 5899999999998


Q ss_pred             ee
Q psy1314         176 VK  177 (275)
Q Consensus       176 ~~  177 (275)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            74

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

Probab=99.76  E-value=1.6e-18  Score=125.74  Aligned_cols=85  Identities=21%  Similarity=0.385  Sum_probs=78.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhccc-CCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ce-eCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQ-YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QV-ICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~-~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~-~~g~~i~v  173 (275)
                      ....++|||+|||+++++++|+++|++ ||.|..|.|+.++ ++.++|||||+|.+.++|++||+.++ .. |.|++|.|
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            445689999999999999999999999 9999999999998 89999999999999999999999875 77 99999999


Q ss_pred             EEeeeCCCC
Q psy1314         174 KRVKFNPET  182 (275)
Q Consensus       174 ~~~~~~~~~  182 (275)
                      .++.++...
T Consensus        85 ~~a~~~~~~   93 (104)
T 2dhg_A           85 SVAIPKASR   93 (104)
T ss_dssp             CBCCCCCSC
T ss_pred             EEccCCCcC
Confidence            999877654

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=7.3e-19  Score=122.76  Aligned_cols=81  Identities=19%  Similarity=0.361  Sum_probs=74.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      +.+.++|||+|||+++++++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++|++. ++..+.++.+.+++
T Consensus         2 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            2 SSGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            45788999999999999999999999999999999999999999999999999999999999984 57788999888876


Q ss_pred             cc
Q psy1314          92 VT   93 (275)
Q Consensus        92 ~~   93 (275)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}

Probab=99.76  E-value=6.3e-19  Score=127.03  Aligned_cols=87  Identities=16%  Similarity=0.418  Sum_probs=73.8

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCC-CCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-HTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~-~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      +........++|||+|||.++|+++|+++|++|| |.+|.|+.++ .+++++|||||+|.+.++|++||++++..+.++.
T Consensus        11 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~   89 (100)
T 2j76_E           11 RSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRR   89 (100)
T ss_dssp             ---------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBC
T ss_pred             CCcCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeE
Confidence            3445567789999999999999999999999999 9999999998 6899999999999999999999977788999999


Q ss_pred             ecccccccc
Q psy1314          87 IDPKRVTKR   95 (275)
Q Consensus        87 i~v~~~~~~   95 (275)
                      |.|+++.++
T Consensus        90 l~V~~a~~~   98 (100)
T 2j76_E           90 IRVDVADQA   98 (100)
T ss_dssp             CCCEECCCS
T ss_pred             EEEEeccCC
Confidence            999998764

>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=99.76  E-value=4.9e-18  Score=122.93  Aligned_cols=86  Identities=21%  Similarity=0.438  Sum_probs=77.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.+..+  ++|||||+|.+.++|++||+.+ +..|.+++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   89 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCC--CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            455689999999999999999999999999999999988653  7999999999999999999986 5899999999999


Q ss_pred             eeeCCCCCC
Q psy1314         176 VKFNPETMG  184 (275)
Q Consensus       176 ~~~~~~~~~  184 (275)
                      +.+++....
T Consensus        90 a~~~~~~~~   98 (103)
T 2cq3_A           90 ATARVMTNS   98 (103)
T ss_dssp             CCSSCCCCC
T ss_pred             cccCCCCCC
Confidence            998876543

>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=2.4e-19  Score=126.69  Aligned_cols=82  Identities=15%  Similarity=0.272  Sum_probs=70.6

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCC--CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G--~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      .+|||+|||+++++++|+++|++||  .|..|.|+.++.+++++|||||+|.+.++|++||+.++ ..|.|++|.|.++.
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  99999999999999999999999999999999998874 89999999999998


Q ss_pred             eCCCC
Q psy1314         178 FNPET  182 (275)
Q Consensus       178 ~~~~~  182 (275)
                      +.+..
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            87654

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

Probab=99.76  E-value=5.1e-18  Score=120.21  Aligned_cols=85  Identities=21%  Similarity=0.328  Sum_probs=76.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||.++|+++|+++|++||+|++|.|+.+  +++++|||||+|.+.++|++|++. ++..+.++.|.|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v   80 (92)
T 2dgv_A            3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDV   80 (92)
T ss_dssp             CSSSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEE
Confidence            34567899999999999999999999999999999999984  789999999999999999999984 788999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      +++.+...
T Consensus        81 ~~a~~~~~   88 (92)
T 2dgv_A           81 RIDRNASG   88 (92)
T ss_dssp             EECSCCSS
T ss_pred             EEcCCCCC
Confidence            99876544

>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=99.76  E-value=5.9e-19  Score=133.95  Aligned_cols=85  Identities=16%  Similarity=0.305  Sum_probs=77.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGE---VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~---v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      .++..+.++|||+|||+++|+++|+++|++||.   |.+|.|+.++. ++++|||||+|.+.++|++||+++++.|.++.
T Consensus        38 ~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~  116 (136)
T 2hgl_A           38 GPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRY  116 (136)
T ss_dssp             CSSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEE
Confidence            355677899999999999999999999999999   89999999977 99999999999999999999997788999999


Q ss_pred             ecccccccc
Q psy1314          87 IDPKRVTKR   95 (275)
Q Consensus        87 i~v~~~~~~   95 (275)
                      |.|.++..+
T Consensus       117 i~V~~a~~~  125 (136)
T 2hgl_A          117 IEVFKSHRT  125 (136)
T ss_dssp             EEEEECCHH
T ss_pred             EEEEECChH
Confidence            999887543

>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=6.3e-18  Score=124.63  Aligned_cols=85  Identities=22%  Similarity=0.287  Sum_probs=77.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (114)
T 2do0_A            9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMH   87 (114)
T ss_dssp             CCCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEE
Confidence            4556678999999999999999999999999999999999996 69999999999999999999998 578899999999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++...
T Consensus        88 v~~a~~~   94 (114)
T 2do0_A           88 VKMDERA   94 (114)
T ss_dssp             EEECSCC
T ss_pred             EEEcccC
Confidence            9987644

>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=3.9e-18  Score=132.90  Aligned_cols=83  Identities=20%  Similarity=0.345  Sum_probs=77.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      ...+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..|.++.|.|+
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            345778999999999999999999999999999999999999999999999999999999999995 6789999999999


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      ++..
T Consensus       115 ~a~~  118 (156)
T 1h2v_Z          115 WDAG  118 (156)
T ss_dssp             EESC
T ss_pred             ECCC
Confidence            9864

>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=99.76  E-value=3.8e-18  Score=125.04  Aligned_cols=86  Identities=17%  Similarity=0.368  Sum_probs=79.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.+
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            345689999999999999999999999999999999999999999999999999999999999976 5899999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      +.+++.+
T Consensus       103 a~~~~~~  109 (110)
T 1oo0_B          103 CFVKGPK  109 (110)
T ss_dssp             SEESSCC
T ss_pred             cccCCCC
Confidence            9987653

>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=124.87  Aligned_cols=86  Identities=19%  Similarity=0.249  Sum_probs=77.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .......++|||+|||+++|+++|+++|++||+|.++.++.++.+++++|||||+|.+.++|++||+. ++..|.++.|.
T Consensus         9 ~~~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   88 (98)
T 2cqp_A            9 SSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (98)
T ss_dssp             CCCCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            34556778999999999999999999999999999998988889999999999999999999999965 56899999999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++..+
T Consensus        89 V~~a~~~   95 (98)
T 2cqp_A           89 LVLGSGP   95 (98)
T ss_dssp             EEESSCS
T ss_pred             EEEcCCC
Confidence            9987643

>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=99.76  E-value=2.3e-18  Score=129.36  Aligned_cols=89  Identities=25%  Similarity=0.423  Sum_probs=80.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      ......+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.++.++|||||+|.+.++|++||+ +++..|.++.|
T Consensus        15 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   94 (126)
T 3ex7_B           15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   94 (126)
T ss_dssp             CBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            34455667899999999999999999999999999999999999899999999999999999999997 57889999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++..+..
T Consensus        95 ~v~~a~~~~~  104 (126)
T 3ex7_B           95 SVDWCFVRGP  104 (126)
T ss_dssp             EEEESEESSS
T ss_pred             EEEEecCCCC
Confidence            9999876544

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.76  E-value=2.3e-18  Score=120.11  Aligned_cols=80  Identities=28%  Similarity=0.550  Sum_probs=74.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|..|.++.++.++.++|||||+|.+.++|++|++.+ +..+.|++|.|.++
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            45689999999999999999999999999999999999899999999999999999999999876 58999999999987


Q ss_pred             e
Q psy1314         177 K  177 (275)
Q Consensus       177 ~  177 (275)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.76  E-value=5.3e-18  Score=122.74  Aligned_cols=85  Identities=24%  Similarity=0.393  Sum_probs=76.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.++.+  ++|||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   89 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEE
Confidence            445689999999999999999999999999999999988654  5899999999999999999976 5889999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +..+....
T Consensus        90 a~~~~~~~   97 (103)
T 2cqi_A           90 ATTPSSQK   97 (103)
T ss_dssp             CCCTTCCC
T ss_pred             CCCCcccc
Confidence            99876543

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=3.4e-18  Score=121.84  Aligned_cols=82  Identities=24%  Similarity=0.459  Sum_probs=76.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..|.+++|.|.+
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   91 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSG   91 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            445689999999999999999999999999999999999999999999999999999999999987 5899999999998


Q ss_pred             eee
Q psy1314         176 VKF  178 (275)
Q Consensus       176 ~~~  178 (275)
                      ++.
T Consensus        92 a~~   94 (95)
T 2cqc_A           92 PSS   94 (95)
T ss_dssp             CSC
T ss_pred             cCC
Confidence            763

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

Probab=99.76  E-value=1.3e-18  Score=125.54  Aligned_cols=89  Identities=27%  Similarity=0.459  Sum_probs=77.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~   95 (275)
                      ++|||+|||.++|+++|+++|++||+|++|.|+.+     ++|||||+|.+.++|++|++. ++..+.++.|.|+++.++
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     689999999999999999995 677899999999988665


Q ss_pred             cCC-----------CcceeeecCCCC
Q psy1314          96 VNP-----------LKCKIFVGGLTT  110 (275)
Q Consensus        96 ~~~-----------~~~~l~V~~l~~  110 (275)
                      ...           ...+|||++|+.
T Consensus        76 ~~~~~~~~~~~~~~~~~~ifvg~L~h  101 (101)
T 2hvz_A           76 PRRSRFDRPPARRKLLEVLFNGPLEH  101 (101)
T ss_dssp             CCSSCCCSCCCSCCCCSCCCSCCCCC
T ss_pred             CCcccCCCCCccccCCCceecCCCCC
Confidence            321           246799999973

>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=99.76  E-value=8.2e-18  Score=122.88  Aligned_cols=79  Identities=16%  Similarity=0.134  Sum_probs=71.7

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC-----eE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICG-----KE  170 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g-----~~  170 (275)
                      ....++|||+|||+++++++|+++|++||+|..|.|+.+       |||||+|.+.++|++||+.++ ..|.+     ++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~   84 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAY   84 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceE
Confidence            345689999999999999999999999999999999876       799999999999999999874 88999     99


Q ss_pred             EEEEEeeeCCCC
Q psy1314         171 VDVKRVKFNPET  182 (275)
Q Consensus       171 i~v~~~~~~~~~  182 (275)
                      |.|.++.+++..
T Consensus        85 i~V~~a~~~~~~   96 (108)
T 1x4c_A           85 IRVKVDGPRSPS   96 (108)
T ss_dssp             EEEEESSCCSCC
T ss_pred             EEEEeCCCCCCC
Confidence            999999886654

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

Probab=99.76  E-value=2.9e-18  Score=133.49  Aligned_cols=81  Identities=21%  Similarity=0.421  Sum_probs=74.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G--~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      +.++|||+|||+++|+++|+++|++||  +|.+|.|+.++.+++++|||||+|.+.++|++||+. ++..|.|+.|.|.+
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            568999999999999999999999999  999999999999999999999999999999999997 57899999999998


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8643

>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=1e-18  Score=124.64  Aligned_cols=83  Identities=19%  Similarity=0.280  Sum_probs=73.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ......++|||+|||+++|+++|+++|++||+|.++.++.++.+++++|||||+|.+.++|++||+ +++..+.+++|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v   89 (95)
T 2ek1_A           10 SGKPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL   89 (95)
T ss_dssp             -----CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEE
Confidence            334557899999999999999999999999999999999988999999999999999999999998 5788999999999


Q ss_pred             cccc
Q psy1314          90 KRVT   93 (275)
Q Consensus        90 ~~~~   93 (275)
                      +.+.
T Consensus        90 ~~a~   93 (95)
T 2ek1_A           90 SGPS   93 (95)
T ss_dssp             ECCC
T ss_pred             Eecc
Confidence            8774

>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=99.76  E-value=2.3e-18  Score=127.11  Aligned_cols=83  Identities=16%  Similarity=0.219  Sum_probs=76.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCe-EEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSI-TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v-~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.| ..|.|+.++ +++++|||||+|.+.++|++||+..+..|.+++|.|.+
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            3456889999999999999999999999999 889999998 89999999999999999999999966899999999999


Q ss_pred             eeeCC
Q psy1314         176 VKFNP  180 (275)
Q Consensus       176 ~~~~~  180 (275)
                      +..++
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98775

>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=99.76  E-value=2.4e-18  Score=127.18  Aligned_cols=81  Identities=27%  Similarity=0.452  Sum_probs=73.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      ..+|||+|||+++++++|+++|++||.|..|+|+.++.  .++|||||+|.+.++|++||+.+ +..|+|++|.|.++..
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 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETT--EEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCC--CCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45799999999999999999999999999999998853  47999999999999999999887 5899999999999887


Q ss_pred             CCCC
Q psy1314         179 NPET  182 (275)
Q Consensus       179 ~~~~  182 (275)
                      +..+
T Consensus        83 ~~~~   86 (115)
T 4f25_A           83 RKER   86 (115)
T ss_dssp             CCC-
T ss_pred             cccc
Confidence            6554

>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=3.5e-18  Score=124.12  Aligned_cols=85  Identities=25%  Similarity=0.313  Sum_probs=77.5

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC---eEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICG---KEVDV  173 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g---~~i~v  173 (275)
                      ...++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.++ ..+.+   ++|.|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456899999999999999999999999999999999987 78899999999999999999999874 77887   99999


Q ss_pred             EEeeeCCCCC
Q psy1314         174 KRVKFNPETM  183 (275)
Q Consensus       174 ~~~~~~~~~~  183 (275)
                      .++..++.+.
T Consensus        92 ~~a~~~~~~~  101 (105)
T 2dnh_A           92 KFADTDKESG  101 (105)
T ss_dssp             EESCSSCCCS
T ss_pred             EECccCcccC
Confidence            9999887654

>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=3.5e-18  Score=122.09  Aligned_cols=82  Identities=17%  Similarity=0.323  Sum_probs=77.0

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      +++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..+.|+.|.|.++.+
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            478999999999999999999999999999999999999999999999999999999999877 5899999999999987


Q ss_pred             CCC
Q psy1314         179 NPE  181 (275)
Q Consensus       179 ~~~  181 (275)
                      ++.
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.2e-18  Score=129.85  Aligned_cols=81  Identities=22%  Similarity=0.337  Sum_probs=73.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCe----eEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEV----ESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v----~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      ..+..+|||+|||+++|+++|+++|++||+|    .+|.|+.+ .+++++|||||+|.+.++|++||+.+++.|.++.|+
T Consensus        20 ~~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~   98 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEE
Confidence            3567899999999999999999999999875    68999998 589999999999999999999999988899999998


Q ss_pred             cccccc
Q psy1314          89 PKRVTK   94 (275)
Q Consensus        89 v~~~~~   94 (275)
                      |..+..
T Consensus        99 V~~a~~  104 (123)
T 2dha_A           99 LFRSTA  104 (123)
T ss_dssp             CEEECH
T ss_pred             EEECCH
Confidence            887644

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.75  E-value=8.6e-19  Score=127.92  Aligned_cols=86  Identities=16%  Similarity=0.288  Sum_probs=78.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC---eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCe
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGE---VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNK   85 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~---v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~   85 (275)
                      ...+..+.++|||+|||+++|+++|+++|+.||.   |.+|.|+.++. ++++|||||+|.+.++|++||+++++.+.++
T Consensus         4 ~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr   82 (107)
T 2lmi_A            4 LEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQR   82 (107)
T ss_dssp             CCCCCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSS
T ss_pred             CcCCCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCe
Confidence            3456678899999999999999999999999988   89999999977 9999999999999999999999888899999


Q ss_pred             eecccccccc
Q psy1314          86 KIDPKRVTKR   95 (275)
Q Consensus        86 ~i~v~~~~~~   95 (275)
                      .|.|.++.++
T Consensus        83 ~i~V~~a~~~   92 (107)
T 2lmi_A           83 YVEVYEINNE   92 (107)
T ss_dssp             CCCCEECCHH
T ss_pred             EEEEEECCHH
Confidence            9999887653

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.75  E-value=7.9e-18  Score=126.05  Aligned_cols=86  Identities=20%  Similarity=0.367  Sum_probs=78.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||.++++++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++|++ +++..+.++.|.|
T Consensus        30 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  108 (124)
T 2kt5_A           30 EGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  108 (124)
T ss_dssp             CCCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            445677899999999999999999999999999999999997 89999999999999999999999 5788999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      +++.....
T Consensus       109 ~~a~~~~~  116 (124)
T 2kt5_A          109 QLVASQID  116 (124)
T ss_dssp             EEECCTTC
T ss_pred             EEeCCCCC
Confidence            99876543

>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=99.75  E-value=5.9e-18  Score=123.80  Aligned_cols=82  Identities=24%  Similarity=0.422  Sum_probs=73.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|..+   +.+++||||+|.+.++|++||+.+ +..|.+++|.|.+
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            345689999999999999999999999999999999765   447899999999999999999877 5899999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      ++.+..
T Consensus        96 a~~~~~  101 (109)
T 1x4a_A           96 PRSGRG  101 (109)
T ss_dssp             CCCCCC
T ss_pred             cccCCC
Confidence            887654

>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=99.75  E-value=6.7e-18  Score=120.68  Aligned_cols=83  Identities=18%  Similarity=0.198  Sum_probs=74.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~----~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      ...+.++|||+|||+++++++|+    ++|++||+|++|.|+.++.+   ++||||+|.+.++|++||+ +++..+.+++
T Consensus         5 ~~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~   81 (96)
T 2dgx_A            5 SSGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKK   81 (96)
T ss_dssp             CCSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            34567899999999999999999    99999999999999998766   8899999999999999998 5788999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.+...
T Consensus        82 l~V~~a~~~~~   92 (96)
T 2dgx_A           82 ILVSLATGASG   92 (96)
T ss_dssp             EEEEECCCSSC
T ss_pred             EEEEEcCCCCC
Confidence            99999876543

>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=5.3e-18  Score=123.03  Aligned_cols=82  Identities=20%  Similarity=0.325  Sum_probs=75.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEE-EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITE-FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~-v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|.. |.|+.+ .+++++|||||+|.+.++|++||+..+..|.++.|+|..+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            45689999999999999999999999999988 888888 7899999999999999999999999668999999999988


Q ss_pred             eeCC
Q psy1314         177 KFNP  180 (275)
Q Consensus       177 ~~~~  180 (275)
                      ..+.
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
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=99.75  E-value=5.7e-19  Score=132.35  Aligned_cols=85  Identities=22%  Similarity=0.360  Sum_probs=76.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ....+.++|||+|||+++|+++|+++|++||.|.++.++.+..+++++|||||+|.+.++|++||+++++.|.++.|.|.
T Consensus        20 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   99 (124)
T 1wel_A           20 SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH   99 (124)
T ss_dssp             SCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEE
Confidence            34456789999999999999999999999999998666666679999999999999999999999988889999999998


Q ss_pred             ccccc
Q psy1314          91 RVTKR   95 (275)
Q Consensus        91 ~~~~~   95 (275)
                      ++..+
T Consensus       100 ~a~~~  104 (124)
T 1wel_A          100 PITKK  104 (124)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            87653

>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=99.75  E-value=1.2e-17  Score=122.14  Aligned_cols=86  Identities=24%  Similarity=0.452  Sum_probs=75.5

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      ......+.++|||+|||.++|+++|+++|++||+|++|.|+.+   +.++|||||+|.+.++|++||+ +++..|.++.|
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           15 RGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             SCCCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            3455667889999999999999999999999999999999654   4689999999999999999995 57889999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++.....
T Consensus        92 ~V~~a~~~~~  101 (109)
T 1x4a_A           92 RVEFPRSGRG  101 (109)
T ss_dssp             EEECCCCCCC
T ss_pred             EEEEcccCCC
Confidence            9999876543

>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=99.75  E-value=3.1e-18  Score=120.20  Aligned_cols=82  Identities=24%  Similarity=0.444  Sum_probs=75.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC-cccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQ-SRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~-~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      ...++|||+|||.++|+++|+++|++||+|.+|.|+.++.++. ++|||||+|.+.++|++|++ +++..+.++.|.|++
T Consensus         2 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   81 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATA   81 (88)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEE
Confidence            3568999999999999999999999999999999999887766 89999999999999999999 578899999999998


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +.+.
T Consensus        82 a~~~   85 (88)
T 4a8x_A           82 VLAP   85 (88)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8654

>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=2.4e-18  Score=125.74  Aligned_cols=86  Identities=26%  Similarity=0.453  Sum_probs=79.1

Q ss_pred             ccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314          95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus        95 ~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      +.....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..|.|++|.|
T Consensus        21 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33456789999999999999999999999999999999999999999999999999999999999876 58899999999


Q ss_pred             EEeeeCC
Q psy1314         174 KRVKFNP  180 (275)
Q Consensus       174 ~~~~~~~  180 (275)
                      .+++++.
T Consensus       101 ~~a~~k~  107 (108)
T 2jrs_A          101 GHVTERT  107 (108)
T ss_dssp             ECSCSSC
T ss_pred             EEcccCC
Confidence            9998765

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

Probab=99.75  E-value=2.1e-18  Score=124.77  Aligned_cols=81  Identities=16%  Similarity=0.287  Sum_probs=74.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ....++|||+|||+++|+++|+++|++||+|..|.|+.++. +.++|||||+|.+.++|++||+..++.|.|+.|.|.++
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            34568999999999999999999999999999999999987 89999999999999999999995568999999999987


Q ss_pred             ee
Q psy1314         177 KF  178 (275)
Q Consensus       177 ~~  178 (275)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            65

>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=4.1e-18  Score=122.40  Aligned_cols=84  Identities=17%  Similarity=0.393  Sum_probs=76.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeE-EEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeE----
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT-EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKE----  170 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~-~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~----  170 (275)
                      ....++|||+|||.++++++|+++|++||.|. .|.|+.++.++.++|||||+|.+.++|++|++.++ ..|.++.    
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            34568999999999999999999999999999 99999999999999999999999999999999874 8899999    


Q ss_pred             EEEEEeeeCC
Q psy1314         171 VDVKRVKFNP  180 (275)
Q Consensus       171 i~v~~~~~~~  180 (275)
                      |.|.++.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            8888887543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1.9e-17  Score=121.98  Aligned_cols=84  Identities=19%  Similarity=0.261  Sum_probs=76.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.+ +..|.+++|.|.+
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            3456899999999999999999999999999999999987 5889999999999999999999976 5899999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +.....
T Consensus        91 a~~~~~   96 (114)
T 2do0_A           91 DERALP   96 (114)
T ss_dssp             CSCCCC
T ss_pred             cccCCC
Confidence            876544

>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=99.75  E-value=1.8e-18  Score=131.30  Aligned_cols=120  Identities=10%  Similarity=0.134  Sum_probs=75.7

Q ss_pred             cEEEEEEccHHHHHHHHHhCCceecCeee-cccccccccCCCcceeeecCCCCCCCHHHHHHhcccCCC---eEEEEecc
Q psy1314          59 GFAFVTFTTQKAVDDLLAAGDHYIGNKKI-DPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS---ITEFQQPF  134 (275)
Q Consensus        59 G~afV~f~~~e~a~~al~~~~~~~~g~~i-~v~~~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~---v~~v~i~~  134 (275)
                      +++|.+|...+++-...........+..- .-...........++|||+|||+++|+++|+++|++||.   |..|.|+.
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~gg~~~g~g~~~~~~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~   81 (136)
T 2hgl_A            2 GSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIY   81 (136)
T ss_dssp             ---------------------------------CCSCSSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEE
T ss_pred             ccccccccchHHHHhhccCCCcccCCCCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEE
Confidence            46666666665554444322112211110 001111222345689999999999999999999999999   88999999


Q ss_pred             CCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         135 DKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       135 ~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      ++. ++++|||||+|.+.++|++||+..+..|.++.|+|.++..+
T Consensus        82 d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           82 TRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             CSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEEECCHH
T ss_pred             CCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEEECChH
Confidence            987 99999999999999999999993358999999999988654

>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=4.6e-18  Score=124.35  Aligned_cols=86  Identities=20%  Similarity=0.339  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEe-eCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecCee
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIK-NDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGNKK   86 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~-v~~~~i~-~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g~~   86 (275)
                      .+.+.++|||+|||+++|+++|+++|++||+ |.+|.|+ .++.+++++|||||+|.+.++|++|++.+   ...+.++.
T Consensus         4 ~s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~   83 (109)
T 2dis_A            4 GSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQ   83 (109)
T ss_dssp             CCCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBC
T ss_pred             cccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCe
Confidence            3457889999999999999999999999998 9999998 78888999999999999999999999965   37899999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.++..
T Consensus        84 l~V~~a~~~~~   94 (109)
T 2dis_A           84 IAVDWAEPEID   94 (109)
T ss_dssp             CEEEESCSSCS
T ss_pred             EEEEEcCCCCC
Confidence            99999876654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.75  E-value=4.5e-18  Score=127.36  Aligned_cols=82  Identities=22%  Similarity=0.504  Sum_probs=76.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~   94 (275)
                      +.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||++++..|.++.|.|+++..
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            36799999999999999999999999999999999999999999999999999999999997778899999999998865


Q ss_pred             cc
Q psy1314          95 RV   96 (275)
Q Consensus        95 ~~   96 (275)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.75  E-value=7.7e-19  Score=126.59  Aligned_cols=81  Identities=19%  Similarity=0.288  Sum_probs=76.1

Q ss_pred             CcceeeecCCCC------CCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCC-eE
Q psy1314          99 LKCKIFVGGLTT------EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICG-KE  170 (275)
Q Consensus        99 ~~~~l~V~~l~~------~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g-~~  170 (275)
                      .+++|||+|||.      ++++++|+++|++||.|..|.|+.++.|++++|||||+|.+.++|++||+.+ +..|.| ++
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      9999999999999999999999999999999999999999999999999887 588999 99


Q ss_pred             EEEEEeeeC
Q psy1314         171 VDVKRVKFN  179 (275)
Q Consensus       171 i~v~~~~~~  179 (275)
                      |.|.++.++
T Consensus        85 l~V~~a~~~   93 (100)
T 3ns6_A           85 LFLYTMKDV   93 (100)
T ss_dssp             CEEEESHHH
T ss_pred             EEEEECchh
Confidence            999998765

>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=99.74  E-value=1.4e-18  Score=125.95  Aligned_cols=84  Identities=20%  Similarity=0.409  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      ..+.++|||+|||.++++++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++|++ +++..+.++.|.|++
T Consensus         5 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            5 DRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CCCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            3467899999999999999999999999999999999999899999999999999999999997 567899999999998


Q ss_pred             ccccc
Q psy1314          92 VTKRV   96 (275)
Q Consensus        92 ~~~~~   96 (275)
                      +.++.
T Consensus        85 a~~~~   89 (104)
T 1p1t_A           85 AASEK   89 (104)
T ss_dssp             TTCTT
T ss_pred             CCCcc
Confidence            87654

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

Probab=99.74  E-value=1.3e-18  Score=119.07  Aligned_cols=76  Identities=33%  Similarity=0.647  Sum_probs=72.8

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ++|||+|||.++++++|+++|++||+|..+.++.++.++.++|||||+|.+.++|++|++.++..++|++|.|.++
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            4799999999999999999999999999999999998999999999999999999999999998899999999876

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

Probab=99.74  E-value=2.7e-18  Score=123.79  Aligned_cols=81  Identities=15%  Similarity=0.210  Sum_probs=72.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC---CceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP---KQVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~---~~~~~g~~i~v  173 (275)
                      ....++|||+|||+++++++|+++|++||.|.+|.|+++      ||||||+|++.++|++||+.+   +..|.|++|.|
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            345689999999999999999999999999999999875      789999999999999999964   27899999999


Q ss_pred             EEeeeCCCCC
Q psy1314         174 KRVKFNPETM  183 (275)
Q Consensus       174 ~~~~~~~~~~  183 (275)
                      .+++.++...
T Consensus        87 ~~A~~~~~~~   96 (105)
T 1sjq_A           87 QFSNHKELKT   96 (105)
T ss_dssp             CCCSSSSCCC
T ss_pred             EEcCCCCCCc
Confidence            9998876554

>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=6.4e-18  Score=124.09  Aligned_cols=84  Identities=17%  Similarity=0.264  Sum_probs=76.0

Q ss_pred             CcceeeecCCCCCCCHHHHH---HhcccCCCeEEEEeccCCCCC---CeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVR---DYFSQYGSITEFQQPFDKSKN---MKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~---~~F~~~G~v~~v~i~~~~~~~---~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      ..++|||+|||+++++++|+   ++|++||+|..|.|+.+..++   .++|||||+|.+.++|++||+.| +..|+|++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            46789999999999999999   999999999999999887643   55699999999999999999986 589999999


Q ss_pred             EEEEeeeCCCC
Q psy1314         172 DVKRVKFNPET  182 (275)
Q Consensus       172 ~v~~~~~~~~~  182 (275)
                      .|.++.+++..
T Consensus        94 ~V~~a~~k~~~  104 (111)
T 2cpi_A           94 KASLGTTKYCS  104 (111)
T ss_dssp             EEESCCCCSCS
T ss_pred             EEEeccccccc
Confidence            99999988743

>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=99.74  E-value=8e-18  Score=120.27  Aligned_cols=82  Identities=10%  Similarity=0.116  Sum_probs=74.4

Q ss_pred             CCcceeeecCCCCCCCHHHHH----HhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVD  172 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~  172 (275)
                      ...++|||+|||+++++++|+    ++|++||+|..|.|+.++.+   ++||||+|.+.++|++||+.+ +..|.|++|.
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            345789999999999999999    99999999999999998776   789999999999999999987 5889999999


Q ss_pred             EEEeeeCCCC
Q psy1314         173 VKRVKFNPET  182 (275)
Q Consensus       173 v~~~~~~~~~  182 (275)
                      |.++++++..
T Consensus        84 V~~a~~~~~~   93 (96)
T 2dgx_A           84 VSLATGASGP   93 (96)
T ss_dssp             EEECCCSSCC
T ss_pred             EEEcCCCCCC
Confidence            9999876543

>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=99.74  E-value=7.6e-18  Score=118.51  Aligned_cols=80  Identities=24%  Similarity=0.417  Sum_probs=74.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      .++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|+...+..+.|++|.|.+++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            57899999999999999999999999999999999998999999999999999999999943468999999999988754

>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=5.6e-19  Score=127.47  Aligned_cols=87  Identities=20%  Similarity=0.265  Sum_probs=77.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ....+.++|||+|||+++|+++|+++|++||.|.. .++.++.+++++|||||+|.+.++|++||++++..+.++.|.|.
T Consensus        12 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   90 (101)
T 1fj7_A           12 SESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLE   90 (101)
T ss_dssp             TTCSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEE
Confidence            44557889999999999999999999999999888 66777778999999999999999999999977889999999999


Q ss_pred             ccccccCC
Q psy1314          91 RVTKRVNP   98 (275)
Q Consensus        91 ~~~~~~~~   98 (275)
                      ++.++...
T Consensus        91 ~a~~~~~~   98 (101)
T 1fj7_A           91 KPKGRDGT   98 (101)
T ss_dssp             CCSCCCCS
T ss_pred             EcCCCCCC
Confidence            99776544

>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=99.74  E-value=2.6e-18  Score=129.52  Aligned_cols=85  Identities=24%  Similarity=0.430  Sum_probs=78.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~  122 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDF  122 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            445689999999999999999999999999999999999999999999999999999999999987 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +.++.+
T Consensus       123 a~~~~p  128 (129)
T 2kxn_B          123 SITKRP  128 (129)
T ss_dssp             CSSSSC
T ss_pred             ecCCCC
Confidence            887653

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=120.85  Aligned_cols=83  Identities=22%  Similarity=0.330  Sum_probs=73.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|+.|.   .|.++.++.++.++|||||+|.+.++|++||+.+ +..|.+++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            44568999999999999999999999773   6777888888999999999999999999999976 5899999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      ++++.+.
T Consensus        89 a~~~~~~   95 (102)
T 2fc8_A           89 AKPKGEG   95 (102)
T ss_dssp             CCCCCSS
T ss_pred             ecCCCCC
Confidence            9887653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.74  E-value=2.8e-18  Score=129.77  Aligned_cols=85  Identities=21%  Similarity=0.327  Sum_probs=76.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--EEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCc----eec
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDH----YIG   83 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~--~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~----~~~   83 (275)
                      ......++|||+|||+++|+++|+++|++||.|..  |+|++++.|++++|||||+|.+. +|++||+. ++.    .+.
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            34466789999999999999999999999999977  99999999999999999999999 99999875 566    899


Q ss_pred             Ceeeccccccccc
Q psy1314          84 NKKIDPKRVTKRV   96 (275)
Q Consensus        84 g~~i~v~~~~~~~   96 (275)
                      ++.|.|+++.+..
T Consensus        97 gr~l~V~~a~~~~  109 (131)
T 2m2b_A           97 GKTINVEFAKGSK  109 (131)
T ss_dssp             GCCCCCEECCCSC
T ss_pred             CEEEEEEECCCCC
Confidence            9999999887653

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.5e-17  Score=117.60  Aligned_cols=82  Identities=17%  Similarity=0.354  Sum_probs=75.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++| .|..|.|+.+ .+++++|||||+|.+.++|++||+ + +..|.|++|.|.+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~   83 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFR   83 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEE
Confidence            3456899999999999999999999999 9999999998 788999999999999999999999 6 5899999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +..++.
T Consensus        84 a~~~~~   89 (91)
T 2dgw_A           84 EKSGPS   89 (91)
T ss_dssp             ESSCCC
T ss_pred             CCcCCC
Confidence            987754

>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=7.4e-18  Score=121.29  Aligned_cols=79  Identities=11%  Similarity=0.113  Sum_probs=70.7

Q ss_pred             CCcceeeecCCCC-CCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEE
Q psy1314          98 PLKCKIFVGGLTT-EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDV  173 (275)
Q Consensus        98 ~~~~~l~V~~l~~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v  173 (275)
                      .+.++|||+|||+ .+++++|+++|++||.|.+|.|+++      ++||||+|++.++|++||+.++   ..|.|++|.|
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   86 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   86 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEE
Confidence            4568899999999 9999999999999999999999865      5799999999999999999763   5699999999


Q ss_pred             EEeeeCCCC
Q psy1314         174 KRVKFNPET  182 (275)
Q Consensus       174 ~~~~~~~~~  182 (275)
                      .++..+...
T Consensus        87 ~~a~~~~~~   95 (102)
T 1x4d_A           87 HLSQKYKRI   95 (102)
T ss_dssp             EEECCCTTS
T ss_pred             EECCCCCCC
Confidence            999876543

>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=99.74  E-value=1.9e-17  Score=119.90  Aligned_cols=80  Identities=20%  Similarity=0.371  Sum_probs=71.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|..|.|+        ++||||+|.+.++|++||+.+ +..|.+++|.|.++
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            456889999999999999999999999999999987        459999999999999999986 58899999999999


Q ss_pred             eeCCCCCCC
Q psy1314         177 KFNPETMGS  185 (275)
Q Consensus       177 ~~~~~~~~~  185 (275)
                      .++......
T Consensus        81 ~~~~~~~~~   89 (103)
T 2dgu_A           81 KPPDQKRKE   89 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCcccchh
Confidence            987765443

>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=99.74  E-value=1.1e-18  Score=132.89  Aligned_cols=84  Identities=18%  Similarity=0.235  Sum_probs=73.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ..+.+.++|||+|||+++|+++|+++|++|| |++|.|+.++. ++++|||||+|.+.++|++||+++.+.|.++.|.|.
T Consensus        41 ~~~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~  118 (139)
T 2hgn_A           41 VQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELF  118 (139)
T ss_dssp             ----CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEE
Confidence            3456678999999999999999999999999 67999999975 999999999999999999999777889999999998


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      .+....
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            876543

>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=99.74  E-value=1.5e-17  Score=121.58  Aligned_cols=85  Identities=13%  Similarity=0.325  Sum_probs=78.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCC-eEEEEec-cCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGS-ITEFQQP-FDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVD  172 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~-v~~v~i~-~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~  172 (275)
                      ...++|||+|||+++++++|+++|++||. |..|.|+ .++.++.++|||||+|.+.++|++|++.++   ..+.|++|.
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            34689999999999999999999999998 9999998 888888999999999999999999999873   789999999


Q ss_pred             EEEeeeCCCC
Q psy1314         173 VKRVKFNPET  182 (275)
Q Consensus       173 v~~~~~~~~~  182 (275)
                      |.++.+++..
T Consensus        86 V~~a~~~~~~   95 (109)
T 2dis_A           86 VDWAEPEIDV   95 (109)
T ss_dssp             EEESCSSCST
T ss_pred             EEEcCCCCCc
Confidence            9999887654

>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=99.74  E-value=1.7e-17  Score=119.40  Aligned_cols=82  Identities=17%  Similarity=0.169  Sum_probs=72.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh---CCceecCee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA---GDHYIGNKK   86 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~---~~~~~~g~~   86 (275)
                      .....+.++|||+|||+++|+++|+++|++||.|++|.|+++      +|||||+|.+.++|++|++.   +...+.|++
T Consensus         9 ~~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   82 (101)
T 2cq1_A            9 KMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQP   82 (101)
T ss_dssp             CCCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcE
Confidence            455567889999999999999999999999999999999875      68999999999999999985   356899999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|.++..+..
T Consensus        83 l~V~~a~~~~~   93 (101)
T 2cq1_A           83 IYIQYSNHKEL   93 (101)
T ss_dssp             CEEEECSCSSC
T ss_pred             EEEEEcCcccC
Confidence            99999876544

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

Probab=99.74  E-value=6.5e-18  Score=125.37  Aligned_cols=81  Identities=25%  Similarity=0.449  Sum_probs=74.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|+|.+
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            345689999999999999999999999999999999999999999999999999999999999987 5899999999988


Q ss_pred             ee
Q psy1314         176 VK  177 (275)
Q Consensus       176 ~~  177 (275)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            64

>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=99.74  E-value=8e-18  Score=119.92  Aligned_cols=80  Identities=21%  Similarity=0.351  Sum_probs=74.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+.+++++|+++|++||+|..|.|+.++. +.++|||||+|.+.++|++|++.+ +..|.+++|.|.+
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            44568999999999999999999999999999999999876 889999999999999999999976 5899999999988


Q ss_pred             ee
Q psy1314         176 VK  177 (275)
Q Consensus       176 ~~  177 (275)
                      ++
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.74  E-value=6.3e-18  Score=118.62  Aligned_cols=82  Identities=24%  Similarity=0.476  Sum_probs=75.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCC-eeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNM-KKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~-~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ..++|||+|||.++++++|+++|++||.|..|.|+.+..++. ++|||||+|.+.++|++|++.+ +..+.|++|.|.++
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            357899999999999999999999999999999999887765 8999999999999999999976 58999999999999


Q ss_pred             eeCC
Q psy1314         177 KFNP  180 (275)
Q Consensus       177 ~~~~  180 (275)
                      .+..
T Consensus        83 ~~~~   86 (88)
T 4a8x_A           83 LAPW   86 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.74  E-value=2.3e-18  Score=130.89  Aligned_cols=90  Identities=26%  Similarity=0.420  Sum_probs=81.1

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i   87 (275)
                      ...+..+.++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.+++|
T Consensus        40 ~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           40 PPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             SCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            345556788999999999999999999999999999999999988999999999999999999999985 6789999999


Q ss_pred             cccccccccCC
Q psy1314          88 DPKRVTKRVNP   98 (275)
Q Consensus        88 ~v~~~~~~~~~   98 (275)
                      .|+++......
T Consensus       120 ~V~~a~~~~~~  130 (135)
T 2lea_A          120 RVQMARYGRPP  130 (135)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEECCCCCCC
Confidence            99998765543

>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=99.74  E-value=1.8e-18  Score=127.65  Aligned_cols=84  Identities=18%  Similarity=0.313  Sum_probs=77.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF  178 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~  178 (275)
                      ..++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||...+..|.|+.|.|.++..
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCC
Confidence            35889999999999999999999999999999999999999999999999999999999993346899999999999987


Q ss_pred             CCCC
Q psy1314         179 NPET  182 (275)
Q Consensus       179 ~~~~  182 (275)
                      +..+
T Consensus       104 ~~~~  107 (114)
T 2cq4_A          104 EKNR  107 (114)
T ss_dssp             HHHH
T ss_pred             CccC
Confidence            7543

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

Probab=99.74  E-value=7.7e-18  Score=131.05  Aligned_cols=81  Identities=17%  Similarity=0.352  Sum_probs=75.5

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCC--CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYG--SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G--~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ..++|||+|||+++++++|+++|++||  .|..|.|+.|+.+++++|||||+|.+.++|++||+.++ ..|.|++|.|.+
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            457999999999999999999999999  99999999999999999999999999999999999984 899999999999


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            8754

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

Probab=99.74  E-value=1.3e-17  Score=127.38  Aligned_cols=83  Identities=27%  Similarity=0.472  Sum_probs=75.5

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.++.|.
T Consensus        57 ~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  136 (140)
T 2ku7_A           57 GGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR  136 (140)
T ss_dssp             CSSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEE
T ss_pred             CCCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            44556789999999999999999999999999999999999999999999999999999999999975 56789999999


Q ss_pred             cccc
Q psy1314          89 PKRV   92 (275)
Q Consensus        89 v~~~   92 (275)
                      |+++
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            8764

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.74  E-value=2.3e-17  Score=113.81  Aligned_cols=72  Identities=17%  Similarity=0.204  Sum_probs=66.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      .+..|||+||++.+||++|+++|.+||+|.++.++.      ++|||||+|.++++|++|++. ++..+.+++|.|+.+
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            477899999999999999999999999999999976      589999999999999999986 577999999998877

>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=2.7e-18  Score=116.91  Aligned_cols=75  Identities=36%  Similarity=0.687  Sum_probs=70.6

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      +|||+|||+++++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|++|++..+..++|++|.|.+|
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            589999999999999999999999999999999998999999999999999999999985568999999999864

>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=5.6e-18  Score=121.94  Aligned_cols=82  Identities=12%  Similarity=0.107  Sum_probs=71.8

Q ss_pred             CCCCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecC
Q psy1314           9 AGPGRNDERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGN   84 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g   84 (275)
                      .....+++++|||+|||+ ++|+++|+++|++||.|.+|.|+++      ++||||+|.+.++|++||+.+   ...+.|
T Consensus         8 ~~~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~G   81 (102)
T 1x4d_A            8 QKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFG   81 (102)
T ss_dssp             CCCCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETT
T ss_pred             CCCCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECC
Confidence            344567889999999999 9999999999999999999999876      479999999999999999853   356999


Q ss_pred             eeeccccccccc
Q psy1314          85 KKIDPKRVTKRV   96 (275)
Q Consensus        85 ~~i~v~~~~~~~   96 (275)
                      ++|.|.++....
T Consensus        82 r~l~V~~a~~~~   93 (102)
T 1x4d_A           82 KPVRVHLSQKYK   93 (102)
T ss_dssp             EECEEEEECCCT
T ss_pred             cEEEEEECCCCC
Confidence            999999987543

>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=99.74  E-value=4.2e-18  Score=122.15  Aligned_cols=83  Identities=18%  Similarity=0.209  Sum_probs=76.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+.++ ..|.|++|.|.+
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            3456889999999999999999999999999988888888899999999999999999999998875 899999999999


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +..+
T Consensus        92 a~~~   95 (98)
T 2cqp_A           92 GSGP   95 (98)
T ss_dssp             SSCS
T ss_pred             cCCC
Confidence            8754

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

Probab=99.74  E-value=8.5e-18  Score=119.99  Aligned_cols=81  Identities=12%  Similarity=0.167  Sum_probs=69.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCC---ceecCee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD---HYIGNKK   86 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~---~~~~g~~   86 (275)
                      .....++++|||+|||.++|+++|+++|++||+|++|.|++.      ||+|||+|.+.++|.+|++.++   ..+.|++
T Consensus        15 ~~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~   88 (100)
T 3r27_A           15 PHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHP   88 (100)
T ss_dssp             --CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEE
T ss_pred             cccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcE
Confidence            344567899999999999999999999999999999999853      6899999999999999998642   3588999


Q ss_pred             eccccccccc
Q psy1314          87 IDPKRVTKRV   96 (275)
Q Consensus        87 i~v~~~~~~~   96 (275)
                      |.|+++..++
T Consensus        89 i~V~~S~~k~   98 (100)
T 3r27_A           89 AFVNYSTSQK   98 (100)
T ss_dssp             EEEEECSCSC
T ss_pred             EEEEeccccc
Confidence            9999987653

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.73  E-value=3.2e-18  Score=123.68  Aligned_cols=83  Identities=29%  Similarity=0.573  Sum_probs=76.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ...+.++|||+|||.++|+++|+++|++||.|.+|.|+.++ +++++|||||+|.+.++|++|++ ++..+.|+.|.|.+
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~   82 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGP   82 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEE
Confidence            34567899999999999999999999999999999999998 99999999999999999999999 88899999999888


Q ss_pred             ccccc
Q psy1314          92 VTKRV   96 (275)
Q Consensus        92 ~~~~~   96 (275)
                      +..+.
T Consensus        83 a~~~~   87 (102)
T 2xs2_A           83 AIRKQ   87 (102)
T ss_dssp             EEECC
T ss_pred             CCcCc
Confidence            86543

>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=6.7e-18  Score=124.66  Aligned_cols=85  Identities=13%  Similarity=0.168  Sum_probs=74.0

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecC
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGN   84 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g   84 (275)
                      .......+.++|||+|||+++|+++|+++|++||.|++|.|+++      ||||||+|.+.++|++|++.+   +..+.|
T Consensus        23 ~~~~~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~G   96 (119)
T 2ad9_A           23 DSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRG   96 (119)
T ss_dssp             CTTSCSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTT
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            34455667899999999999999999999999999999999975      689999999999999999864   357999


Q ss_pred             eeecccccccccCC
Q psy1314          85 KKIDPKRVTKRVNP   98 (275)
Q Consensus        85 ~~i~v~~~~~~~~~   98 (275)
                      ++|.|.++..+...
T Consensus        97 r~l~V~~a~~k~~~  110 (119)
T 2ad9_A           97 QPIYIQFSNHKELK  110 (119)
T ss_dssp             BCCEEEECSSSSCC
T ss_pred             eEEEEEEccCCCCC
Confidence            99999998765443

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.73  E-value=7e-18  Score=121.24  Aligned_cols=81  Identities=27%  Similarity=0.372  Sum_probs=75.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE--------EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE--------FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~--------v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      ....++|||+|||.++++++|+++|++||.|..        |.|+.++.+++++|||||+|.+.++|++|++.+ +..|.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            445689999999999999999999999999999        999999999999999999999999999999976 58899


Q ss_pred             CeEEEEEEee
Q psy1314         168 GKEVDVKRVK  177 (275)
Q Consensus       168 g~~i~v~~~~  177 (275)
                      |++|.|.+++
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999998874

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2e-17  Score=119.31  Aligned_cols=81  Identities=19%  Similarity=0.303  Sum_probs=71.8

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|   .++.+ .+++++|||||+|.+.++|++||+.+ +..|.+++|.|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            4457899999999999999999999999987   55655 67889999999999999999999977 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +.+++.
T Consensus        88 a~~~~~   93 (101)
T 2fc9_A           88 QGPRGS   93 (101)
T ss_dssp             CSSCCC
T ss_pred             cCCCCC
Confidence            987654

>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=99.73  E-value=2.1e-18  Score=117.40  Aligned_cols=75  Identities=29%  Similarity=0.746  Sum_probs=71.4

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      +|||+|||.++++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|++|++.++..+.|++|.|.++
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            589999999999999999999999999999999999999999999999999999999998778999999999864

>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=99.73  E-value=1.9e-17  Score=129.23  Aligned_cols=87  Identities=24%  Similarity=0.373  Sum_probs=79.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ......++|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+. ++..+.+++|.|
T Consensus        65 ~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  144 (158)
T 2kn4_A           65 MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV  144 (158)
T ss_dssp             CCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999985 678999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      .++.+...
T Consensus       145 ~~a~~~~~  152 (158)
T 2kn4_A          145 QMARYGRP  152 (158)
T ss_dssp             EEECCSSC
T ss_pred             EECCCCCC
Confidence            99876543

>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=99.73  E-value=1.7e-17  Score=120.85  Aligned_cols=80  Identities=16%  Similarity=0.348  Sum_probs=74.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+.+. ++.++|||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3456899999999999999999999999999999999998 8899999999999999999999986 5899999999998


Q ss_pred             ee
Q psy1314         176 VK  177 (275)
Q Consensus       176 ~~  177 (275)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

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

Probab=99.73  E-value=1.1e-17  Score=118.51  Aligned_cols=83  Identities=22%  Similarity=0.369  Sum_probs=75.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.+  ++.++|||||+|.+.++|++|++.+ +..|.|++|.|.+
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            345689999999999999999999999999999999874  6789999999999999999999986 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +++...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.2e-17  Score=121.88  Aligned_cols=79  Identities=18%  Similarity=0.243  Sum_probs=72.5

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      .++|||+|||+++++++|+++|++| .|..|.|+.++. ++++|||||+|.+.++|++||+..++.|.++.|+|..+..+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCHH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCcc
Confidence            4789999999999999999999999 899999999876 88999999999999999999976579999999999888765


Q ss_pred             C
Q psy1314         180 P  180 (275)
Q Consensus       180 ~  180 (275)
                      +
T Consensus        94 ~   94 (109)
T 2dnn_A           94 Q   94 (109)
T ss_dssp             H
T ss_pred             c
Confidence            3

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

Probab=99.73  E-value=1.4e-17  Score=121.92  Aligned_cols=86  Identities=21%  Similarity=0.399  Sum_probs=76.5

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      .......+.++|||+|||.++|+++|+++|++||+|++|.|+.++  +.++|||||+|.+.++|++|++ +++..+.++.
T Consensus        21 ~~~~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~   98 (109)
T 2err_A           21 MNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRK   98 (109)
T ss_dssp             -CCSCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEE
T ss_pred             CCccCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            345566778999999999999999999999999999999999885  3589999999999999999998 4788999999


Q ss_pred             ecccccccc
Q psy1314          87 IDPKRVTKR   95 (275)
Q Consensus        87 i~v~~~~~~   95 (275)
                      |.|+++.++
T Consensus        99 l~V~~a~~~  107 (109)
T 2err_A           99 IEVNNATAR  107 (109)
T ss_dssp             CEEEECCCS
T ss_pred             EEEEECCCC
Confidence            999988654

>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=99.73  E-value=2.3e-17  Score=121.59  Aligned_cols=83  Identities=20%  Similarity=0.404  Sum_probs=71.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceec-----
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIG-----   83 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~-----   83 (275)
                      .....+.++|||+|||+++|+++|+++|++||+|.+|.|+.++ +++++|||||+|.+.++|++||+. ++..+.     
T Consensus        19 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~   97 (114)
T 1x5o_A           19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   97 (114)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccc
Confidence            3445678899999999999999999999999999999999997 899999999999999999999984 566674     


Q ss_pred             ---Ceeecccccc
Q psy1314          84 ---NKKIDPKRVT   93 (275)
Q Consensus        84 ---g~~i~v~~~~   93 (275)
                         +++|.|.++.
T Consensus        98 ~~~~~~l~v~~a~  110 (114)
T 1x5o_A           98 SAPTEPLLCKFSG  110 (114)
T ss_dssp             CCCSSCBEEEECC
T ss_pred             cCCCCceeEEccC
Confidence               4455555544

>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=99.72  E-value=1.4e-17  Score=122.19  Aligned_cols=86  Identities=16%  Similarity=0.337  Sum_probs=76.9

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH---HHHhhcCCeeEEEEeeCCCCC---CcccEEEEEEccHHHHHHHHHh-CCceec
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEIN---DYFSQYGEVESISIKNDPHTG---QSRGFAFVTFTTQKAVDDLLAA-GDHYIG   83 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~---~~f~~~G~v~~~~i~~~~~tg---~~~G~afV~f~~~e~a~~al~~-~~~~~~   83 (275)
                      ....+.++|||+|||+++++++|+   ++|++||+|++|.|+.++.++   +++|||||+|.+.++|++||+. ++..+.
T Consensus        10 ~r~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~   89 (111)
T 2cpi_A           10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVD   89 (111)
T ss_dssp             CCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEET
T ss_pred             ccccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEEC
Confidence            345568899999999999999999   999999999999999987754   5669999999999999999996 788999


Q ss_pred             Ceeeccccccccc
Q psy1314          84 NKKIDPKRVTKRV   96 (275)
Q Consensus        84 g~~i~v~~~~~~~   96 (275)
                      +++|.|+++.++.
T Consensus        90 gr~l~V~~a~~k~  102 (111)
T 2cpi_A           90 GRTLKASLGTTKY  102 (111)
T ss_dssp             TEEEEEESCCCCS
T ss_pred             CEEEEEEeccccc
Confidence            9999999987654

>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=99.72  E-value=2.4e-17  Score=129.64  Aligned_cols=86  Identities=27%  Similarity=0.393  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      ...+.++|||+|||+++|+++|+++|++||+|.+|.|+.++.++.++|||||+|.+.++|++||+ +++..|.++.|.|.
T Consensus        68 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  147 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD  147 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            44567789999999999999999999999999999999999999999999999999999999998 47889999999999


Q ss_pred             ccccccC
Q psy1314          91 RVTKRVN   97 (275)
Q Consensus        91 ~~~~~~~   97 (275)
                      ++..+..
T Consensus       148 ~a~~~~~  154 (165)
T 1rk8_A          148 WCFVKGP  154 (165)
T ss_dssp             ESEECC-
T ss_pred             EecCCCC
Confidence            9876543

>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=2.5e-17  Score=118.92  Aligned_cols=88  Identities=24%  Similarity=0.387  Sum_probs=77.6

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      ........+.++|||+|||.++|+++|+++|+.|   ..|.++.++.+++++|||||+|.+.++|++||+ +++..|.++
T Consensus         6 ~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   82 (102)
T 2fc8_A            6 SGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGN   82 (102)
T ss_dssp             CTTSSSSCCCSSEEEECCCTTCCHHHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCCCCCEEEEeCCCCccCHHHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCe
Confidence            3345566788999999999999999999999977   478888888899999999999999999999998 578899999


Q ss_pred             eecccccccccC
Q psy1314          86 KIDPKRVTKRVN   97 (275)
Q Consensus        86 ~i~v~~~~~~~~   97 (275)
                      .|.|+++.++..
T Consensus        83 ~l~V~~a~~~~~   94 (102)
T 2fc8_A           83 KVTLDWAKPKGE   94 (102)
T ss_dssp             ECEEEECCCCCS
T ss_pred             EEEEEEecCCCC
Confidence            999999977654

>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=2.4e-17  Score=118.88  Aligned_cols=84  Identities=17%  Similarity=0.351  Sum_probs=73.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||.|   .++.+ .+++++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   84 (101)
T 2fc9_A            9 STWSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIR   84 (101)
T ss_dssp             CCCSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            3456778999999999999999999999999976   56666 678999999999999999999999 567899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.++..
T Consensus        85 v~~a~~~~~   93 (101)
T 2fc9_A           85 LELQGPRGS   93 (101)
T ss_dssp             EEECSSCCC
T ss_pred             EEEcCCCCC
Confidence            999876543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.72  E-value=2.3e-17  Score=123.42  Aligned_cols=83  Identities=27%  Similarity=0.413  Sum_probs=75.8

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF  178 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~  178 (275)
                      ..++|||+|||.++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+..+..|.|+.|.|.+++.
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            35889999999999999999999999999999999998899999999999999999999994336899999999999886


Q ss_pred             CCC
Q psy1314         179 NPE  181 (275)
Q Consensus       179 ~~~  181 (275)
                      ...
T Consensus       115 ~~~  117 (124)
T 2jwn_A          115 NMP  117 (124)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            543

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.72  E-value=3.8e-18  Score=129.07  Aligned_cols=85  Identities=20%  Similarity=0.296  Sum_probs=77.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE--EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c----eeCCe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE--FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q----VICGK  169 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~--v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~----~~~g~  169 (275)
                      ....++|||+|||+++++++|+++|++||.|..  |+|++|+.+++++|||||+|.+. +|++||+.++ .    .|+|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            445689999999999999999999999999977  99999999999999999999999 9999999885 6    89999


Q ss_pred             EEEEEEeeeCCCC
Q psy1314         170 EVDVKRVKFNPET  182 (275)
Q Consensus       170 ~i~v~~~~~~~~~  182 (275)
                      +|.|.++.++...
T Consensus        99 ~l~V~~a~~~~~~  111 (131)
T 2m2b_A           99 TINVEFAKGSKRD  111 (131)
T ss_dssp             CCCCEECCCSCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876544

>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=99.72  E-value=5.1e-17  Score=118.64  Aligned_cols=81  Identities=20%  Similarity=0.285  Sum_probs=72.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC----
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN----   84 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g----   84 (275)
                      .+.....++|||+|||+++|+++|+++|++||+|++|.|+.+       |||||+|.+.++|++||+. ++..|.+    
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~   81 (108)
T 1x4c_A            9 PPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   81 (108)
T ss_dssp             CCCCSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCc
Confidence            344567889999999999999999999999999999999886       7999999999999999995 5778999    


Q ss_pred             -eeecccccccccC
Q psy1314          85 -KKIDPKRVTKRVN   97 (275)
Q Consensus        85 -~~i~v~~~~~~~~   97 (275)
                       +.|.|+++.++..
T Consensus        82 ~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           82 TAYIRVKVDGPRSP   95 (108)
T ss_dssp             EEEEEEEESSCCSC
T ss_pred             ceEEEEEeCCCCCC
Confidence             9999999876543

>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=99.72  E-value=4.5e-17  Score=117.17  Aligned_cols=81  Identities=11%  Similarity=0.142  Sum_probs=72.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC---CceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP---KQVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~---~~~~~g~~i~v  173 (275)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.+      +|||||+|++.++|++|++.+   ...|.|++|.|
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V   85 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   85 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEE
Confidence            345688999999999999999999999999999998865      789999999999999999865   36799999999


Q ss_pred             EEeeeCCCCC
Q psy1314         174 KRVKFNPETM  183 (275)
Q Consensus       174 ~~~~~~~~~~  183 (275)
                      .+++.+....
T Consensus        86 ~~a~~~~~~~   95 (101)
T 2cq1_A           86 QYSNHKELKT   95 (101)
T ss_dssp             EECSCSSCCC
T ss_pred             EEcCcccCcC
Confidence            9998776543

>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=99.72  E-value=9.6e-18  Score=120.79  Aligned_cols=83  Identities=17%  Similarity=0.389  Sum_probs=73.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCC-CCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK-SKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++|| |..|.|+.++ .+++++|||||+|.+.++|++||...+..|.|+.|.|.+
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            34568999999999999999999999999 9999999998 689999999999999999999994336899999999999


Q ss_pred             eeeCC
Q psy1314         176 VKFNP  180 (275)
Q Consensus       176 ~~~~~  180 (275)
                      +..++
T Consensus        95 a~~~~   99 (100)
T 2j76_E           95 ADQAQ   99 (100)
T ss_dssp             CCCSC
T ss_pred             ccCCC
Confidence            88764

>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=99.72  E-value=9.5e-18  Score=138.74  Aligned_cols=80  Identities=20%  Similarity=0.351  Sum_probs=73.3

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcC--CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYG--EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G--~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ..++|||+|||+++|+++|+++|++||  +|++|.|+.++.|++++|||||+|.+.++|++||+. +++.|.++.|.|++
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  999999999999999999999999999999999995 57899999999888


Q ss_pred             ccc
Q psy1314          92 VTK   94 (275)
Q Consensus        92 ~~~   94 (275)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            753

>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=99.72  E-value=5.6e-18  Score=120.73  Aligned_cols=80  Identities=19%  Similarity=0.258  Sum_probs=73.3

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++||+.+ +..|.+++|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a   92 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGP   92 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEec
Confidence            34589999999999999999999999999999999998899999999999999999999999976 58999999999876


Q ss_pred             e
Q psy1314         177 K  177 (275)
Q Consensus       177 ~  177 (275)
                      .
T Consensus        93 ~   93 (95)
T 2ek1_A           93 S   93 (95)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.72  E-value=8.1e-18  Score=125.74  Aligned_cols=80  Identities=21%  Similarity=0.341  Sum_probs=73.3

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeE--EEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSIT--EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~--~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~  175 (275)
                      ...++|||+|||+++|+++|+++|++| .|+  .|.|+.++. ++++|||||+|.+.++|++||+.++..|.++.|+|..
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 677  899999987 8999999999999999999999888999999999988


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +..+
T Consensus       118 a~~~  121 (126)
T 2hgm_A          118 SSQE  121 (126)
T ss_dssp             ECHH
T ss_pred             CCHH
Confidence            8654

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

Probab=99.56  E-value=4.1e-19  Score=131.52  Aligned_cols=86  Identities=27%  Similarity=0.353  Sum_probs=78.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEE--------EEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE--------FQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~--------v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      ....++|||+|||.++++++|+++|++||.|..        |.|+.++.++.++|||||+|.+.++|++||+.+ +..|.
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            345688999999999999999999999999998        899999888999999999999999999999987 48899


Q ss_pred             CeEEEEEEeeeCCCC
Q psy1314         168 GKEVDVKRVKFNPET  182 (275)
Q Consensus       168 g~~i~v~~~~~~~~~  182 (275)
                      |++|.|.++.+++..
T Consensus        84 g~~l~V~~a~~~~~~   98 (116)
T 2lcw_A           84 GNPIKVSFATRRADF   98 (116)
Confidence            999999999887654

>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=5.6e-17  Score=117.38  Aligned_cols=80  Identities=14%  Similarity=0.178  Sum_probs=70.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g~~i   87 (275)
                      ....++++|||+|||+++++++|+++|++||+|.+|.|+++      ||||||+|.+.++|++|++.+   ...+.+++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l   83 (104)
T 1wex_A           10 HKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQA   83 (104)
T ss_dssp             CCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBC
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEE
Confidence            34567889999999999999999999999999999999864      689999999999999999853   346999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++..+.
T Consensus        84 ~V~~a~~~~   92 (104)
T 1wex_A           84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEccCcc
Confidence            999987654

>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=5.2e-18  Score=122.97  Aligned_cols=83  Identities=24%  Similarity=0.484  Sum_probs=77.4

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.+ +..|.|++|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            4578999999999999999999999999999999999889999999999999999999999877 588999999999998


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      .+..
T Consensus        87 ~~~~   90 (104)
T 1p1t_A           87 SEKN   90 (104)
T ss_dssp             CTTH
T ss_pred             Cccc
Confidence            7654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.72  E-value=1.6e-17  Score=123.28  Aligned_cols=82  Identities=12%  Similarity=0.234  Sum_probs=75.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCC---eEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGS---ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~---v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~  174 (275)
                      ...++|||+|||+++|+++|+++|++||.   |..|+|+.++. ++++|||||+|.+.++|++||+..++.|.++.|+|.
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            45688999999999999999999999998   89999999877 899999999999999999999955689999999999


Q ss_pred             EeeeCC
Q psy1314         175 RVKFNP  180 (275)
Q Consensus       175 ~~~~~~  180 (275)
                      ++..+.
T Consensus        94 ~a~~~~   99 (118)
T 2db1_A           94 KSHRTE   99 (118)
T ss_dssp             EECHHH
T ss_pred             ECCHHH
Confidence            987653

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.71  E-value=2.2e-17  Score=119.96  Aligned_cols=83  Identities=12%  Similarity=0.247  Sum_probs=73.7

Q ss_pred             CCCCCCCeEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceec
Q psy1314          11 PGRNDERKLFVGGLHRNT------GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIG   83 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~------t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~   83 (275)
                      ......++|||+|||+++      |+++|+++|++||+|.+|.|+  +.+++++|||||+|.+.++|++||+. ++..+.
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            344557899999999999      789999999999999999998  36889999999999999999999995 678999


Q ss_pred             Ce-eecccccccc
Q psy1314          84 NK-KIDPKRVTKR   95 (275)
Q Consensus        84 g~-~i~v~~~~~~   95 (275)
                      ++ +|.|.++...
T Consensus        88 g~~~l~V~~a~~~  100 (105)
T 2nlw_A           88 KQHTFRVNLFTDF  100 (105)
T ss_dssp             TTCEEEEECSCCC
T ss_pred             CCceEEEEEcchH
Confidence            98 9999988643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.4e-17  Score=116.30  Aligned_cols=79  Identities=28%  Similarity=0.515  Sum_probs=71.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.++        ++||||+|.+.++|++|++.+ +..|++++|.|.+
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            3456899999999999999999999999999999987        579999999999999999877 4789999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +.+++...
T Consensus        77 a~~~~~~~   84 (90)
T 2dnq_A           77 SKNKSKAS   84 (90)
T ss_dssp             SSCCCCCC
T ss_pred             CCCCCCCC
Confidence            98876543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.71  E-value=1.3e-17  Score=115.07  Aligned_cols=72  Identities=14%  Similarity=0.266  Sum_probs=67.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      +..|+|+||++.+|+++|+++|.+||+|.++.+..      ++|||||+|.++++|++|++.|+ ..|.+++|.|.+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            46799999999999999999999999999999875      58999999999999999999985 89999999999884

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=5.6e-17  Score=114.88  Aligned_cols=78  Identities=19%  Similarity=0.352  Sum_probs=70.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.+++        +||||+|.+.++|++|++.+ +..|.|++|.|.+
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            45568999999999999999999999999999999873        39999999999999999886 5899999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      +.+++..
T Consensus        79 a~~~~~~   85 (92)
T 2dgt_A           79 STSRLRT   85 (92)
T ss_dssp             SSCCCSC
T ss_pred             ccCCCCC
Confidence            9877654

>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=99.71  E-value=9e-17  Score=111.98  Aligned_cols=78  Identities=22%  Similarity=0.439  Sum_probs=70.2

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh--CCceecCee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA--GDHYIGNKK   86 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~--~~~~~~g~~   86 (275)
                      ..+...+.++|||+|||.++|+++|+++|++||+|.+|.++++      +|||||+|.+.++|++|++.  ++..+.+++
T Consensus         5 ~~~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~   78 (85)
T 2ytc_A            5 SSGEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRR   78 (85)
T ss_dssp             CCCSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEE
T ss_pred             CCCCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCE
Confidence            3455677889999999999999999999999999999999874      68999999999999999995  567999999


Q ss_pred             eccccc
Q psy1314          87 IDPKRV   92 (275)
Q Consensus        87 i~v~~~   92 (275)
                      |.|+++
T Consensus        79 l~v~~a   84 (85)
T 2ytc_A           79 LNVKWG   84 (85)
T ss_dssp             CCEEEC
T ss_pred             EEEEec
Confidence            999876

>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=1.9e-17  Score=121.19  Aligned_cols=80  Identities=18%  Similarity=0.150  Sum_probs=69.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCC-CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYG-SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G-~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ...++|||+|||+++++++|+++|++|| +|..+.|..+    .++|||||+|.+.++|++||+.+ +..|.|++|.|.+
T Consensus        26 ~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~  101 (111)
T 2jvr_A           26 AKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVER  101 (111)
T ss_dssp             CCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3568999999999999999999999999 8999998643    36899999999999999999987 4899999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +...+.
T Consensus       102 a~~~p~  107 (111)
T 2jvr_A          102 DDNPPP  107 (111)
T ss_dssp             SCC---
T ss_pred             CCCCCC
Confidence            876543

>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=99.71  E-value=6.5e-18  Score=119.17  Aligned_cols=79  Identities=23%  Similarity=0.479  Sum_probs=71.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~   95 (275)
                      ++|||+|||.++++++|+++|++||+|++|.|+.++.+++++|||||+|.+.+ |++|++. ++..+.++.|.|+++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            58999999999999999999999999999999999999999999999999999 9999986 577899999999998765


Q ss_pred             c
Q psy1314          96 V   96 (275)
Q Consensus        96 ~   96 (275)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=7.2e-17  Score=113.82  Aligned_cols=79  Identities=27%  Similarity=0.470  Sum_probs=71.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||.++|+++|+++|++||+|++|.|+        ++||||+|.+.++|++|++ +++..+.+++|.|
T Consensus         3 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   74 (90)
T 2dnq_A            3 SGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINV   74 (90)
T ss_dssp             SCSSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEE
Confidence            346778999999999999999999999999999999997        4799999999999999997 5677999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      +++.++..
T Consensus        75 ~~a~~~~~   82 (90)
T 2dnq_A           75 EASKNKSK   82 (90)
T ss_dssp             ECSSCCCC
T ss_pred             EECCCCCC
Confidence            99876654

>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=99.71  E-value=2.4e-17  Score=121.66  Aligned_cols=81  Identities=15%  Similarity=0.210  Sum_probs=72.7

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v  173 (275)
                      ..+.++|||+|||+++++++|+++|++||.|.+|.|+.+      +|||||+|++.++|++|++.++   ..|.|++|.|
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            345688999999999999999999999999999999875      7899999999999999999763   5799999999


Q ss_pred             EEeeeCCCCC
Q psy1314         174 KRVKFNPETM  183 (275)
Q Consensus       174 ~~~~~~~~~~  183 (275)
                      .+++.++...
T Consensus       102 ~~a~~k~~~~  111 (119)
T 2ad9_A          102 QFSNHKELKT  111 (119)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCCCCCc
Confidence            9998876654

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

Probab=99.71  E-value=1.1e-16  Score=113.73  Aligned_cols=81  Identities=25%  Similarity=0.495  Sum_probs=70.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      .....++|||+|||+++|+++|+++|++||+|.+|  +.++.+++   ||||+|.+.++|++||+++++.+.++.|.|++
T Consensus         4 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~   78 (94)
T 2e5g_A            4 GSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRP   78 (94)
T ss_dssp             CCTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBC
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEE
Confidence            34567899999999999999999999999999987  55556665   99999999999999999778899999999998


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +..+..
T Consensus        79 a~~~~~   84 (94)
T 2e5g_A           79 REQKEF   84 (94)
T ss_dssp             SCCSCC
T ss_pred             CCcCCC
Confidence            865543

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.71  E-value=2.7e-17  Score=118.82  Aligned_cols=83  Identities=23%  Similarity=0.520  Sum_probs=76.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++ .+..|+|++|.|.++.
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            346899999999999999999999999999999999998 89999999999999999999999 6688999999999998


Q ss_pred             eCCCC
Q psy1314         178 FNPET  182 (275)
Q Consensus       178 ~~~~~  182 (275)
                      .+...
T Consensus        85 ~~~~~   89 (102)
T 2xs2_A           85 RKQNL   89 (102)
T ss_dssp             ECC--
T ss_pred             cCcch
Confidence            87654

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

Probab=99.70  E-value=3.2e-17  Score=116.98  Aligned_cols=78  Identities=18%  Similarity=0.224  Sum_probs=69.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v  173 (275)
                      ..++++|||+|||+++|+++|+++|++||.|.+|.+++.      ||+|||+|++.++|.+|++.++   ..|.|++|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            345788999999999999999999999999999998853      7899999999999999999874   3589999999


Q ss_pred             EEeeeCC
Q psy1314         174 KRVKFNP  180 (275)
Q Consensus       174 ~~~~~~~  180 (275)
                      .+++.+.
T Consensus        92 ~~S~~k~   98 (100)
T 3r27_A           92 NYSTSQK   98 (100)
T ss_dssp             EECSCSC
T ss_pred             Eeccccc
Confidence            9987653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.70  E-value=2.2e-17  Score=114.12  Aligned_cols=72  Identities=13%  Similarity=0.308  Sum_probs=65.0

Q ss_pred             CCeEEEcCCCCCC------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCe-ee
Q psy1314          16 ERKLFVGGLHRNT------GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNK-KI   87 (275)
Q Consensus        16 ~~~l~v~~Lp~~~------t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~-~i   87 (275)
                      +++|||+|||.++      |+++|+++|++||+|.+|.|+  +.+++++|||||+|.+.++|++|++. ++..+.++ +|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l   78 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   78 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeE
Confidence            4789999999999      789999999999999999987  46889999999999999999999995 57788888 77


Q ss_pred             cc
Q psy1314          88 DP   89 (275)
Q Consensus        88 ~v   89 (275)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            66

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.1e-17  Score=124.63  Aligned_cols=81  Identities=16%  Similarity=0.205  Sum_probs=73.3

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCe----EEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSI----TEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDV  173 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v----~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v  173 (275)
                      ...++|||+|||+++|+++|+++|++||.|    ..|.|+.+ .+++++|||||+|.+.++|++||+++++.|.++.|+|
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V   99 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL   99 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEE
Confidence            346789999999999999999999999875    68999888 4799999999999999999999998778999999999


Q ss_pred             EEeeeC
Q psy1314         174 KRVKFN  179 (275)
Q Consensus       174 ~~~~~~  179 (275)
                      ..+..+
T Consensus       100 ~~a~~~  105 (123)
T 2dha_A          100 FRSTAA  105 (123)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            888655

>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=99.70  E-value=3.3e-17  Score=119.85  Aligned_cols=82  Identities=26%  Similarity=0.525  Sum_probs=74.1

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      .....++|||+|||..+++++|+++|++||.|..|.|+.+      +|||||+|.+.++|++||+.+ +..|.|++|.|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3455689999999999999999999999999999999876      789999999999999999886 589999999999


Q ss_pred             EeeeCCCCC
Q psy1314         175 RVKFNPETM  183 (275)
Q Consensus       175 ~~~~~~~~~  183 (275)
                      ++.+++...
T Consensus        95 ~a~~~~~~~  103 (109)
T 1x4g_A           95 WGKESPDMT  103 (109)
T ss_dssp             CCCCCCSSC
T ss_pred             ecCCCCCCC
Confidence            999877654

>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=6.5e-18  Score=119.16  Aligned_cols=81  Identities=21%  Similarity=0.477  Sum_probs=71.9

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~~  179 (275)
                      ++|||+|||.++++++|+++|++||+|..|.++.++.++.++|||||+|.+.+ |++|++.++ ..+.|++|.|.++.++
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            57999999999999999999999999999999999999999999999999999 999999984 8899999999999877


Q ss_pred             CCC
Q psy1314         180 PET  182 (275)
Q Consensus       180 ~~~  182 (275)
                      +..
T Consensus        81 ~~~   83 (90)
T 2ki2_A           81 KSL   83 (90)
T ss_dssp             ---
T ss_pred             CCC
Confidence            543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=1.2e-16  Score=113.11  Aligned_cols=82  Identities=22%  Similarity=0.403  Sum_probs=73.3

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      .+.....+.++|||+|||.++|+++|+++|++||.|++|.|+++        ||||+|.+.++|++|++ +++..+.++.
T Consensus         2 ~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~   73 (92)
T 2dgt_A            2 SSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKR   73 (92)
T ss_dssp             CCSCCCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            34566788899999999999999999999999999999999743        99999999999999997 5788999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.++..
T Consensus        74 l~V~~a~~~~~   84 (92)
T 2dgt_A           74 MHVQLSTSRLR   84 (92)
T ss_dssp             EEEEESSCCCS
T ss_pred             EEEEEccCCCC
Confidence            99999976544

>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=99.70  E-value=1.1e-16  Score=114.43  Aligned_cols=80  Identities=20%  Similarity=0.385  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceec--Ceee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIG--NKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~--g~~i   87 (275)
                      ....+.++|||+|||.++|+++|+++|++||+|++|.++.+      +|||||+|.+.++|++|++ +++..+.  ++.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l   85 (97)
T 1why_A           12 GKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRL   85 (97)
T ss_dssp             CCCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEE
Confidence            44567799999999999999999999999999999999864      6799999999999999998 5778898  8999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++.++.
T Consensus        86 ~V~~a~~~~   94 (97)
T 1why_A           86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999987653

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

Probab=99.70  E-value=8.3e-17  Score=122.88  Aligned_cols=80  Identities=26%  Similarity=0.534  Sum_probs=74.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.++ ..|.|++|+|.+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  139 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL  139 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456899999999999999999999999999999999999999999999999999999999998875 889999999986


Q ss_pred             e
Q psy1314         176 V  176 (275)
Q Consensus       176 ~  176 (275)
                      |
T Consensus       140 A  140 (140)
T 2ku7_A          140 A  140 (140)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=5.9e-17  Score=121.48  Aligned_cols=83  Identities=12%  Similarity=0.234  Sum_probs=72.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN   84 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~----~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g   84 (275)
                      .....+.++|||+|||+++++++|+    ++|++||+|.+|.+..   +++++|||||+|.+.++|++|++. ++..+.+
T Consensus        23 ~~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~g   99 (127)
T 2a3j_A           23 PPHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQG   99 (127)
T ss_dssp             CCCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTT
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCC
Confidence            3445668899999999999999876    6999999999988753   578899999999999999999975 5779999


Q ss_pred             eeecccccccc
Q psy1314          85 KKIDPKRVTKR   95 (275)
Q Consensus        85 ~~i~v~~~~~~   95 (275)
                      ++|.|.++..+
T Consensus       100 r~l~V~~a~~~  110 (127)
T 2a3j_A          100 NPLVITFSETP  110 (127)
T ss_dssp             SCCEEEECCCC
T ss_pred             CEEEEEEccCc
Confidence            99999998754

>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=99.70  E-value=4.9e-17  Score=117.70  Aligned_cols=81  Identities=16%  Similarity=0.201  Sum_probs=71.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v  173 (275)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.++.+      ||||||+|++.++|++|++.++   ..|.|++|.|
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            345689999999999999999999999999999998764      7899999999999999999762   4699999999


Q ss_pred             EEeeeCCCCC
Q psy1314         174 KRVKFNPETM  183 (275)
Q Consensus       174 ~~~~~~~~~~  183 (275)
                      .++..+....
T Consensus        86 ~~a~~~~~~~   95 (104)
T 1wex_A           86 NYSTSKRITR   95 (104)
T ss_dssp             EECSSSSCCC
T ss_pred             EEccCccccC
Confidence            9998776543

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

Probab=99.70  E-value=6.4e-17  Score=128.50  Aligned_cols=84  Identities=20%  Similarity=0.377  Sum_probs=76.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      ...+.++|||+|||+++++++|+++|++||+|++|.|+.++ +++++|||||+|.+.++|++||+. ++..+.++.|.|+
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            44567899999999999999999999999999999999997 899999999999999999999994 6779999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++....
T Consensus       163 ~a~~~~  168 (177)
T 2f3j_A          163 LVASQI  168 (177)
T ss_dssp             EESSGG
T ss_pred             EecCCC
Confidence            886543

>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=99.70  E-value=2.5e-17  Score=121.68  Aligned_cols=74  Identities=19%  Similarity=0.168  Sum_probs=63.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeE-----E
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKE-----V  171 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~-----i  171 (275)
                      ...++|||+|||+++++++|+++|++||+|..|.|+.+       |||||+|.+.++|++||+.| +..|+|++     |
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i   86 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   86 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEE
Confidence            34689999999999999999999999999999999865       79999999999999999987 48899988     5


Q ss_pred             EEEEeee
Q psy1314         172 DVKRVKF  178 (275)
Q Consensus       172 ~v~~~~~  178 (275)
                      +|....+
T Consensus        87 ~v~~~~~   93 (115)
T 3beg_B           87 RVKVDGP   93 (115)
T ss_dssp             EEEECC-
T ss_pred             EeccCCC
Confidence            5554444

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.70  E-value=8.1e-17  Score=120.51  Aligned_cols=85  Identities=16%  Similarity=0.334  Sum_probs=77.8

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++|++.+ +..|.|++|.|.+
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            3456899999999999999999999999999999999998 8899999999999999999999976 5889999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      +......
T Consensus       111 a~~~~~~  117 (124)
T 2kt5_A          111 VASQIDL  117 (124)
T ss_dssp             ECCTTCC
T ss_pred             eCCCCCC
Confidence            9876554

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.70  E-value=4.5e-17  Score=116.25  Aligned_cols=85  Identities=19%  Similarity=0.269  Sum_probs=72.9

Q ss_pred             cccccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeE
Q psy1314          92 VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKE  170 (275)
Q Consensus        92 ~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~  170 (275)
                      .........++|||+|||..+++++|+++|++||.|..+     ..++.++|||||+|.+.++|++|++.++ ..|.|++
T Consensus         8 ~~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   82 (96)
T 1fjc_A            8 CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS   82 (96)
T ss_dssp             TTTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE
T ss_pred             cccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            333445567899999999999999999999999887665     3467889999999999999999999875 8899999


Q ss_pred             EEEEEeeeCCC
Q psy1314         171 VDVKRVKFNPE  181 (275)
Q Consensus       171 i~v~~~~~~~~  181 (275)
                      |.|.++.++..
T Consensus        83 l~v~~a~~~~~   93 (96)
T 1fjc_A           83 VSLYYTGEKGG   93 (96)
T ss_dssp             EEEEECSSSCC
T ss_pred             EEEEEcCCCCC
Confidence            99999887654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.69  E-value=4.3e-17  Score=118.39  Aligned_cols=82  Identities=17%  Similarity=0.240  Sum_probs=73.3

Q ss_pred             CCCcceeeecCCCCCC------CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCe
Q psy1314          97 NPLKCKIFVGGLTTEI------SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGK  169 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~  169 (275)
                      ....++|||+|||+.+      ++++|+++|++||.|..|.|+  +.++.++|||||+|.+.++|++||+.+ +..|.|+
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~   89 (105)
T 2nlw_A           12 DGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ   89 (105)
T ss_dssp             CSCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTT
T ss_pred             CCCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            3446899999999999      789999999999999999988  467889999999999999999999987 5889998


Q ss_pred             -EEEEEEeeeCC
Q psy1314         170 -EVDVKRVKFNP  180 (275)
Q Consensus       170 -~i~v~~~~~~~  180 (275)
                       +|.|.++....
T Consensus        90 ~~l~V~~a~~~~  101 (105)
T 2nlw_A           90 HTFRVNLFTDFD  101 (105)
T ss_dssp             CEEEEECSCCCC
T ss_pred             ceEEEEEcchHh
Confidence             99999987543

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

Probab=99.69  E-value=1.2e-16  Score=115.05  Aligned_cols=77  Identities=10%  Similarity=0.252  Sum_probs=69.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      .+...++|||+|||.++|+++|+++|++||+|.+|.++.      ++|||||+|.+.++|++|++. ++..+.++.|.|+
T Consensus        23 ~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   96 (101)
T 2la4_A           23 APPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTG   96 (101)
T ss_dssp             SCSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCC
T ss_pred             CCCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            345678999999999999999999999999999999983      478999999999999999975 7889999999999


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      ++.+
T Consensus        97 ~a~~  100 (101)
T 2la4_A           97 WGKE  100 (101)
T ss_dssp             BCCC
T ss_pred             eccC
Confidence            8864

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=7.5e-18  Score=117.56  Aligned_cols=77  Identities=22%  Similarity=0.407  Sum_probs=69.4

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~  174 (275)
                      ...++|||+|||+++++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++|++.++ ..|.++.|++.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   80 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQS   80 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeec
Confidence            346799999999999999999999999999999999999999999999999999999999999864 66777766554

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

Probab=99.69  E-value=4.1e-17  Score=119.37  Aligned_cols=82  Identities=21%  Similarity=0.454  Sum_probs=74.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++.  .++|||||+|.+.++|++|++.+ +..|.|++|.|.+
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            44568999999999999999999999999999999998853  47999999999999999999986 5889999999999


Q ss_pred             eeeCC
Q psy1314         176 VKFNP  180 (275)
Q Consensus       176 ~~~~~  180 (275)
                      +.+++
T Consensus       104 a~~~~  108 (109)
T 2err_A          104 ATARV  108 (109)
T ss_dssp             CCCSC
T ss_pred             CCCCc
Confidence            88653

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

Probab=99.69  E-value=5.4e-17  Score=119.70  Aligned_cols=81  Identities=26%  Similarity=0.426  Sum_probs=70.6

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCC---CCcccEEEEEEccHHHHHHHHHhCCceecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHT---GQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~t---g~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i   87 (275)
                      ....+.++|||+|||+++|+++|+++|++||+|. +.++.++.+   ++++|||||+|.+.++|++||+.+ +.++|+.+
T Consensus         3 ~~~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~-~~~~G~~~   80 (114)
T 2dnl_A            3 SGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC-LEEDGKLY   80 (114)
T ss_dssp             CSSSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS-EEETTEEE
T ss_pred             CCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh-hhcCCcEE
Confidence            3456789999999999999999999999999999 888888777   799999999999999999999986 45788887


Q ss_pred             cccccc
Q psy1314          88 DPKRVT   93 (275)
Q Consensus        88 ~v~~~~   93 (275)
                      .+..+.
T Consensus        81 ~~~~~~   86 (114)
T 2dnl_A           81 LCVSSP   86 (114)
T ss_dssp             EEECCS
T ss_pred             EeccCC
Confidence            776543

>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=99.69  E-value=1.3e-17  Score=124.95  Aligned_cols=83  Identities=16%  Similarity=0.229  Sum_probs=74.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ...++|||+|||+++++++|+++|++||.|..+.++.+..+++++|||||+|.+.++|++||+..+..|.|+.|.|.++.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            34589999999999999999999999999988777777788999999999999999999999944689999999999987


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      .+.
T Consensus       103 ~~~  105 (124)
T 1wel_A          103 KKG  105 (124)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>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=99.69  E-value=7.3e-17  Score=118.16  Aligned_cols=90  Identities=19%  Similarity=0.462  Sum_probs=74.7

Q ss_pred             cCeeeccccccccc----CCCcceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHH
Q psy1314          83 GNKKIDPKRVTKRV----NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ  157 (275)
Q Consensus        83 ~g~~i~v~~~~~~~----~~~~~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~  157 (275)
                      .+..|.+..+....    ....++|||+|||+. +++++|+++|++||.|..|.|        +++||||+|.+.++|++
T Consensus         6 ~g~~~~~~~s~~~~~~~~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~   77 (110)
T 1wf1_A            6 SGMSLKLQASNVTNKNDPKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARA   77 (110)
T ss_dssp             CSCCCCCCCCCSCCSCCCTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHH
T ss_pred             CCcccccccCCCCCCCCCCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHH
Confidence            44556555543322    223479999999999 999999999999999999988        47899999999999999


Q ss_pred             HHhcC-CceeCCeEEEEEEeeeCC
Q psy1314         158 VLANP-KQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       158 Ai~~~-~~~~~g~~i~v~~~~~~~  180 (275)
                      ||+.+ +..|+|++|.|.++..+.
T Consensus        78 A~~~l~g~~~~g~~l~V~~a~~~~  101 (110)
T 1wf1_A           78 AVLGENGRVLAGQTLDINMAGEPK  101 (110)
T ss_dssp             HHHHHTTCEETTEECCEEESCCCC
T ss_pred             HHHHcCCCEECCeEEEEEECCCCC
Confidence            99886 589999999999997543

>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=99.69  E-value=9.6e-18  Score=123.85  Aligned_cols=87  Identities=17%  Similarity=0.250  Sum_probs=72.7

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||.|..+.+..+..++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            45689999999999999999999999999843322222236778999999999999999999987 58899999999999


Q ss_pred             eeCCCCCC
Q psy1314         177 KFNPETMG  184 (275)
Q Consensus       177 ~~~~~~~~  184 (275)
                      ..+..+..
T Consensus       103 ~~~~~~~~  110 (115)
T 2cpx_A          103 KNKKQRSS  110 (115)
T ss_dssp             CCCSCCCC
T ss_pred             cCCCCCCC
Confidence            98766543

>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=1e-16  Score=115.06  Aligned_cols=82  Identities=21%  Similarity=0.413  Sum_probs=72.6

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i   87 (275)
                      ......+.++|||+|||+++|+++|+++|++||+|++|.|+++      +|||||+|.+.++|++|++. ++..+.+++|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l   81 (99)
T 2cpj_A            8 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQL   81 (99)
T ss_dssp             CSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceE
Confidence            3455677889999999999999999999999999999999865      68999999999999999965 6789999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++.++.
T Consensus        82 ~v~~a~~~~   90 (99)
T 2cpj_A           82 RVRFACHSA   90 (99)
T ss_dssp             EEEESSCCS
T ss_pred             EEEEcCCCC
Confidence            999987643

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.2e-16  Score=112.69  Aligned_cols=78  Identities=21%  Similarity=0.385  Sum_probs=70.3

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|..|.+++        +||||+|.+.++|++|++.+ +..|.+++|.|.+
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            44568999999999999999999999999999999973        38999999999999999986 5899999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      +.++...
T Consensus        78 a~~~~~~   84 (90)
T 2dnp_A           78 STKGQKK   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9877543

>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=6e-17  Score=116.29  Aligned_cols=81  Identities=27%  Similarity=0.475  Sum_probs=72.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||..+++++|+++|++||.|..|.+..+      ++||||+|.+.++|++|++.+ +..|.|++|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   85 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   85 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEE
Confidence            345689999999999999999999999999999999854      789999999999999999887 5889999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +.++....
T Consensus        86 a~~~~~~~   93 (99)
T 2cpj_A           86 ACHSASLT   93 (99)
T ss_dssp             SSCCSCCC
T ss_pred             cCCCCCCC
Confidence            98876543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=1.7e-16  Score=111.91  Aligned_cols=80  Identities=21%  Similarity=0.371  Sum_probs=71.6

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      ...+.+.++|||+|||.++|+++|+++|++||+|.+|.|+++        ||||+|.+.++|++|++ +++..+.++.|.
T Consensus         3 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   74 (90)
T 2dnp_A            3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRIN   74 (90)
T ss_dssp             CCSSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            345677899999999999999999999999999999999843        99999999999999998 578899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.+...
T Consensus        75 v~~a~~~~~   83 (90)
T 2dnp_A           75 VELSTKGQK   83 (90)
T ss_dssp             EEESCCCCC
T ss_pred             EEECCCCCC
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=99.69  E-value=7.5e-17  Score=118.83  Aligned_cols=82  Identities=13%  Similarity=0.252  Sum_probs=73.7

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee--------C
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI--------C  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~--------~  167 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.|+.++ ++.++|||||+|.+.++|++||+.++ ..|        .
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            3456899999999999999999999999999999999998 88999999999999999999999874 667        5


Q ss_pred             CeEEEEEEeeeC
Q psy1314         168 GKEVDVKRVKFN  179 (275)
Q Consensus       168 g~~i~v~~~~~~  179 (275)
                      +++|.|.++.++
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            788999988743

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

Probab=99.51  E-value=1.9e-18  Score=127.86  Aligned_cols=86  Identities=26%  Similarity=0.432  Sum_probs=78.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE--------EEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCcee
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVES--------ISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYI   82 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~--------~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~   82 (275)
                      +..+.++|||+|||.++|+++|+++|++||+|.+        |.|+.++.+++++|||||+|.+.++|++||+. ++..+
T Consensus         3 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   82 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   82 (116)
Confidence            4567889999999999999999999999999998        99999988999999999999999999999994 67899


Q ss_pred             cCeeecccccccccC
Q psy1314          83 GNKKIDPKRVTKRVN   97 (275)
Q Consensus        83 ~g~~i~v~~~~~~~~   97 (275)
                      .++.|.|+++.++..
T Consensus        83 ~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           83 SGNPIKVSFATRRAD   97 (116)
Confidence            999999999876644

>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=99.69  E-value=1.9e-16  Score=115.72  Aligned_cols=80  Identities=15%  Similarity=0.371  Sum_probs=72.2

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      .....++|||+|||.++|+++|+++|++||+|.+|.|+.+      +|||||+|.+.++|++||+ +++..+.++.|.|.
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   94 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCY   94 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            4556789999999999999999999999999999999986      6899999999999999996 47889999999999


Q ss_pred             ccccccC
Q psy1314          91 RVTKRVN   97 (275)
Q Consensus        91 ~~~~~~~   97 (275)
                      ++..+..
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9876544

>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=99.68  E-value=2.2e-17  Score=121.84  Aligned_cols=85  Identities=19%  Similarity=0.264  Sum_probs=71.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ..+.++|||+|||.++|+++|+++|++||.|..+.+..+..+++++|||||+|.+.++|++||+. ++..+.++.|.|++
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            45678999999999999999999999999985443333323788999999999999999999985 67899999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.++..
T Consensus       102 a~~~~~  107 (115)
T 2cpx_A          102 GKNKKQ  107 (115)
T ss_dssp             CCCCSC
T ss_pred             ccCCCC
Confidence            876644

>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=99.68  E-value=2.2e-16  Score=114.19  Aligned_cols=80  Identities=19%  Similarity=0.332  Sum_probs=71.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||+++|+++|+++|++||+|++|.|++        +||||+|.+.++|++||+ +++..+.++.|.
T Consensus         5 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   76 (103)
T 2dgu_A            5 SSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENIE   76 (103)
T ss_dssp             CCCCCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEEE
Confidence            34456789999999999999999999999999999999873        499999999999999998 478899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.++..
T Consensus        77 v~~a~~~~~   85 (103)
T 2dgu_A           77 IVFAKPPDQ   85 (103)
T ss_dssp             EEECCCCCC
T ss_pred             EEEcCCCcc
Confidence            999876544

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=114.26  Aligned_cols=82  Identities=16%  Similarity=0.323  Sum_probs=71.2

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .......++|||+|||+++|+++|+++|++||.|. +.++.+    +++|||||+|.+.++|++|++. ++..+.++.|.
T Consensus        13 ~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   87 (97)
T 2e5j_A           13 GEGAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLR   87 (97)
T ss_dssp             CSSSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             CCCCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            34556688999999999999999999999999997 666654    5789999999999999999965 78899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |+++.++.
T Consensus        88 V~~a~~~~   95 (97)
T 2e5j_A           88 VALARQQR   95 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEEcCCCC
Confidence            99987653

>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=99.68  E-value=5.5e-17  Score=114.19  Aligned_cols=80  Identities=30%  Similarity=0.487  Sum_probs=63.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ...+..+|||+|||+++|+++|+++|++||+|++|.|+.+     ++|||||+|.+.++|+++.. ....+.++.|.|.+
T Consensus         7 ~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~-~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            7 HHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCG-EDLIIKGISVHISN   80 (89)
T ss_dssp             ----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTT-CEEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcC-CCcccCCEEEEEEE
Confidence            4567889999999999999999999999999999999875     68999999999999985432 23456799999998


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.++..
T Consensus        81 a~~k~~   86 (89)
T 3d2w_A           81 AEPKHN   86 (89)
T ss_dssp             CC----
T ss_pred             cCCCCc
Confidence            876543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.3e-16  Score=113.24  Aligned_cols=77  Identities=17%  Similarity=0.310  Sum_probs=69.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccC--CCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQY--GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~--G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      ....++|||+|||+.+++++|+++|++|  |.|..|.+.        ++||||+|.+.++|++||+.+ +..|.+++|.|
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            3456899999999999999999999999  999999875        679999999999999999976 58999999999


Q ss_pred             EEeeeCCC
Q psy1314         174 KRVKFNPE  181 (275)
Q Consensus       174 ~~~~~~~~  181 (275)
                      .+++++..
T Consensus        84 ~~a~~~~~   91 (99)
T 2cpd_A           84 TLAKPVDK   91 (99)
T ss_dssp             ECCCCCCC
T ss_pred             EECCCCCC
Confidence            99987654

>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=99.68  E-value=7.9e-17  Score=115.24  Aligned_cols=78  Identities=21%  Similarity=0.371  Sum_probs=70.7

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC--CeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC--GKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~--g~~i~v~  174 (275)
                      ...++|||+|||.++++++|+++|++||.|..|.+..+      ++||||+|.+.++|++|++.+ +..|.  +++|.|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            45689999999999999999999999999999998754      789999999999999999986 58889  9999999


Q ss_pred             EeeeCCC
Q psy1314         175 RVKFNPE  181 (275)
Q Consensus       175 ~~~~~~~  181 (275)
                      ++++++.
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9988654

>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=5.5e-18  Score=122.24  Aligned_cols=83  Identities=17%  Similarity=0.284  Sum_probs=74.3

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|.. .++.+..++.++|||||+|.+.++|++||+ + +..|.|++|.|.++
T Consensus        15 ~~~~~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           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            35689999999999999999999999999887 677777788899999999999999999999 6 58899999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      .++..+
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            876543

>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=99.68  E-value=7.2e-17  Score=113.32  Aligned_cols=78  Identities=26%  Similarity=0.552  Sum_probs=68.5

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF  178 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~  178 (275)
                      ..++|||+|||+++++++|+++|++||+|..|.|+.+     ++|||||+|.+.++|++|+.. ...+.+++|.|.++.+
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            4689999999999999999999999999999999865     689999999999999876444 4667999999999887


Q ss_pred             CCCC
Q psy1314         179 NPET  182 (275)
Q Consensus       179 ~~~~  182 (275)
                      +...
T Consensus        78 ~~~~   81 (88)
T 1wf0_A           78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

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

Probab=99.68  E-value=7.3e-17  Score=116.28  Aligned_cols=77  Identities=30%  Similarity=0.519  Sum_probs=70.9

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      ++|||+|||.++++++|+++|++||+|..|.++.+     ++|||||+|.+.++|++|++.+ +..+.|++|.|.++..+
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     5899999999999999999987 48899999999999887


Q ss_pred             CCC
Q psy1314         180 PET  182 (275)
Q Consensus       180 ~~~  182 (275)
                      +..
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.68  E-value=8.9e-17  Score=117.57  Aligned_cols=80  Identities=11%  Similarity=0.132  Sum_probs=69.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G-~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      .+....+|||+|||+++|+++|+++|++|| +|..+.|+.+    .++|||||+|.+.++|++||+. ++..+.++.|.|
T Consensus        24 ~p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V   99 (111)
T 2jvr_A           24 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            455678999999999999999999999999 8999988643    4789999999999999999975 678999999999


Q ss_pred             cccccc
Q psy1314          90 KRVTKR   95 (275)
Q Consensus        90 ~~~~~~   95 (275)
                      +++...
T Consensus       100 ~~a~~~  105 (111)
T 2jvr_A          100 ERDDNP  105 (111)
T ss_dssp             EESCC-
T ss_pred             EECCCC
Confidence            988643

>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=99.68  E-value=6.7e-17  Score=118.02  Aligned_cols=80  Identities=10%  Similarity=0.186  Sum_probs=70.2

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC---CceecCee
Q psy1314          11 PGRNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGNKK   86 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g~~   86 (275)
                      ....++++|||+|||++ +|+++|+++|++||+|.+|.|++.      +|||||+|.+.++|++|++.+   ...+.|++
T Consensus        20 ~~~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~   93 (112)
T 1x4f_A           20 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRC   93 (112)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             ccCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            34567889999999998 999999999999999999999753      689999999999999999853   45799999


Q ss_pred             eccccccccc
Q psy1314          87 IDPKRVTKRV   96 (275)
Q Consensus        87 i~v~~~~~~~   96 (275)
                      |.|.++..+.
T Consensus        94 l~V~~a~~~~  103 (112)
T 1x4f_A           94 VKVDLSEKYK  103 (112)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEECcccc
Confidence            9999986543

>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=99.68  E-value=2.1e-17  Score=120.53  Aligned_cols=83  Identities=14%  Similarity=0.207  Sum_probs=75.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCC---eEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGS---ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~---v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v  173 (275)
                      ....++|||+|||+++|+++|+++|++||.   |..|.|+.++. ++++|||||+|.+.++|++||+..+..|.++.|.|
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            345688999999999999999999999988   89999999987 89999999999999999999994468899999999


Q ss_pred             EEeeeCC
Q psy1314         174 KRVKFNP  180 (275)
Q Consensus       174 ~~~~~~~  180 (275)
                      .++..+.
T Consensus        87 ~~a~~~~   93 (107)
T 2lmi_A           87 YEINNED   93 (107)
T ss_dssp             EECCHHH
T ss_pred             EECCHHH
Confidence            9887653

>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=2.4e-16  Score=109.76  Aligned_cols=76  Identities=26%  Similarity=0.476  Sum_probs=68.8

Q ss_pred             cCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-C-ceeCCeEEEE
Q psy1314          96 VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-K-QVICGKEVDV  173 (275)
Q Consensus        96 ~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~-~~~~g~~i~v  173 (275)
                      .....++|||+|||.++++++|+++|++||.|..|.++.+      +|||||+|.+.++|++|++.+ + ..+.|++|.|
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            3456689999999999999999999999999999999864      789999999999999999976 5 8899999999


Q ss_pred             EEee
Q psy1314         174 KRVK  177 (275)
Q Consensus       174 ~~~~  177 (275)
                      .+++
T Consensus        82 ~~ak   85 (85)
T 2ytc_A           82 KWGR   85 (85)
T ss_dssp             EECC
T ss_pred             EecC
Confidence            9874

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=5.4e-16  Score=111.28  Aligned_cols=81  Identities=20%  Similarity=0.299  Sum_probs=71.0

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhc--CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQY--GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~--G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      ......+.++|||+|||+++|+++|+++|++|  |.|.+|.++        +|||||+|.+.++|++||+ +++..+.++
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (99)
T 2cpd_A            8 DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGS   79 (99)
T ss_dssp             CCSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTE
T ss_pred             cccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            34445678899999999999999999999999  889988875        4699999999999999999 678899999


Q ss_pred             eecccccccccC
Q psy1314          86 KIDPKRVTKRVN   97 (275)
Q Consensus        86 ~i~v~~~~~~~~   97 (275)
                      .|.|+++.++..
T Consensus        80 ~l~v~~a~~~~~   91 (99)
T 2cpd_A           80 PIEVTLAKPVDK   91 (99)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            999999876543

>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=99.67  E-value=1.9e-16  Score=127.39  Aligned_cols=84  Identities=35%  Similarity=0.688  Sum_probs=76.1

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      ...++|||+|||.++|+++|+++|++||.|++|.|+.++.+++++|||||+|.+.++|++||+.+++.+.|+.|.|.++.
T Consensus       102 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             -CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEECC
T ss_pred             CCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHhCCcEECCEEEEEEecC
Confidence            45689999999999999999999999999999999999989999999999999999999999998899999999999987


Q ss_pred             cccC
Q psy1314          94 KRVN   97 (275)
Q Consensus        94 ~~~~   97 (275)
                      ++..
T Consensus       182 ~k~~  185 (196)
T 1l3k_A          182 SKQE  185 (196)
T ss_dssp             ----
T ss_pred             ChhH
Confidence            7654

>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=99.67  E-value=7.2e-17  Score=115.36  Aligned_cols=83  Identities=18%  Similarity=0.358  Sum_probs=72.7

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHH----HHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCe
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEIN----DYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNK   85 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~----~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~   85 (275)
                      .+..+.++|||+|||.++++++|+    ++|++||.|.+|.++.   ++.++|||||+|.+.++|++|++. ++..+.++
T Consensus         3 ~~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (97)
T 1nu4_A            3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDK   79 (97)
T ss_dssp             ---CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCc
Confidence            456778999999999999999999    9999999999999874   467889999999999999999984 78899999


Q ss_pred             eeccccccccc
Q psy1314          86 KIDPKRVTKRV   96 (275)
Q Consensus        86 ~i~v~~~~~~~   96 (275)
                      .|.|+++.++.
T Consensus        80 ~l~v~~a~~~~   90 (97)
T 1nu4_A           80 PMRIQYAKTDS   90 (97)
T ss_dssp             ECEEEECSSCC
T ss_pred             EEEEEEccCCC
Confidence            99999987654

>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=99.67  E-value=8.4e-17  Score=117.48  Aligned_cols=81  Identities=19%  Similarity=0.190  Sum_probs=71.1

Q ss_pred             CCCcceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEE
Q psy1314          97 NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVD  172 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~  172 (275)
                      ..+.++|||+|||++ +++++|+++|++||.|.+|.|++      ++|||||+|++.++|++||+.++   ..|.|++|.
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            345789999999998 99999999999999999999974      37899999999999999999762   569999999


Q ss_pred             EEEeeeCCCCC
Q psy1314         173 VKRVKFNPETM  183 (275)
Q Consensus       173 v~~~~~~~~~~  183 (275)
                      |.++..+....
T Consensus        96 V~~a~~~~~~~  106 (112)
T 1x4f_A           96 VDLSEKYKKLV  106 (112)
T ss_dssp             EEEECSCSSSS
T ss_pred             EEECccccccc
Confidence            99998766543

>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=99.67  E-value=8.5e-17  Score=114.13  Aligned_cols=78  Identities=21%  Similarity=0.338  Sum_probs=68.2

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCC-eEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-C-ceeCCeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGS-ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-K-QVICGKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~-v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~-~~~~g~~i~v~  174 (275)
                      ...++|||+|||.++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.+ + ..|+|++|.|.
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            45689999999999999999999999999 5555552       4789999999999999999976 5 78999999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      ++.++..+
T Consensus        79 ~a~~~~~~   86 (93)
T 2cqh_A           79 YSVSKKLR   86 (93)
T ss_dssp             ECCCCCCC
T ss_pred             EccCcccc
Confidence            99877654

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=7.2e-17  Score=115.17  Aligned_cols=83  Identities=18%  Similarity=0.319  Sum_probs=72.0

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i   87 (275)
                      ......+.++|||+|||.++|+++|+++|++||.|..+     ..+++++|||||+|.+.++|++|++. ++..+.++.|
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   83 (96)
T 1fjc_A            9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             ccccCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            34455678999999999999999999999999987666     35688999999999999999999995 5679999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++.++.
T Consensus        84 ~v~~a~~~~   92 (96)
T 1fjc_A           84 SLYYTGEKG   92 (96)
T ss_dssp             EEEECSSSC
T ss_pred             EEEEcCCCC
Confidence            999987654

>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=99.67  E-value=4.5e-16  Score=113.92  Aligned_cols=76  Identities=18%  Similarity=0.483  Sum_probs=68.1

Q ss_pred             CCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          13 RNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      ....++|||+|||++ +|+++|+++|++||+|++|.|        ++|||||+|.+.++|++||+ +++..+.++.|.|+
T Consensus        24 ~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   95 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDIN   95 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            344589999999999 999999999999999999999        46899999999999999995 57889999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++....
T Consensus        96 ~a~~~~  101 (110)
T 1wf1_A           96 MAGEPK  101 (110)
T ss_dssp             ESCCCC
T ss_pred             ECCCCC
Confidence            987543

>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=99.67  E-value=2.7e-16  Score=110.65  Aligned_cols=79  Identities=24%  Similarity=0.522  Sum_probs=64.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      .....+|||+|||+++|+++|+++|++||.|.+|.|+.+     ++|||||+|.+.++|+++. .....+.+++|.|.++
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-----FRAFAFVTFADDKVAQSLC-GEDLIIKGISVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHT-TCEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHc-CCCcccCCEEEEEEEc
Confidence            345689999999999999999999999999999999875     6899999999999998543 3345678999999999


Q ss_pred             eeCCC
Q psy1314         177 KFNPE  181 (275)
Q Consensus       177 ~~~~~  181 (275)
                      .++..
T Consensus        82 ~~k~~   86 (89)
T 3d2w_A           82 EPKHN   86 (89)
T ss_dssp             C----
T ss_pred             CCCCc
Confidence            87754

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.67  E-value=5.5e-17  Score=112.11  Aligned_cols=71  Identities=20%  Similarity=0.310  Sum_probs=64.6

Q ss_pred             ceeeecCCCCCC------CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCe-EEE
Q psy1314         101 CKIFVGGLTTEI------SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGK-EVD  172 (275)
Q Consensus       101 ~~l~V~~l~~~~------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~-~i~  172 (275)
                      ++|||+|||..+      ++++|+++|++||+|..|.++  +.++.++|||||+|.+.++|++|++.++ ..|.|+ +|.
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      679999999999999999987  4678899999999999999999999874 889998 776


Q ss_pred             E
Q psy1314         173 V  173 (275)
Q Consensus       173 v  173 (275)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            5

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

Probab=99.67  E-value=4.6e-16  Score=110.55  Aligned_cols=79  Identities=20%  Similarity=0.433  Sum_probs=68.4

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||.|..|  +.++.++.   ||||+|.+.++|++||+ + +..|.|++|.|.++
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a   79 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEEC
Confidence            345789999999999999999999999999987  55555554   99999999999999999 6 59999999999988


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      ..+...
T Consensus        80 ~~~~~~   85 (94)
T 2e5g_A           80 EQKEFQ   85 (94)
T ss_dssp             CCSCCC
T ss_pred             CcCCCC
Confidence            766543

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

Probab=99.67  E-value=3.1e-16  Score=114.43  Aligned_cols=79  Identities=22%  Similarity=0.415  Sum_probs=70.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||+|++|.|+        +|||||+|.+.++|++|++ +++..+.++.|.
T Consensus        25 ~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   96 (108)
T 2jvo_A           25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLE   96 (108)
T ss_dssp             ---CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3445678899999999999999999999999999999998        5799999999999999998 478899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |+++..+.
T Consensus        97 V~~a~~~~  104 (108)
T 2jvo_A           97 VVYSKLPA  104 (108)
T ss_dssp             EESCSCCC
T ss_pred             EEEecCCC
Confidence            99987654

>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=99.66  E-value=7.6e-17  Score=113.19  Aligned_cols=79  Identities=29%  Similarity=0.488  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ..+.++|||+|||+++|+++|+++|++||+|.+|.|+.+     ++|||||+|.+.++|++|+.. ...+.++.|.|.++
T Consensus         2 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a   75 (88)
T 1wf0_A            2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNA   75 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEec
Confidence            356799999999999999999999999999999999865     689999999999999876543 45678999999988


Q ss_pred             ccccC
Q psy1314          93 TKRVN   97 (275)
Q Consensus        93 ~~~~~   97 (275)
                      .++..
T Consensus        76 ~~~~~   80 (88)
T 1wf0_A           76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76544

>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=99.66  E-value=8.2e-16  Score=123.81  Aligned_cols=112  Identities=15%  Similarity=0.257  Sum_probs=87.1

Q ss_pred             cHHHHHHHHHhC--Cc-eecCeeeccccccccc----------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEec
Q psy1314          67 TQKAVDDLLAAG--DH-YIGNKKIDPKRVTKRV----------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP  133 (275)
Q Consensus        67 ~~e~a~~al~~~--~~-~~~g~~i~v~~~~~~~----------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~  133 (275)
                      +.+.+..|++..  .. .+......+.......          ....++|||+|||+++++++|+++|++||.|..|.|+
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            556777777765  22 3433323333221111          1134789999999999999999999999999999999


Q ss_pred             cCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         134 FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       134 ~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      ++. ++.++|||||+|++.++|++|++.++..+.|++|.|.++..-
T Consensus       143 ~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          143 RTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             ECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             ECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            876 488999999999999999999999888999999999876643

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

Probab=99.66  E-value=2.2e-16  Score=112.74  Aligned_cols=79  Identities=24%  Similarity=0.430  Sum_probs=68.3

Q ss_pred             CCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeec
Q psy1314          11 PGRNDERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKID   88 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~   88 (275)
                      .+..+.++|||+|||+ ++|+++|+++|++||+|.+|.|.        +|||||+|.+.++|++|++. ++..+.+++|.
T Consensus         5 ~~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   76 (96)
T 2kvi_A            5 HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLI   76 (96)
T ss_dssp             ----CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBC
T ss_pred             ccCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEE
Confidence            4567789999999998 99999999999999999999994        57999999999999999995 77899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.....
T Consensus        77 V~~a~~~~~   85 (96)
T 2kvi_A           77 LEVSSSNAR   85 (96)
T ss_dssp             EEEEECCCC
T ss_pred             EEEcCcCCC
Confidence            999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.66  E-value=7.2e-16  Score=120.46  Aligned_cols=84  Identities=24%  Similarity=0.426  Sum_probs=77.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||.++|+++|+++|++||.|.++.++.++.++.++|+|||+|.+.++|.+|++ +++..+.+++|.
T Consensus        81 ~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  160 (166)
T 3md3_A           81 QSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR  160 (166)
T ss_dssp             CCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Confidence            3456678899999999999999999999999999999999999999999999999999999999998 578899999999


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      |.++.
T Consensus       161 v~~a~  165 (166)
T 3md3_A          161 INWAA  165 (166)
T ss_dssp             EEESC
T ss_pred             EEecC
Confidence            99875

>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=99.66  E-value=3.3e-16  Score=141.09  Aligned_cols=85  Identities=19%  Similarity=0.408  Sum_probs=78.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||+++|+++|.++|++||+|+.|.|+.++.+++++|||||+|.+.++|.+||+. ++..|.++.|.|
T Consensus        97 ~~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V  176 (437)
T 3pgw_S           97 AQGDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLV  176 (437)
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEE
Confidence            3445678999999999999999999999999999999999999999999999999999999999975 678999999999


Q ss_pred             cccccc
Q psy1314          90 KRVTKR   95 (275)
Q Consensus        90 ~~~~~~   95 (275)
                      .++...
T Consensus       177 ~~a~~~  182 (437)
T 3pgw_S          177 DVERGR  182 (437)
T ss_pred             EEeCCC
Confidence            998754

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.66  E-value=2.2e-16  Score=118.34  Aligned_cols=82  Identities=12%  Similarity=0.198  Sum_probs=72.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHH----HhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.+..   ++.++|||||+|.+.++|++|++.+ +..|.|++|
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            3456889999999999999876    6999999999988754   4678999999999999999999988 488999999


Q ss_pred             EEEEeeeCCC
Q psy1314         172 DVKRVKFNPE  181 (275)
Q Consensus       172 ~v~~~~~~~~  181 (275)
                      .|.++..+..
T Consensus       103 ~V~~a~~~~~  112 (127)
T 2a3j_A          103 VITFSETPQS  112 (127)
T ss_dssp             EEEECCCCCH
T ss_pred             EEEEccCcch
Confidence            9999987654

>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=99.66  E-value=6.2e-16  Score=110.57  Aligned_cols=78  Identities=26%  Similarity=0.461  Sum_probs=68.4

Q ss_pred             CCCCCCCCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314          10 GPGRNDERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      .....+.++|||+|||. ++++++|+++|++||+|.+|.|.        +|||||+|.+.++|++|++ +++..+.++.|
T Consensus        16 ~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   87 (97)
T 2xnq_A           16 PRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKL   87 (97)
T ss_dssp             ---CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEEC
T ss_pred             cCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            45567789999999998 99999999999999999999983        6899999999999999999 56789999999


Q ss_pred             cccccccc
Q psy1314          88 DPKRVTKR   95 (275)
Q Consensus        88 ~v~~~~~~   95 (275)
                      .|+++..+
T Consensus        88 ~V~~a~~~   95 (97)
T 2xnq_A           88 ILEVSSSN   95 (97)
T ss_dssp             EEEECCCC
T ss_pred             EEEecCCC
Confidence            99988653

>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=3.7e-16  Score=111.42  Aligned_cols=81  Identities=21%  Similarity=0.322  Sum_probs=71.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESI-SIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~-~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      +.....++|||+|||+++|+++|+++|++||+|.+| .|+.++.++    .|||+|.+.++|++||+ +++..+.+++|.
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~----~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   85 (96)
T 2e44_A           10 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETA----VVNVTYSSKDQARQALDKLNGFQLENFTLK   85 (96)
T ss_dssp             CCCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSE----EEEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCC----EEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            444567899999999999999999999999999999 588876643    39999999999999998 578899999999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++.++
T Consensus        86 V~~a~~~   92 (96)
T 2e44_A           86 VAYIPDE   92 (96)
T ss_dssp             EEECCCC
T ss_pred             EEEcCcc
Confidence            9998765

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

Probab=99.66  E-value=1e-16  Score=114.46  Aligned_cols=78  Identities=26%  Similarity=0.493  Sum_probs=68.9

Q ss_pred             CCCcceeeecCCCC-CCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          97 NPLKCKIFVGGLTT-EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        97 ~~~~~~l~V~~l~~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ....++|||+|||+ .+++++|+++|++||.|..|.|.        +|||||+|.+.++|++|++.+ +..+.|++|.|.
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            34578999999998 99999999999999999999984        789999999999999999986 588999999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      ++..++..
T Consensus        79 ~a~~~~~~   86 (96)
T 2kvi_A           79 VSSSNARP   86 (96)
T ss_dssp             EEECCCC-
T ss_pred             EcCcCCCC
Confidence            99876543

>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=99.65  E-value=2.5e-16  Score=111.72  Aligned_cols=79  Identities=15%  Similarity=0.268  Sum_probs=68.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCC-ceecCeeec
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGD-HYIGNKKID   88 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~-v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~-~~~~g~~i~   88 (275)
                      ...+.++|||+|||.++|+++|+++|++||+ |..+.++       ++|||||+|.+.++|++|++ +++ ..+.++.|.
T Consensus         4 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~   76 (93)
T 2cqh_A            4 GSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIME   76 (93)
T ss_dssp             CCCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEE
Confidence            4567889999999999999999999999999 6666663       36899999999999999998 467 899999999


Q ss_pred             ccccccccC
Q psy1314          89 PKRVTKRVN   97 (275)
Q Consensus        89 v~~~~~~~~   97 (275)
                      |+++.++..
T Consensus        77 v~~a~~~~~   85 (93)
T 2cqh_A           77 VDYSVSKKL   85 (93)
T ss_dssp             EEECCCCCC
T ss_pred             EEEccCccc
Confidence            999876543

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

Probab=99.65  E-value=3.2e-16  Score=115.50  Aligned_cols=77  Identities=22%  Similarity=0.407  Sum_probs=67.4

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCC---CCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSK---NMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~---~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~  174 (275)
                      ...++|||+|||+++++++|+++|++||+|. +.++.+..+   ++++|||||+|.+.++|++||+.+ ..++|+.+.+.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~-~~~~G~~~~~~   83 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDAC-LEEDGKLYLCV   83 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHS-EEETTEEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhh-hhcCCcEEEec
Confidence            3468899999999999999999999999999 888888777   689999999999999999999987 34777777665


Q ss_pred             Ee
Q psy1314         175 RV  176 (275)
Q Consensus       175 ~~  176 (275)
                      .+
T Consensus        84 ~~   85 (114)
T 2dnl_A           84 SS   85 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.65  E-value=1.8e-16  Score=116.34  Aligned_cols=77  Identities=13%  Similarity=0.141  Sum_probs=68.8

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      ...+.++|||+|||+++|+++|+++|++||.|.+|.|+.      +++||||+|.+.++|++||+ +++..+.+++|.|+
T Consensus         6 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   79 (111)
T 1whx_A            6 SGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             TSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            344578999999999999999999999999999999875      46899999999999999998 46789999999999


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      ++..
T Consensus        80 ~a~~   83 (111)
T 1whx_A           80 WAPI   83 (111)
T ss_dssp             EEET
T ss_pred             ECCC
Confidence            9864

>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=2.1e-15  Score=107.78  Aligned_cols=82  Identities=18%  Similarity=0.306  Sum_probs=70.7

Q ss_pred             CCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCee
Q psy1314           8 TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKK   86 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~   86 (275)
                      .......+.++|||+||  ++|+++|+++|++||+|.+|.|.      +++|||||+|.+.++|++||+. ++..+.++.
T Consensus         7 ~~~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~   78 (97)
T 1x5p_A            7 GERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQ   78 (97)
T ss_dssp             SCCCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEE
T ss_pred             CccCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            33455567889999996  99999999999999999999995      4578999999999999999975 678999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|+++.++..
T Consensus        79 l~v~~a~~~~~   89 (97)
T 1x5p_A           79 LKVNIARKQPM   89 (97)
T ss_dssp             EEEECCSSCCC
T ss_pred             EEEEECCCCCC
Confidence            99999876543

>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=4.7e-16  Score=120.24  Aligned_cols=81  Identities=21%  Similarity=0.375  Sum_probs=73.1

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .......++|||+|||+++|+++|+++|++||+|.+|.|+.+     ++|||||+|.+.++|++||+ +++..+.+++|.
T Consensus        67 ~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  141 (150)
T 2i2y_A           67 RDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVR  141 (150)
T ss_dssp             SSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCE
T ss_pred             ccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            444567889999999999999999999999999999999886     57999999999999999998 578899999999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++.++
T Consensus       142 v~~a~~~  148 (150)
T 2i2y_A          142 VELSNGE  148 (150)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9988654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.64  E-value=3.6e-16  Score=115.04  Aligned_cols=77  Identities=17%  Similarity=0.273  Sum_probs=68.2

Q ss_pred             CeEEEcCC----CCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEcc----HHH----HHHHHH--h-CCce
Q psy1314          17 RKLFVGGL----HRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT----QKA----VDDLLA--A-GDHY   81 (275)
Q Consensus        17 ~~l~v~~L----p~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~----~e~----a~~al~--~-~~~~   81 (275)
                      ..|||+||    |+++++++|+++|+.||+|.+|.++.|+.|++++|||||+|.+    +++    |.+|+.  . ++..
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    322    778877  3 6789


Q ss_pred             ecCeeecccccc
Q psy1314          82 IGNKKIDPKRVT   93 (275)
Q Consensus        82 ~~g~~i~v~~~~   93 (275)
                      |.|+.|.|..-.
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999988654

>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=99.64  E-value=1.6e-16  Score=124.54  Aligned_cols=82  Identities=37%  Similarity=0.613  Sum_probs=76.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      ...++|||+|||.++|+++|+++|++||+|.++.++.++.+++++|||||+|.+.++|++|+++++..+.+++|.|.++.
T Consensus        85 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~V~~a~  164 (167)
T 2cjk_A           85 DKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE  164 (167)
T ss_dssp             HHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHHCSEECSSSSCEEEEECC
T ss_pred             cCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHhCCCEEeCCeEEEEeecC
Confidence            34678999999999999999999999999999999999889999999999999999999999977789999999999987


Q ss_pred             cc
Q psy1314          94 KR   95 (275)
Q Consensus        94 ~~   95 (275)
                      ++
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.64  E-value=5.7e-16  Score=126.76  Aligned_cols=81  Identities=23%  Similarity=0.376  Sum_probs=75.2

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      +.++|||+|||+++|+++|+++|++||+|.+|+|++|+.+++++|||||+|.+.++|++||+.++ ..+.++.|.+.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            45789999999999999999999999999999999999999999999999999999999999874 88999999998876


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=1.6e-15  Score=108.32  Aligned_cols=79  Identities=16%  Similarity=0.305  Sum_probs=69.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+||  ++++++|+++|++||.|..|.|.      .++|||||+|.+.++|++||+.+ +..|.+++|.|.+
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  89999999999999999999984      35889999999999999999887 4889999999999


Q ss_pred             eeeCCCCC
Q psy1314         176 VKFNPETM  183 (275)
Q Consensus       176 ~~~~~~~~  183 (275)
                      +.+++...
T Consensus        84 a~~~~~~~   91 (97)
T 1x5p_A           84 ARKQPMLD   91 (97)
T ss_dssp             CSSCCCCC
T ss_pred             CCCCCCCC
Confidence            98776543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=1.7e-16  Score=113.55  Aligned_cols=80  Identities=16%  Similarity=0.346  Sum_probs=69.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||.|. +.++.+    .++|||||+|.+.++|++|++.+ +..|.|++|.|.+
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            34468999999999999999999999999986 666654    46899999999999999999887 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +.+++.
T Consensus        91 a~~~~~   96 (97)
T 2e5j_A           91 ARQQRD   96 (97)
T ss_dssp             CCCCCC
T ss_pred             cCCCCC
Confidence            987653

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

Probab=99.64  E-value=3.5e-16  Score=124.25  Aligned_cols=83  Identities=17%  Similarity=0.356  Sum_probs=76.4

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+.+++++|+++|++||+|..|.|+.+. ++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            346899999999999999999999999999999999998 8899999999999999999999987 58899999999998


Q ss_pred             eeCCC
Q psy1314         177 KFNPE  181 (275)
Q Consensus       177 ~~~~~  181 (275)
                      .....
T Consensus       165 ~~~~~  169 (177)
T 2f3j_A          165 ASQID  169 (177)
T ss_dssp             SSGGG
T ss_pred             cCCCC
Confidence            76543

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

Probab=99.64  E-value=3.7e-16  Score=114.02  Aligned_cols=77  Identities=17%  Similarity=0.456  Sum_probs=69.8

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||.|..|.++        +|||||+|.+.++|++|++.+ +..|.|++|.|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            3456899999999999999999999999999999987        689999999999999999986 5899999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +..++.
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987654

>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=5e-16  Score=113.49  Aligned_cols=81  Identities=12%  Similarity=0.178  Sum_probs=70.5

Q ss_pred             CCcceeee--cCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee-----CCe
Q psy1314          98 PLKCKIFV--GGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI-----CGK  169 (275)
Q Consensus        98 ~~~~~l~V--~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~-----~g~  169 (275)
                      .+..+|||  +||++++++++|+++|++||+|..|.|+.+      +|||||+|.+.++|++|++.|+ ..|     .++
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  779999999999999999999999988643      7899999999999999999885 777     688


Q ss_pred             EEEEEEeeeCCCCCC
Q psy1314         170 EVDVKRVKFNPETMG  184 (275)
Q Consensus       170 ~i~v~~~~~~~~~~~  184 (275)
                      +|.|.++...|...+
T Consensus        97 ~l~v~~a~~~p~~~~  111 (114)
T 2cq2_A           97 TLYLNFVEKVQWSGP  111 (114)
T ss_dssp             ECEEEEESCCCCSSC
T ss_pred             EEEEEecccCcccCC
Confidence            999999987766543

>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=99.64  E-value=5e-16  Score=108.98  Aligned_cols=75  Identities=13%  Similarity=0.257  Sum_probs=68.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      +...++|||+|||+++++++|+++|++| +|.+|.|.      +++|||||+|.+.++|++|++ +++..+.+++|.|++
T Consensus         2 s~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   74 (88)
T 1wg1_A            2 SSGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQL   74 (88)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEE
Confidence            3467899999999999999999999999 99999884      568999999999999999998 568899999999998


Q ss_pred             ccc
Q psy1314          92 VTK   94 (275)
Q Consensus        92 ~~~   94 (275)
                      +..
T Consensus        75 a~~   77 (88)
T 1wg1_A           75 QPT   77 (88)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=6.3e-16  Score=108.08  Aligned_cols=73  Identities=23%  Similarity=0.474  Sum_probs=66.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhc----C-------CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCce
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQY----G-------EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHY   81 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~----G-------~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~   81 (275)
                      +.+.++|||+|||+++|+++|+++|++|    |       +|.++.+..+      +|||||+|.+.++|++|+.+++..
T Consensus         3 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~   76 (87)
T 2hzc_A            3 LGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGII   76 (87)
T ss_dssp             SGGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCE
Confidence            4568899999999999999999999999    8       8999999765      689999999999999999667889


Q ss_pred             ecCeeecccc
Q psy1314          82 IGNKKIDPKR   91 (275)
Q Consensus        82 ~~g~~i~v~~   91 (275)
                      +.++.|.|+.
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999998864

>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=99.64  E-value=1.4e-15  Score=119.80  Aligned_cols=81  Identities=25%  Similarity=0.546  Sum_probs=75.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      .....++|||+|||.++|+++|+++|++||+|.+|.++.++.+++++|+|||+|.+.++|++|++. ++..+.+++|.|+
T Consensus        90 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  169 (172)
T 2g4b_A           90 PLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQ  169 (172)
T ss_dssp             CCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            345578999999999999999999999999999999999988999999999999999999999984 7889999999998


Q ss_pred             cc
Q psy1314          91 RV   92 (275)
Q Consensus        91 ~~   92 (275)
                      ++
T Consensus       170 ~A  171 (172)
T 2g4b_A          170 RA  171 (172)
T ss_dssp             EC
T ss_pred             eC
Confidence            76

>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=99.63  E-value=1e-15  Score=123.25  Aligned_cols=79  Identities=13%  Similarity=0.276  Sum_probs=73.5

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~~~   95 (275)
                      .++|||+|||+++|+++|+++|++||+|.+|.|+++. +++++|||||+|.+.++|++||+.++..+.|++|.|.+....
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y  187 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDY  187 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHH
Confidence            5889999999999999999999999999999999985 589999999999999999999998888999999999887543

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

Probab=99.63  E-value=2.3e-16  Score=113.59  Aligned_cols=76  Identities=22%  Similarity=0.412  Sum_probs=68.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||.|..|.+..      ++|||||+|.+.++|++|++.+ +..|.|++|.|.++
T Consensus        25 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   98 (101)
T 2la4_A           25 PRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYP------EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWG   98 (101)
T ss_dssp             SSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBC
T ss_pred             CCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEec
Confidence            3468999999999999999999999999999999873      4789999999999999999886 58999999999988


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      +++
T Consensus        99 ~~~  101 (101)
T 2la4_A           99 KER  101 (101)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            753

>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=99.63  E-value=3.2e-16  Score=111.99  Aligned_cols=82  Identities=17%  Similarity=0.338  Sum_probs=72.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHH----HhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      ....++|||+|||.++++++|+    ++|++||.|..|.++.   ++.++|||||+|.+.++|++|++.+ +..+.|++|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   81 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPM   81 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEE
Confidence            3456899999999999999999    9999999999999874   4567899999999999999999986 589999999


Q ss_pred             EEEEeeeCCC
Q psy1314         172 DVKRVKFNPE  181 (275)
Q Consensus       172 ~v~~~~~~~~  181 (275)
                      .|.++.+++.
T Consensus        82 ~v~~a~~~~~   91 (97)
T 1nu4_A           82 RIQYAKTDSD   91 (97)
T ss_dssp             EEEECSSCCT
T ss_pred             EEEEccCCCc
Confidence            9999987654

>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=99.63  E-value=6e-16  Score=113.48  Aligned_cols=76  Identities=13%  Similarity=0.151  Sum_probs=69.2

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+.+++++|+++|++||.|..|.|+.      +++||||+|.+.++|++||+.+ +..|.+++|.|.++.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            467999999999999999999999999999999874      4789999999999999999987 488999999999998


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ...
T Consensus        83 ~~~   85 (111)
T 1whx_A           83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            653

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.63  E-value=2.2e-15  Score=121.30  Aligned_cols=84  Identities=24%  Similarity=0.547  Sum_probs=78.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ..+.++|||+|||.++|+++|+++|++||.|.+|.++.++.++.++|||||+|.+.++|++|++. ++..+.++.|.|++
T Consensus       111 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  190 (198)
T 2yh0_A          111 PDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQR  190 (198)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            36779999999999999999999999999999999999988999999999999999999999984 78899999999999


Q ss_pred             ccccc
Q psy1314          92 VTKRV   96 (275)
Q Consensus        92 ~~~~~   96 (275)
                      +.++.
T Consensus       191 a~~~~  195 (198)
T 2yh0_A          191 ASVGA  195 (198)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            87654

>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=1.5e-15  Score=108.63  Aligned_cols=75  Identities=25%  Similarity=0.516  Sum_probs=68.1

Q ss_pred             CCCcceeeecCCCC-CCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          97 NPLKCKIFVGGLTT-EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        97 ~~~~~~l~V~~l~~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ....++|||+|||+ ++++++|+++|++||.|..|.+.        +|||||+|.+.++|++|++.+ +..+.|++|.|.
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            34568999999998 99999999999999999999983        789999999999999999977 588999999999


Q ss_pred             EeeeC
Q psy1314         175 RVKFN  179 (275)
Q Consensus       175 ~~~~~  179 (275)
                      +++.+
T Consensus        91 ~a~~~   95 (97)
T 2xnq_A           91 VSSSN   95 (97)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            98764

>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=99.62  E-value=4.8e-16  Score=114.72  Aligned_cols=71  Identities=17%  Similarity=0.296  Sum_probs=61.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      ....++|||+|||+++|+++|+++|++||+|++|.|+.+       |||||+|.+.++|++||+ +++..|.++.|.+.
T Consensus        13 ~r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~   84 (115)
T 3beg_B           13 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETA   84 (115)
T ss_dssp             ----CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeE
Confidence            356789999999999999999999999999999999875       799999999999999999 56788999884443

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.62  E-value=1.6e-15  Score=123.86  Aligned_cols=84  Identities=17%  Similarity=0.487  Sum_probs=77.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~   92 (275)
                      ...++|||+|||.++|+++|+++|++||.|++|.|+.++.+++++|||||+|.+.++|.+|++ +++..|.++.|.|.++
T Consensus       123 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a  202 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKA  202 (216)
T ss_dssp             TTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEe
Confidence            456899999999999999999999999999999999999999999999999999999999999 5788999999999998


Q ss_pred             ccccC
Q psy1314          93 TKRVN   97 (275)
Q Consensus        93 ~~~~~   97 (275)
                      ..+..
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            76543

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.62  E-value=6.5e-16  Score=113.69  Aligned_cols=76  Identities=25%  Similarity=0.396  Sum_probs=67.9

Q ss_pred             ceeeecCC----CCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECC----HHH----HHHHHh--cC-Cce
Q psy1314         101 CKIFVGGL----TTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD----QNV----AEQVLA--NP-KQV  165 (275)
Q Consensus       101 ~~l~V~~l----~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~----~e~----a~~Ai~--~~-~~~  165 (275)
                      .+|+|+||    |+.+++++|+++|++||+|.+|.++.|+.|++++|||||+|.+    +++    |.+|++  .+ +..
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    9999999999999999999999999999999999999999996    322    888988  65 589


Q ss_pred             eCCeEEEEEEe
Q psy1314         166 ICGKEVDVKRV  176 (275)
Q Consensus       166 ~~g~~i~v~~~  176 (275)
                      |.|++|.|..-
T Consensus        83 I~Gr~irV~ln   93 (136)
T 2j8a_A           83 IMGFKFEVILN   93 (136)
T ss_dssp             ETTEEEEEEEC
T ss_pred             ecCcEEEEEEC
Confidence            99999999754

>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=99.62  E-value=1.7e-15  Score=118.39  Aligned_cols=82  Identities=20%  Similarity=0.323  Sum_probs=76.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      +++|||+|||.++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++|++.+ +..+.+++|.|.++.+
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            478999999999999999999999999999999999989999999999999999999999976 5899999999999876


Q ss_pred             CCC
Q psy1314         179 NPE  181 (275)
Q Consensus       179 ~~~  181 (275)
                      ...
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>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=99.62  E-value=2.1e-16  Score=121.27  Aligned_cols=84  Identities=20%  Similarity=0.288  Sum_probs=71.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEE--E---eeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESIS--I---KNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~--i---~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      ...+.++|||+|||+++|+++|+++|++||.|..+.  +   +....+++++|||||+|.+.++|.+||+ +++..+.++
T Consensus        41 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           41 PGEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CCSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            356778999999999999999999999999987641  0   1112468899999999999999999999 578899999


Q ss_pred             eecccccccc
Q psy1314          86 KIDPKRVTKR   95 (275)
Q Consensus        86 ~i~v~~~~~~   95 (275)
                      .|.|+++...
T Consensus       121 ~l~V~~a~~~  130 (143)
T 3egn_A          121 PMVVQFARSA  130 (143)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998654

>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=8.7e-16  Score=109.47  Aligned_cols=79  Identities=13%  Similarity=0.145  Sum_probs=70.5

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEE-EeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEF-QQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v-~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ...++|||+|||+++++++|+++|++||.|..| .|+.++.++    .|||+|.+.++|++||+.+ +..|.|++|.|.+
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            346889999999999999999999999999999 588876654    3999999999999999977 5889999999999


Q ss_pred             eeeCC
Q psy1314         176 VKFNP  180 (275)
Q Consensus       176 ~~~~~  180 (275)
                      +.++.
T Consensus        89 a~~~~   93 (96)
T 2e44_A           89 IPDEM   93 (96)
T ss_dssp             CCCCC
T ss_pred             cCccc
Confidence            98874

>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=99.61  E-value=1.5e-15  Score=118.98  Aligned_cols=83  Identities=14%  Similarity=0.275  Sum_probs=76.7

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .+++|||+|||.++++++|+++|++||+|..|.++.++.++.++|||||+|.+.++|++|++.+ +..+.+++|.|.++.
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            3578999999999999999999999999999999999889999999999999999999999876 589999999999987


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      +...
T Consensus        82 ~~~~   85 (168)
T 1b7f_A           82 PGGE   85 (168)
T ss_dssp             CCSS
T ss_pred             CCcc
Confidence            6543

>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=99.61  E-value=8.8e-16  Score=113.22  Aligned_cols=80  Identities=15%  Similarity=0.289  Sum_probs=72.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||..+++++|+++|++||.|..|.|+.+.   .++|||||+|.+.++|++|++.+ +..+.|+.|.|.++
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 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYY   82 (115)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEe
Confidence            356799999999999999999999999999999998763   44899999999999999999976 58899999999999


Q ss_pred             eeCC
Q psy1314         177 KFNP  180 (275)
Q Consensus       177 ~~~~  180 (275)
                      .++.
T Consensus        83 ~~~~   86 (115)
T 3lqv_A           83 NANR   86 (115)
T ss_dssp             CHHH
T ss_pred             cCCh
Confidence            8654

>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=99.61  E-value=2e-15  Score=105.95  Aligned_cols=75  Identities=17%  Similarity=0.213  Sum_probs=67.9

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+++++++|+++|++| .|..+.|.      +++|||||+|.+.++|++|++.+ +..+.|++|.|.++.
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      46899999999999999999987 588999999999986


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            654

>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=99.61  E-value=2e-15  Score=110.32  Aligned_cols=78  Identities=13%  Similarity=0.251  Sum_probs=63.9

Q ss_pred             CCCCCCCCeEEE--cCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCcee----
Q psy1314          10 GPGRNDERKLFV--GGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYI----   82 (275)
Q Consensus        10 ~~~~~~~~~l~v--~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~----   82 (275)
                      ....++.++|||  +||++++|+++|+++|++||+|++|.|+.+      +|||||+|.+.++|++|++. +++.+    
T Consensus        19 ~~~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~l   92 (114)
T 2cq2_A           19 ETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDL   92 (114)
T ss_dssp             CCCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTT
T ss_pred             cCCCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEcccc
Confidence            344566789999  779999999999999999999999988643      68999999999999999985 45566    


Q ss_pred             -cCeeecccccc
Q psy1314          83 -GNKKIDPKRVT   93 (275)
Q Consensus        83 -~g~~i~v~~~~   93 (275)
                       .+++|.+..+.
T Consensus        93 g~g~~l~v~~a~  104 (114)
T 2cq2_A           93 GQKITLYLNFVE  104 (114)
T ss_dssp             SCEEECEEEEES
T ss_pred             CCCcEEEEEecc
Confidence             46666665543

>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=99.58  E-value=3.6e-15  Score=115.57  Aligned_cols=79  Identities=14%  Similarity=0.176  Sum_probs=69.4

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC--eEEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICG--KEVDVKR  175 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g--~~i~v~~  175 (275)
                      ...+|||+||++.+|+++|+++|++||+|++|.|..+.    +++||||+|.+.++|++|++.|+ ..|.+  ++|+|.+
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            34679999999999999999999999999999987542    47899999999999999999984 78865  9999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      ++++..
T Consensus       121 Ak~~~l  126 (164)
T 1sjr_A          121 SKLTSL  126 (164)
T ss_dssp             CSSSSC
T ss_pred             ecCCcc
Confidence            987643

>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=99.58  E-value=7e-15  Score=113.95  Aligned_cols=80  Identities=14%  Similarity=0.144  Sum_probs=68.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC--eeec
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN--KKID   88 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g--~~i~   88 (275)
                      .+....+|||+||++++|+++|+++|++||+|++|.|..+.    ++|||||+|.+.++|++|++. ++..|.+  +.|.
T Consensus        42 ~ps~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           42 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CCCCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             CCCceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            34455679999999999999999999999999999997542    578999999999999999986 5678855  8999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++..+
T Consensus       118 V~~Ak~~  124 (164)
T 1sjr_A          118 IDFSKLT  124 (164)
T ss_dssp             EEECSSS
T ss_pred             EEEecCC
Confidence            9988765

>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=99.58  E-value=5.1e-16  Score=119.07  Aligned_cols=86  Identities=23%  Similarity=0.410  Sum_probs=71.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEE--eccC---CCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQ--QPFD---KSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKE  170 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~--i~~~---~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~  170 (275)
                      ....++|||+|||+.+++++|+++|++||.|..+.  ++.+   ..++.++|||||+|.+.++|.+||+.+ +..|.|++
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            34568999999999999999999999999987641  1111   235778999999999999999999987 58999999


Q ss_pred             EEEEEeeeCCCC
Q psy1314         171 VDVKRVKFNPET  182 (275)
Q Consensus       171 i~v~~~~~~~~~  182 (275)
                      |.|.++.....+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999876543

>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=99.57  E-value=9.5e-15  Score=102.00  Aligned_cols=71  Identities=23%  Similarity=0.473  Sum_probs=64.2

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccC----C-------CeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-Cce
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQY----G-------SITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQV  165 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~----G-------~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~  165 (275)
                      ...++|||+|||+++++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|++|+ .+ +..
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~   76 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGII   76 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCE
Confidence            346899999999999999999999999    8       8999998755      789999999999999999 65 589


Q ss_pred             eCCeEEEEEE
Q psy1314         166 ICGKEVDVKR  175 (275)
Q Consensus       166 ~~g~~i~v~~  175 (275)
                      +.|++|.|.+
T Consensus        77 ~~g~~l~V~r   86 (87)
T 2hzc_A           77 FQGQSLKIRR   86 (87)
T ss_dssp             ETTEECEEEC
T ss_pred             ECCeEEEEeC
Confidence            9999999874

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.56  E-value=1.7e-14  Score=104.46  Aligned_cols=82  Identities=13%  Similarity=0.200  Sum_probs=71.2

Q ss_pred             CCCCCeEEEcCCCC-----CCCHHHHHHHHhhcCCeeEEEEeeCCCC-CCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314          13 RNDERKLFVGGLHR-----NTGEKEINDYFSQYGEVESISIKNDPHT-GQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~-----~~t~~~l~~~f~~~G~v~~~~i~~~~~t-g~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      +.++++|+|.||..     +.++++|+++|++||+|++|.|++++.+ ++++|++||+|.+.++|.+|++ +++..+.|+
T Consensus         5 ~~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr   84 (105)
T 2pe8_A            5 KCPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGR   84 (105)
T ss_dssp             GSCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTE
T ss_pred             CCCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCc
Confidence            45788999999962     2478999999999999999999998754 6899999999999999999997 578899999


Q ss_pred             eeccccccc
Q psy1314          86 KIDPKRVTK   94 (275)
Q Consensus        86 ~i~v~~~~~   94 (275)
                      .|.+.++..
T Consensus        85 ~i~v~~a~~   93 (105)
T 2pe8_A           85 VVKACFYNL   93 (105)
T ss_dssp             ECEEEECCH
T ss_pred             EEEEEEcCH
Confidence            999988754

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.55  E-value=1.3e-14  Score=108.30  Aligned_cols=77  Identities=16%  Similarity=0.246  Sum_probs=68.1

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeE-EEEEECCHHHHHHHHhcCC-ceeCC--eEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF-CFISFDDQNVAEQVLANPK-QVICG--KEVDVK  174 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~-afV~f~~~e~a~~Ai~~~~-~~~~g--~~i~v~  174 (275)
                      .-.+|||+||++.+|+++|+++|++||+|.+|.|..+     ++|| |||+|.+.++|++|++.|+ ..|.+  +.|+|.
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            4467899999999999999999999999999988754     2677 9999999999999999985 88888  889999


Q ss_pred             EeeeCC
Q psy1314         175 RVKFNP  180 (275)
Q Consensus       175 ~~~~~~  180 (275)
                      +++.+.
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            988764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.55  E-value=2e-14  Score=100.09  Aligned_cols=75  Identities=21%  Similarity=0.221  Sum_probs=64.0

Q ss_pred             CCCCCe-EEEcCCCCCCCHHH----HHHHHhhc-CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCe
Q psy1314          13 RNDERK-LFVGGLHRNTGEKE----INDYFSQY-GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNK   85 (275)
Q Consensus        13 ~~~~~~-l~v~~Lp~~~t~~~----l~~~f~~~-G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~   85 (275)
                      ..++.+ |||+|||.++++++    |+++|++| |+|.+|       |+   |+|||+|.+.++|++|++ +++..+.++
T Consensus         5 ~~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr   74 (96)
T 2diu_A            5 SSGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGN   74 (96)
T ss_dssp             CCCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSS
T ss_pred             CCCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCc
Confidence            345566 99999999999988    55899999 599888       23   999999999999999997 578899999


Q ss_pred             eecccccccccC
Q psy1314          86 KIDPKRVTKRVN   97 (275)
Q Consensus        86 ~i~v~~~~~~~~   97 (275)
                      +|.|+.+..+.+
T Consensus        75 ~i~v~~A~~~sd   86 (96)
T 2diu_A           75 RIIVSFTPKNRE   86 (96)
T ss_dssp             CCEEESSCCSCC
T ss_pred             eEEEEecCCCcc
Confidence            999999976543

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.54  E-value=2.7e-14  Score=106.67  Aligned_cols=80  Identities=15%  Similarity=0.194  Sum_probs=67.4

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccE-EEEEEccHHHHHHHHHh-CCceecC--ee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF-AFVTFTTQKAVDDLLAA-GDHYIGN--KK   86 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~-afV~f~~~e~a~~al~~-~~~~~~g--~~   86 (275)
                      ..+..-.+|||+||++.+|+++|+++|++||+|.+|.|+.+.     +|+ |||+|.+.++|++|++. ++..|.+  +.
T Consensus        23 ~~ps~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~   97 (130)
T 3zzy_A           23 AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCT   97 (130)
T ss_dssp             --CCSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEE
T ss_pred             CCCCceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcE
Confidence            334555678899999999999999999999999999987642     578 99999999999999985 5778877  88


Q ss_pred             ecccccccc
Q psy1314          87 IDPKRVTKR   95 (275)
Q Consensus        87 i~v~~~~~~   95 (275)
                      |.|+++...
T Consensus        98 LrI~~ak~~  106 (130)
T 3zzy_A           98 LRIDFSKLT  106 (130)
T ss_dssp             EEEEECSCS
T ss_pred             EEEEecCCC
Confidence            999988654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=5.8e-14  Score=104.32  Aligned_cols=73  Identities=16%  Similarity=0.094  Sum_probs=62.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccE-EEEEEccHHHHHHHHHh-CCceecC--eeeccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGF-AFVTFTTQKAVDDLLAA-GDHYIGN--KKIDPKRV   92 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~-afV~f~~~e~a~~al~~-~~~~~~g--~~i~v~~~   92 (275)
                      ..|||+|||+.+|+++|+++|++||+|++|.|+..      .|| |||+|.+.++|++|++. ++..|.+  +.|.|+++
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            34679999999999999999999999999999752      286 99999999999999985 6778876  58889888


Q ss_pred             ccc
Q psy1314          93 TKR   95 (275)
Q Consensus        93 ~~~   95 (275)
                      .++
T Consensus       100 k~~  102 (124)
T 2e5i_A          100 RPT  102 (124)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=2.1e-14  Score=106.75  Aligned_cols=75  Identities=9%  Similarity=0.073  Sum_probs=65.6

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeE-EEEEECCHHHHHHHHhcCC-ceeCC--eEEEEEE
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF-CFISFDDQNVAEQVLANPK-QVICG--KEVDVKR  175 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~-afV~f~~~e~a~~Ai~~~~-~~~~g--~~i~v~~  175 (275)
                      ...|||+||++.+++++|+++|++||.|.+|.|...      .|| |||+|.+.++|++|++.|+ ..|.+  ++|.|.+
T Consensus        25 vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~   98 (124)
T 2e5i_A           25 VLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEY   98 (124)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEEC
T ss_pred             EEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEE
Confidence            356789999999999999999999999999998642      276 9999999999999999884 78877  6899999


Q ss_pred             eeeCC
Q psy1314         176 VKFNP  180 (275)
Q Consensus       176 ~~~~~  180 (275)
                      ++++.
T Consensus        99 Ak~~~  103 (124)
T 2e5i_A           99 ARPTR  103 (124)
T ss_dssp             CSCSC
T ss_pred             ecCCc
Confidence            88764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.53  E-value=1.1e-14  Score=101.40  Aligned_cols=71  Identities=17%  Similarity=0.226  Sum_probs=63.3

Q ss_pred             eeeecCCCCCCCHHH----HHHhcccC-CCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314         102 KIFVGGLTTEISEQD----VRDYFSQY-GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~----l~~~F~~~-G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      .|||.|||+.+++++    |+++|++| |.|.+|.       +   |+|||+|.+.++|++|++.| +..|.|++|+|.+
T Consensus        11 ~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt-------g---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A           11 LLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT-------G---CSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             EEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC-------T---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe-------c---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            499999999999988    55899999 5998882       2   89999999999999999987 5899999999999


Q ss_pred             eeeCCCC
Q psy1314         176 VKFNPET  182 (275)
Q Consensus       176 ~~~~~~~  182 (275)
                      ++.+.+.
T Consensus        81 A~~~sd~   87 (96)
T 2diu_A           81 TPKNREL   87 (96)
T ss_dssp             SCCSCCC
T ss_pred             cCCCcce
Confidence            9988764

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.53  E-value=2.4e-14  Score=112.78  Aligned_cols=80  Identities=33%  Similarity=0.502  Sum_probs=69.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceec---Ceee
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIG---NKKI   87 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~---g~~i   87 (275)
                      ...+.++|||+|||.++|+++|+++|++||.|++|.++.++ +++++|||||+|.+.++|.+|++. ++..+.   +++|
T Consensus        91 ~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l  169 (175)
T 3nmr_A           91 NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPM  169 (175)
T ss_dssp             SCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCC
T ss_pred             ccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCe
Confidence            34467899999999999999999999999999999999985 689999999999999999999975 455554   3888


Q ss_pred             ccccc
Q psy1314          88 DPKRV   92 (275)
Q Consensus        88 ~v~~~   92 (275)
                      .|.++
T Consensus       170 ~V~~a  174 (175)
T 3nmr_A          170 VVKFA  174 (175)
T ss_dssp             EEEEC
T ss_pred             EEEec
Confidence            88765

>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=99.52  E-value=2.5e-14  Score=116.29  Aligned_cols=77  Identities=17%  Similarity=0.288  Sum_probs=69.8

Q ss_pred             CcceeeecCCC-CCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          99 LKCKIFVGGLT-TEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        99 ~~~~l~V~~l~-~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ..++|||+||| +.+++++|+++|++||.|.+|+|+.+     ++|||||+|.+.++|++||+.| +..|.|++|.|.++
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            45789999999 89999999999999999999999875     3789999999999999999987 59999999999998


Q ss_pred             eeCC
Q psy1314         177 KFNP  180 (275)
Q Consensus       177 ~~~~  180 (275)
                      +.+.
T Consensus        78 ~~~~   81 (205)
T 3tyt_A           78 KQPA   81 (205)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            7543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=5.1e-14  Score=101.92  Aligned_cols=81  Identities=11%  Similarity=0.103  Sum_probs=69.8

Q ss_pred             CCcceeeecCCCC-----CCCHHHHHHhcccCCCeEEEEeccCCCC-CCeeeEEEEEECCHHHHHHHHhcC-CceeCCeE
Q psy1314          98 PLKCKIFVGGLTT-----EISEQDVRDYFSQYGSITEFQQPFDKSK-NMKKGFCFISFDDQNVAEQVLANP-KQVICGKE  170 (275)
Q Consensus        98 ~~~~~l~V~~l~~-----~~~~~~l~~~F~~~G~v~~v~i~~~~~~-~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~  170 (275)
                      .++++|+|.||..     +.++++|+++|++||.|.+|.|+.++.+ +.++|++||+|.+.++|.+|++.| +..+.|+.
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            3467899999963     2378999999999999999999988654 578999999999999999999988 48999999


Q ss_pred             EEEEEeee
Q psy1314         171 VDVKRVKF  178 (275)
Q Consensus       171 i~v~~~~~  178 (275)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999865

>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=99.52  E-value=3.2e-14  Score=112.33  Aligned_cols=80  Identities=19%  Similarity=0.341  Sum_probs=70.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ....+.++|||+|||.++|+++|+++|++||+|..+     ..++.++|||||+|.+.++|.+|++. ++..+.+++|.|
T Consensus        94 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  168 (175)
T 1fje_B           94 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL  168 (175)
T ss_dssp             STTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEE
T ss_pred             cccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            344567899999999999999999999999987665     46789999999999999999999995 778999999999


Q ss_pred             cccccc
Q psy1314          90 KRVTKR   95 (275)
Q Consensus        90 ~~~~~~   95 (275)
                      +++.++
T Consensus       169 ~~a~~k  174 (175)
T 1fje_B          169 YYTGEK  174 (175)
T ss_dssp             EECSSC
T ss_pred             EecCCC
Confidence            998654

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

Probab=99.52  E-value=2e-14  Score=118.54  Aligned_cols=104  Identities=20%  Similarity=0.200  Sum_probs=76.9

Q ss_pred             HHHHhCCceecCeeeccccccc-----ccCCCcceeeecCCCCCC---------CHHHHHHhcccCCCeEEEEeccCCCC
Q psy1314          73 DLLAAGDHYIGNKKIDPKRVTK-----RVNPLKCKIFVGGLTTEI---------SEQDVRDYFSQYGSITEFQQPFDKSK  138 (275)
Q Consensus        73 ~al~~~~~~~~g~~i~v~~~~~-----~~~~~~~~l~V~~l~~~~---------~~~~l~~~F~~~G~v~~v~i~~~~~~  138 (275)
                      .+|......+.++.........     ......++|||+||+..+         ++++|+++|++||+|..|.|+.+   
T Consensus       102 ~~~~~~~~D~fGr~k~~~~~d~~~g~gs~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~---  178 (240)
T 3u1l_A          102 LALRTEVLDCFGREKFADYREDMGGIGSFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES---  178 (240)
T ss_dssp             HHHHCSSBCTTSSBCGGGTC---------CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG---
T ss_pred             hcccccCcccccchhcccchhcccCcCccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC---
Confidence            3444344445565544333221     123456899999999998         79999999999999999999853   


Q ss_pred             CCeeeEEEEEECCHHHHHHHHhcC-Ccee------------CCeEEEEEEeeeCCCC
Q psy1314         139 NMKKGFCFISFDDQNVAEQVLANP-KQVI------------CGKEVDVKRVKFNPET  182 (275)
Q Consensus       139 ~~~~G~afV~f~~~e~a~~Ai~~~-~~~~------------~g~~i~v~~~~~~~~~  182 (275)
                         +|||||+|.+.++|++|++.| +..|            .|+.|.|.++...+..
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               899999999999999999988 4777            8999999999987654

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

Probab=99.50  E-value=3.7e-14  Score=116.97  Aligned_cols=81  Identities=21%  Similarity=0.329  Sum_probs=67.9

Q ss_pred             CCCCCCCeEEEcCCCCCC---------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCc
Q psy1314          11 PGRNDERKLFVGGLHRNT---------GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDH   80 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~---------t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~   80 (275)
                      +...+.++|||+|||.++         ++++|+++|++||+|++|.|+.+      +|||||+|.+.++|++|++. ++.
T Consensus       129 s~~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~  202 (240)
T 3u1l_A          129 SFRKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQ  202 (240)
T ss_dssp             --CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             ccccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCC
Confidence            345678999999999998         79999999999999999999864      78999999999999999975 566


Q ss_pred             ee------------cCeeecccccccccC
Q psy1314          81 YI------------GNKKIDPKRVTKRVN   97 (275)
Q Consensus        81 ~~------------~g~~i~v~~~~~~~~   97 (275)
                      .|            .++.|.|+++....+
T Consensus       203 ~l~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          203 TLLLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCCCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             EEeccccccccccCCCCEEEEEEccCCCC
Confidence            77            789999999876543

>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=99.49  E-value=1.1e-13  Score=117.81  Aligned_cols=82  Identities=18%  Similarity=0.342  Sum_probs=73.5

Q ss_pred             CCCcceeeecCCCCCCCHHHHH----HhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~----~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      ...+++|||+|||+++++++|+    ++|++||.|..|.|++   +++++|||||+|.+.++|++||+.+ +..|.|+.|
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    8999999999999886   5678999999999999999999887 589999999


Q ss_pred             EEEEeeeCCC
Q psy1314         172 DVKRVKFNPE  181 (275)
Q Consensus       172 ~v~~~~~~~~  181 (275)
                      .|.++..+..
T Consensus        83 ~v~~a~~~~~   92 (282)
T 3pgw_A           83 RIQYAKTDSD   92 (282)
T ss_pred             EEEEeccCcc
Confidence            9999976653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.48  E-value=2.7e-13  Score=96.99  Aligned_cols=69  Identities=14%  Similarity=0.262  Sum_probs=60.1

Q ss_pred             CCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeCCCCCC
Q psy1314         110 TEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPETMG  184 (275)
Q Consensus       110 ~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~~~~~~  184 (275)
                      ..+++++|+++|++||+|..|.|+     ++++|||||+|.+.++|++||+.+. .+.+++|.|.++..++....
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~-~~~g~~l~V~~a~~~~~~~~   95 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV-GLVDNPLKISWLEGQPQDAS   95 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC-BCSSSBCEEECSSCCCCCCS
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC-CCCCCeEEEEEccCCCCCCC
Confidence            578999999999999999999988     2579999999999999999999853 36799999999988765443

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.47  E-value=5.1e-13  Score=95.54  Aligned_cols=78  Identities=17%  Similarity=0.190  Sum_probs=65.2

Q ss_pred             CCCCCeEEEcCCC-------CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCe
Q psy1314          13 RNDERKLFVGGLH-------RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNK   85 (275)
Q Consensus        13 ~~~~~~l~v~~Lp-------~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~   85 (275)
                      .+..++|.|.-..       .++|+++|+++|++||+|++|.|+.     +++|||||+|.+.++|++||+. ...+.++
T Consensus         7 ~~~~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~-----~~rGfaFVeF~~~~~A~~Ai~~-~~~~~g~   80 (100)
T 2d9o_A            7 GQGTPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSS-----KKPGTAVVEFATVKAAELAVQN-EVGLVDN   80 (100)
T ss_dssp             CCSSCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEES-----SSSSEEEEEESCHHHHHHHHHT-CCBCSSS
T ss_pred             CCccceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEcc-----CCCCEEEEEECCHHHHHHHHHh-cCCCCCC
Confidence            4457788887654       4589999999999999999999983     5789999999999999999997 3446789


Q ss_pred             eeccccccccc
Q psy1314          86 KIDPKRVTKRV   96 (275)
Q Consensus        86 ~i~v~~~~~~~   96 (275)
                      +|.|+++..+.
T Consensus        81 ~l~V~~a~~~~   91 (100)
T 2d9o_A           81 PLKISWLEGQP   91 (100)
T ss_dssp             BCEEECSSCCC
T ss_pred             eEEEEEccCCC
Confidence            99999886553

>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=99.46  E-value=3.6e-13  Score=98.71  Aligned_cols=82  Identities=16%  Similarity=0.297  Sum_probs=68.2

Q ss_pred             CCCcceeeecCCCCCCC-----------HHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c
Q psy1314          97 NPLKCKIFVGGLTTEIS-----------EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q  164 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~-----------~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~  164 (275)
                      ...+++|+|.||....+           +++|+++|++||.|..|.| .++   .++|||||+|.+.++|++|++.++ .
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCC
Confidence            34568899999944332           5899999999999999966 443   269999999999999999999885 8


Q ss_pred             eeCCeEEEEEEeeeCCCC
Q psy1314         165 VICGKEVDVKRVKFNPET  182 (275)
Q Consensus       165 ~~~g~~i~v~~~~~~~~~  182 (275)
                      .|.|++|.|.++.++...
T Consensus        88 ~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           88 WFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             EETTEECEEEECCSCCCS
T ss_pred             EECCcEEEEEEeCCCCCc
Confidence            999999999999876553

>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=5.1e-13  Score=97.89  Aligned_cols=82  Identities=15%  Similarity=0.310  Sum_probs=68.0

Q ss_pred             CCCCCCCeEEEcCCCCCC-----------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-C
Q psy1314          11 PGRNDERKLFVGGLHRNT-----------GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-G   78 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~-----------t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~   78 (275)
                      ..+.++++|+|.||....           ++++|+++|++||+|++|.| .++   .++|||||+|.+.++|++|++. +
T Consensus        10 ~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~ln   85 (112)
T 2dit_A           10 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLD   85 (112)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcC
Confidence            356778999999994332           26899999999999999966 443   3799999999999999999975 5


Q ss_pred             CceecCeeeccccccccc
Q psy1314          79 DHYIGNKKIDPKRVTKRV   96 (275)
Q Consensus        79 ~~~~~g~~i~v~~~~~~~   96 (275)
                      +..+.+++|.|.++.++.
T Consensus        86 g~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           86 GRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             TCEETTEECEEEECCSCC
T ss_pred             CCEECCcEEEEEEeCCCC
Confidence            779999999999986543

>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=99.43  E-value=1.6e-13  Score=113.31  Aligned_cols=79  Identities=19%  Similarity=0.332  Sum_probs=71.5

Q ss_pred             CCCcceeeecCCCC-CCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEE
Q psy1314          97 NPLKCKIFVGGLTT-EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVK  174 (275)
Q Consensus        97 ~~~~~~l~V~~l~~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~  174 (275)
                      ....++|||+|||. ++++++|+++|++||.|..|.|+.++     +|||||+|.+.++|++|++.+ +..|.|++|.|.
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            44578999999999 99999999999999999999999874     789999999999999999876 588999999999


Q ss_pred             EeeeCC
Q psy1314         175 RVKFNP  180 (275)
Q Consensus       175 ~~~~~~  180 (275)
                      ++....
T Consensus       106 ~a~~~~  111 (229)
T 2adc_A          106 LSKHQN  111 (229)
T ss_dssp             CCSCCC
T ss_pred             EecCcc
Confidence            987653

>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=99.43  E-value=3e-13  Score=113.94  Aligned_cols=82  Identities=20%  Similarity=0.289  Sum_probs=72.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC--Cceec---Ceeec
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG--DHYIG---NKKID   88 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~--~~~~~---g~~i~   88 (275)
                      .+..+|||+|||.++|+++|+++|++||.|.+|.|+.+ .+++++|||||+|.+.++|.+||+.+  ...+.   +++|.
T Consensus        94 ~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~  172 (261)
T 3sde_A           94 THGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVI  172 (261)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCE
T ss_pred             ccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEE
Confidence            34679999999999999999999999999999999999 58999999999999999999999975  33444   88888


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |.++....
T Consensus       173 v~~~~~~~  180 (261)
T 3sde_A          173 VEPMEQFD  180 (261)
T ss_dssp             EEECCCEE
T ss_pred             EeeccccC
Confidence            88876553

>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=99.42  E-value=4.3e-13  Score=97.00  Aligned_cols=81  Identities=20%  Similarity=0.214  Sum_probs=69.0

Q ss_pred             CCCCeEEEcCC--CCCCC--------HHHHHHHHhhcCCeeEEEEeeCCCC--CCcccEEEEEEccHHHHHHHHH-hCCc
Q psy1314          14 NDERKLFVGGL--HRNTG--------EKEINDYFSQYGEVESISIKNDPHT--GQSRGFAFVTFTTQKAVDDLLA-AGDH   80 (275)
Q Consensus        14 ~~~~~l~v~~L--p~~~t--------~~~l~~~f~~~G~v~~~~i~~~~~t--g~~~G~afV~f~~~e~a~~al~-~~~~   80 (275)
                      .+++.|.|.|+  |.++.        +++|++.|++||+|++|.|++++.+  ++++|++||+|.+.++|.+|++ +++.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            46889999998  44443        4799999999999999999988754  4689999999999999999997 4688


Q ss_pred             eecCeeeccccccc
Q psy1314          81 YIGNKKIDPKRVTK   94 (275)
Q Consensus        81 ~~~g~~i~v~~~~~   94 (275)
                      .+.++.|.+.....
T Consensus        83 ~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           83 KFANRVVVTKYCDP   96 (105)
T ss_dssp             EETTEECEEEEECH
T ss_pred             EeCCCEEEEEEeCH
Confidence            99999999987754

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.40  E-value=1e-12  Score=105.88  Aligned_cols=76  Identities=16%  Similarity=0.267  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcC-CeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceec-Ceeeccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYG-EVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIG-NKKIDPK   90 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G-~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~-g~~i~v~   90 (275)
                      .+.++|||+|||.++|+++|+++|++|| +|.+|.|+.+.     +|+|||+|.+.++|.+|++ +++..+. +++|.|.
T Consensus       118 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~  192 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS  192 (198)
T ss_dssp             CCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEE
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEE
Confidence            4578999999999999999999999999 99999997642     6899999999999999999 5677888 9999999


Q ss_pred             cccc
Q psy1314          91 RVTK   94 (275)
Q Consensus        91 ~~~~   94 (275)
                      ++.+
T Consensus       193 ~a~~  196 (198)
T 1qm9_A          193 FSKS  196 (198)
T ss_dssp             EECC
T ss_pred             eecc
Confidence            8764

>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=99.40  E-value=6.9e-13  Score=95.91  Aligned_cols=81  Identities=17%  Similarity=0.200  Sum_probs=67.5

Q ss_pred             CcceeeecCC--CCCCC--------HHHHHHhcccCCCeEEEEeccCCCC--CCeeeEEEEEECCHHHHHHHHhcCC-ce
Q psy1314          99 LKCKIFVGGL--TTEIS--------EQDVRDYFSQYGSITEFQQPFDKSK--NMKKGFCFISFDDQNVAEQVLANPK-QV  165 (275)
Q Consensus        99 ~~~~l~V~~l--~~~~~--------~~~l~~~F~~~G~v~~v~i~~~~~~--~~~~G~afV~f~~~e~a~~Ai~~~~-~~  165 (275)
                      +++.|.|.|+  |..+.        +++|+++|++||.|.+|.|+++..+  ..++|++||+|.+.++|++|++.|+ ..
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            4566778887  33332        3799999999999999999988765  3578999999999999999999985 89


Q ss_pred             eCCeEEEEEEeeeC
Q psy1314         166 ICGKEVDVKRVKFN  179 (275)
Q Consensus       166 ~~g~~i~v~~~~~~  179 (275)
                      +.|++|.|.++...
T Consensus        84 f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           84 FANRVVVTKYCDPD   97 (105)
T ss_dssp             ETTEECEEEEECHH
T ss_pred             eCCCEEEEEEeCHH
Confidence            99999999987643

>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=99.38  E-value=2.5e-13  Score=98.13  Aligned_cols=71  Identities=17%  Similarity=0.421  Sum_probs=60.4

Q ss_pred             EcCCCCCCCHHHHHHHH------------hhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeee
Q psy1314          21 VGGLHRNTGEKEINDYF------------SQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKI   87 (275)
Q Consensus        21 v~~Lp~~~t~~~l~~~f------------~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i   87 (275)
                      +.+||+++++++|+++|            ++||+|++|.|++++ +++++|||||+|.+.++|++|++ +++..+.|++|
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            45666777777777666            999999999999885 47899999999999999999998 57889999999


Q ss_pred             ccccc
Q psy1314          88 DPKRV   92 (275)
Q Consensus        88 ~v~~~   92 (275)
                      .|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            98765

>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=99.37  E-value=2.1e-13  Score=98.54  Aligned_cols=71  Identities=15%  Similarity=0.368  Sum_probs=60.4

Q ss_pred             ecCCCCCCCHHHHHHhc------------ccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314         105 VGGLTTEISEQDVRDYF------------SQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus       105 V~~l~~~~~~~~l~~~F------------~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      +.+|++.+++++|+++|            ++||.|.+|.|+.+.. ++++|||||+|.+.++|++|++.+ +..++|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~-~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLG-DHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSS-SSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCC-CCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            55677777777666665            9999999999998764 688999999999999999999987 489999999


Q ss_pred             EEEEe
Q psy1314         172 DVKRV  176 (275)
Q Consensus       172 ~v~~~  176 (275)
                      .|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99875

>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=99.37  E-value=1.2e-12  Score=96.53  Aligned_cols=80  Identities=13%  Similarity=0.277  Sum_probs=68.6

Q ss_pred             CCCeEEEcCCC--CCC---CHHHHHHHHhhcCCeeEEEEeeCCC----CCCcccEEEEEEccHHHHHHHHHh-CCceecC
Q psy1314          15 DERKLFVGGLH--RNT---GEKEINDYFSQYGEVESISIKNDPH----TGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN   84 (275)
Q Consensus        15 ~~~~l~v~~Lp--~~~---t~~~l~~~f~~~G~v~~~~i~~~~~----tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g   84 (275)
                      ++++|+|.|+-  .++   .+++|++.|++||+|++|.|++++.    +++++|++||+|.+.++|.+|++. ++..+.|
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            68899999993  222   4799999999999999999998864    457889999999999999999985 6889999


Q ss_pred             eeeccccccc
Q psy1314          85 KKIDPKRVTK   94 (275)
Q Consensus        85 ~~i~v~~~~~   94 (275)
                      +.|.+..+..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999987753

>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=99.34  E-value=2.2e-12  Score=95.13  Aligned_cols=80  Identities=11%  Similarity=0.166  Sum_probs=67.7

Q ss_pred             CcceeeecCCCC--CC---CHHHHHHhcccCCCeEEEEeccCCC----CCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC
Q psy1314          99 LKCKIFVGGLTT--EI---SEQDVRDYFSQYGSITEFQQPFDKS----KNMKKGFCFISFDDQNVAEQVLANPK-QVICG  168 (275)
Q Consensus        99 ~~~~l~V~~l~~--~~---~~~~l~~~F~~~G~v~~v~i~~~~~----~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g  168 (275)
                      ++++|+|.|+-.  ++   .+++|++.|++||+|.+|.|++++.    +++++|++||+|.+.++|.+|++.|+ ..+.|
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            456788888732  22   3689999999999999999998764    45778999999999999999999985 89999


Q ss_pred             eEEEEEEeee
Q psy1314         169 KEVDVKRVKF  178 (275)
Q Consensus       169 ~~i~v~~~~~  178 (275)
                      +.|.|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998754

>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=99.27  E-value=8.6e-12  Score=108.20  Aligned_cols=69  Identities=10%  Similarity=0.203  Sum_probs=58.9

Q ss_pred             CCCCCCCCCCeEEEcC--CCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-Ccee
Q psy1314           8 TAGPGRNDERKLFVGG--LHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYI   82 (275)
Q Consensus         8 ~~~~~~~~~~~l~v~~--Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~   82 (275)
                      .....+.++++|||+|  |+..+|+++|+++|++||+|++|.|..      +||||||+|.+.++|++|++.+ +..+
T Consensus        10 ~v~~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~   81 (345)
T 3tht_A           10 GIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEV   81 (345)
T ss_dssp             TCCCCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CceecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCcc
Confidence            4455678889999999  588999999999999999999987754      4789999999999999999974 4444

>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=99.23  E-value=1.9e-11  Score=106.01  Aligned_cols=74  Identities=12%  Similarity=0.248  Sum_probs=60.8

Q ss_pred             CCCcceeeecC--CCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee---CCe-
Q psy1314          97 NPLKCKIFVGG--LTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI---CGK-  169 (275)
Q Consensus        97 ~~~~~~l~V~~--l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~---~g~-  169 (275)
                      ..++.+|||+|  |+..+|+++|+++|++||+|..|.+..      +||||||+|.+.++|++||+.|+ ..+   .|+ 
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            44567899999  578999999999999999999988754      37999999999999999999985 555   244 


Q ss_pred             -EEEEEEe
Q psy1314         170 -EVDVKRV  176 (275)
Q Consensus       170 -~i~v~~~  176 (275)
                       .+.|.++
T Consensus        89 ~~ly~~~~   96 (345)
T 3tht_A           89 ITLYLNFV   96 (345)
T ss_dssp             EECEEEEC
T ss_pred             eEEEEEEe
Confidence             4555555

>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=99.17  E-value=1.2e-10  Score=85.09  Aligned_cols=77  Identities=12%  Similarity=0.173  Sum_probs=63.8

Q ss_pred             CCCCCeEEEcCCC--CCC--------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCce
Q psy1314          13 RNDERKLFVGGLH--RNT--------GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHY   81 (275)
Q Consensus        13 ~~~~~~l~v~~Lp--~~~--------t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~   81 (275)
                      +-++++|.|.|+=  .+.        .+++|++.|++||.|++|.|.++.    ++|++||+|.+.++|++|++ +++..
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~   79 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRW   79 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCE
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            4567889999982  221        346889999999999999997653    58999999999999999997 47889


Q ss_pred             ecCeeecccccc
Q psy1314          82 IGNKKIDPKRVT   93 (275)
Q Consensus        82 ~~g~~i~v~~~~   93 (275)
                      +.|+.|.+.++.
T Consensus        80 f~GR~i~v~~~~   91 (114)
T 3s6e_A           80 FAGKMITAAYVP   91 (114)
T ss_dssp             ETTEECEEEEEC
T ss_pred             ECCEEEEEEEEc
Confidence            999999998874

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=7.2e-11  Score=86.67  Aligned_cols=76  Identities=17%  Similarity=0.159  Sum_probs=66.2

Q ss_pred             CCCcceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECC-HHHHHHHHhcC---CceeCCeEE
Q psy1314          97 NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD-QNVAEQVLANP---KQVICGKEV  171 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~-~e~a~~Ai~~~---~~~~~g~~i  171 (275)
                      ....+.|+|+||+.. +++++|+++|++||+|..|.+..++.      .|||+|.+ .++|.+|++++   +..|++..+
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            345688999999999 99999999999999999999998854      49999999 89999999987   478899888


Q ss_pred             EEEEeee
Q psy1314         172 DVKRVKF  178 (275)
Q Consensus       172 ~v~~~~~  178 (275)
                      ++....-
T Consensus        89 ~~evL~G   95 (121)
T 1owx_A           89 TWEVLEG   95 (121)
T ss_dssp             EEEECCH
T ss_pred             EEEECCC
Confidence            8876653

>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=99.09  E-value=1e-10  Score=85.50  Aligned_cols=76  Identities=11%  Similarity=0.125  Sum_probs=61.5

Q ss_pred             cceeeecCCCCCC----------CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC
Q psy1314         100 KCKIFVGGLTTEI----------SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICG  168 (275)
Q Consensus       100 ~~~l~V~~l~~~~----------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g  168 (275)
                      ++.|.|.|+=...          .+++|+++|++||.|.+|.|.++.    ++|++||+|.+.++|++|++.|+ ..+.|
T Consensus         7 s~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~G   82 (114)
T 3s6e_A            7 TQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAG   82 (114)
T ss_dssp             CSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             CcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            4456666663221          246899999999999999997653    48999999999999999999884 89999


Q ss_pred             eEEEEEEeeeC
Q psy1314         169 KEVDVKRVKFN  179 (275)
Q Consensus       169 ~~i~v~~~~~~  179 (275)
                      +.|.|.++...
T Consensus        83 R~i~v~~~~~~   93 (114)
T 3s6e_A           83 KMITAAYVPLP   93 (114)
T ss_dssp             EECEEEEECHH
T ss_pred             EEEEEEEEcHH
Confidence            99999988643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=3.8e-10  Score=82.83  Aligned_cols=74  Identities=16%  Similarity=0.146  Sum_probs=61.1

Q ss_pred             CCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEcc-HHHHHHHHHhC---CceecCe
Q psy1314          11 PGRNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT-QKAVDDLLAAG---DHYIGNK   85 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~-~e~a~~al~~~---~~~~~g~   85 (275)
                      ..-.....|+|+||+.+ +++++|+++|++||+|..|.++.+..      .|||.|.+ +++|.+|+..+   +..|.+.
T Consensus        13 ~~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~   86 (121)
T 1owx_A           13 LEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNK   86 (121)
T ss_dssp             CSCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSS
T ss_pred             ccccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCc
Confidence            34466788999999999 99999999999999999999998865      69999999 78898888864   3456665


Q ss_pred             eeccc
Q psy1314          86 KIDPK   90 (275)
Q Consensus        86 ~i~v~   90 (275)
                      .+.++
T Consensus        87 ~~~~e   91 (121)
T 1owx_A           87 EVTWE   91 (121)
T ss_dssp             SEEEE
T ss_pred             EEEEE
Confidence            44443

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.00  E-value=1.7e-09  Score=74.51  Aligned_cols=73  Identities=12%  Similarity=0.208  Sum_probs=59.0

Q ss_pred             CcceeeecCCCC----CCCH----HHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeE
Q psy1314          99 LKCKIFVGGLTT----EISE----QDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKE  170 (275)
Q Consensus        99 ~~~~l~V~~l~~----~~~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~  170 (275)
                      +..+|+|.-++.    ++-+    .+|.+.|++||+|..++|+.++        +||+|.+.++|.+||+..+..++|+.
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            445666665541    2323    6789999999999999999873        89999999999999994469999999


Q ss_pred             EEEEEeeeC
Q psy1314         171 VDVKRVKFN  179 (275)
Q Consensus       171 i~v~~~~~~  179 (275)
                      |+|..+.+.
T Consensus        78 LkV~lkt~d   86 (91)
T 2dnr_A           78 ITIALKSPS   86 (91)
T ss_dssp             EEEEECCCS
T ss_pred             EEEEeCCCC
Confidence            999988764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.96  E-value=1.4e-09  Score=74.97  Aligned_cols=73  Identities=21%  Similarity=0.243  Sum_probs=61.4

Q ss_pred             CCCCeEEEcCCCC----CCCH----HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCe
Q psy1314          14 NDERKLFVGGLHR----NTGE----KEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNK   85 (275)
Q Consensus        14 ~~~~~l~v~~Lp~----~~t~----~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~   85 (275)
                      .+..||+|.-+|.    ++-+    .+|.+.|++||+|..++++.++        +||+|.+.++|.+||++++..+.++
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCCe
Confidence            4556777776662    3333    6799999999999999999873        8999999999999999999999999


Q ss_pred             eeccccccc
Q psy1314          86 KIDPKRVTK   94 (275)
Q Consensus        86 ~i~v~~~~~   94 (275)
                      .|+|+.+.+
T Consensus        77 ~LkV~lkt~   85 (91)
T 2dnr_A           77 TITIALKSP   85 (91)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEeCCC
Confidence            999998764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.85  E-value=3.5e-08  Score=69.13  Aligned_cols=91  Identities=20%  Similarity=0.269  Sum_probs=77.6

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQY-----GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~-----G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      ...-..+|.|.|||.+++++.|.-+|++-     |+|++++...+        -|+|+|.+.+.|++.|+...+.+.+.+
T Consensus         4 ~~~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~~--------~AvItF~d~~va~rVL~k~~H~L~~~~   75 (104)
T 2dhx_A            4 GSSGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGC--------GGVLTFREPADAERVLAQADHELHGAQ   75 (104)
T ss_dssp             SCCCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEETT--------EEEEEESSHHHHHHHHTCSCCBSSSSB
T ss_pred             CccCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcCC--------cEEEEEcChHHHHHHhcCCcceecCeE
Confidence            34567899999999999999999999983     67998888652        699999999999999998899999998


Q ss_pred             ecccccccccCCCcceeeecCCCCCCC
Q psy1314          87 IDPKRVTKRVNPLKCKIFVGGLTTEIS  113 (275)
Q Consensus        87 i~v~~~~~~~~~~~~~l~V~~l~~~~~  113 (275)
                      |.|....+   ....+|++.+|++.++
T Consensus        76 LsV~P~~~---~~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           76 LSLRPAPP---RAPARLLLQGLPPGTS   99 (104)
T ss_dssp             CEEEECCC---CCCCCCCCCSCCCCCC
T ss_pred             EEEEcCCC---CCcceEeeecCCCCCC
Confidence            88876553   3457899999999875

>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=98.83  E-value=6.1e-09  Score=72.09  Aligned_cols=75  Identities=12%  Similarity=0.147  Sum_probs=62.9

Q ss_pred             CCCCCCCeEEEcCCCCC-----CCH----HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCce
Q psy1314          11 PGRNDERKLFVGGLHRN-----TGE----KEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHY   81 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~-----~t~----~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~   81 (275)
                      ..-.+..||+|.-++.+     +-+    .+|.+.|++||+|..++++.++        +||+|.+.++|.+||++++..
T Consensus        10 ~~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~   81 (95)
T 1ufw_A           10 FQGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMK   81 (95)
T ss_dssp             CCCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSE
T ss_pred             ecCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCee
Confidence            34456778999888743     222    5688999999999999999983        999999999999999988999


Q ss_pred             ecCeeecccccc
Q psy1314          82 IGNKKIDPKRVT   93 (275)
Q Consensus        82 ~~g~~i~v~~~~   93 (275)
                      +.++.|+|+...
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998754

>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=98.73  E-value=8.7e-09  Score=71.34  Aligned_cols=73  Identities=18%  Similarity=0.278  Sum_probs=59.1

Q ss_pred             CCCcceeeecCCCCC-----CCH----HHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeC
Q psy1314          97 NPLKCKIFVGGLTTE-----ISE----QDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVIC  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~-----~~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~  167 (275)
                      -++..+|+|.-++..     +-+    .+|.+.|++||+|..++|+.++        +||+|.+.++|.+||+.....++
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~ldG~~v~   83 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVK   83 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHHGGGSEET
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHhcCCeeeC
Confidence            345677888777632     222    5688999999999999999873        99999999999999994469999


Q ss_pred             CeEEEEEEee
Q psy1314         168 GKEVDVKRVK  177 (275)
Q Consensus       168 g~~i~v~~~~  177 (275)
                      |+.|+|....
T Consensus        84 Gr~L~V~~k~   93 (95)
T 1ufw_A           84 GRAVKISGPS   93 (95)
T ss_dssp             TEEEEEECCC
T ss_pred             CeEEEEeccC
Confidence            9999997643

>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=98.70  E-value=6.6e-08  Score=79.03  Aligned_cols=79  Identities=13%  Similarity=0.261  Sum_probs=63.3

Q ss_pred             CCCeEEEcCCC-----CCCCHHHHHHHHhhcCCeeEEEEeeCC----CCCCcccEEEEEEccHHHHHHHHHh-CCceecC
Q psy1314          15 DERKLFVGGLH-----RNTGEKEINDYFSQYGEVESISIKNDP----HTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN   84 (275)
Q Consensus        15 ~~~~l~v~~Lp-----~~~t~~~l~~~f~~~G~v~~~~i~~~~----~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g   84 (275)
                      ....+.+.++-     .+-.+++|++.|++||.|.++.|+++.    .+++++|++||+|.+.++|.+|++. ++..+.|
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            34455555552     234678999999999999999998554    3458999999999999999999985 6789999


Q ss_pred             eeecccccc
Q psy1314          85 KKIDPKRVT   93 (275)
Q Consensus        85 ~~i~v~~~~   93 (275)
                      |.|.+....
T Consensus       203 r~i~~~~~~  211 (222)
T 3dxb_A          203 RKVVAEVYD  211 (222)
T ss_dssp             SBCEEEECC
T ss_pred             eEEEEEEcC
Confidence            999888764

>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=98.66  E-value=3.7e-08  Score=80.58  Aligned_cols=67  Identities=10%  Similarity=0.128  Sum_probs=58.6

Q ss_pred             CCHHHHHHhcccCCCeEEEEeccC----CCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         112 ISEQDVRDYFSQYGSITEFQQPFD----KSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       112 ~~~~~l~~~F~~~G~v~~v~i~~~----~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      -.+++|++.|++||.|..+.|+++    ..+++++|++||+|.+.++|++|++.|+ ..+.|+.|.+.+...
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            356899999999999999999844    4455899999999999999999999984 899999999988753

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.39  E-value=2.9e-06  Score=59.96  Aligned_cols=74  Identities=14%  Similarity=0.161  Sum_probs=64.1

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhc-----CCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHH-HHhCCceecCe
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQY-----GEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL-LAAGDHYIGNK   85 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~-----G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~a-l~~~~~~~~g~   85 (275)
                      ..+..++|-|-+||..++++.|+.+++++     +.++.|.++.|-      +=|+|+|++..+|.+| |..++..|.++
T Consensus        17 ~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr   90 (117)
T 2l9w_A           17 SKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGK   90 (117)
T ss_dssp             TTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTE
T ss_pred             CccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCe
Confidence            34568899999999999999999999999     999999999984      3699999999877765 57888999999


Q ss_pred             eecccc
Q psy1314          86 KIDPKR   91 (275)
Q Consensus        86 ~i~v~~   91 (275)
                      .|.+-.
T Consensus        91 ~Lr~gT   96 (117)
T 2l9w_A           91 VIRSGT   96 (117)
T ss_dssp             EEEEEC
T ss_pred             EEEecC
Confidence            887653

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.33  E-value=1.4e-06  Score=61.52  Aligned_cols=72  Identities=18%  Similarity=0.163  Sum_probs=62.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccC-----CCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQY-----GSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEV  171 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~-----G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i  171 (275)
                      ...++|-+-+||..+++..|+.+++++     +.++.+.+..|.      +-|+|+|.|...|-+|...+ +.+|.|++|
T Consensus        19 ~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~L   92 (117)
T 2l9w_A           19 ELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVI   92 (117)
T ss_dssp             TTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEE
T ss_pred             cCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEE
Confidence            345788899999999999999999999     999999988773      24999999999999988766 689999999


Q ss_pred             EEEE
Q psy1314         172 DVKR  175 (275)
Q Consensus       172 ~v~~  175 (275)
                      .|.-
T Consensus        93 r~gT   96 (117)
T 2l9w_A           93 RSGT   96 (117)
T ss_dssp             EEEC
T ss_pred             EecC
Confidence            9864

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.22  E-value=1.1e-05  Score=56.56  Aligned_cols=74  Identities=19%  Similarity=0.272  Sum_probs=62.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhccc-----CCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQ-----YGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVD  172 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~-----~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~  172 (275)
                      ....+|.|.|||..++++.|+-+|++     -|+|..++...        .-|+|+|.+.+.|++.|++..+.|++.+|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~Ls   77 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLS   77 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEE
Confidence            34578999999999999999999997     26888888653        348999999999999999988999999999


Q ss_pred             EEEeeeC
Q psy1314         173 VKRVKFN  179 (275)
Q Consensus       173 v~~~~~~  179 (275)
                      |....++
T Consensus        78 V~P~~~~   84 (104)
T 2dhx_A           78 LRPAPPR   84 (104)
T ss_dssp             EEECCCC
T ss_pred             EEcCCCC
Confidence            9765544

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=98.07  E-value=1.7e-05  Score=54.80  Aligned_cols=55  Identities=22%  Similarity=0.393  Sum_probs=46.9

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      ...+.++| .+|+++...||.++|+.||.| .|..+.|-       .|||.|.+++.|..|+++
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~   68 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            33455666 999999999999999999955 68888873       799999999999999985

>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=97.75  E-value=0.00012  Score=52.99  Aligned_cols=78  Identities=17%  Similarity=0.240  Sum_probs=57.8

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecC-e
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGN-K   85 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g-~   85 (275)
                      .....+..+.+.|.|-++|++. ...|.++|++||+|.+......      .....|.|.++.+|++||..++..+.+ -
T Consensus        15 ~l~~~~~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~------~NWihI~Y~s~~~A~rAL~kNG~ii~g~~   87 (119)
T 1wwh_A           15 SLTSEDHLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESI   87 (119)
T ss_dssp             ------CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTE
T ss_pred             ccCCCCCCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCC------CCeEEEEeCCHHHHHHHHHhCCeEecCCE
Confidence            3344556667889999999985 6778888999999988877322      348999999999999999999988875 4


Q ss_pred             eecccc
Q psy1314          86 KIDPKR   91 (275)
Q Consensus        86 ~i~v~~   91 (275)
                      .|-|.+
T Consensus        88 mIGV~p   93 (119)
T 1wwh_A           88 MIGVKP   93 (119)
T ss_dssp             ECEEEE
T ss_pred             EEEEEE
Confidence            444444

>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=97.68  E-value=7e-05  Score=51.96  Aligned_cols=52  Identities=23%  Similarity=0.392  Sum_probs=45.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      +.++| .+|+++...||.++|+.||.| .|..+.|-       .|||.|.+++.|..||++
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEEE-EEEEEETT-------EEEEEEEEECHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            34555 999999999999999999944 78888873       899999999999999985

>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=97.54  E-value=0.00039  Score=48.81  Aligned_cols=74  Identities=8%  Similarity=0.052  Sum_probs=59.4

Q ss_pred             CCCCeEEEcCCCCCC-C----HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeee
Q psy1314          14 NDERKLFVGGLHRNT-G----EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKI   87 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~-t----~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i   87 (275)
                      +-.++|+|+||+.++ +    ++.++++|..|+++.....++.-      .-..|.|.++++|.+|-.. ++..+.|+.+
T Consensus         3 ~~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~   76 (104)
T 1wey_A            3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCcee
Confidence            345789999999876 2    36789999999999888888752      2578999999999998654 5678999988


Q ss_pred             cccccc
Q psy1314          88 DPKRVT   93 (275)
Q Consensus        88 ~v~~~~   93 (275)
                      ++-.++
T Consensus        77 r~YFgq   82 (104)
T 1wey_A           77 KLYFAQ   82 (104)
T ss_dssp             EEECCC
T ss_pred             EEEecC
Confidence            877765

>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=0.00075  Score=46.49  Aligned_cols=61  Identities=10%  Similarity=0.132  Sum_probs=49.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC--cccEEEEEEccHHHHHHHHHh
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQ--SRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~--~~G~afV~f~~~e~a~~al~~   77 (275)
                      .+|.|++||+.+||+++.+.+..+.++.....+.-+.+..  .-.-|||.|.+.+++....+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~   64 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDR   64 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            5799999999999999999999988777666665443322  234699999999999988875

>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=97.30  E-value=0.00071  Score=47.52  Aligned_cols=75  Identities=17%  Similarity=0.126  Sum_probs=59.8

Q ss_pred             cceeeecCCCCCC-CH----HHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEE
Q psy1314         100 KCKIFVGGLTTEI-SE----QDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDV  173 (275)
Q Consensus       100 ~~~l~V~~l~~~~-~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v  173 (275)
                      .++|+|.||+..+ ..    +.++++|..|.++......+.=      .-..|.|.++++|.+|-..++ ..+.|++++|
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            4679999998866 22    5678999999988776665431      127899999999999998884 8899999999


Q ss_pred             EEeeeCC
Q psy1314         174 KRVKFNP  180 (275)
Q Consensus       174 ~~~~~~~  180 (275)
                      .++++.+
T Consensus        79 YFgq~~~   85 (104)
T 1wey_A           79 YFAQTLH   85 (104)
T ss_dssp             ECCCCSS
T ss_pred             EecCCCC
Confidence            9988543

>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=97.25  E-value=0.0019  Score=46.61  Aligned_cols=72  Identities=17%  Similarity=0.183  Sum_probs=57.7

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCC-eEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICG-KEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g-~~i~v~~~~  177 (275)
                      ..+-|.|-++|... ...|-+.|++||+|.+.....      ...+-.|+|+++.+|++||.+.+..|.+ -.|-|....
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~~   95 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   95 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEECC
Confidence            35678888999885 567778899999999887621      2458999999999999999998888875 667776654

>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=97.22  E-value=0.00045  Score=47.74  Aligned_cols=54  Identities=19%  Similarity=0.315  Sum_probs=42.8

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      .+.++| .+|.++...||.++|++||.| .|..+-|.       .|||.|.+++.|..|+..+
T Consensus        16 ~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           16 DHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             CeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            455666 999999999999999999853 34444332       5999999999999998853

>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=96.94  E-value=0.00073  Score=46.85  Aligned_cols=52  Identities=17%  Similarity=0.289  Sum_probs=42.2

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      +.++| ++|.++...||.++|++||. ..|..+-|.       .|||.|.+++.|..|+..
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~   58 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVKIAVNT   58 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-------EEEEEEEEECHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHh
Confidence            45666 99999999999999999983 445555442       499999999999998885

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.61  E-value=0.003  Score=43.79  Aligned_cols=63  Identities=5%  Similarity=0.040  Sum_probs=44.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC--cccEEEEEEccHHHHHHHHHh
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQ--SRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~--~~G~afV~f~~~e~a~~al~~   77 (275)
                      .+-+|.|+.||+.+||+++.+.+..+=++.....+.-+.+-.  .-.-|||.|.+.|+.....+.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~   72 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDR   72 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHH
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHH
Confidence            456899999999999999999888764443333322222111  123589999999999998886

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.55  E-value=0.0012  Score=59.20  Aligned_cols=58  Identities=17%  Similarity=0.330  Sum_probs=44.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG   78 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~   78 (275)
                      ..++|+|. .|.++++.+|.++|++||+|.++.+-.+..     -||.|+|++.+++.++++..
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g-----~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG-----LYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS-----EEEEEECC---CCHHHHSSC
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC-----eEEEEEeCCHHHHHHHHhcc
Confidence            35789998 799999999999999999999999876542     49999999999999887653

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=96.49  E-value=0.0079  Score=41.35  Aligned_cols=62  Identities=10%  Similarity=0.128  Sum_probs=48.8

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCC--eeeEEEEEECCHHHHHHHHhcC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNM--KKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~--~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      ++|.|++||+.+|++++.+.+.....+.....+..+.+..  .-.-|+|.|.+.+++....+..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~   65 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRF   65 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHH
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHh
Confidence            4789999999999999999999888877766654433221  2244899999999998888875

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.19  E-value=0.0076  Score=44.09  Aligned_cols=78  Identities=22%  Similarity=0.312  Sum_probs=54.7

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEE-EEeccCCC---------CC----CeeeEEEEEECCHHHHHHHHhcCCce
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITE-FQQPFDKS---------KN----MKKGFCFISFDDQNVAEQVLANPKQV  165 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~-v~i~~~~~---------~~----~~~G~afV~f~~~e~a~~Ai~~~~~~  165 (275)
                      ...|.|=+.|+..+. .+-+.|++||.|.+ +.+.....         +.    ....+..|+|+++.+|.+||.+.+..
T Consensus         7 e~~VtVFGFp~~~~~-~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMAN-QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGHH-HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHHH-HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            345777788777655 56678999999866 22221000         00    12467899999999999999999999


Q ss_pred             eCCeEEEEEEeee
Q psy1314         166 ICGKEVDVKRVKF  178 (275)
Q Consensus       166 ~~g~~i~v~~~~~  178 (275)
                      |.|..|-|....+
T Consensus        86 i~G~mIGV~Py~~   98 (132)
T 3p3d_A           86 FNGVLLGVIPYTK   98 (132)
T ss_dssp             ETTEECEEEECCH
T ss_pred             eCcEEEEEEECCH
Confidence            9998877776543

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.11  E-value=0.0067  Score=44.38  Aligned_cols=78  Identities=13%  Similarity=0.240  Sum_probs=51.8

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeE-EEEeeC--------CCCCC-----cccEEEEEEccHHHHHHHHHhCC
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVES-ISIKND--------PHTGQ-----SRGFAFVTFTTQKAVDDLLAAGD   79 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~-~~i~~~--------~~tg~-----~~G~afV~f~~~e~a~~al~~~~   79 (275)
                      ..+..|.|=+.|++.+ ..+.++|++||.|.+ ..+...        +.+.+     ......|+|.++.+|.+||+.++
T Consensus         5 ~~e~~VtVFGFp~~~~-~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG   83 (132)
T 3p3d_A            5 NGELAILVFGYPETMA-NQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENG   83 (132)
T ss_dssp             ---CEEEEECCCGGGH-HHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTT
T ss_pred             cCceEEEEEecCHHHH-HHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCC
Confidence            4456678888866654 567778999999765 222110        00011     24577999999999999999999


Q ss_pred             ceecCeeeccccc
Q psy1314          80 HYIGNKKIDPKRV   92 (275)
Q Consensus        80 ~~~~g~~i~v~~~   92 (275)
                      ..|.+..|-|.+.
T Consensus        84 ~ii~G~mIGV~Py   96 (132)
T 3p3d_A           84 AVFNGVLLGVIPY   96 (132)
T ss_dssp             CEETTEECEEEEC
T ss_pred             eEeCcEEEEEEEC
Confidence            9999875555544

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.56  E-value=0.0053  Score=55.02  Aligned_cols=60  Identities=15%  Similarity=0.227  Sum_probs=44.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      ....+.|+|. .|..+++.+|.++|++||+|.++....+.     .-|+.|||.+.+++.+++...
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~~  109 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNGT  109 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSSC
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhcc
Confidence            3445789997 79999999999999999999999876542     369999999999999887663

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.49  E-value=0.033  Score=38.57  Aligned_cols=64  Identities=6%  Similarity=0.047  Sum_probs=45.9

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCC--eeeEEEEEECCHHHHHHHHhcCC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNM--KKGFCFISFDDQNVAEQVLANPK  163 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~--~~G~afV~f~~~e~a~~Ai~~~~  163 (275)
                      +.+|.|+.||+.+|++++.+.+...-++.....+..+.+..  .-.-|+|.|.+.+++....+..+
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~   74 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFD   74 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHST
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcC
Confidence            46799999999999999988888765554433333222211  12348999999999999888853

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.26  E-value=0.26  Score=44.82  Aligned_cols=54  Identities=22%  Similarity=0.395  Sum_probs=44.8

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      ..+.++|+ +|..+...+|.++|+.||.| +|..+.+.       .|||.|.+.+.|..+++.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-------~a~V~~~~~~~a~~~l~~  492 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNT  492 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-------EEEEECSCHHHHHHHHHH
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-------eEEEEECCHHHHHHHHHH
Confidence            34566676 99999999999999999954 67666652       799999999999999885

>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=85.38  E-value=2.1  Score=38.79  Aligned_cols=54  Identities=19%  Similarity=0.308  Sum_probs=42.0

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      +..++|+ +|..+...+|.++|+.||.| .|..+.+       -.|||.|.+.+.|..++..+
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widd-------t~a~V~~~~~~~a~~~l~~~  493 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDD-------TSAFVSLSQPEQVQIAVNTS  493 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSS-------SEEEEECSCHHHHHHHHHHH
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcC-------CeEEEEECCHHHHHHHHHHH
Confidence            3456665 88899999999999999954 4554433       25999999999999888764

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=83.75  E-value=3.7  Score=27.56  Aligned_cols=57  Identities=12%  Similarity=0.124  Sum_probs=45.1

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      ..+|-|.|-|+|..+-..++.-.....|---.|..+        .|-|.|.|.+.++..-|+.++
T Consensus        10 kqnclikiinipqgtlkaevvlavrhlgyefycdyi--------dgqamirfqnsdeqrlaiqkl   66 (129)
T 4eyt_A           10 KQNCLIKIINIPQGTLKAEVVLAVRHLGYEFYCDYI--------DGQAMIRFQNSDEQRLAIQKL   66 (129)
T ss_dssp             CCSCEEEEECCCTTCCHHHHHHHHHTTCCCEEEEEC--------SSCEEEEESSHHHHHHHHHHH
T ss_pred             hhCcEEEEEecCCCceeeeeEEeehhcCeeEeeeee--------cCeeEEEecCChHHHHHHHHH
Confidence            346778899999999988888777777765666654        235999999999999998874

---

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	275
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	1e-31
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	3e-18
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-17
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-18
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	3e-17
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-17
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-15
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	3e-17
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-17
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-16
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-16
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-15
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	1e-13
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-15
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-15
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	5e-14
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	2e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	6e-12
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	6e-14
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-12
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-13
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-09
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	4e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-12
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-12
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-11
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-12
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	7e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	1e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-11
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	5e-11
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-10
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	8e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-10
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	9e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-10
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	8e-09
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-10
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-10
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	3e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-10
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	9e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	4e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-09
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-10
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	5e-08
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-10
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-09
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	8e-10
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-10
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-09
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-09
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	5e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	2e-09
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	5e-09
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	3e-09
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	9e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	3e-09
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	9e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-09
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-08
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-09
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	1e-08
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	6e-09
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-08
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-09
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	7e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-07
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	8e-09
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	9e-08
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	8e-09
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-08
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	4e-08
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	3e-07
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-08
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	3e-06
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	4e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	6e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	9e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	2e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-05
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-07
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	6e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-06
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-06
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	3e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	1e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	9e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 1e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	2e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	1e-04
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-05
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-05
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	4e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	4e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	9e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	1e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	1e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	8e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.002
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	0.001
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.001
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	0.004
d2b0ga1	83	d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosoph	0.002
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.003
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	0.003
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	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 =  113 bits (283), Expect = 1e-31
 Identities = 56/175 (32%), Positives = 92/175 (52%), Gaps = 7/175 (4%)

Query: 14  NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
              RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD 
Sbjct: 4   EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA 63

Query: 74  LLAAGDHYIGNKKIDPKRVTKRVNPLKC-------KIFVGGLTTEISEQDVRDYFSQYGS 126
            + A  H +  + ++PKR   R +  +        KIFVGG+  +  E  +RDYF QYG 
Sbjct: 64  AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGK 123

Query: 127 ITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFNPE 181
           I   +   D+    K+GF F++FDD +  ++++      + G   +V++     E
Sbjct: 124 IEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 178

>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 = 55.8 bits (133), Expect = 3e-10
 Identities = 19/82 (23%), Positives = 43/82 (52%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ E +++ +R +F Q+G++T+     D +    +GF F+++      +  +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 162 PKQVICGKEVDVKRVKFNPETM 183
               + G+ V+ KR     ++ 
Sbjct: 68  RPHKVDGRVVEPKRAVSREDSQ 89

>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 = 75.0 bits (184), Expect = 3e-18
 Identities = 25/75 (33%), Positives = 44/75 (58%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           CK+F+GGL+ + +++ +R+YF Q+G + E     D      +GF F++F DQ   ++VLA
Sbjct: 1   CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA 60

Query: 161 NPKQVICGKEVDVKR 175
             +  +  K +D K 
Sbjct: 61  QSRHELDSKTIDPKV 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 = 72.7 bits (178), Expect = 2e-17
 Identities = 34/74 (45%), Positives = 47/74 (63%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL   T ++ + +YF Q+GEV+   +  DP T +SRGF FVTF  Q  VD +LA 
Sbjct: 2  KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ 61

Query: 78 GDHYIGNKKIDPKR 91
            H + +K IDPK 
Sbjct: 62 SRHELDSKTIDPKV 75

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.7 bits (183), Expect = 8e-18
 Identities = 32/83 (38%), Positives = 50/83 (60%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          +   RKLF+GGL   T E+ + +Y+ Q+G++    +  DP + +SRGF FVTF++   VD
Sbjct: 17 KEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVD 76

Query: 73 DLLAAGDHYIGNKKIDPKRVTKR 95
            +AA  H I  + ++PKR   R
Sbjct: 77 AAMAARPHSIDGRVVEPKRAVAR 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 = 73.2 bits (179), Expect = 3e-17
 Identities = 26/89 (29%), Positives = 45/89 (50%)

Query: 89  PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
           P    KR      K+F+GGL+ E +E+ +R+Y+ Q+G +T+     D +    +GF F++
Sbjct: 9   PLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 68

Query: 149 FDDQNVAEQVLANPKQVICGKEVDVKRVK 177
           F      +  +A     I G+ V+ KR  
Sbjct: 69  FSSMAEVDAAMAARPHSIDGRVVEPKRAV 97

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 73.5 bits (180), Expect = 1e-17
 Identities = 29/77 (37%), Positives = 46/77 (59%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
            RKLF+GGL   T ++ +  +F Q+G +    +  DP+T +SRGF FVT+ T + VD  
Sbjct: 5  QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA 64

Query: 75 LAAGDHYIGNKKIDPKR 91
          + A  H +  + ++PKR
Sbjct: 65 MNARPHKVDGRVVEPKR 81

>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 = 68.1 bits (166), Expect = 1e-15
 Identities = 19/74 (25%), Positives = 41/74 (55%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ E +++ +R +F Q+G++T+     D +    +GF F+++      +  +  
Sbjct: 8   KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67

Query: 162 PKQVICGKEVDVKR 175
               + G+ V+ KR
Sbjct: 68  RPHKVDGRVVEPKR 81

>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 = 72.3 bits (177), Expect = 3e-17
 Identities = 30/74 (40%), Positives = 45/74 (60%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  +T E++I +YF  +GEVESI +  D  T + RGF F+TF  ++ V  ++  
Sbjct: 1  KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 78 GDHYIGNKKIDPKR 91
            H +G  K + K 
Sbjct: 61 KYHNVGLSKCEIKV 74

>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 = 71.9 bits (176), Expect = 5e-17
 Identities = 22/74 (29%), Positives = 43/74 (58%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+ +  E+ +R+YF  +G +   + P D   N ++GFCFI+F ++   ++++  
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

Query: 162 PKQVICGKEVDVKR 175
               +   + ++K 
Sbjct: 61  KYHNVGLSKCEIKV 74

>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 = 70.8 bits (173), Expect = 1e-16
 Identities = 35/74 (47%), Positives = 52/74 (70%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+F+GGL  +T +K++ DYFS++GEV   ++K DP TG+SRGF FV F   ++VD ++  
Sbjct: 1  KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 78 GDHYIGNKKIDPKR 91
           +H +  K IDPKR
Sbjct: 61 KEHKLNGKVIDPKR 74

>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 = 69.6 bits (170), Expect = 3e-16
 Identities = 22/74 (29%), Positives = 44/74 (59%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL+ + +++D++DYFS++G + +     D      +GF F+ F +    ++V+  
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ 60

Query: 162 PKQVICGKEVDVKR 175
            +  + GK +D KR
Sbjct: 61  KEHKLNGKVIDPKR 74

>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 = 68.5 bits (167), Expect = 1e-15
 Identities = 20/87 (22%), Positives = 38/87 (43%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
          P   D R +F   L      +++ D+FS  G+V  + I +D ++ +S+G A+V F   ++
Sbjct: 13 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 72

Query: 71 VDDLLAAGDHYIGNKKIDPKRVTKRVN 97
          V   +      +    I  +      N
Sbjct: 73 VPLAIGLTGQRLLGVPIIVQASQAEKN 99

>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 = 63.5 bits (154), Expect = 1e-13
 Identities = 15/78 (19%), Positives = 32/78 (41%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
              +F   L   I  +D+ D+FS  G + + +   D++    KG  ++ F +       +
Sbjct: 18  ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI 77

Query: 160 ANPKQVICGKEVDVKRVK 177
               Q + G  + V+  +
Sbjct: 78  GLTGQRLLGVPIIVQASQ 95

>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 = 67.3 bits (164), Expect = 3e-15
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 1/82 (1%)

Query: 94  KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           KR       + V GL  + +EQD+++YFS +G +   Q   D      KGF F+ F +  
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 154 VAEQVLANPKQVICGKEVDVKR 175
              +V++  + +I G+  D K 
Sbjct: 62  TQVKVMSQ-RHMIDGRWCDCKL 82

>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 = 66.9 bits (163), Expect = 5e-15
 Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            L V GL   T E+++ +YFS +GEV  + +K D  TG S+GF FV FT  +    +++
Sbjct: 9  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS 68

Query: 77 AGDHYIGNKKIDPKRVTKR 95
             H I  +  D K    +
Sbjct: 69 QR-HMIDGRWCDCKLPNSK 86

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 63.6 bits (154), Expect = 5e-14
 Identities = 25/74 (33%), Positives = 42/74 (56%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGG+  +  E  +RDYF QYG I   +   D+    K+GF F++FDD +  ++++  
Sbjct: 4   KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ 63

Query: 162 PKQVICGKEVDVKR 175
               + G   +V++
Sbjct: 64  KYHTVNGHNCEVRK 77

>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 = 62.0 bits (150), Expect = 2e-13
 Identities = 29/75 (38%), Positives = 45/75 (60%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          +K+FVGG+  +T E  + DYF QYG++E I I  D  +G+ RGFAFVTF    +VD ++ 
Sbjct: 3  KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 77 AGDHYIGNKKIDPKR 91
             H +     + ++
Sbjct: 63 QKYHTVNGHNCEVRK 77

>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 = 64.2 bits (156), Expect = 6e-14
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-HTGQSRGFAFVTFTTQK 69
          P +    K+ V  +     ++EI + FS +GE++++ +      TG  RGF FV F T++
Sbjct: 3  PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 70 AVDDLLAAGDH--YIGNKKI 87
                 A  H  ++  +++
Sbjct: 63 DAKKAFNALCHSTHLYGRRL 82

>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 = 58.4 bits (141), Expect = 6e-12
 Identities = 14/86 (16%), Positives = 35/86 (40%), Gaps = 3/86 (3%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK-GFCFISFDDQNVAEQV 158
             KI V  +  + +++++R+ FS +G +   + P   +      GF F+ F  +  A++ 
Sbjct: 8   TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 67

Query: 159 LA--NPKQVICGKEVDVKRVKFNPET 182
                    + G+ + ++        
Sbjct: 68  FNALCHSTHLYGRRLVLEWADSEVTV 93

>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 = 63.2 bits (153), Expect = 6e-14
 Identities = 27/74 (36%), Positives = 45/74 (60%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           KIFVGGL+   + +DV+ YF Q+G + +    FDK+ N  +GF F++F+ +++ E+V   
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 162 PKQVICGKEVDVKR 175
               I  K V+ K+
Sbjct: 61  HFHEINNKMVECKK 74

>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 = 59.4 bits (143), Expect = 2e-12
 Identities = 28/74 (37%), Positives = 44/74 (59%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          K+FVGGL  NT  +++  YF Q+G+V+   +  D  T + RGF FVTF ++  V+ +   
Sbjct: 1  KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60

Query: 78 GDHYIGNKKIDPKR 91
            H I NK ++ K+
Sbjct: 61 HFHEINNKMVECKK 74

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 62.0 bits (150), Expect = 3e-13
 Identities = 14/95 (14%), Positives = 37/95 (38%), Gaps = 9/95 (9%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEF--QQPFDKSKNMKKGFCFISFDDQNVAE-- 156
           C++F+GG+      +++ +  ++                K   +GF F+ ++    A   
Sbjct: 2   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 61

Query: 157 -QVLANPKQVICGKEVDVKRVK----FNPETMGSV 186
            + L   +  + G ++ V   +     + + M +V
Sbjct: 62  RRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 96

>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 = 52.0 bits (124), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 10/84 (11%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVES--ISIKNDPHTGQSRGFAFVTFTTQKAVD--- 72
          +LF+GG+ +    +EI +  ++  E     I   +     ++RGFAFV + + +A     
Sbjct: 3  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 73 DLLAAGDHYIGNKKI-----DPKR 91
            L  G   +   +I     +P+ 
Sbjct: 63 RKLMPGRIQLWGHQIAVDWAEPEI 86

>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 = 60.1 bits (145), Expect = 1e-12
 Identities = 14/87 (16%), Positives = 31/87 (35%), Gaps = 5/87 (5%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN-----DPHTGQSRGFAFVTFTTQKAV 71
          R+L+VG +     E+ + D+F+    +  ++             Q + FAF+ F +    
Sbjct: 2  RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 72 DDLLAAGDHYIGNKKIDPKRVTKRVNP 98
             +A        + +  +R       
Sbjct: 62 TQAMAFDGIIFQGQSLKIRRPHDYQPL 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 = 56.3 bits (135), Expect = 4e-11
 Identities = 15/81 (18%), Positives = 33/81 (40%), Gaps = 5/81 (6%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITE-----FQQPFDKSKNMKKGFCFISFDDQNVAE 156
           +++VG +   I+E+ + D+F+    +                N  K F F+ F   +   
Sbjct: 3   RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62

Query: 157 QVLANPKQVICGKEVDVKRVK 177
           Q +A    +  G+ + ++R  
Sbjct: 63  QAMAFDGIIFQGQSLKIRRPH 83

>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 = 59.7 bits (144), Expect = 2e-12
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 2/79 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             ++V GL   ++++++   FSQYG I   +   D+   + +G  FI FD +  AE+ + 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 161 NP-KQVICGKEVDVKRVKF 178
               Q   G    +  VKF
Sbjct: 67  GLNGQKPSGATEPI-TVKF 84

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 22/78 (28%), Positives = 37/78 (47%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           +  L+V GL +   +KE+   FSQYG + +  I  D  TG SRG  F+ F  +   ++ 
Sbjct: 5  RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 64

Query: 75 LAAGDHYIGNKKIDPKRV 92
          +   +    +   +P  V
Sbjct: 65 IKGLNGQKPSGATEPITV 82

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 5e-12
 Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 3/89 (3%)

Query: 10 GPG--RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
          GP   RN +  ++VGGL     E  + + F Q G V +  +  D  TGQ +G+ FV F +
Sbjct: 1  GPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 60

Query: 68 QKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
          ++  D  +   D   +  K I   + +  
Sbjct: 61 EEDADYAIKIMDMIKLYGKPIRVNKASAH 89

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.3 bits (138), Expect = 2e-11
 Identities = 18/84 (21%), Positives = 38/84 (45%), Gaps = 1/84 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             ++VGGL  ++SE  + + F Q G +     P D+     +G+ F+ F  +  A+  + 
Sbjct: 10  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 69

Query: 161 N-PKQVICGKEVDVKRVKFNPETM 183
                 + GK + V +   + + +
Sbjct: 70  IMDMIKLYGKPIRVNKASAHNKNL 93

>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 = 58.4 bits (141), Expect = 6e-12
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 1/74 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C ++VG L+   +E+ + + FS+ G I +     DK K    GFCF+ +  +  AE  + 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 161 NP-KQVICGKEVDV 173
                 +  + +  
Sbjct: 68  YINGTRLDDRIIRT 81

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.4 bits (128), Expect = 4e-10
 Identities = 17/72 (23%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            L+VG L   T E++I + FS+ G+++ I +  D     + GF FV + ++   ++ + 
Sbjct: 8  CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 77 AGD-HYIGNKKI 87
            +   + ++ I
Sbjct: 68 YINGTRLDDRII 79

>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 = 57.6 bits (139), Expect = 8e-12
 Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           L+VG LH +  E  + + FS  G + SI +  D  T +S G+A+V F      +  L  
Sbjct: 2  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 78 GD-HYIGNKKI 87
           +   I  K +
Sbjct: 62 MNFDVIKGKPV 72

>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 = 56.9 bits (137), Expect = 2e-11
 Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++VG L  +++E  + + FS  G I   +   D       G+ +++F     AE+ L  
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 162 -PKQVICGKEVDVK 174
               VI GK V + 
Sbjct: 62  MNFDVIKGKPVRIM 75

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.7 bits (139), Expect = 1e-11
 Identities = 19/76 (25%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           +  L+V  L R   + +++  F +YG +   +I  D  TG+ RG AFV +  ++   + 
Sbjct: 5  KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 75 LAAGDHYI---GNKKI 87
          ++A ++ I   G++ +
Sbjct: 65 ISALNNVIPEGGSQPL 80

>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 = 55.3 bits (133), Expect = 7e-11
 Identities = 13/61 (21%), Positives = 29/61 (47%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             ++V  L   I++  +   F +YGSI +     DK     +G  F+ ++ +  A++ ++
Sbjct: 7   TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 66

Query: 161 N 161
            
Sbjct: 67  A 67

>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 = 57.4 bits (138), Expect = 1e-11
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  ++VGGL  E+ ++ +   F  +G IT+ Q P D      +GF F+ F+    A   +
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 160 ANP-KQVICGKEVDVKRVK 177
            N  +  + G+ + V   K
Sbjct: 65  DNMNESELFGRTIRVNLAK 83

>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 = 55.1 bits (132), Expect = 9e-11
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 6/84 (7%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           +R L+VGGL     +K ++  F  +G++  I I  D  T + RGFAFV F   +     
Sbjct: 4  TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63

Query: 75 LAAGD-HYIGNKKID-----PKRV 92
          +   +   +  + I      P R+
Sbjct: 64 IDNMNESELFGRTIRVNLAKPMRI 87

>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 = 5e-11
 Identities = 21/114 (18%), Positives = 44/114 (38%), Gaps = 11/114 (9%)

Query: 17  RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           R L++  L      +E+ D F +YG +  I      +T ++RG A+V +       +   
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNACD 64

Query: 77  AGDHY-IGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITE 129
               + + N+ +        V           + T+  E+ ++    +YG  T+
Sbjct: 65  HLSGFNVCNRYL-------VVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTD 111

>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 = 52.7 bits (126), Expect = 1e-09
 Identities = 13/82 (15%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +++  L  +I+ +++ D F +YG I + +          +G  ++ ++D   A+    
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACD 64

Query: 161 N-PKQVICGKEVDVKRVKFNPE 181
           +     +C + + V     N  
Sbjct: 65  HLSGFNVCNRYLVVLYYNANRA 86

>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 = 56.3 bits (135), Expect = 5e-11
 Identities = 23/75 (30%), Positives = 39/75 (52%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            KIFVGGL    ++  +R YF  +G I E     D+     +G+ F++  D+  AE+   
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 70

Query: 161 NPKQVICGKEVDVKR 175
           +P  +I G++ +V  
Sbjct: 71  DPNPIIDGRKANVNL 85

>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 = 55.1 bits (132), Expect = 1e-10
 Identities = 24/84 (28%), Positives = 39/84 (46%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
             K+FVGGL  +T +  +  YF  +G++E   +  D  TG+SRG+ FVT   + A +  
Sbjct: 9  TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 68

Query: 75 LAAGDHYIGNKKIDPKRVTKRVNP 98
              +  I  +K +         P
Sbjct: 69 CKDPNPIIDGRKANVNLAYLGAKP 92

>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 = 55.0 bits (132), Expect = 8e-11
 Identities = 20/80 (25%), Positives = 42/80 (52%), Gaps = 1/80 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
           KLF+GGL     + ++ +  + +G +++ ++  D  TG S+G+AF  +      D  +A
Sbjct: 2  HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 77 AGD-HYIGNKKIDPKRVTKR 95
            +   +G+KK+  +R +  
Sbjct: 62 GLNGMQLGDKKLLVQRASVG 81

>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 = 54.6 bits (131), Expect = 1e-10
 Identities = 20/81 (24%), Positives = 41/81 (50%), Gaps = 1/81 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+F+GGL   +++  V++  + +G +  F    D +  + KG+ F  + D NV +Q +A 
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62

Query: 162 P-KQVICGKEVDVKRVKFNPE 181
                +  K++ V+R     +
Sbjct: 63  LNGMQLGDKKLLVQRASVGAK 83

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C + V GL+   +E+D+R+ FS+YG I +    +D+     +GF F+ F++ + A++   
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 161 NP-KQVICGKEVDV 173
                 + G+ + V
Sbjct: 70  RANGMELDGRRIRV 83

>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 = 52.0 bits (124), Expect = 9e-10
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            L V GL   T E+++ + FS+YG +  +SI  D  + +SRGFAFV F       +   
Sbjct: 10 CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 77 AGD-HYIGNKKI 87
            +   +  ++I
Sbjct: 70 RANGMELDGRRI 81

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK---SKNMKKGFCFISFDDQNVAEQVL 159
           +F+  L    +E+ ++  FS+ G+I        K      +  GF F+ +     A++ L
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 160 ANP-KQVICGKEVDVKRVK 177
                  + G +++V+  +
Sbjct: 61  KQLQGHTVDGHKLEVRISE 79

>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 = 53.5 bits (128), Expect = 3e-10
 Identities = 20/84 (23%), Positives = 35/84 (41%), Gaps = 4/84 (4%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVES---ISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
          LF+  L+ +T E+ +   FS+ G ++S      KN      S GF FV +   +     L
Sbjct: 1  LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKAL 60

Query: 76 AAGD-HYIGNKKIDPKRVTKRVNP 98
               H +   K++ +   +   P
Sbjct: 61 KQLQGHTVDGHKLEVRISERATKP 84

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 11/79 (13%), Positives = 30/79 (37%), Gaps = 1/79 (1%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
              + V  L  +++++++   F   G I   +   D       G+ F+ F  +  +++ +
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 160 ANP-KQVICGKEVDVKRVK 177
                  +  K + V   +
Sbjct: 62  KVLNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 49.6 bits (118), Expect = 8e-09
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 1/71 (1%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           L V  L ++  ++E+   F   G + +  I  D  TG S G+AFV FT++      +  
Sbjct: 4  NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 78 GD-HYIGNKKI 87
           +   + NK++
Sbjct: 64 LNGITVRNKRL 74

>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 = 53.9 bits (129), Expect = 3e-10
 Identities = 18/82 (21%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++ V  +     + D+R  F Q+G I + +  F+  +   KGF F++F++   A++    
Sbjct: 13  RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREK 70

Query: 162 -PKQVICGKEVDVKRVKFNPET 182
               V+ G++++V        T
Sbjct: 71  LHGTVVEGRKIEVNNATARVMT 92

>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 = 51.6 bits (123), Expect = 2e-09
 Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 3/87 (3%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
           ++  ++L V  +     + ++   F Q+G++  + I  +     S+GF FVTF      
Sbjct: 7  SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADA 64

Query: 72 DDLLAAGD-HYIGNKKIDPKRVTKRVN 97
          D          +  +KI+    T RV 
Sbjct: 65 DRAREKLHGTVVEGRKIEVNNATARVM 91

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 3e-10
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +FVG  T +++E ++R++FSQYG + +            + F F++F D  +A+ +  
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMD-----VFIPKPFRAFAFVTFADDQIAQSLCG 60

Query: 161 NPKQVICGKEVDVKRVK 177
               +I G  V +   +
Sbjct: 61  ED-LIIKGISVHISNAE 76

>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 = 50.8 bits (121), Expect = 3e-09
 Identities = 21/84 (25%), Positives = 32/84 (38%), Gaps = 6/84 (7%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G +    +FVG    +  E E+ ++FSQYG+V  + I           FAFVTF   +  
Sbjct: 1  GSSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR-----AFAFVTFADDQIA 55

Query: 72 DDLLAAGDHYIGNKKIDPKRVTKR 95
            L       I    +       +
Sbjct: 56 QSLCGED-LIIKGISVHISNAEPK 78

>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 = 53.8 bits (129), Expect = 3e-10
 Identities = 23/98 (23%), Positives = 44/98 (44%), Gaps = 7/98 (7%)

Query: 84  NKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKG 143
            K++  + V  + +P  C ++ GG+ + +++Q +R  FS +G I E +         +KG
Sbjct: 2   TKQLRFEDVVNQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVF------PEKG 55

Query: 144 FCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNP 180
           + F+ F     A   + +     I G  V     K +P
Sbjct: 56  YSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESP 93

>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 = 46.9 bits (111), Expect = 9e-08
 Identities = 11/74 (14%), Positives = 31/74 (41%), Gaps = 7/74 (9%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
              ++ GG+     ++ +   FS +G++  I +  +        ++FV F+T ++    
Sbjct: 17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTHESAAHA 70

Query: 75 LAAGD-HYIGNKKI 87
          + + +   I    +
Sbjct: 71 IVSVNGTTIEGHVV 84

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 4e-10
 Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          DE KLFVGGL  +T E+ +   FS+YG++  + +  D  T +SRGF FVTF       D 
Sbjct: 4  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 75 LAAGD-HYIGNKKIDPKRVTKR 95
          + A +   +  ++I   +  K 
Sbjct: 64 MMAMNGKSVDGRQIRVDQAGKS 85

>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 = 50.1 bits (119), Expect = 6e-09
 Identities = 22/79 (27%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           + K+FVGGL+ + +EQ +   FS+YG I+E     D+     +GF F++F++ + A+  +
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 160 AN-PKQVICGKEVDVKRVK 177
                + + G+++ V +  
Sbjct: 65  MAMNGKSVDGRQIRVDQAG 83

>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 = 52.9 bits (126), Expect = 5e-10
 Identities = 10/75 (13%), Positives = 25/75 (33%), Gaps = 1/75 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C +++       +++++RD       +    +      N  + F +I    +  A   + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 161 NP-KQVICGKEVDVK 174
                 I G  +  K
Sbjct: 62  KLNGLKIEGYTLVTK 76

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.1 bits (111), Expect = 5e-08
 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 5/85 (5%)

Query: 16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLL 75
          E  L++     +  ++ I D       V             SR FA++  T+++     +
Sbjct: 1  ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCV 60

Query: 76 AAGD-HYIGNKKIDPKRVTKRVNPL 99
             +   I    +      K  NPL
Sbjct: 61 EKLNGLKIEGYTL---VT-KVSNPL 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 = 52.8 bits (126), Expect = 6e-10
 Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKK-GFCFISFDDQNVAEQVL-A 160
           IF+G L  EI E+ + D FS +G I +  +           G+ FI+F   + ++  + A
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 161 NPKQVICGKEVDVKR 175
              Q +C + + V  
Sbjct: 61  MNGQYLCNRPITVSY 75

>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 = 51.3 bits (122), Expect = 2e-09
 Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 2/79 (2%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESIS-IKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          +F+G L     EK + D FS +G +     I  DP TG S+G+AF+ F +  A D  + A
Sbjct: 1  IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 78 GD-HYIGNKKIDPKRVTKR 95
           +  Y+ N+ I      K+
Sbjct: 61 MNGQYLCNRPITVSYAFKK 79

>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 = 52.9 bits (126), Expect = 8e-10
 Identities = 13/82 (15%), Positives = 28/82 (34%)

Query: 96  VNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
           VN  K    +  +   I++ DV  +                +     G   + F +++ A
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 156 EQVLANPKQVICGKEVDVKRVK 177
            +     ++ + G+E  V  V 
Sbjct: 64  RKSERLHRKKLNGREAFVHVVT 85

>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 = 46.8 bits (110), Expect = 1e-07
 Identities = 10/86 (11%), Positives = 25/86 (29%)

Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          G   + +    +  +  +  + ++  +       E+       + GQ  G A V F  + 
Sbjct: 2  GDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNED 61

Query: 70 AVDDLLAAGDHYIGNKKIDPKRVTKR 95
                      +  ++     VT  
Sbjct: 62 DARKSERLHRKKLNGREAFVHVVTLE 87

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.6 bits (126), Expect = 9e-10
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 10/83 (12%)

Query: 97  NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
             +  ++F+G L T  + + DV   FS+YG I           ++ KGF F+ + ++  A
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGC--------SVHKGFAFVQYVNERNA 63

Query: 156 EQVLAN-PKQVICGKEVDVKRVK 177
              +A    ++I G+ +D+    
Sbjct: 64  RAAVAGEDGRMIAGQVLDINLAA 86

>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 = 49.9 bits (119), Expect = 8e-09
 Identities = 20/95 (21%), Positives = 43/95 (45%), Gaps = 12/95 (12%)

Query: 5  ANGTAG--PGRNDERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFA 61
          ++G++G    R+   ++F+G L+     + ++   FS+YG++   S+          GFA
Sbjct: 2  SSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK--------GFA 53

Query: 62 FVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
          FV +  ++     +A  D   I  + +D     + 
Sbjct: 54 FVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP 88

>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 = 51.5 bits (123), Expect = 1e-09
 Identities = 12/74 (16%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           K+ V  L   +S+ D+++ F+++G++ +    +D+S         + F+ +  A + +  
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLG-TADVHFERKADALKAMKQ 60

Query: 162 -PKQVICGKEVDVK 174
                + G+ ++++
Sbjct: 61  YNGVPLDGRPMNIQ 74

>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 = 48.8 bits (116), Expect = 1e-08
 Identities = 13/71 (18%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KL V  L     + +I + F+++G ++  ++     +G+S G A V F  +      +  
Sbjct: 2  KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHY-DRSGRSLGTADVHFERKADALKAMKQ 60

Query: 78 GD-HYIGNKKI 87
           +   +  + +
Sbjct: 61 YNGVPLDGRPM 71

>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 = 52.0 bits (124), Expect = 1e-09
 Identities = 22/78 (28%), Positives = 36/78 (46%), Gaps = 1/78 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             I V  L+ +  E D+++ F  +GSI+      DK+    KGF FISF  +  A + +A
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 68

Query: 161 N-PKQVICGKEVDVKRVK 177
                      ++V+  K
Sbjct: 69  GVSGFGYDHLILNVEWAK 86

>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 = 50.4 bits (120), Expect = 5e-09
 Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 1/86 (1%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
           +D   + V  L  +T E ++ + F  +G +  I +  D  TGQS+GFAF++F  ++   
Sbjct: 5  ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAA 64

Query: 73 DLLAAGD-HYIGNKKIDPKRVTKRVN 97
            +A        +  ++ +      N
Sbjct: 65 RAIAGVSGFGYDHLILNVEWAKPSTN 90

>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 = 51.2 bits (122), Expect = 2e-09
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 8/76 (10%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA- 160
           K+++G L+  ++  D+R  F                  +K G+ F+ + DQN A + +  
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 161 -NPKQVICGKEVDVKR 175
            + K  + GK ++V  
Sbjct: 57  LSGKVELHGKIMEVDY 72

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 5e-09
 Identities = 12/80 (15%), Positives = 23/80 (28%), Gaps = 8/80 (10%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
          KL++G L       ++   F                     G+AFV +  Q      +  
Sbjct: 3  KLYIGNLSPAVTADDLRQLFGDRKLPL------AGQVLLKSGYAFVDYPDQNWAIRAIET 56

Query: 78 --GDHYIGNKKIDPKRVTKR 95
            G   +  K ++      +
Sbjct: 57 LSGKVELHGKIMEVDYSVSK 76

>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 = 50.6 bits (120), Expect = 3e-09
 Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 2/75 (2%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            + V  L    ++  V  YF   G I         S      F  I F   + A   +  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA--DSLKKNFRFARIEFARYDGALAAITK 59

Query: 162 PKQVICGKEVDVKRV 176
             +V+   E+ V  +
Sbjct: 60  THKVVGQNEIIVSHL 74

>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 = 49.1 bits (116), Expect = 9e-09
 Identities = 11/76 (14%), Positives = 28/76 (36%), Gaps = 2/76 (2%)

Query: 18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA 77
           + V  L ++  + ++  YF   G +  + + +     ++  FA + F         +  
Sbjct: 2  TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITK 59

Query: 78 GDHYIGNKKIDPKRVT 93
              +G  +I    +T
Sbjct: 60 THKVVGQNEIIVSHLT 75

>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 = 51.3 bits (122), Expect = 3e-09
 Identities = 26/86 (30%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            ++FV  L+   SE+D+   FS YG ++E   P D      KGF F++F     A +  A
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 161 N-PKQVICGKEVDVKRVKFNPETMGS 185
               QV  G+ + V       E   S
Sbjct: 69  EVDGQVFQGRMLHVLPSTIKKEASQS 94

>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 = 47.0 bits (111), Expect = 9e-08
 Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 1/85 (1%)

Query: 12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAV 71
          G +   +LFV  L   + E+++   FS YG +  +    D  T + +GFAFVTF   +  
Sbjct: 4  GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHA 63

Query: 72 DDLLAAGD-HYIGNKKIDPKRVTKR 95
              A  D      + +     T +
Sbjct: 64 VKAYAEVDGQVFQGRMLHVLPSTIK 88

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 4e-09
 Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 3/77 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++VG L+ +++E  +   FSQ G     +   +        +CF+ F +   A   LA 
Sbjct: 10  TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAALAA 67

Query: 162 -PKQVICGKEVDVKRVK 177
              + I GKEV V    
Sbjct: 68  MNGRKILGKEVKVNWAT 84

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.1 bits (114), Expect = 3e-08
 Identities = 21/76 (27%), Positives = 32/76 (42%), Gaps = 3/76 (3%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
              R L+VG L R+  E  I   FSQ G  +S  +  +     +  + FV F   +   
Sbjct: 5  DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAA 62

Query: 73 DLLAAGD-HYIGNKKI 87
            LAA +   I  K++
Sbjct: 63 AALAAMNGRKILGKEV 78

>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 = 50.9 bits (121), Expect = 4e-09
 Identities = 16/93 (17%), Positives = 37/93 (39%), Gaps = 2/93 (2%)

Query: 5  ANGTAGPGRNDE--RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G           F+G L  +  E+ I ++F           +   +  + +GF +
Sbjct: 2  SSGSSGSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGY 61

Query: 63 VTFTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
            F    ++   L+  +  +GNK+I      + 
Sbjct: 62 AEFEDLDSLLSALSLNEESLGNKRIRVDVADQA 94

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 13/75 (17%), Positives = 31/75 (41%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
              F+G L  +++E+ ++++F               +    KGF +  F+D +     L+
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75

Query: 161 NPKQVICGKEVDVKR 175
             ++ +  K + V  
Sbjct: 76  LNEESLGNKRIRVDV 90

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 50.3 bits (119), Expect = 6e-09
 Identities = 17/91 (18%), Positives = 37/91 (40%), Gaps = 1/91 (1%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
          ++   G        LF+G L+ N    E+    S+      +++ +   TG +R F +V 
Sbjct: 2  SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVD 60

Query: 65 FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
          F + + ++  L      +   +I  ++   R
Sbjct: 61 FESAEDLEKALELTGLKVFGNEIKLEKPKGR 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 = 49.2 bits (116), Expect = 1e-08
 Identities = 12/77 (15%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +F+G L    S  +++   S+  +  +      ++    + F ++ F+     E+ L 
Sbjct: 14  FNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRT-GTNRKFGYVDFESAEDLEKALE 72

Query: 161 NPKQVICGKEVDVKRVK 177
                + G E+ +++ K
Sbjct: 73  LTGLKVFGNEIKLEKPK 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 = 50.1 bits (119), Expect = 7e-09
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 4/79 (5%)

Query: 10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          GP  N++ +++VG L  +   K+I D F +YG +  I +KN         FAFV F   +
Sbjct: 8  GPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG---PPFAFVEFEDPR 64

Query: 70 AVDDLLAAGD-HYIGNKKI 87
            +D +   D +     ++
Sbjct: 65 DAEDAVYGRDGYDYDGYRL 83

>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 = 50.1 bits (119), Expect = 7e-09
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 4/78 (5%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
           C+I+VG L  +I  +D+ D F +YG+I +              F F+ F+D   AE  + 
Sbjct: 15  CRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVY 71

Query: 161 NP-KQVICGKEVDVKRVK 177
                   G  + V+  +
Sbjct: 72  GRDGYDYDGYRLRVEFPR 89

>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 = 49.7 bits (118), Expect = 7e-09
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           K  + V  L   +++++ R  F   G I   +   DK      G+ F+++ D   AE+ +
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 160 ANP-KQVICGKEVDVKRVK 177
                  +  K + V   +
Sbjct: 62  NTLNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 4e-07
 Identities = 21/72 (29%), Positives = 32/72 (44%), Gaps = 1/72 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
            L V  L +N  ++E    F   GE+ES  +  D  TGQS G+ FV +   K  +  + 
Sbjct: 3  TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62

Query: 77 AGD-HYIGNKKI 87
            +   +  K I
Sbjct: 63 TLNGLRLQTKTI 74

>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 = 49.8 bits (118), Expect = 8e-09
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +F+  L+ +  E+ + +   Q+G +   +          KG  F  F  Q  A++ LA
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 161 --NPKQVICGKEVDVKRVK 177
             + +    G ++D +++K
Sbjct: 69  AASLEAEGGGLKLDGRQLK 87

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.1 bits (111), Expect = 9e-08
 Identities = 22/87 (25%), Positives = 45/87 (51%), Gaps = 4/87 (4%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
           + + +F+  L  ++ E+ + +   Q+G+++ + +   P T  S+G AF  F TQ+A   
Sbjct: 6  TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 65

Query: 74 LLAAGDHYI--GNKKIDPKRVTKRVNP 98
           LAA       G  K+D +++  +V+ 
Sbjct: 66 CLAAASLEAEGGGLKLDGRQL--KVDL 90

>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 = 50.1 bits (119), Expect = 8e-09
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 1/86 (1%)

Query: 93  TKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ 152
           +++  P    +F+  L  E  +QD+   F  +G++   +   DK  N+ K F F+S+D+ 
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 153 NVAEQVLAN-PKQVICGKEVDVKRVK 177
             A+  + +     I  K + V+  +
Sbjct: 71  VSAQAAIQSMNGFQIGMKRLKVQLKR 96

>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 = 47.8 bits (113), Expect = 6e-08
 Identities = 20/98 (20%), Positives = 44/98 (44%), Gaps = 3/98 (3%)

Query: 1  MAYRANGTAGPGRN--DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSR 58
          +  ++ G AG  +   +   LF+  L +  G++++   F  +G V S  +  D  T  S+
Sbjct: 1  LTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSK 60

Query: 59 GFAFVTFTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
           F FV++    +    + + +   IG K++  +    +
Sbjct: 61 CFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSK 98

>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 = 49.3 bits (117), Expect = 1e-08
 Identities = 16/80 (20%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 9  AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ 68
          A  G+     + V  +       EI D+F  Y  +           G   G A V F ++
Sbjct: 2  ASSGKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESR 61

Query: 69 KAVDDLLAAGD-HYIGNKKI 87
                +   +   IG++K+
Sbjct: 62 DEATAAVIDLNDRPIGSRKV 81

>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 = 45.4 bits (107), Expect = 2e-07
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 98  PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQ 157
           P    I V  +   +S  ++ D+F  Y  I          K M  G   ++F+ ++ A  
Sbjct: 7   PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 66

Query: 158 VLAN-PKQVICGKEVDVK 174
            + +   + I  ++V + 
Sbjct: 67  AVIDLNDRPIGSRKVKLV 84

>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 = 48.4 bits (115), Expect = 2e-08
 Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 7/77 (9%)

Query: 100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVL 159
           + ++FVG L  +I+E+++R  F +YG   E         +  KGF FI  + + +AE   
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAK 61

Query: 160 AN-PKQVICGKEVDVKR 175
                  + GK++ V+ 
Sbjct: 62  VELDNMPLRGKQLRVRF 78

>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 = 41.9 bits (98), Expect = 5e-06
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 7/75 (9%)

Query: 14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDD 73
              +LFVG L  +  E+E+   F +YG+   + I  D        F F+   T+   + 
Sbjct: 6  TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEI 59

Query: 74 LLAAGD-HYIGNKKI 87
               D   +  K++
Sbjct: 60 AKVELDNMPLRGKQL 74

>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 = 47.8 bits (113), Expect = 4e-08
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 101 CKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMK-KGFCFISFDDQNVAEQV 158
            +I +  L+TE + E  +R+ F  +GSI +   P  + ++       F+ F++++ AE+ 
Sbjct: 5   REIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA 64

Query: 159 LANPKQVICGKEVDVKRVKFNP 180
           L   + ++  +E+ V      P
Sbjct: 65  LQMNRSLLGNREISVSLADKKP 86

>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 = 45.1 bits (106), Expect = 3e-07
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 15 DERKLFVGGLHRN-TGEKEINDYFSQYGEV-ESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          + R++ +  L      E  + + F  +G + +            +   AF+ F  + + +
Sbjct: 3  EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAE 62

Query: 73 DLLAAGDHYIGNKKIDPKRVTKR 95
            L      +GN++I      K+
Sbjct: 63 RALQMNRSLLGNREISVSLADKK 85

>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 = 47.8 bits (113), Expect = 4e-08
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 89  PKRVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFIS 148
           P+R  +        +FV  +  E  E ++++ F  YG I       D+     KG+  + 
Sbjct: 1   PQRSVE-----GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVE 55

Query: 149 FDDQNVAEQVLAN-PKQVICGKEVDVKR 175
           ++    A           I G+ + V  
Sbjct: 56  YETHKQALAAKEALNGAEIMGQTIQVDW 83

>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 = 42.4 bits (99), Expect = 3e-06
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 11 PGRNDE-RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          P R+ E   LFV  +H    E EI + F  YGE+++I +  D  TG S+G+A V + T K
Sbjct: 1  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHK 60

Query: 70 AVDDLLAAGD-HYIGNKKI 87
                 A +   I  + I
Sbjct: 61 QALAAKEALNGAEIMGQTI 79

>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 = 47.8 bits (113), Expect = 4e-08
 Identities = 13/76 (17%), Positives = 30/76 (39%), Gaps = 1/76 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +++ G  T+ +  D++++    G +   Q      K  K    F+ FD    A++ +  
Sbjct: 8   SVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKG-SIFVVFDSIESAKKFVET 66

Query: 162 PKQVICGKEVDVKRVK 177
           P Q     ++ +    
Sbjct: 67  PGQKYKETDLLILFKD 82

>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 = 45.5 bits (107), Expect = 2e-07
 Identities = 10/73 (13%), Positives = 25/73 (34%), Gaps = 1/73 (1%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
            R +++ G   +    +I ++    G+V +I           +G  FV F + ++    
Sbjct: 5  KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNI-QMRRTLHKAFKGSIFVVFDSIESAKKF 63

Query: 75 LAAGDHYIGNKKI 87
          +           +
Sbjct: 64 VETPGQKYKETDL 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 = 47.9 bits (113), Expect = 5e-08
 Identities = 14/77 (18%), Positives = 32/77 (41%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + + GL    S++++  +FS    +          +    G  F+ F  Q +AE+ L 
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 161 NPKQVICGKEVDVKRVK 177
             K+ I  + +++ +  
Sbjct: 76  KHKERIGHRYIEIFKSS 92

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 6e-08
 Identities = 20/84 (23%), Positives = 41/84 (48%), Gaps = 3/84 (3%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
          ++    +F+  L ++   K + D FS +G + S  +  D +   S+G+ FV F TQ+A +
Sbjct: 5  KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAE 62

Query: 73 DLLAAGD-HYIGNKKIDPKRVTKR 95
            +   +   + ++K+   R   R
Sbjct: 63 RAIEKMNGMLLNDRKVFVGRFKSR 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 = 47.0 bits (111), Expect = 7e-08
 Identities = 19/77 (24%), Positives = 37/77 (48%), Gaps = 3/77 (3%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            IF+  L   I  + + D FS +G+I   +   D++ +    + F+ F+ Q  AE+ +  
Sbjct: 10  NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKG--YGFVHFETQEAAERAIEK 67

Query: 162 -PKQVICGKEVDVKRVK 177
               ++  ++V V R K
Sbjct: 68  MNGMLLNDRKVFVGRFK 84

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 47.0 bits (111), Expect = 8e-08
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 6/82 (7%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
            R L    L  N  E E+ + F        + I+     G+S+G A++ F ++   +  
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKN 69

Query: 75 LAAGD-HYIGNKKIDPKRVTKR 95
          L       I  + +      ++
Sbjct: 70 LEEKQGAEIDGRSVSLYYTGEK 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 = 44.6 bits (105), Expect = 6e-07
 Identities = 14/77 (18%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +    L+  I+E ++++ F         +          KG  +I F  +  AE+ L  
Sbjct: 18  TLLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72

Query: 162 P-KQVICGKEVDVKRVK 177
                I G+ V +    
Sbjct: 73  KQGAEIDGRSVSLYYTG 89

>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 = 47.1 bits (111), Expect = 9e-08
 Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 9/92 (9%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKN--------DPHTGQSRGFAFVT 64
           +D   ++V GL+ +    ++ D+F Q G V+              D  TG+ +G A V+
Sbjct: 5  DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 65 FTTQKAVDDLLAAGD-HYIGNKKIDPKRVTKR 95
          +         +   D       K+      K+
Sbjct: 65 YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 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 = 47.1 bits (111), Expect = 1e-07
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 9/93 (9%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPF--------DKSKNMKKGFCFIS 148
           +     I+V GL   ++  D+ D+F Q G +   ++          DK     KG   +S
Sbjct: 5   DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVS 64

Query: 149 FDDQNVAEQVLANP-KQVICGKEVDVKRVKFNP 180
           ++D   A+  +     +   G ++ V   +  P
Sbjct: 65  YEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 97

>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 = 45.8 bits (108), Expect = 2e-07
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 8/83 (9%)

Query: 100 KCKIFVGGLTTEISEQDVR----DYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVA 155
              I++  L  +I + +++      FS++    +            +G  F+ F + + A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRF---GQILDILVSRSLKMRGQAFVIFKEVSSA 59

Query: 156 EQVLAN-PKQVICGKEVDVKRVK 177
              L +        K + ++  K
Sbjct: 60  TNALRSMQGFPFYDKPMRIQYAK 82

>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 = 40.4 bits (94), Expect = 1e-05
 Identities = 14/76 (18%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 17 RKLFVGGLHRNTGEKEI----NDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
            +++  L+    + E+    +  FS++G++  I +         RG AFV F    +  
Sbjct: 4  HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK---MRGQAFVIFKEVSSAT 60

Query: 73 DLLAAGD-HYIGNKKI 87
          + L +       +K +
Sbjct: 61 NALRSMQGFPFYDKPM 76

>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 = 46.0 bits (108), Expect = 2e-07
 Identities = 13/77 (16%), Positives = 29/77 (37%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +++ GL  E   + V D+F +   + +             G  F+ F ++   +  L 
Sbjct: 19  FCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC 78

Query: 161 NPKQVICGKEVDVKRVK 177
             KQ +  + + V  + 
Sbjct: 79  RHKQYMGNRFIQVHPIT 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 = 45.3 bits (106), Expect = 6e-07
 Identities = 19/83 (22%), Positives = 32/83 (38%)

Query: 13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVD 72
                +++ GL      K + D+F +   VE          G++ G  FV F  +    
Sbjct: 15 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYK 74

Query: 73 DLLAAGDHYIGNKKIDPKRVTKR 95
            L     Y+GN+ I    +TK+
Sbjct: 75 AALCRHKQYMGNRFIQVHPITKK 97

>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 = 45.4 bits (107), Expect = 2e-07
 Identities = 15/72 (20%), Positives = 30/72 (41%), Gaps = 7/72 (9%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          + L+V  L  +T E+ I   F+         +K      + R +AFV F+ ++   + + 
Sbjct: 9  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMK 62

Query: 77 AGD-HYIGNKKI 87
          A +   +    I
Sbjct: 63 ALNGKVLDGSPI 74

>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 = 43.1 bits (101), Expect = 2e-06
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 7/77 (9%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            ++V  L    SE+ +   F+        +          + + F+ F ++  A + +  
Sbjct: 10  ILYVRNLMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKA 63

Query: 162 -PKQVICGKEVDVKRVK 177
              +V+ G  ++V   K
Sbjct: 64  LNGKVLDGSPIEVTLAK 80

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 20/77 (25%), Positives = 37/77 (48%), Gaps = 1/77 (1%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
            +FVG +  E +E+ ++D FS+ G +  F+  +D+     KG+ F  + DQ  A   + N
Sbjct: 10  SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69

Query: 162 -PKQVICGKEVDVKRVK 177
              +   G+ + V    
Sbjct: 70  LNGREFSGRALRVDNAA 86

>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 = 42.4 bits (99), Expect = 4e-06
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 1/94 (1%)

Query: 15  DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
             R +FVG +     E+++ D FS+ G V S  +  D  TG+ +G+ F  +  Q+     
Sbjct: 7   SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66

Query: 75  LAAGD-HYIGNKKIDPKRVTKRVNPLKCKIFVGG 107
           +   +      + +         N  + K    G
Sbjct: 67  MRNLNGREFSGRALRVDNAASEKNKEELKSLGTG 100

>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 = 44.0 bits (103), Expect = 5e-07
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           +++ GL    ++QD+      YG I   +   DK+ N  KG+ F+ FD  + A++ +   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTA- 59

Query: 163 KQVICGKEVDVKRVK 177
              +    V  +  K
Sbjct: 60  ---LKASGVQAQMAK 71

>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 = 36.3 bits (83), Expect = 3e-04
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG 78
          L++ GL   T ++++      YG++ S     D  T + +G+ FV F +  A    + A 
Sbjct: 1  LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 79 DHYIGNKKIDPKRV 92
                  +  +  
Sbjct: 61 K----ASGVQAQMA 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 = 44.9 bits (105), Expect = 1e-06
 Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 2/94 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + V  + T + E  +R  F +YG I   +   D+     +G+ F+ F   + A+Q +A
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102

Query: 161 NP-KQVICGKEVDVKRVKFNPETMGSVSGAVRGA 193
                 I  K + V       +  G  +GAV   
Sbjct: 103 GLNGFNILNKRLKVALAASGHQRPGI-AGAVGDG 135

>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 = 39.1 bits (90), Expect = 1e-04
 Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
           P  +  R L V  +     E ++   F +YG +ES+ I  D  T QSRG+ FV F +  +
Sbjct: 37  PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS 96

Query: 71  VDDLLAAGD-HYIGNKKIDPKRVTKR 95
               +A  +   I NK++        
Sbjct: 97  AQQAIAGLNGFNILNKRLKVALAASG 122

>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 = 44.0 bits (103), Expect = 1e-06
 Identities = 15/78 (19%), Positives = 35/78 (44%), Gaps = 1/78 (1%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             +++  L+  ++E+D+   F+++         F       +G  FI+F ++ +A Q L 
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 161 NP-KQVICGKEVDVKRVK 177
                 + GK + ++  K
Sbjct: 79  LVNGYKLYGKILVIEFGK 96

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
          + L++  L     E+++   F+++ E +   I+    TG+ RG AF+TF  ++     L 
Sbjct: 19 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 77 AGD-HYIGNKKI 87
            + + +  K +
Sbjct: 79 LVNGYKLYGKIL 90

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 12/76 (15%), Positives = 26/76 (34%), Gaps = 8/76 (10%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + V G     +   +   F+QYG+I +              +  I +  +  A + L+
Sbjct: 5   TWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKALS 57

Query: 161 NPKQVICGKE-VDVKR 175
              ++      + VK 
Sbjct: 58  KDGRIFGESIMIGVKP 73

>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 = 38.0 bits (88), Expect = 9e-05
 Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 7/73 (9%)

Query: 15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
          D+  + V G  + +    I   F+QYG +    + N         +  + + ++      
Sbjct: 3  DDTWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKA 55

Query: 75 LAAGDHYIGNKKI 87
          L+      G   +
Sbjct: 56 LSKDGRIFGESIM 68

>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 = 41.2 bits (96), Expect = 1e-05
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 8  TAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTT 67
          +A   R+    + +   +    E+   +   +YGEVE +++  D       G  +V F  
Sbjct: 19 SADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRR 77

Query: 68 QKAVDDLLAAGD-HYIGNKKI 87
          ++  +  +   +  +   + I
Sbjct: 78 EEDAEKAVIDLNNRWFNGQPI 98

>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 = 38.1 bits (88), Expect = 1e-04
 Identities = 14/97 (14%), Positives = 38/97 (39%), Gaps = 8/97 (8%)

Query: 88  DPKRVTKRVNPLKCKI---FVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGF 144
           +P+  ++  + L+  +    +     E  E+   +   +YG + E     D   +   G 
Sbjct: 12  NPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEM-NVCDNLGDHLVGN 70

Query: 145 CFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNP 180
            ++ F  +  AE+ + +   +   G+ +     + +P
Sbjct: 71  VYVKFRREEDAEKAVIDLNNRWFNGQPI---HAELSP 104

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 113

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 2e-05
 Identities = 13/88 (14%), Positives = 24/88 (27%), Gaps = 9/88 (10%)

Query: 98  PLKCK-IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDD--QNV 154
            + C   F G L  +   +D+   FS +G I                   I F +  +  
Sbjct: 8   KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDF------VRGAKEGIILFKEKAKEA 61

Query: 155 AEQVLANPKQVICGKEVDVKRVKFNPET 182
             +        +  +  +V       E 
Sbjct: 62  LGKAKDANNGNLQLRNKEVTWEVLEGEV 89

>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 = 1e-04
 Identities = 12/79 (15%), Positives = 26/79 (32%), Gaps = 4/79 (5%)

Query: 17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA 76
             F G L   T  ++++  FS +GE++ I        G            ++A+     
Sbjct: 12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKE----KAKEALGKAKD 67

Query: 77 AGDHYIGNKKIDPKRVTKR 95
          A +  +  +  +       
Sbjct: 68 ANNGNLQLRNKEVTWEVLE 86

>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 = 40.0 bits (93), Expect = 2e-05
 Identities = 14/81 (17%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             ++V G   +++   +R  FS       F    D S +  +   F++++    A+Q +A
Sbjct: 6   NTLYVYGE--DMTPTLLRGAFSP------FGNIIDLSMDPPRNCAFVTYEKMESADQAVA 57

Query: 161 NP-KQVICGKEVDVKRVKFNP 180
                 +   ++ V   +  P
Sbjct: 58  ELNGTQVESVQLKVNIARKQP 78

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 15/87 (17%), Positives = 31/87 (35%), Gaps = 9/87 (10%)

Query: 94  KRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQN 153
           + + P    + +  +   +SE+D++  FS  G + +  + F       +    I      
Sbjct: 4   QNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVE 59

Query: 154 VAEQVLA--NPKQVICGKEVDVKRVKF 178
            A Q L   +   +     +   RV F
Sbjct: 60  EAVQALIDLHNHDLGENHHL---RVSF 83

>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 = 40.1 bits (93), Expect = 3e-05
 Identities = 12/77 (15%), Positives = 24/77 (31%), Gaps = 2/77 (2%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             + + GL    +E D+ ++FS                    G   + F     A   +A
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLN--PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA 73

Query: 161 NPKQVICGKEVDVKRVK 177
             K  +  + V++    
Sbjct: 74  KDKANMQHRYVELFLNS 90

>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 = 38.6 bits (89), Expect = 9e-05
 Identities = 13/91 (14%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 5  ANGTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVT 64
           +  +         + + GL     E +I ++FS    +           G+  G A V 
Sbjct: 4  GSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIG--PDGRVTGEADVE 61

Query: 65 FTTQKAVDDLLAAGDHYIGNKKIDPKRVTKR 95
          F T +     +A     + ++ ++    +  
Sbjct: 62 FATHEDAVAAMAKDKANMQHRYVELFLNSTA 92

>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 = 40.0 bits (93), Expect = 3e-05
 Identities = 18/110 (16%), Positives = 37/110 (33%), Gaps = 12/110 (10%)

Query: 11  PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKA 70
            G++   ++ V  L        ++  FS++G V  I          ++  A + +    +
Sbjct: 2   AGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVS 57

Query: 71  VDDLLAAGDHYIGNKKIDPKRVTKRVNPLKCKIFVGGLTTEISEQDVRDY 120
                 + D     + I     T R++  K       L  + +    RDY
Sbjct: 58  AQHAKLSLD----GQNIYNACCTLRIDFSKLT----SLNVKYNNDKSRDY 99

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 4e-05
 Identities = 8/60 (13%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           +I V  L   ++   +   FS++G++ +       +    +    + + D   A+    +
Sbjct: 9   RIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNN----QFQALLQYADPVSAQHAKLS 64

>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 = 39.8 bits (92), Expect = 4e-05
 Identities = 10/93 (10%), Positives = 27/93 (29%), Gaps = 5/93 (5%)

Query: 91  RVTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFD 150
           ++ K+       +++  L   + EQ++ +    +G +   +   D S   +         
Sbjct: 9   QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 68

Query: 151 DQNVAEQVLANPKQVICGKEVDVK-----RVKF 178
            +     +     + I               KF
Sbjct: 69  TEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKF 101

>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 = 35.9 bits (82), Expect = 9e-04
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 4/88 (4%)

Query: 15  DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDL 74
           D   L++  L  +  E+E+ +    +G+V S  I  D              +T+K    +
Sbjct: 17  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVI 76

Query: 75  LAAGDHYIGNKKIDPKRVTKRVNPLKCK 102
                 +I         V+    PL CK
Sbjct: 77  GHFNGKFIKTPPG----VSAPTEPLLCK 100

>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 = 38.3 bits (88), Expect = 1e-04
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 7/78 (8%)

Query: 17 RKLFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPHTGQS---RGFAFVTFTTQKA 70
            +FV GL +   + E+    +YF ++G++  + I N      S      A+VT+   + 
Sbjct: 9  NLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED 68

Query: 71 VDDLLAAGD-HYIGNKKI 87
              +   +   +  + +
Sbjct: 69 ALRAIQCVNNVVVDGRTL 86

>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 = 36.7 bits (84), Expect = 3e-04
 Identities = 15/84 (17%), Positives = 34/84 (40%), Gaps = 10/84 (11%)

Query: 100 KCKIFVGGLTTEISEQDVR---DYFSQYGSITEFQQPFDKSKN---MKKGFCFISFDDQN 153
           K  +FV GL+  +++ +V    +YF ++G I +       S           ++++    
Sbjct: 8   KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 154 VAEQVLANPKQVICGKEVDVKRVK 177
            A + +      +    VD + +K
Sbjct: 68  DALRAIQC----VNNVVVDGRTLK 87

>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 = 1e-04
 Identities = 7/81 (8%), Positives = 16/81 (19%), Gaps = 11/81 (13%)

Query: 12 GRNDERKLFVGGLH-----RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFT 66
          G +    L     +      +    +    F  Y +  +                 + F+
Sbjct: 1  GSSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFS 54

Query: 67 TQKAVDDLLAAGDHYIGNKKI 87
             +  D            K 
Sbjct: 55 NPLSAADARLRLHKTEFLGKE 75

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.6 bits (84), Expect = 4e-04
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 10/76 (13%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA-- 160
           +  GGL   +S   +     + G +              K + F  +     +++     
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLM------PPNKPYSFARYRTTEESKRAYVTL 76

Query: 161 NPKQVI--CGKEVDVK 174
           N K+V+   G+++ + 
Sbjct: 77  NGKEVVDDLGQKITLY 92

>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 = 35.7 bits (82), Expect = 8e-04
 Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 5/62 (8%)

Query: 114 EQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVD 172
            +D+R   S++G I +             G   +SF D   A+  +     +   G+++ 
Sbjct: 33  REDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 88

Query: 173 VK 174
            +
Sbjct: 89  AQ 90

>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 = 34.5 bits (79), Expect = 0.002
 Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 5/59 (8%)

Query: 30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGD-HYIGNKKI 87
           +++    S++G++  + + +        G A V+F   +  D  +   D  + G ++I
Sbjct: 33 REDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQI 87

>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 = 35.1 bits (80), Expect = 0.001
 Identities = 13/78 (16%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
             I V  L  + + Q+V D    Y              +  K   F++  +   A+  + 
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQ 58

Query: 161 N-PKQVICGKEVDVKRVK 177
              +    GK++ V+   
Sbjct: 59  MFHQYSFRGKDLIVQLQP 76

>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 = 35.1 bits (80), Expect = 0.001
 Identities = 13/94 (13%), Positives = 35/94 (37%), Gaps = 10/94 (10%)

Query: 5  ANGTAG--PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAF 62
          ++G++G  P R  + ++ V GL  +   +++ D+  +                Q  G   
Sbjct: 2  SSGSSGGPPTRRSDFRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGM 54

Query: 63 VTFTTQKAVDDLLAAGDHY-IGNKKIDPKRVTKR 95
          V +  ++ ++  L   D     + + +   +   
Sbjct: 55 VEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVY 88

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 34.0 bits (77), Expect = 0.004
 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 9/90 (10%)

Query: 101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLA 160
            ++ V GL    S QD++D+  +             +   K G   + +  +   E  L 
Sbjct: 16  FRVLVSGLPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGMVEYLRKEDMEYALR 68

Query: 161 N-PKQVICGKEVDVKRVKFNPE-TMGSVSG 188
                     E +   ++  PE + G  SG
Sbjct: 69  KLDDTKFRSHEGETSYIRVYPERSSGPSSG 98

>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 = 34.1 bits (77), Expect = 0.002
 Identities = 11/83 (13%), Positives = 26/83 (31%), Gaps = 7/83 (8%)

Query: 97  NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAE 156
            P    +F+  L  E +E  +   F+Q+    E +         +    F+ F  +  + 
Sbjct: 5   QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVP-----NRHDIAFVEFTTELQSN 59

Query: 157 QVLA--NPKQVICGKEVDVKRVK 177
                    ++     + +   K
Sbjct: 60  AAKEALQGFKITPTHAMKITFAK 82

>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 = 33.9 bits (77), Expect = 0.003
 Identities = 11/81 (13%), Positives = 25/81 (30%), Gaps = 11/81 (13%)

Query: 12 GRNDE-RKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQK 69
          GR +  R + +    R      ++      +G + +  I N  +       AF+   T +
Sbjct: 3  GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN------EAFIEMATTE 56

Query: 70 AVDDLLAAGD---HYIGNKKI 87
               +         +  K +
Sbjct: 57 DAQAAVDYYTTTPALVFGKPV 77

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.7 bits (76), Expect = 0.003
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 8/73 (10%)

Query: 103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP 162
           I + GL  +++ Q+V D  S Y       +      +  KG  F++  +   AE  +   
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDY-------ELKYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 163 KQVIC-GKEVDVK 174
            Q     +E+ V+
Sbjct: 54  HQSRLRERELSVQ 66

>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 = 33.7 bits (76), Expect = 0.004
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 6/81 (7%)

Query: 102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN 161
           ++ V GL    S QD++D+  +           D  ++      F+  +D   A + L N
Sbjct: 2   RVVVSGLPPSGSWQDLKDHMREA----GDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDN 57

Query: 162 PKQVICGKEVDVKRVKFNPET 182
                   E +   ++   + 
Sbjct: 58  --TKFRSHEGETAYIRVKVDG 76

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	275
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.85
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.85
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.84
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.84
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.84
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.84
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.84
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.83
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.83
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.83
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.83
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.83
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.82
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.82
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.81
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.81
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.81
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.81
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.8
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.8
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.79
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.79
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.78
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.78
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.78
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.78
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.78
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.77
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.77
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.77
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.76
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.76
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.76
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.76
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.76
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.75
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.75
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.75
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.74
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.74
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.73
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.73
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.73
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.73
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.72
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.71
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.71
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.71
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.71
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.71
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.7
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.69
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.69
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.69
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.69
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.69
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.69
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.69
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.68
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.68
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.68
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.67
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.67
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.67
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.67
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.67
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.66
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.66
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.66
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.66
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.65
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.65
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.64
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.64
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.62
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.56
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.55
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	99.48
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	99.45
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.43
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.43
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.41
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.39
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.39
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.33
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.31
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.21
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.17
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.53
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.5
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.44
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.28
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.98
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.54
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.51
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.51

>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=5e-36  Score=239.01  Aligned_cols=171  Identities=33%  Similarity=0.633  Sum_probs=154.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      +++..++|||+|||+++|+++|+++|++||+|+++.+++++.++.++|+|||+|.+.++|++|+.++...+..+.+.+..
T Consensus         2 ep~~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (183)
T ss_dssp             CCHHHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhh
Confidence            45566899999999999999999999999999999999999999999999999999999999999988888888777665


Q ss_pred             ccccc-------CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCc
Q psy1314          92 VTKRV-------NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQ  164 (275)
Q Consensus        92 ~~~~~-------~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~  164 (275)
                      .....       .....+|||+|||+.+|+++|+++|+.||.|..+.|+.+..++.++|||||+|.++++|++||+.+++
T Consensus        82 ~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~  161 (183)
T d1u1qa_          82 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH  161 (183)
T ss_dssp             CCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCE
T ss_pred             hhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCC
Confidence            43332       23457899999999999999999999999999999999999999999999999999999999987778


Q ss_pred             eeCCeEEEEEEeeeCCCC
Q psy1314         165 VICGKEVDVKRVKFNPET  182 (275)
Q Consensus       165 ~~~g~~i~v~~~~~~~~~  182 (275)
                      .|+|++|+|.++.++.++
T Consensus       162 ~~~G~~i~V~~A~~k~e~  179 (183)
T d1u1qa_         162 TVNGHNCEVRKALSKQEM  179 (183)
T ss_dssp             EETTEEEEEEECCCHHHH
T ss_pred             eECCEEEEEEecCCcccc
Confidence            999999999998877543

>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=99.87  E-value=2.4e-22  Score=138.47  Aligned_cols=82  Identities=35%  Similarity=0.656  Sum_probs=77.4

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ++++.++|||+|||+++|+++|+++|++||+|.++.|+.++.|++++|||||+|.++++|++||+++++.|.|+.|.|+.
T Consensus         2 epe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            45667899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cc
Q psy1314          92 VT   93 (275)
Q Consensus        92 ~~   93 (275)
                      +.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            64

>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=1.4e-21  Score=136.12  Aligned_cols=85  Identities=32%  Similarity=0.531  Sum_probs=78.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ..+..++|||+|||+++|+++|+++|++||+|.+|.|+.++.|++++|||||+|.++++|++||+. .+.++|+.|.|++
T Consensus         4 ~~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~-~~~l~Gr~i~v~~   82 (90)
T d2cqga1           4 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMIDGRWCDCKL   82 (90)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS-CEEETTEEEEEEC
T ss_pred             CCcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc-CCccCCEEeEEEe
Confidence            455678899999999999999999999999999999999999999999999999999999999985 5689999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.+++.
T Consensus        83 a~~k~~   88 (90)
T d2cqga1          83 PNSKQS   88 (90)
T ss_dssp             CCTTCC
T ss_pred             CCCCCC
Confidence            877543

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.9e-21  Score=139.21  Aligned_cols=83  Identities=28%  Similarity=0.506  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      .+.++|||+|||+++|+++|+++|++||+|++|.|+.++.|++++|||||+|.+.++|++||+.+++.+.|++|.|+++.
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            34567999999999999999999999999999999999999999999999999999999999998889999999999876


Q ss_pred             ccc
Q psy1314          94 KRV   96 (275)
Q Consensus        94 ~~~   96 (275)
                      ...
T Consensus        88 ~~~   90 (103)
T d2cqda1          88 LGA   90 (103)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=3.4e-21  Score=137.85  Aligned_cols=84  Identities=27%  Similarity=0.551  Sum_probs=78.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      +...++|||+|||+.+++++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+.++..|+|++|.|.++
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a   86 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLA   86 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEES
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEc
Confidence            34457799999999999999999999999999999999999999999999999999999999999988899999999988


Q ss_pred             eeCC
Q psy1314         177 KFNP  180 (275)
Q Consensus       177 ~~~~  180 (275)
                      ..+.
T Consensus        87 ~~~~   90 (103)
T d2cqda1          87 YLGA   90 (103)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7654

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=9.4e-22  Score=132.48  Aligned_cols=75  Identities=47%  Similarity=0.878  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      +|||+|||+++|+++|+++|++||+|.+|.|+.++.|++++|||||+|.++++|++||+++++.+.|+.|.|+.+
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            599999999999999999999999999999999999999999999999999999999999889999999988754

>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=3.4e-22  Score=135.25  Aligned_cols=76  Identities=45%  Similarity=0.777  Sum_probs=72.8

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ++|||+|||+++|+++|+++|++||+|+++.|++++.|++++|||||+|.++++|++||+++++.++|+.|.|+.+
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            5899999999999999999999999999999999999999999999999999999999999899999999988765

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=1.1e-21  Score=140.21  Aligned_cols=84  Identities=38%  Similarity=0.710  Sum_probs=78.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      ++.++|||+|||+++|+++|+++|++||+|.++.|++++.++.++|||||+|.+.++|++||+++++.|.|+.|.|+++.
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            34578999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cccC
Q psy1314          94 KRVN   97 (275)
Q Consensus        94 ~~~~   97 (275)
                      ++++
T Consensus        98 ~ke~  101 (103)
T d1x4ba1          98 AREE  101 (103)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            6643

>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=7.6e-22  Score=132.68  Aligned_cols=75  Identities=40%  Similarity=0.721  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      +|||+|||+++|+++|+++|++||+|.+|.|+.++.|++++|||||+|.+.++|++||+.+.+.+.++.|+|+.+
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            599999999999999999999999999999999999999999999999999999999998888999998887653

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=1.1e-21  Score=139.75  Aligned_cols=83  Identities=22%  Similarity=0.363  Sum_probs=77.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      ..+.++|||+|||+++|+++|+++|+.||+|.+|.|++++.|++++|||||+|.+.++|++||++++..|.|+.|.|+++
T Consensus        15 ~~~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          15 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ccc
Q psy1314          93 TKR   95 (275)
Q Consensus        93 ~~~   95 (275)
                      ..+
T Consensus        95 ~~~   97 (101)
T d2cq4a1          95 QAE   97 (101)
T ss_dssp             HHH
T ss_pred             CCC
Confidence            543

>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=99.84  E-value=8e-21  Score=134.98  Aligned_cols=86  Identities=29%  Similarity=0.453  Sum_probs=79.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||+++++++|+++|++||+|..|.|+.++.+++++|||||+|.+.++|++||+.+ +..|.|++|+|.++
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            34578999999999999999999999999999999999999999999999999999999999987 48899999999999


Q ss_pred             eeCCCCC
Q psy1314         177 KFNPETM  183 (275)
Q Consensus       177 ~~~~~~~  183 (275)
                      ..+++..
T Consensus        86 ~~~~~~~   92 (99)
T d1whwa_          86 TIKKEAS   92 (99)
T ss_dssp             CCCSTTC
T ss_pred             CCCCccC
Confidence            9876543

>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=4.2e-21  Score=134.75  Aligned_cols=85  Identities=26%  Similarity=0.422  Sum_probs=78.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      +.++.++|||+|||.++|+++|+++|++||+|.+|.|+.++.|++++|||||+|.+.++|++||+. ++..+.++.|.|+
T Consensus         5 ~~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   84 (93)
T d1x5ua1           5 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   84 (93)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            445568999999999999999999999999999999999999999999999999999999999975 6779999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++.++.
T Consensus        85 ~A~~~~   90 (93)
T d1x5ua1          85 KASAHN   90 (93)
T ss_dssp             ETTTTS
T ss_pred             EcCCCC
Confidence            987654

>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=99.84  E-value=7.2e-21  Score=132.52  Aligned_cols=83  Identities=27%  Similarity=0.436  Sum_probs=76.8

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ....+|||+|||+++|+++|+++|++||.|..|.|+.|+.++.++|||||+|.+.++|++||+.+ +.|+|+.|.|+++.
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 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR-HMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC-EEETTEEEEEECCC
T ss_pred             cCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC-CccCCEEeEEEeCC
Confidence            45678999999999999999999999999999999999999999999999999999999999864 57999999999988


Q ss_pred             eCCC
Q psy1314         178 FNPE  181 (275)
Q Consensus       178 ~~~~  181 (275)
                      ++..
T Consensus        85 ~k~~   88 (90)
T d2cqga1          85 SKQS   88 (90)
T ss_dssp             TTCC
T ss_pred             CCCC
Confidence            7654

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=8e-21  Score=130.70  Aligned_cols=79  Identities=24%  Similarity=0.486  Sum_probs=75.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+++++++|+++|++||.|..+.|+.|+.++.++|||||+|.+.++|++||+.+++.|+|+.|+|++|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            3468999999999999999999999999999999999999999999999999999999999988899999999998874

>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=99.84  E-value=9.6e-21  Score=135.22  Aligned_cols=86  Identities=20%  Similarity=0.362  Sum_probs=78.9

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~   90 (275)
                      +..+.++|||+|||+++|+++|+++|++||.|.++.++.++.+++++|||||+|.+.++|++||+ +++..|.+++|.|+
T Consensus        14 ~~p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          14 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            33566789999999999999999999999999999999999999999999999999999999996 57889999999999


Q ss_pred             ccccccC
Q psy1314          91 RVTKRVN   97 (275)
Q Consensus        91 ~~~~~~~   97 (275)
                      ++.++.+
T Consensus        94 ~a~~k~~  100 (102)
T d2cpza1          94 LKRSKND  100 (102)
T ss_dssp             CCCCSCC
T ss_pred             EeCCCCC
Confidence            9977654

>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=99.84  E-value=7.7e-21  Score=132.05  Aligned_cols=83  Identities=28%  Similarity=0.428  Sum_probs=76.6

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      +.+.++|||+|||+++|+++|+++|++||+|++|+|+.++.+++++|||||+|.+.++|++|++ +++..+.++.|.|++
T Consensus         4 s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           4 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999997 478899999999999


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +.++
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            8654

>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=99.84  E-value=8.2e-21  Score=130.48  Aligned_cols=79  Identities=29%  Similarity=0.445  Sum_probs=73.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      ..++++++|||+|||+++|+++|+++|++||+|.+|.|+.++.+++++|||||+|.+.++|++||+ +++..+.+++|.|
T Consensus         4 ~~p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           4 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345678899999999999999999999999999999999999999999999999999999999997 5788999998875

>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=1.2e-20  Score=132.45  Aligned_cols=83  Identities=20%  Similarity=0.350  Sum_probs=77.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      -.++++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++||+. ++..+.+++|.|++
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35678999999999999999999999999999999999999999999999999999999999985 67899999999999


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            8644

>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=1.1e-20  Score=134.32  Aligned_cols=86  Identities=24%  Similarity=0.412  Sum_probs=78.7

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      .++..++|||+|||+++|+++|+++|++||+|.+|.|+.++.|++++|||||+|.+.++|++||+. ++..|.++.|.|+
T Consensus         4 ~~~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~   83 (99)
T d1whwa_           4 GSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVL   83 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            345677899999999999999999999999999999999999999999999999999999999985 5789999999999


Q ss_pred             ccccccC
Q psy1314          91 RVTKRVN   97 (275)
Q Consensus        91 ~~~~~~~   97 (275)
                      ++..+..
T Consensus        84 ~a~~~~~   90 (99)
T d1whwa_          84 PSTIKKE   90 (99)
T ss_dssp             ECCCCST
T ss_pred             ECCCCCc
Confidence            9876543

>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=99.83  E-value=1.3e-21  Score=132.33  Aligned_cols=76  Identities=33%  Similarity=0.647  Sum_probs=73.0

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      |+|||+|||+++|+++|+++|++||.|.+++|++|+.+++++|||||+|.++++|++||+..++.|+|++|+|+.|
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            6899999999999999999999999999999999999999999999999999999999997679999999999876

>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=99.83  E-value=8.3e-21  Score=132.48  Aligned_cols=86  Identities=22%  Similarity=0.429  Sum_probs=78.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ...++.++|||+|||.++|+++|+++|++||+|.+|.|+.++.++.++|||||+|.+.++|++||+. ++..+.++.|.|
T Consensus         3 ~~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v   82 (90)
T d2cq0a1           3 RRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNV   82 (90)
T ss_dssp             CCCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456778999999999999999999999999999999999999999999999999999999999986 567999999999


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      +++.++.
T Consensus        83 ~~akp~~   89 (90)
T d2cq0a1          83 EWAKPST   89 (90)
T ss_dssp             EESSCCC
T ss_pred             EeeeCCC
Confidence            9987653

>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=99.83  E-value=7.1e-21  Score=130.55  Aligned_cols=79  Identities=24%  Similarity=0.393  Sum_probs=74.4

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~~   94 (275)
                      .++|||+|||+++|+++|+++|++||+|++|.|++++.+++++|||||+|.+.++|++||+ +++..+.+++|.|+++.+
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            4679999999999999999999999999999999999999999999999999999999997 578899999999998854

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=1.1e-20  Score=128.54  Aligned_cols=77  Identities=38%  Similarity=0.759  Sum_probs=73.7

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      -++|||+|||+++|+++|+++|++||+|..+.++.++.+++++|||||+|.++++|++|++++++.|.|++|.|+.+
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            47899999999999999999999999999999999999999999999999999999999999999999999999765

>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=99.83  E-value=5.6e-21  Score=133.07  Aligned_cols=83  Identities=25%  Similarity=0.436  Sum_probs=77.2

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ...++|||+|||+++|+++|+++|++||+|++|.|+.++.+++++|||||+|.+.++|++|++. ++..+.+++|.|+++
T Consensus         3 ~~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           3 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            4568999999999999999999999999999999999999999999999999999999999975 788999999999998


Q ss_pred             cccc
Q psy1314          93 TKRV   96 (275)
Q Consensus        93 ~~~~   96 (275)
                      .++.
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>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=6.4e-21  Score=131.53  Aligned_cols=80  Identities=25%  Similarity=0.567  Sum_probs=75.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~   95 (275)
                      ++|||+|||+++|+++|+++|++||+|++|+|+.|+.|++++|||||+|.++++|++|++. ++..+.+++|.|+++...
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            5899999999999999999999999999999999999999999999999999999999995 577999999999998754


Q ss_pred             c
Q psy1314          96 V   96 (275)
Q Consensus        96 ~   96 (275)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.83  E-value=1.7e-20  Score=130.81  Aligned_cols=84  Identities=26%  Similarity=0.351  Sum_probs=78.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ....++|||+|||.++++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++|++||+.++ ..|.|++|.|.+
T Consensus         5 ~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3456789999999999999999999999999999999999999999999999999999999999885 899999999999


Q ss_pred             eeeCC
Q psy1314         176 VKFNP  180 (275)
Q Consensus       176 ~~~~~  180 (275)
                      ++++.
T Consensus        85 akp~~   89 (90)
T d2cq0a1          85 AKPST   89 (90)
T ss_dssp             SSCCC
T ss_pred             eeCCC
Confidence            98764

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.3e-21  Score=130.34  Aligned_cols=75  Identities=29%  Similarity=0.746  Sum_probs=71.9

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      +|||+|||+++|+++|+++|++||+|..|.|+.++.+++++|||||+|.+.++|++||+.+++.|+|+.|+|+.|
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            599999999999999999999999999999999999999999999999999999999998888999999999865

>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=99.83  E-value=1.6e-20  Score=130.47  Aligned_cols=81  Identities=19%  Similarity=0.403  Sum_probs=76.2

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||.++++++|+++|++||+|..|+|+.++.++.++|||||+|.+.++|++|++.+ +..|.|++|.|.++.
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            4578999999999999999999999999999999999999999999999999999999999986 589999999999998


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      ++
T Consensus        86 ~k   87 (88)
T d1rk8a_          86 VK   87 (88)
T ss_dssp             EC
T ss_pred             CC
Confidence            75

>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=99.83  E-value=3e-20  Score=130.33  Aligned_cols=83  Identities=22%  Similarity=0.365  Sum_probs=77.2

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ...+++|||+|||+++|+++|+++|++||+|.+|.|+.++.++.++|||||+|.+.++|++||+.+ +..|+|++|.|.+
T Consensus         4 ~~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           4 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345689999999999999999999999999999999999999999999999999999999999987 5899999999999


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +...
T Consensus        84 a~~~   87 (93)
T d1h2vz_          84 DAGF   87 (93)
T ss_dssp             ESCC
T ss_pred             cCCC
Confidence            7643

>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=99.83  E-value=6.3e-21  Score=128.37  Aligned_cols=75  Identities=29%  Similarity=0.685  Sum_probs=71.3

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      +|||+|||+++++++|+++|++||+|..+.|+.++.+++++|||||+|.++++|++||+..++.|+|++|.|++|
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            599999999999999999999999999999999999999999999999999999999997778999999998654

>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=99.82  E-value=1.9e-20  Score=127.71  Aligned_cols=76  Identities=28%  Similarity=0.386  Sum_probs=72.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      +|||+|||+++|+++|+++|++||+|.+|+|++++.|++++|||||+|.++++|++|++. ++..+.+++|.|+++.
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            699999999999999999999999999999999999999999999999999999999975 6789999999999874

>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=1.1e-20  Score=129.50  Aligned_cols=79  Identities=14%  Similarity=0.287  Sum_probs=74.7

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      +++|||+|||+++++++|+++|++||+|..+.|++++.++.++|||||+|.++++|++||+.+ +..+.+++|.|.++++
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            467999999999999999999999999999999999999999999999999999999999887 5899999999999864

>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=99.82  E-value=2.4e-20  Score=140.85  Aligned_cols=87  Identities=28%  Similarity=0.449  Sum_probs=79.2

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      .+.+..++|||+|||+++|+++|+++|++||+|++|.|++++.|++++|||||+|.+.++|++||+. ++..|.++.|.|
T Consensus        37 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V  116 (139)
T d1u6fa1          37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            4455567899999999999999999999999999999999999999999999999999999999985 678999999999


Q ss_pred             cccccccC
Q psy1314          90 KRVTKRVN   97 (275)
Q Consensus        90 ~~~~~~~~   97 (275)
                      +++..+..
T Consensus       117 ~~a~~~~~  124 (139)
T d1u6fa1         117 ALAASGHQ  124 (139)
T ss_dssp             EESSCCCC
T ss_pred             EEcCCCCC
Confidence            99876544

>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=1.5e-20  Score=131.25  Aligned_cols=85  Identities=33%  Similarity=0.604  Sum_probs=78.5

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      +++.++|||+|||+++|+++|+++|++||+|..|.++.++.++.++|||||+|.++++|++||+ +++..+.|++|.|++
T Consensus         2 ~~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   81 (90)
T d1x5sa1           2 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567889999999999999999999999999999999998999999999999999999999996 578899999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.++.+
T Consensus        82 a~~~~~   87 (90)
T d1x5sa1          82 AGKSSD   87 (90)
T ss_dssp             EECCCC
T ss_pred             cCCCCC
Confidence            876654

>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=99.82  E-value=1.6e-20  Score=134.02  Aligned_cols=83  Identities=29%  Similarity=0.540  Sum_probs=78.1

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      .++|||+|||+++++++|+++|++||.|..+.|++|+.++.++|||||+|.+.++|++||+.+++.|+|+.|.|.++.++
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~k   99 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAR   99 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSC
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECccc
Confidence            37899999999999999999999999999999999999999999999999999999999988789999999999999887


Q ss_pred             CCC
Q psy1314         180 PET  182 (275)
Q Consensus       180 ~~~  182 (275)
                      .++
T Consensus       100 e~~  102 (103)
T d1x4ba1         100 EES  102 (103)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.82  E-value=3.6e-20  Score=126.98  Aligned_cols=79  Identities=27%  Similarity=0.414  Sum_probs=74.1

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~~   94 (275)
                      .++|||+|||+++|+++|+++|++||+|.+|+|+.++.+++++|||||+|.++++|++|++ +++..+.+++|.|+++.+
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            4579999999999999999999999999999999999999999999999999999999997 578899999999998854

>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=99.82  E-value=1.2e-20  Score=131.32  Aligned_cols=82  Identities=27%  Similarity=0.509  Sum_probs=76.8

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .+++|||+|||+++++++|+++|++||+|..|.|+.|+.++.++|||||+|.+.++|++|++.+ +..|.|++|.|.+++
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            4578999999999999999999999999999999999999999999999999999999999886 588999999999998


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ++.
T Consensus        84 p~~   86 (89)
T d2cqba1          84 PMR   86 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.82  E-value=4.6e-20  Score=125.72  Aligned_cols=76  Identities=25%  Similarity=0.401  Sum_probs=73.0

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.++++|++|++.+ +..|.|++|+|.+++
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            5999999999999999999999999999999999999999999999999999999999987 589999999999885

>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=99.82  E-value=2e-20  Score=129.04  Aligned_cols=80  Identities=25%  Similarity=0.539  Sum_probs=75.8

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      .+|||+|||+++|+++|+++|++||+|..|+|+.|+.++.++|||||+|.++++|++|++.+ +..|.|++|.|.++.+.
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            47999999999999999999999999999999999999999999999999999999999988 58999999999999865


Q ss_pred             C
Q psy1314         180 P  180 (275)
Q Consensus       180 ~  180 (275)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.82  E-value=2e-20  Score=131.28  Aligned_cols=84  Identities=21%  Similarity=0.407  Sum_probs=78.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++|++||+.+ +..|.|++|+|.+|
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            34578999999999999999999999999999999999999999999999999999999999987 48899999999999


Q ss_pred             eeCCC
Q psy1314         177 KFNPE  181 (275)
Q Consensus       177 ~~~~~  181 (275)
                      .++..
T Consensus        87 ~~~~~   91 (93)
T d1x5ua1          87 SAHNK   91 (93)
T ss_dssp             TTTSC
T ss_pred             CCCCC
Confidence            87653

>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=99.81  E-value=5.4e-20  Score=138.88  Aligned_cols=83  Identities=22%  Similarity=0.376  Sum_probs=77.5

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      .++|||+|||+++|+++|+++|++||+|..|.|+.++.+++++|||||+|.+.++|++||+.+ +..|+|++|.|.++..
T Consensus        42 ~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~  121 (139)
T d1u6fa1          42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAAS  121 (139)
T ss_dssp             TSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            467999999999999999999999999999999999999999999999999999999999987 5899999999999987


Q ss_pred             CCCC
Q psy1314         179 NPET  182 (275)
Q Consensus       179 ~~~~  182 (275)
                      +..+
T Consensus       122 ~~~~  125 (139)
T d1u6fa1         122 GHQR  125 (139)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6544

>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=99.81  E-value=4.3e-20  Score=126.57  Aligned_cols=78  Identities=19%  Similarity=0.320  Sum_probs=74.1

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      .+|||+|||.++++++|+++|++||+|..|+++.+..++.++|||||+|.++++|++|++.+ +..+.|++|.|.+++|
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            57999999999999999999999999999999999999999999999999999999999886 5899999999999875

>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=3.2e-20  Score=132.48  Aligned_cols=85  Identities=24%  Similarity=0.391  Sum_probs=79.2

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      +..++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++||+.+ +..|.|++|.|.++
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            44578999999999999999999999999999999999999999999999999999999999887 58999999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      .++.++
T Consensus        96 ~~k~~~  101 (102)
T d2cpza1          96 RSKNDS  101 (102)
T ss_dssp             CCSCCC
T ss_pred             CCCCCC
Confidence            887654

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.81  E-value=4.9e-20  Score=127.10  Aligned_cols=80  Identities=21%  Similarity=0.453  Sum_probs=71.3

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC--eeecc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN--KKIDP   89 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g--~~i~v   89 (275)
                      ....++|||+|||+++|+++|+++|++||+|.+|+|++++.+++++|||||+|.+.++|++||+. ++..+.+  ++|.|
T Consensus         3 ~~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V   82 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV   82 (85)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEE
Confidence            34566799999999999999999999999999999999999999999999999999999999985 5666765  77877


Q ss_pred             ccc
Q psy1314          90 KRV   92 (275)
Q Consensus        90 ~~~   92 (275)
                      +++
T Consensus        83 ~~A   85 (85)
T d1b7fa2          83 RLA   85 (85)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            764

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=2e-20  Score=126.06  Aligned_cols=75  Identities=37%  Similarity=0.658  Sum_probs=71.7

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.+++||||+|.+.++|++||+++++.+.|++|.|+++
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            599999999999999999999999999999999999999999999999999999999998899999999998764

>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=99.81  E-value=6.6e-20  Score=128.82  Aligned_cols=86  Identities=23%  Similarity=0.478  Sum_probs=77.0

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCC-CCCCcccEEEEEEccHHHHHHHHHh--CCceecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-HTGQSRGFAFVTFTTQKAVDDLLAA--GDHYIGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~-~tg~~~G~afV~f~~~e~a~~al~~--~~~~~~g~~i   87 (275)
                      +...++++|||+|||.++++++|+++|++||.|.+|.|+.++ .+++++|||||+|.+.++|++||+.  ++..+.|++|
T Consensus         3 p~~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l   82 (94)
T d2cpha1           3 PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   82 (94)
T ss_dssp             CCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEE
Confidence            345677889999999999999999999999999999998875 4789999999999999999999985  5678999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|+++....
T Consensus        83 ~V~~A~~~~   91 (94)
T d2cpha1          83 VLEWADSEV   91 (94)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999997653

>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=99.81  E-value=1.1e-19  Score=123.59  Aligned_cols=76  Identities=33%  Similarity=0.727  Sum_probs=72.7

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      ++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.++++|++|++..++.|+|++|+|.+|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            6899999999999999999999999999999999999999999999999999999999987679999999999876

>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=125.77  Aligned_cols=78  Identities=13%  Similarity=0.289  Sum_probs=72.9

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~~   93 (275)
                      ..++|||+|||.++|+++|+++|++||+|.+|.|+.+ .+++++|||||+|.++++|++||++++..+.++.|.|.+..
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            4679999999999999999999999999999999887 48999999999999999999999998999999999998754

>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=99.80  E-value=6.8e-20  Score=126.33  Aligned_cols=78  Identities=28%  Similarity=0.490  Sum_probs=69.6

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC--eeecccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN--KKIDPKR   91 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g--~~i~v~~   91 (275)
                      ..++|||+|||+++|+++|+++|++||+|.+++|+.++.+++++|||||+|.++++|++|++. ++..+.|  ++|.|++
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            456799999999999999999999999999999999999999999999999999999999974 6778876  4466655


Q ss_pred             c
Q psy1314          92 V   92 (275)
Q Consensus        92 ~   92 (275)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=9.1e-20  Score=125.16  Aligned_cols=76  Identities=26%  Similarity=0.523  Sum_probs=71.4

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      .++++|||+|||+.+|+++|+++|++||.|.+|.|+.++.+++++|||||+|.+.++|++||+.+ +..|.|++|+|
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            34678999999999999999999999999999999999999999999999999999999999876 58999999986

>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=99.80  E-value=1.7e-19  Score=125.66  Aligned_cols=83  Identities=27%  Similarity=0.380  Sum_probs=74.5

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      +..+.++|||+|||.++|+++|+++|++||+|++|.|+.++.++  ++||||+|.+.++|++|++. ++..+.++.|.|.
T Consensus         4 d~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~   81 (90)
T d2cqia1           4 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVN   81 (90)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45667899999999999999999999999999999999987654  78999999999999999985 7889999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++.++.
T Consensus        82 ~a~~~~   87 (90)
T d2cqia1          82 WATTPS   87 (90)
T ss_dssp             ECCCTT
T ss_pred             EcCCCC
Confidence            987543

>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=99.80  E-value=4.4e-20  Score=127.60  Aligned_cols=82  Identities=20%  Similarity=0.384  Sum_probs=71.3

Q ss_pred             CCCCeEEEcCCCCCCC-HHHHHHHHhhcCCeeEEEEeeC-CCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          14 NDERKLFVGGLHRNTG-EKEINDYFSQYGEVESISIKND-PHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t-~~~l~~~f~~~G~v~~~~i~~~-~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      -+.++|||+|||+++| +++|+++|++||+|++|.|+.+ +.+++++|||||+|.+.++|++||+++++.+.++.|.|++
T Consensus         2 ~e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSL   81 (86)
T ss_dssp             CTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEE
T ss_pred             CCCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEE
Confidence            3678999999999976 5669999999999999998764 5688999999999999999999999889999999999999


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +.++
T Consensus        82 a~~k   85 (86)
T d2ghpa3          82 ADKK   85 (86)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8754

>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=1.4e-19  Score=128.18  Aligned_cols=85  Identities=22%  Similarity=0.436  Sum_probs=77.0

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-------CceecC
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-------DHYIGN   84 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-------~~~~~g   84 (275)
                      +.++.++|||+|||+++|+++|+++|++||+|.++.++.++.++.++|||||+|.+.++|++||+.+       +..+.+
T Consensus         4 ~~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~g   83 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   83 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECC
Confidence            4566789999999999999999999999999999999999999999999999999999999999853       357889


Q ss_pred             eeeccccccccc
Q psy1314          85 KKIDPKRVTKRV   96 (275)
Q Consensus        85 ~~i~v~~~~~~~   96 (275)
                      +.|.|+++.++.
T Consensus        84 r~l~v~~a~~k~   95 (98)
T d1x4ha1          84 RQLKVDLAVTRD   95 (98)
T ss_dssp             CEEEEECCCCCC
T ss_pred             EEEEEEECCCCC
Confidence            999999987654

>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=99.80  E-value=1.3e-19  Score=122.83  Aligned_cols=75  Identities=21%  Similarity=0.387  Sum_probs=70.3

Q ss_pred             eEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          18 KLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        18 ~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      +|||+|||+++|+++|+++|++||+|.+|+|+.++ +++++|||||+|.+.++|++|++. ++..+.+++|.|+.+.
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            69999999999999999999999999999999985 799999999999999999999984 7889999999998764

>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=99.79  E-value=6e-20  Score=131.59  Aligned_cols=81  Identities=21%  Similarity=0.434  Sum_probs=75.2

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      +.++|||+|||+++|+++|+++|++||+|.+|.|++++.|++++|||||+|.+.++|++||+. ++..+.++.|.|+++.
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            457899999999999999999999999999999999999999999999999999999999986 5789999999999876


Q ss_pred             cc
Q psy1314          94 KR   95 (275)
Q Consensus        94 ~~   95 (275)
                      +.
T Consensus        87 ~~   88 (104)
T d1p1ta_          87 SE   88 (104)
T ss_dssp             CT
T ss_pred             CC
Confidence            53

>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=1.8e-19  Score=129.05  Aligned_cols=87  Identities=23%  Similarity=0.311  Sum_probs=77.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecc
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDP   89 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v   89 (275)
                      .++..+..+|||+|||+++|+++|+++|+.++.|..+.++.+..+++++|+|||+|.++++|++||+++++.|.++.|.|
T Consensus         9 ~~~~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V   88 (104)
T d1wg5a_           9 SPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI   88 (104)
T ss_dssp             CSSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEE
T ss_pred             CCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEE
Confidence            44556667899999999999999999999999988877777778899999999999999999999998899999999999


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      ..+.+.+
T Consensus        89 ~~~~~~~   95 (104)
T d1wg5a_          89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9887654

>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=99.79  E-value=9.4e-20  Score=124.51  Aligned_cols=79  Identities=15%  Similarity=0.157  Sum_probs=67.2

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~~   94 (275)
                      .++|||+|||+++|+++|+++|++||+|..+.++.+..+++++|||||+|.+.++|++|++ +++..+.+++|.|+++.+
T Consensus         1 d~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           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            4699999999999999999999999999999998888899999999999999999999997 578899999999998754

>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=99.79  E-value=9.9e-20  Score=125.01  Aligned_cols=78  Identities=33%  Similarity=0.600  Sum_probs=71.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEE-EEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccccccc
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESI-SIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTKRV   96 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~-~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~~~   96 (275)
                      |||+|||+++|+++|+++|++||.|.++ .|++++.+++++|||||+|.+.++|++||+. ++..+.+++|.|+++.++.
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            8999999999999999999999998764 7888999999999999999999999999974 6789999999999987653

>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=99.79  E-value=1.6e-19  Score=124.58  Aligned_cols=78  Identities=23%  Similarity=0.443  Sum_probs=70.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCC---CcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccccc
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTG---QSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg---~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~~   94 (275)
                      |||+|||+++|+++|+++|++||+|++|.|++++.++   +++|||||+|.+.++|++|++. ++..+.+++|.|+++..
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   4799999999999999999975 67899999999999865


Q ss_pred             cc
Q psy1314          95 RV   96 (275)
Q Consensus        95 ~~   96 (275)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.79  E-value=1e-19  Score=124.90  Aligned_cols=79  Identities=27%  Similarity=0.465  Sum_probs=72.9

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEE-EeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeCC
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEF-QQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFNP  180 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v-~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~~  180 (275)
                      |||+|||+++++++|+++|++||.|..+ .|++++.+++++|||||+|.+.++|++||+.+ +..+.|++|.|.++.++.
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 78889899999999999999999999999987 589999999999998765


Q ss_pred             C
Q psy1314         181 E  181 (275)
Q Consensus       181 ~  181 (275)
                      .
T Consensus        81 ~   81 (83)
T d1x5ta1          81 S   81 (83)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.79  E-value=5.5e-19  Score=123.80  Aligned_cols=85  Identities=22%  Similarity=0.429  Sum_probs=75.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .......++|||+|||+++|+++|+++|++||+|.+|.++.++.  .++|||||+|.+.++|++||+ +++..+.++.|.
T Consensus         5 ~~~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~   82 (93)
T d2cq3a1           5 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   82 (93)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            34456677899999999999999999999999999999998864  478999999999999999997 478899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |+++.++.
T Consensus        83 V~~A~~r~   90 (93)
T d2cq3a1          83 VNNATARV   90 (93)
T ss_dssp             EEECCSSC
T ss_pred             EEecCcCC
Confidence            99997654

>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=99.79  E-value=1.3e-19  Score=124.91  Aligned_cols=78  Identities=19%  Similarity=0.408  Sum_probs=71.7

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCC--eEEEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICG--KEVDVKR  175 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g--~~i~v~~  175 (275)
                      .+.+|||+|||+++++++|+++|++||+|..++|++++.++.++|||||+|.+.++|++||+.++ ..+.+  ++|.|.+
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            34679999999999999999999999999999999999999999999999999999999999874 67766  8899987


Q ss_pred             e
Q psy1314         176 V  176 (275)
Q Consensus       176 ~  176 (275)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=1.2e-19  Score=124.99  Aligned_cols=77  Identities=27%  Similarity=0.500  Sum_probs=71.0

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCC--eEEEEEEe
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICG--KEVDVKRV  176 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g--~~i~v~~~  176 (275)
                      +++|||+|||+.+|+++|+++|++||+|.+++|+.++.++.++|||||+|.++++|++|++.+ +..+.|  ++|.|++|
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            467999999999999999999999999999999999999999999999999999999999987 478887  55888875

>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=99.79  E-value=7.8e-20  Score=127.52  Aligned_cols=84  Identities=26%  Similarity=0.521  Sum_probs=77.9

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ...+|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.++++|++||+.+ +..|.|++|.|.++.
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            3567999999999999999999999999999999999999999999999999999999999886 588999999999998


Q ss_pred             eCCCC
Q psy1314         178 FNPET  182 (275)
Q Consensus       178 ~~~~~  182 (275)
                      ++.+.
T Consensus        84 ~~~~~   88 (90)
T d1x5sa1          84 KSSDN   88 (90)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.79  E-value=1.7e-20  Score=130.97  Aligned_cols=85  Identities=19%  Similarity=0.321  Sum_probs=76.8

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      ...++....+|||+|||+++|+++|+++|++||.|.++.|+.+ .+++++|||||+|.+.++|++||++++..+.+++|.
T Consensus         6 e~~~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~   84 (91)
T d1fjeb1           6 EGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIK   84 (91)
T ss_dssp             SSSSCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEE
T ss_pred             CCCCCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEE
Confidence            3455667779999999999999999999999999999988765 689999999999999999999999889999999999


Q ss_pred             cccccc
Q psy1314          89 PKRVTK   94 (275)
Q Consensus        89 v~~~~~   94 (275)
                      |.++..
T Consensus        85 V~~ak~   90 (91)
T d1fjeb1          85 LEKPKG   90 (91)
T ss_dssp             EECCCC
T ss_pred             EEecCC
Confidence            998864

>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=99.79  E-value=6.9e-20  Score=125.19  Aligned_cols=79  Identities=13%  Similarity=0.214  Sum_probs=67.8

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      +|+|||+|||+++|+++|+++|++||.|..+.++.+..++.++|||||+|.+.++|++|++.+ +..+.|++|.|.+++|
T Consensus         1 d~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           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            378999999999999999999999999999988888888999999999999999999999987 5999999999999875

>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=99.79  E-value=1.7e-19  Score=122.22  Aligned_cols=75  Identities=17%  Similarity=0.402  Sum_probs=70.6

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      +|||+|||+++++++|+++|++||+|..++|+.++ +++++|||||+|.+.++|++|++.+ +..+.|++|.|.++.
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            69999999999999999999999999999999886 6889999999999999999999986 589999999999875

>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=126.64  Aligned_cols=84  Identities=17%  Similarity=0.391  Sum_probs=76.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCC-CCCeeeEEEEEECCHHHHHHHHhcC-C-ceeCCeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKS-KNMKKGFCFISFDDQNVAEQVLANP-K-QVICGKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~-~~~~~G~afV~f~~~e~a~~Ai~~~-~-~~~~g~~i~v~  174 (275)
                      ....+|||+|||+++++++|+++|++||.|..|.|+.+.. ++.++|||||+|.+.++|.+||+.+ + ..|.|++|.|.
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            4567899999999999999999999999999999998754 7889999999999999999999986 4 78999999999


Q ss_pred             EeeeCCC
Q psy1314         175 RVKFNPE  181 (275)
Q Consensus       175 ~~~~~~~  181 (275)
                      +++.+..
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9987653

>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=99.78  E-value=1.3e-19  Score=128.88  Aligned_cols=80  Identities=19%  Similarity=0.344  Sum_probs=75.1

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeeeC
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKFN  179 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~~  179 (275)
                      .++|||+|||+++++++|+++|++||+|.+|.|+.+..+++++|||||+|.+.++|.+|++..+..|.|++|.|.+++++
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~~   97 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE   97 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCCC
Confidence            46899999999999999999999999999999999999999999999999999999999985579999999999988654

>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=99.78  E-value=2e-19  Score=124.17  Aligned_cols=81  Identities=25%  Similarity=0.480  Sum_probs=70.1

Q ss_pred             cceeeecCCCCCCC-HHHHHHhcccCCCeEEEEeccC-CCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314         100 KCKIFVGGLTTEIS-EQDVRDYFSQYGSITEFQQPFD-KSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus       100 ~~~l~V~~l~~~~~-~~~l~~~F~~~G~v~~v~i~~~-~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      .++|||+|||++++ +++|+++|++||.|..|.|+.+ ..+++++|||||+|.+.++|++||+..+..|.|++|+|.+++
T Consensus         4 ~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a~   83 (86)
T d2ghpa3           4 GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLAD   83 (86)
T ss_dssp             TTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECC
T ss_pred             CCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEcC
Confidence            46899999999986 5569999999999999998764 567889999999999999999999755699999999999999


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ++|
T Consensus        84 ~kP   86 (86)
T d2ghpa3          84 KKP   86 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            875

>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=99.78  E-value=2.5e-19  Score=123.52  Aligned_cols=77  Identities=21%  Similarity=0.424  Sum_probs=70.5

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCC---CeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKN---MKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~---~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      |||+|||+++|+++|+++|++||+|..|.|++++.+.   .++|||||+|.+.++|++|++.+ +..|+|++|.|.+++.
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            7999999999999999999999999999999887665   46999999999999999999987 5899999999999864


Q ss_pred             C
Q psy1314         179 N  179 (275)
Q Consensus       179 ~  179 (275)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.78  E-value=3.2e-19  Score=124.02  Aligned_cols=80  Identities=28%  Similarity=0.469  Sum_probs=73.2

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      ..+|||+|||+++++++|+++|++||.|..+.|+.+..+  ++|||||+|.+.++|++||+.++ ..|.|++|.|.++++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~--~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTB--CCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            357999999999999999999999999999999988643  68999999999999999999885 899999999999987


Q ss_pred             CCC
Q psy1314         179 NPE  181 (275)
Q Consensus       179 ~~~  181 (275)
                      +.+
T Consensus        86 ~~~   88 (89)
T d1cvja2          86 RKE   88 (89)
T ss_dssp             TTT
T ss_pred             CCC
Confidence            764

>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=99.78  E-value=1.7e-19  Score=121.36  Aligned_cols=75  Identities=36%  Similarity=0.687  Sum_probs=71.1

Q ss_pred             eeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         102 KIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       102 ~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      +|||+|||+++|+++|+++|++||.|..+.++.++.++.+++||||+|.+.++|++|++..++.|+|++|+|.+|
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            599999999999999999999999999999999999999999999999999999999985579999999999875

>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=99.78  E-value=7.5e-19  Score=123.10  Aligned_cols=83  Identities=20%  Similarity=0.451  Sum_probs=74.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ....++|||+|||+++++++|+++|++||+|..|.++.++.+  ++|||||+|.++++|++||+.+ +..|.|++|.|.+
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 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN   85 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTT--TCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccC--CcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            344678999999999999999999999999999999988654  6899999999999999999886 5899999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      +++++.
T Consensus        86 A~~r~~   91 (93)
T d2cq3a1          86 ATARVM   91 (93)
T ss_dssp             CCSSCC
T ss_pred             cCcCCC
Confidence            988754

>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=99.78  E-value=6.2e-19  Score=122.78  Aligned_cols=82  Identities=26%  Similarity=0.416  Sum_probs=74.0

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||+|..|.|+.+..++  ++||||+|.+.++|++|++.+ +..|.|++|+|.++
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            345789999999999999999999999999999999887654  789999999999999999986 58899999999999


Q ss_pred             eeCCC
Q psy1314         177 KFNPE  181 (275)
Q Consensus       177 ~~~~~  181 (275)
                      .++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            86544

>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=99.77  E-value=5e-19  Score=126.74  Aligned_cols=84  Identities=18%  Similarity=0.453  Sum_probs=74.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCC-CCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDP-HTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~-~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      .++.++|||+|||+++|+++|+++|++|| |+++.++.++ .+++++|||||+|.+.++|++|+++++..|.++.|.|++
T Consensus        12 ~~p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45678999999999999999999999998 6677777654 578899999999999999999999889999999999998


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.++..
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=99.77  E-value=5.2e-19  Score=125.27  Aligned_cols=84  Identities=19%  Similarity=0.322  Sum_probs=76.7

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-------CceeCCeE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-------KQVICGKE  170 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-------~~~~~g~~  170 (275)
                      ...++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.+.++|++||+.+       +..|.|++
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            34578999999999999999999999999999999999999999999999999999999999864       25689999


Q ss_pred             EEEEEeeeCCC
Q psy1314         171 VDVKRVKFNPE  181 (275)
Q Consensus       171 i~v~~~~~~~~  181 (275)
                      |.|.++.++++
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999988765

>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=1.1e-19  Score=130.28  Aligned_cols=81  Identities=25%  Similarity=0.500  Sum_probs=75.8

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      .++|||+|||+++++++|+++|++||+|..|.|+.++.+++++|||||+|.+.++|++||+.+ +..|.|++|.|.++..
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            467999999999999999999999999999999999999999999999999999999999987 5889999999999876


Q ss_pred             CC
Q psy1314         179 NP  180 (275)
Q Consensus       179 ~~  180 (275)
                      +.
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            53

>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=99.77  E-value=4.1e-19  Score=123.46  Aligned_cols=80  Identities=25%  Similarity=0.476  Sum_probs=72.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      ...+|||+|||+++|+++|+++|++||.|.++.|+.++.  .++|||||+|.+.++|++||+. ++..+.+++|.|+++.
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 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            456799999999999999999999999999999998864  4789999999999999999975 5789999999999987


Q ss_pred             ccc
Q psy1314          94 KRV   96 (275)
Q Consensus        94 ~~~   96 (275)
                      +++
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>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=99.77  E-value=9.9e-19  Score=124.49  Aligned_cols=87  Identities=22%  Similarity=0.346  Sum_probs=77.1

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCee--------EEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCce
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVE--------SISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHY   81 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~--------~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~   81 (275)
                      .+..+.++|||+|||.++|+++|+++|++||+|.        .+.+..++.++++++||||+|.++++|++||+. ++..
T Consensus         3 ~~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~   82 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   82 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             CCCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCE
Confidence            3456678999999999999999999999999874        577788888999999999999999999999985 6889


Q ss_pred             ecCeeecccccccccC
Q psy1314          82 IGNKKIDPKRVTKRVN   97 (275)
Q Consensus        82 ~~g~~i~v~~~~~~~~   97 (275)
                      |.+++|.|+++.++..
T Consensus        83 ~~gr~i~V~~a~~~~p   98 (101)
T d2cpea1          83 FQGSKLKVSLARKKPP   98 (101)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             ECCEEEEEEEcCCCCC
Confidence            9999999999976543

>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=99.77  E-value=4.4e-19  Score=126.50  Aligned_cols=88  Identities=16%  Similarity=0.186  Sum_probs=76.7

Q ss_pred             CCCCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCee
Q psy1314           7 GTAGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK   86 (275)
Q Consensus         7 ~~~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~   86 (275)
                      +-+...+.+.++|||+|||+++|+++|+++|+.++ +.+|.++.+ .+++++|||||+|.++++|++||+++++.|.++.
T Consensus         6 ~~~~~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~   83 (102)
T d1weza_           6 SGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMAKDKANMQHRY   83 (102)
T ss_dssp             CCSSCCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSC
T ss_pred             CCCCCcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHHcCCCEECCEE
Confidence            33455667778999999999999999999999997 457888887 4689999999999999999999999899999999


Q ss_pred             eccccccccc
Q psy1314          87 IDPKRVTKRV   96 (275)
Q Consensus        87 i~v~~~~~~~   96 (275)
                      |+|.++....
T Consensus        84 I~V~~s~~~~   93 (102)
T d1weza_          84 VELFLNSTAG   93 (102)
T ss_dssp             CEEEEECCCC
T ss_pred             EEEEEcCCCC
Confidence            9999877654

>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=6.6e-19  Score=128.25  Aligned_cols=104  Identities=18%  Similarity=0.288  Sum_probs=85.0

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~   91 (275)
                      ++.+++|||+|||.++|+++|+++|++||.|++|++..+   +.++|||||+|.+.++|.+||+ ++++.|.++.|.|.+
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~   80 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLY   80 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            355789999999999999999999999999999999765   5678999999999999999997 578899999999998


Q ss_pred             cccccCCCcceeeecCCCCCCCHHHHHHhcccCCC
Q psy1314          92 VTKRVNPLKCKIFVGGLTTEISEQDVRDYFSQYGS  126 (275)
Q Consensus        92 ~~~~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~  126 (275)
                      +.......       .......+++++.+.+++|.
T Consensus        81 a~~~~~~~-------~~~~~~~~~~~~~~~~~~g~  108 (114)
T d2f9da1          81 YNANRAFQ-------KMDTKKKEEQLKLLKEKYGI  108 (114)
T ss_dssp             CCHHHHTT-------TSCHHHHHHHHHHHHHHHCC
T ss_pred             cCCCchhh-------hhHHHHHHHHHHHHHHHhCC
Confidence            76432211       22333456778888887764

>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=99.77  E-value=1.3e-18  Score=124.44  Aligned_cols=86  Identities=16%  Similarity=0.195  Sum_probs=76.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ....+|||+|||+++|+++|+++|+.++.|..+.++.++.++.++|+|||+|.++++|++|++.+++.|.++.|.|.++.
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECC
Confidence            34567999999999999999999999999988777777788999999999999999999999866799999999999998


Q ss_pred             eCCCCC
Q psy1314         178 FNPETM  183 (275)
Q Consensus       178 ~~~~~~  183 (275)
                      .++...
T Consensus        93 ~~~~~~   98 (104)
T d1wg5a_          93 RAEVRT   98 (104)
T ss_dssp             TTTSCC
T ss_pred             HHHhcc
Confidence            775443

>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=1.6e-18  Score=123.25  Aligned_cols=84  Identities=19%  Similarity=0.373  Sum_probs=74.7

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .....+.++|||+|||+++|+++|+++|++||+|..+.++.+ .+++++|||||+|.+.++|++||+ +++..|.++++.
T Consensus        12 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~   90 (101)
T d1x5oa1          12 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGV   90 (101)
T ss_dssp             SCCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTS
T ss_pred             ccccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCc
Confidence            344556789999999999999999999999999999999988 578999999999999999999997 578899999988


Q ss_pred             cccccc
Q psy1314          89 PKRVTK   94 (275)
Q Consensus        89 v~~~~~   94 (275)
                      +.++.+
T Consensus        91 v~~~~P   96 (101)
T d1x5oa1          91 SAPTEP   96 (101)
T ss_dssp             CCCSSC
T ss_pred             cCCCCC
Confidence            877643

>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=2.5e-18  Score=123.00  Aligned_cols=84  Identities=18%  Similarity=0.381  Sum_probs=73.0

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCC-CCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDK-SKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~-~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      +.++|||+|||+++++++|+++|++|| |..+.++.+. .++.++|||||+|.+.++|++|++..+..|.+++|.|.++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            458999999999999999999999998 6777777654 56789999999999999999888755799999999999998


Q ss_pred             eCCCCC
Q psy1314         178 FNPETM  183 (275)
Q Consensus       178 ~~~~~~  183 (275)
                      .+....
T Consensus        93 ~~~~~~   98 (104)
T d1wi8a_          93 QAQDKD   98 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            776543

>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=2.3e-18  Score=118.48  Aligned_cols=77  Identities=17%  Similarity=0.332  Sum_probs=71.3

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      .++|||+|||.++|+++|+++|++||+|..|.++.++ ++.++|||||+|.++++|++||+..+..+.|++|.|.+.+
T Consensus         6 ~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           6 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             cCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            4689999999999999999999999999999998764 7889999999999999999999877899999999998754

>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=99.76  E-value=5.8e-19  Score=124.31  Aligned_cols=79  Identities=27%  Similarity=0.554  Sum_probs=72.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      .+..++|||+|||..+++++|+++|++||+|..|+|+.+      +|||||+|.+.++|++||+.+ +..|.|++|+|.+
T Consensus        15 ~~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~   88 (96)
T d1x4ga1          15 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   88 (96)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345678999999999999999999999999999999876      789999999999999999887 5889999999999


Q ss_pred             eeeCCC
Q psy1314         176 VKFNPE  181 (275)
Q Consensus       176 ~~~~~~  181 (275)
                      ++.+|.
T Consensus        89 ak~~p~   94 (96)
T d1x4ga1          89 GKESPD   94 (96)
T ss_dssp             CCCCCS
T ss_pred             cCCCCC
Confidence            987765

>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=99.76  E-value=9.4e-19  Score=124.62  Aligned_cols=86  Identities=22%  Similarity=0.369  Sum_probs=76.9

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeE--------EEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeC
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSIT--------EFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVIC  167 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~--------~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~  167 (275)
                      .....+|||+|||+.+|+++|+++|++||.|.        .+.+..++.++++++||||+|.++++|++||+.+ +..|.
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            44568999999999999999999999999874        4667778888999999999999999999999987 58999


Q ss_pred             CeEEEEEEeeeCCCC
Q psy1314         168 GKEVDVKRVKFNPET  182 (275)
Q Consensus       168 g~~i~v~~~~~~~~~  182 (275)
                      |++|.|.++++++++
T Consensus        85 gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          85 GSKLKVSLARKKPPM   99 (101)
T ss_dssp             TEECEEECSSCCCCS
T ss_pred             CEEEEEEEcCCCCCC
Confidence            999999999987654

>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=99.76  E-value=1.4e-18  Score=116.56  Aligned_cols=74  Identities=14%  Similarity=0.312  Sum_probs=67.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      .+|||+|||+++++++|+++|++||+|.+|.|+.++..  .+++|||+|.++++|++||+++++.|.+++|.|+.+
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            48999999999999999999999999999999998653  357999999999999999999999999999998764

>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=99.75  E-value=6.6e-19  Score=125.85  Aligned_cols=82  Identities=11%  Similarity=0.062  Sum_probs=73.1

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      .....+|||+|||+++|+++|+++|+.||.|..+.++....+++++|+|||+|.+.++|++||+++++.|.++.|.|.++
T Consensus         5 ~~~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           5 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEE
T ss_pred             CCCceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEEC
Confidence            44567899999999999999999999999988765656557899999999999999999999998899999999999876


Q ss_pred             cc
Q psy1314          93 TK   94 (275)
Q Consensus        93 ~~   94 (275)
                      ..
T Consensus        85 ~~   86 (103)
T d2cpya1          85 TL   86 (103)
T ss_dssp             CH
T ss_pred             CH
Confidence            43

>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=4.7e-18  Score=119.45  Aligned_cols=82  Identities=24%  Similarity=0.456  Sum_probs=72.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v   89 (275)
                      +..+++++|||+|||+++|+++|+++|++||.|..+.+..+   ..+++||||+|.+.++|++||+ ++++.|.+++|.|
T Consensus         9 p~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V   85 (95)
T d1x4aa1           9 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   85 (95)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            44567789999999999999999999999999999888654   4568999999999999999997 4788999999999


Q ss_pred             cccccc
Q psy1314          90 KRVTKR   95 (275)
Q Consensus        90 ~~~~~~   95 (275)
                      +++...
T Consensus        86 ~~a~~~   91 (95)
T d1x4aa1          86 EFPRSG   91 (95)
T ss_dssp             ECCCCC
T ss_pred             EeccCC
Confidence            998653

>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=99.75  E-value=1.2e-18  Score=120.81  Aligned_cols=79  Identities=25%  Similarity=0.530  Sum_probs=69.5

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF  178 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~  178 (275)
                      .+++|||+|||+++|+++|+++|++||.|.+|++..+     +++||||+|.+.++|++||. .++.|+|++|.|.++++
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            4678999999999999999999999999999987543     58899999999999999986 45789999999999987


Q ss_pred             CCCCC
Q psy1314         179 NPETM  183 (275)
Q Consensus       179 ~~~~~  183 (275)
                      +....
T Consensus        78 k~~~~   82 (88)
T d1wf0a_          78 KHNSN   82 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            66543

>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=2e-18  Score=121.65  Aligned_cols=83  Identities=13%  Similarity=0.354  Sum_probs=73.9

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCC-eEEEEeccCC-CCCCeeeEEEEEECCHHHHHHHHhcCC---ceeCCeEEEEE
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGS-ITEFQQPFDK-SKNMKKGFCFISFDDQNVAEQVLANPK---QVICGKEVDVK  174 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~-v~~v~i~~~~-~~~~~~G~afV~f~~~e~a~~Ai~~~~---~~~~g~~i~v~  174 (275)
                      +|+|||+|||.++++++|+++|++||+ |..+.++.+. .+++++|||||+|.++++|.+|++.++   ..+.+++|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            478999999999999999999999996 8999998875 467899999999999999999999873   46689999999


Q ss_pred             EeeeCCCC
Q psy1314         175 RVKFNPET  182 (275)
Q Consensus       175 ~~~~~~~~  182 (275)
                      +|+++++.
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99877654

>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=8.3e-19  Score=121.59  Aligned_cols=79  Identities=29%  Similarity=0.485  Sum_probs=69.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKRV   92 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~~   92 (275)
                      +..+++|||+|||+++|+++|+++|++||+|.+|++..+     +++||||+|.+.++|++||. +++.|.+++|.|+++
T Consensus         2 s~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~-----~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a   75 (88)
T d1wf0a_           2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNA   75 (88)
T ss_dssp             CSCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec-----cCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeC
Confidence            456889999999999999999999999999999887543     57899999999999999996 678999999999998


Q ss_pred             ccccC
Q psy1314          93 TKRVN   97 (275)
Q Consensus        93 ~~~~~   97 (275)
                      .++..
T Consensus        76 ~~k~~   80 (88)
T d1wf0a_          76 EPKHN   80 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            76544

>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=99.74  E-value=2.6e-18  Score=121.06  Aligned_cols=83  Identities=19%  Similarity=0.312  Sum_probs=72.6

Q ss_pred             CCeEEEcCCCCCCCHHHHHHHHhhcCC-eeEEEEeeCC-CCCCcccEEEEEEccHHHHHHHHHhC---CceecCeeeccc
Q psy1314          16 ERKLFVGGLHRNTGEKEINDYFSQYGE-VESISIKNDP-HTGQSRGFAFVTFTTQKAVDDLLAAG---DHYIGNKKIDPK   90 (275)
Q Consensus        16 ~~~l~v~~Lp~~~t~~~l~~~f~~~G~-v~~~~i~~~~-~tg~~~G~afV~f~~~e~a~~al~~~---~~~~~g~~i~v~   90 (275)
                      +++|||+|||.++|+++|+++|++||+ |+++.|+.++ .+++++|||||+|.+.++|.+|++.+   ...+.+++|.|+
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            368999999999999999999999996 9999999875 46889999999999999999999865   235678999999


Q ss_pred             ccccccCC
Q psy1314          91 RVTKRVNP   98 (275)
Q Consensus        91 ~~~~~~~~   98 (275)
                      |+.++...
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99776543

>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=99.73  E-value=7.2e-18  Score=119.02  Aligned_cols=74  Identities=26%  Similarity=0.556  Sum_probs=66.4

Q ss_pred             CCcceeeecCCC-CCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEE
Q psy1314          98 PLKCKIFVGGLT-TEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~-~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~  175 (275)
                      ...++|||+||| ..+++++|+++|++||.|..|.|        ++|||||+|++.++|++||+.++ ..|.|++|.|.+
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            445789999997 57888999999999999999998        37899999999999999999985 899999999999


Q ss_pred             eeeC
Q psy1314         176 VKFN  179 (275)
Q Consensus       176 ~~~~  179 (275)
                      +..+
T Consensus        85 a~~~   88 (98)
T d1wf2a_          85 AAEP   88 (98)
T ss_dssp             TTSC
T ss_pred             CCCC
Confidence            8754

>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=6.2e-18  Score=113.36  Aligned_cols=74  Identities=22%  Similarity=0.321  Sum_probs=67.6

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      .+|||+|||+++++++|+++|++||+|..|+++.++...  +++|||+|+++++|++|+...++.|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~--~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKN--FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSS--SEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecccc--ceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            379999999999999999999999999999999887643  57999999999999999987679999999999875

>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=5.2e-18  Score=120.83  Aligned_cols=83  Identities=14%  Similarity=0.168  Sum_probs=72.0

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      .....+|||+|||+++|+++|+++|+.++. ..|.++.+. ++.++|||||+|.+.++|++|++..++.|.++.|+|.++
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            344578999999999999999999999974 567777764 478899999999999999999986679999999999998


Q ss_pred             eeCCC
Q psy1314         177 KFNPE  181 (275)
Q Consensus       177 ~~~~~  181 (275)
                      ..++.
T Consensus        90 ~~~~~   94 (102)
T d1weza_          90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.73  E-value=6.8e-18  Score=118.63  Aligned_cols=79  Identities=25%  Similarity=0.443  Sum_probs=70.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      ...+++|||+|||+++++++|+++|++||.|..+.+..+   ..+++||||+|.+.++|++||+.+ +..|.|++|+|.+
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~   87 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF   87 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            345678999999999999999999999999999988654   346899999999999999999987 5899999999998


Q ss_pred             eee
Q psy1314         176 VKF  178 (275)
Q Consensus       176 ~~~  178 (275)
                      ++.
T Consensus        88 a~~   90 (95)
T d1x4aa1          88 PRS   90 (95)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            764

>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=99.73  E-value=8e-19  Score=125.22  Aligned_cols=85  Identities=19%  Similarity=0.264  Sum_probs=77.7

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      .+++++|||+|||.++|+++|+++|++||.|..+.++.+..++++++||||+|.+.++|++||+. ++..+.+++|.|++
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            34678999999999999999999999999999999998888899999999999999999999986 57799999999999


Q ss_pred             cccccC
Q psy1314          92 VTKRVN   97 (275)
Q Consensus        92 ~~~~~~   97 (275)
                      +.++..
T Consensus        95 ak~k~~  100 (102)
T d2cpxa1          95 GKNKKQ  100 (102)
T ss_dssp             CCCCSC
T ss_pred             CCCccc
Confidence            987654

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.73  E-value=3.1e-18  Score=118.15  Aligned_cols=79  Identities=19%  Similarity=0.256  Sum_probs=68.2

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      .+...+|||+|||+++++++|+++|+.|+.|....++.+..+++++|+|||+|.++++|++||+. ++..+.+++|+|+.
T Consensus         6 ~p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34466799999999999999999999999987644444446899999999999999999999975 78899999998875

>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=99.73  E-value=1.2e-18  Score=126.25  Aligned_cols=87  Identities=22%  Similarity=0.352  Sum_probs=75.7

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeec
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKID   88 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~   88 (275)
                      ........++|||+|||+++|+++|+++|+.+|.|..+.++.+..++.++|+|||+|.+.++|++||+++++.|.++.|.
T Consensus        11 ~~~~~~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~   90 (112)
T d1wela1          11 SRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQ   90 (112)
T ss_dssp             CSSCCCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBE
T ss_pred             CCCCCCCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEE
Confidence            33445667799999999999999999999999998776666656789999999999999999999999989999999999


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |..+.+.
T Consensus        91 V~~~~~~   97 (112)
T d1wela1          91 VHPITKK   97 (112)
T ss_dssp             EEEECHH
T ss_pred             EEEcChH
Confidence            9876543

>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=99.73  E-value=1.2e-17  Score=117.53  Aligned_cols=76  Identities=16%  Similarity=0.392  Sum_probs=69.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      .+.++|||+|||.++++++|+++|++||+|++|+|+.+      +|||||+|.+.++|++||+. ++..+.++.|.|.|+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~a   89 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   89 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45678999999999999999999999999999999976      57999999999999999974 788999999999998


Q ss_pred             ccc
Q psy1314          93 TKR   95 (275)
Q Consensus        93 ~~~   95 (275)
                      .++
T Consensus        90 k~~   92 (96)
T d1x4ga1          90 KES   92 (96)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.72  E-value=3.9e-19  Score=123.95  Aligned_cols=82  Identities=15%  Similarity=0.255  Sum_probs=72.6

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEe
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRV  176 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~  176 (275)
                      .....+|||+|||+++++++|+++|++||.|..+.|+. +.+++++|||||+|.+.++|++||+..+..|.|++|.|.++
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 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVD-VRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCE-EEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeee-cCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            33457899999999999999999999999999888864 46788999999999999999999985569999999999988


Q ss_pred             eeC
Q psy1314         177 KFN  179 (275)
Q Consensus       177 ~~~  179 (275)
                      +.+
T Consensus        89 k~k   91 (91)
T d1fjeb1          89 KGR   91 (91)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.72  E-value=8.3e-18  Score=118.40  Aligned_cols=82  Identities=20%  Similarity=0.279  Sum_probs=71.6

Q ss_pred             ccCCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEE
Q psy1314          95 RVNPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDV  173 (275)
Q Consensus        95 ~~~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v  173 (275)
                      +.....++|||+|||+++|+++|+++|++||.|..+..     ++.+++||||+|.+.++|++|++.++ ..|.|++|.|
T Consensus        11 ~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~-----~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V   85 (96)
T d1fjca_          11 KKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL   85 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE-----TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEE
T ss_pred             CcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee-----cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEE
Confidence            33445689999999999999999999999998766542     46789999999999999999999885 8999999999


Q ss_pred             EEeeeCCC
Q psy1314         174 KRVKFNPE  181 (275)
Q Consensus       174 ~~~~~~~~  181 (275)
                      .++.++..
T Consensus        86 ~~a~~k~~   93 (96)
T d1fjca_          86 YYTGEKGG   93 (96)
T ss_dssp             EECSSSCC
T ss_pred             EEeCCCCC
Confidence            99987754

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.7e-18  Score=114.41  Aligned_cols=69  Identities=22%  Similarity=0.430  Sum_probs=64.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeee
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKI   87 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i   87 (275)
                      |||+|||+++|+++|+++|++||+|..++++.++.++.++|+|||+|.+.++|++|++. ++..+.|+.+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            89999999999999999999999999999999999999999999999999999999975 5667777765

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=4.2e-18  Score=118.16  Aligned_cols=77  Identities=18%  Similarity=0.418  Sum_probs=68.3

Q ss_pred             CCCCeEEEcCCCCCCCHHHH---HHHHhhcCCeeEEEEeeCCCCCCc---ccEEEEEEccHHHHHHHHH-hCCceecCee
Q psy1314          14 NDERKLFVGGLHRNTGEKEI---NDYFSQYGEVESISIKNDPHTGQS---RGFAFVTFTTQKAVDDLLA-AGDHYIGNKK   86 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l---~~~f~~~G~v~~~~i~~~~~tg~~---~G~afV~f~~~e~a~~al~-~~~~~~~g~~   86 (275)
                      -+.++|||+|||+++++++|   .++|++||+|++|.|++++.++.+   +|||||+|.+.++|++|++ +++..+.|+.
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            34678999999999999999   778999999999999999877654   4899999999999999997 5788999999


Q ss_pred             eccc
Q psy1314          87 IDPK   90 (275)
Q Consensus        87 i~v~   90 (275)
                      |+++
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            8763

>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=99.72  E-value=5.5e-18  Score=116.90  Aligned_cols=79  Identities=19%  Similarity=0.241  Sum_probs=69.3

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      +....|+|+|||+++++++|+++|+.|+.|....++.+..++.++|+|||+|.+.++|++||+++ +..|.+++|+|+.+
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34567999999999999999999999999876544455567899999999999999999999987 59999999999864

>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=1.7e-17  Score=113.50  Aligned_cols=78  Identities=19%  Similarity=0.267  Sum_probs=67.8

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCcee-cCeeec
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYI-GNKKID   88 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~-~g~~i~   88 (275)
                      .+..++++|||+|||.++|+++|+++|++||+|.+|++++++     +|||||+|.+.++|.+|++. ++..+ .+++|.
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~   77 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMK   77 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEE
Confidence            455678899999999999999999999999999999998653     68999999999999999986 56666 468888


Q ss_pred             ccccc
Q psy1314          89 PKRVT   93 (275)
Q Consensus        89 v~~~~   93 (275)
                      |+++.
T Consensus        78 v~~ak   82 (83)
T d2b0ga1          78 ITFAK   82 (83)
T ss_dssp             EEECC
T ss_pred             EEEec
Confidence            88874

>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=1.2e-18  Score=124.26  Aligned_cols=85  Identities=18%  Similarity=0.260  Sum_probs=78.1

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      .++++|||+|||.++++++|+++|++||.|..+.++.+..++.+++||||+|.+.++|++||+.+ +..|.|++|.|.++
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45688999999999999999999999999999988888888899999999999999999999987 58899999999999


Q ss_pred             eeCCCC
Q psy1314         177 KFNPET  182 (275)
Q Consensus       177 ~~~~~~  182 (275)
                      +++.++
T Consensus        96 k~k~~r  101 (102)
T d2cpxa1          96 KNKKQR  101 (102)
T ss_dssp             CCCSCC
T ss_pred             CCcccC
Confidence            987654

>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=99.71  E-value=1e-17  Score=118.22  Aligned_cols=81  Identities=17%  Similarity=0.242  Sum_probs=72.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKR  175 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~  175 (275)
                      .....+|||+|||+.+++++|+++|++||+|+.++|..       +|||||+|.+.++|++||++| +..|.++.|.|.+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~   84 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSY   84 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34567899999999999999999999999999999863       479999999999999999987 5899999999999


Q ss_pred             eeeCCCCCC
Q psy1314         176 VKFNPETMG  184 (275)
Q Consensus       176 ~~~~~~~~~  184 (275)
                      +..++++..
T Consensus        85 ~~~~~~~~~   93 (98)
T d1wg4a_          85 IRVYPERSS   93 (98)
T ss_dssp             EEEECCCSS
T ss_pred             EecCCCCCC
Confidence            998876543

>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=99.71  E-value=1e-17  Score=117.91  Aligned_cols=84  Identities=19%  Similarity=0.324  Sum_probs=72.3

Q ss_pred             CCCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeee
Q psy1314           9 AGPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKI   87 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i   87 (275)
                      .....++.++|||+|||+++|+++|+++|++||+|..+.     .++++++||||+|.+.++|++|++. ++..+.+++|
T Consensus         9 ~~~~~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i   83 (96)
T d1fjca_           9 TSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTSTTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             ccCcCCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            345556789999999999999999999999999876553     3577899999999999999999975 5779999999


Q ss_pred             cccccccccC
Q psy1314          88 DPKRVTKRVN   97 (275)
Q Consensus        88 ~v~~~~~~~~   97 (275)
                      .|+++.++..
T Consensus        84 ~V~~a~~k~~   93 (96)
T d1fjca_          84 SLYYTGEKGG   93 (96)
T ss_dssp             EEEECSSSCC
T ss_pred             EEEEeCCCCC
Confidence            9999887643

>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=99.71  E-value=1.6e-17  Score=120.82  Aligned_cols=78  Identities=17%  Similarity=0.335  Sum_probs=70.6

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .+++|||+|||.++++++|+++|++||+|..|.+..+   +.++|||||+|.+.++|.+||+.+ +..|.|++|.|.++.
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            4578999999999999999999999999999999865   446899999999999999999887 589999999999886


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      ..
T Consensus        83 ~~   84 (114)
T d2f9da1          83 AN   84 (114)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.71  E-value=2.2e-18  Score=123.05  Aligned_cols=82  Identities=13%  Similarity=0.182  Sum_probs=72.2

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEee
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVK  177 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~  177 (275)
                      ....+|||+|||+++|+++|+++|+.||.|..+.++.+..++.++|+|||+|.+.++|++||+..+..|.|++|.|.++.
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            34567999999999999999999999999887555566678899999999999999999999865699999999999876


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      ..
T Consensus        86 ~~   87 (103)
T d2cpya1          86 LE   87 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=99.70  E-value=8.9e-18  Score=115.70  Aligned_cols=76  Identities=29%  Similarity=0.527  Sum_probs=69.4

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||.++++++|+++|++||+|.+|.+.++      ++||||+|.+.++|++|++.+ +..|.|++|.|.++.
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            3568999999999999999999999999999999865      679999999999999999987 589999999999987


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      .+.
T Consensus        81 ~~~   83 (86)
T d2cpja1          81 HSA   83 (86)
T ss_dssp             CCS
T ss_pred             CcC
Confidence            654

>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=99.70  E-value=1.2e-17  Score=115.82  Aligned_cols=75  Identities=19%  Similarity=0.362  Sum_probs=67.4

Q ss_pred             cceeeecCCCCCCCHHHH---HHhcccCCCeEEEEeccCCCCCCe---eeEEEEEECCHHHHHHHHhcC-CceeCCeEEE
Q psy1314         100 KCKIFVGGLTTEISEQDV---RDYFSQYGSITEFQQPFDKSKNMK---KGFCFISFDDQNVAEQVLANP-KQVICGKEVD  172 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l---~~~F~~~G~v~~v~i~~~~~~~~~---~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~  172 (275)
                      .++|||+|||+++++++|   +++|++||+|..|.|++++.++.+   +|||||+|.+.++|++||+.+ +..|.|++|+
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   778999999999999988776554   499999999999999999987 5899999998


Q ss_pred             EE
Q psy1314         173 VK  174 (275)
Q Consensus       173 v~  174 (275)
                      |+
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            85

>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=99.70  E-value=2.1e-17  Score=113.80  Aligned_cols=75  Identities=23%  Similarity=0.472  Sum_probs=68.4

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      ..++|||+|||.++++++|+++|++||+|.+|.++++      ++||||+|.+.++|++|++. ++..+.+++|.|+++.
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            4567999999999999999999999999999999876      57999999999999999985 6789999999999987


Q ss_pred             cc
Q psy1314          94 KR   95 (275)
Q Consensus        94 ~~   95 (275)
                      ..
T Consensus        81 ~~   82 (86)
T d2cpja1          81 HS   82 (86)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>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=99.70  E-value=4e-18  Score=113.53  Aligned_cols=69  Identities=25%  Similarity=0.482  Sum_probs=64.4

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEE
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEV  171 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i  171 (275)
                      |||+|||.++|+++|+++|++||.|..++++.++.++.++|+|||+|.+.++|++|++.++ ..+.|+.|
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            7999999999999999999999999999999999999999999999999999999999874 67777654

>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=99.70  E-value=5.4e-17  Score=112.30  Aligned_cols=80  Identities=18%  Similarity=0.190  Sum_probs=71.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh---CCceecCeee
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA---GDHYIGNKKI   87 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~---~~~~~~g~~i   87 (275)
                      .+.+++++|||+|||.++|+++|+++|++||.|.++.++.+      +++|||+|.+.++|++|++.   ++..+.+++|
T Consensus         3 ~~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l   76 (88)
T d2cq1a1           3 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   76 (88)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEE
Confidence            45678999999999999999999999999999999999865      46999999999999999874   4678999999


Q ss_pred             ccccccccc
Q psy1314          88 DPKRVTKRV   96 (275)
Q Consensus        88 ~v~~~~~~~   96 (275)
                      .|.++..++
T Consensus        77 ~v~~sk~~~   85 (88)
T d2cq1a1          77 YIQYSNHKE   85 (88)
T ss_dssp             EEEECSCSS
T ss_pred             EEEECCCCC
Confidence            999987554

>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=3.9e-18  Score=117.84  Aligned_cols=75  Identities=16%  Similarity=0.192  Sum_probs=67.2

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      ++|||+|||+++++++|+++|++||+|..+.|..+       |||||+|.+.++|++||+.| +..|.|+.|.|.++..+
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            37999999999999999999999999999998753       79999999999999999887 58899999998887766


Q ss_pred             CCC
Q psy1314         180 PET  182 (275)
Q Consensus       180 ~~~  182 (275)
                      ++.
T Consensus        74 ~~~   76 (87)
T d3begb1          74 VDG   76 (87)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            554

>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=99.70  E-value=1.1e-17  Score=120.97  Aligned_cols=79  Identities=13%  Similarity=0.136  Sum_probs=69.3

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      .....+++|||+|||+++++++|+++|++||+|+.|.|..      +++||||+|.+.++|++||+. ++..|.+++|.|
T Consensus         5 ~~~r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v   78 (111)
T d1whxa_           5 SSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYL   78 (111)
T ss_dssp             GTSEEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEE
Confidence            4455678999999999999999999999999999998853      468999999999999999974 788999999999


Q ss_pred             cccccc
Q psy1314          90 KRVTKR   95 (275)
Q Consensus        90 ~~~~~~   95 (275)
                      +++...
T Consensus        79 ~~a~~~   84 (111)
T d1whxa_          79 EWAPIG   84 (111)
T ss_dssp             EEEETT
T ss_pred             EECCCC
Confidence            887543

>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=99.69  E-value=1.5e-17  Score=114.90  Aligned_cols=72  Identities=14%  Similarity=0.259  Sum_probs=65.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeecccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~~~   95 (275)
                      ++|||+|||+++|+++|+++|++||+|.++.|+.+       |||||+|.+.++|++||+ +++..|.++.|.|.++..+
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            47999999999999999999999999999998654       799999999999999996 5788999999998876544

>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=99.69  E-value=6e-17  Score=114.20  Aligned_cols=80  Identities=15%  Similarity=0.293  Sum_probs=69.9

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeec
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKID   88 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~   88 (275)
                      .+.....++|||+|||+++++++|+++|++||+|+++.|..       +|||||+|.+.++|++||+ +++..|.++.|.
T Consensus         9 p~~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~   81 (98)
T d1wg4a_           9 PPTRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGE   81 (98)
T ss_dssp             CCCCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSC
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEE
Confidence            34456677899999999999999999999999999999864       4799999999999999997 478899999999


Q ss_pred             cccccccc
Q psy1314          89 PKRVTKRV   96 (275)
Q Consensus        89 v~~~~~~~   96 (275)
                      |.+...+.
T Consensus        82 v~~~~~~~   89 (98)
T d1wg4a_          82 TSYIRVYP   89 (98)
T ss_dssp             EEEEEEEC
T ss_pred             EEEEecCC
Confidence            98876543

>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=99.69  E-value=9.1e-17  Score=110.64  Aligned_cols=78  Identities=19%  Similarity=0.278  Sum_probs=68.6

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ...++|||+|||+++|+++|+++|++||.|..+.+..      ++|||||+|.+.++|.+||+. ++..+.++.|.|+++
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~a   79 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   79 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            3457899999999999999999999999998887754      368999999999999999985 788999999999998


Q ss_pred             ccccC
Q psy1314          93 TKRVN   97 (275)
Q Consensus        93 ~~~~~   97 (275)
                      .++..
T Consensus        80 kP~~~   84 (86)
T d2cpda1          80 KPVDK   84 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            76543

>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=99.69  E-value=8.1e-18  Score=119.59  Aligned_cols=79  Identities=13%  Similarity=0.244  Sum_probs=69.8

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ...++|||+|||.++++++|+++|++||.|..+.+..+. ++.++|||||+|.+.++|++||+.+ +..|.|+++.|.++
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            345789999999999999999999999999999988774 6789999999999999999999987 58888888777554


Q ss_pred             e
Q psy1314         177 K  177 (275)
Q Consensus       177 ~  177 (275)
                      +
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.69  E-value=4e-17  Score=115.15  Aligned_cols=75  Identities=23%  Similarity=0.516  Sum_probs=66.0

Q ss_pred             CCCCCeEEEcCCC-CCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccc
Q psy1314          13 RNDERKLFVGGLH-RNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPK   90 (275)
Q Consensus        13 ~~~~~~l~v~~Lp-~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~   90 (275)
                      .....+|||+||| ..+++++|+++|++||+|++|.|.        +|||||+|.+.++|++||+. ++..+.++.|.|+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~   83 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDIN   83 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3456789999997 568899999999999999999983        58999999999999999986 5789999999999


Q ss_pred             ccccc
Q psy1314          91 RVTKR   95 (275)
Q Consensus        91 ~~~~~   95 (275)
                      ++.++
T Consensus        84 ~a~~~   88 (98)
T d1wf2a_          84 LAAEP   88 (98)
T ss_dssp             ETTSC
T ss_pred             ECCCC
Confidence            98654

>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=99.69  E-value=9.5e-18  Score=113.96  Aligned_cols=75  Identities=15%  Similarity=0.236  Sum_probs=66.0

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCc-eecCeeeccccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDH-YIGNKKIDPKRVTK   94 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~-~~~g~~i~v~~~~~   94 (275)
                      ++|||+|||.++|+++|+++|++||.|.++.++..      +|||||+|.+.++|++|++. ++. .+.|++|.|+++.+
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            57999999999999999999999999887777654      68999999999999999985 454 69999999999987


Q ss_pred             ccC
Q psy1314          95 RVN   97 (275)
Q Consensus        95 ~~~   97 (275)
                      +..
T Consensus        76 k~~   78 (80)
T d2cqha1          76 KKL   78 (80)
T ss_dssp             CCC
T ss_pred             cCc
Confidence            544

>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=99.69  E-value=8.1e-18  Score=114.31  Aligned_cols=76  Identities=22%  Similarity=0.376  Sum_probs=66.9

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c-eeCCeEEEEEEeee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q-VICGKEVDVKRVKF  178 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~-~~~g~~i~v~~~~~  178 (275)
                      .+|||+|||.++|+++|+++|++||.|..+.+..      ++|||||+|.+.++|++|++.++ . .+.|++|.|.++.+
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 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            4799999999999999999999999987766553      47899999999999999999874 4 69999999999998


Q ss_pred             CCCC
Q psy1314         179 NPET  182 (275)
Q Consensus       179 ~~~~  182 (275)
                      +..+
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            7653

>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=5.5e-17  Score=116.92  Aligned_cols=75  Identities=17%  Similarity=0.258  Sum_probs=67.3

Q ss_pred             CCeEEEcCCCC-CCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          16 ERKLFVGGLHR-NTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        16 ~~~l~v~~Lp~-~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      +++|||+|||+ .+|+++|+++|++||+|++|.|++++     +|||||+|.+.++|++||+. ++..|.++.|.|+++.
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            57999999965 59999999999999999999999874     68999999999999999985 6789999999999875


Q ss_pred             cc
Q psy1314          94 KR   95 (275)
Q Consensus        94 ~~   95 (275)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.68  E-value=7.5e-17  Score=126.87  Aligned_cols=86  Identities=34%  Similarity=0.666  Sum_probs=79.5

Q ss_pred             CCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeeccc
Q psy1314          11 PGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPK   90 (275)
Q Consensus        11 ~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~   90 (275)
                      ......++|||+|||.++|+++|+++|+.||+|..+.|+.++.+++++|||||+|.+.++|++||+++++.+.|++|.|.
T Consensus        92 ~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~  171 (183)
T d1u1qa_          92 GAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVR  171 (183)
T ss_dssp             TTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEE
T ss_pred             ccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEE
Confidence            44566789999999999999999999999999999999999999999999999999999999999988889999999999


Q ss_pred             cccccc
Q psy1314          91 RVTKRV   96 (275)
Q Consensus        91 ~~~~~~   96 (275)
                      ++.+++
T Consensus       172 ~A~~k~  177 (183)
T d1u1qa_         172 KALSKQ  177 (183)
T ss_dssp             ECCCHH
T ss_pred             ecCCcc
Confidence            886543

>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=9.8e-17  Score=110.97  Aligned_cols=77  Identities=14%  Similarity=0.173  Sum_probs=66.5

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCcee-cCeeecccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYI-GNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~-~g~~i~v~~   91 (275)
                      .++++|||+|||.++|+++|+++|++||.|..+.++..    +++++|||+|.+.++|.+|+.. ++..+ .+++|.|++
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            45789999999999999999999999999988877654    3478999999999999999975 56666 589999998


Q ss_pred             ccc
Q psy1314          92 VTK   94 (275)
Q Consensus        92 ~~~   94 (275)
                      +++
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            754

>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=99.68  E-value=5.2e-17  Score=111.06  Aligned_cols=76  Identities=16%  Similarity=0.230  Sum_probs=67.4

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-Ccee-CCeEEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVI-CGKEVDVK  174 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~-~g~~i~v~  174 (275)
                      .+++++|||+|||.++++++|+++|++||+|..|+++.+     .++||||+|.+.++|.+|++.+ +..| .+++|.|.
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            456789999999999999999999999999999999865     2689999999999999999987 4666 56899999


Q ss_pred             Eee
Q psy1314         175 RVK  177 (275)
Q Consensus       175 ~~~  177 (275)
                      +++
T Consensus        80 ~ak   82 (83)
T d2b0ga1          80 FAK   82 (83)
T ss_dssp             ECC
T ss_pred             Eec
Confidence            886

>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=99.67  E-value=4.6e-17  Score=117.72  Aligned_cols=76  Identities=13%  Similarity=0.151  Sum_probs=68.7

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      .+++|||+|||+.+++++|+++|++||+|..|.|..      +++||||+|.+.++|++||+.| +..|.|++|.|.++.
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            457899999999999999999999999999998853      4789999999999999999987 589999999999987


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            654

>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=99.67  E-value=3.8e-17  Score=113.82  Aligned_cols=79  Identities=18%  Similarity=0.351  Sum_probs=69.1

Q ss_pred             CCCeEEEcCCCCCCCHHHHHH----HHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecc
Q psy1314          15 DERKLFVGGLHRNTGEKEIND----YFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDP   89 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~----~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v   89 (275)
                      ++++|||+|||+++|+++|++    +|++||+|.+|.+..   +++++|||||+|.+.++|.+|++. ++..+.+++|.|
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            578999999999999999865    589999999988754   466899999999999999999975 678999999999


Q ss_pred             ccccccc
Q psy1314          90 KRVTKRV   96 (275)
Q Consensus        90 ~~~~~~~   96 (275)
                      .++.++.
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9987543

>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=99.67  E-value=7.1e-17  Score=111.59  Aligned_cols=75  Identities=17%  Similarity=0.231  Sum_probs=63.8

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~  178 (275)
                      +.+|||+|||+++++++|+++|++|| +..+.+      ...++||||+|.+.++|++||+.+ +..|.|++|.|.++..
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~   77 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            46899999999999999999999999 233333      235889999999999999999987 5899999999999865


Q ss_pred             CCC
Q psy1314         179 NPE  181 (275)
Q Consensus       179 ~~~  181 (275)
                      +..
T Consensus        78 ~~~   80 (88)
T d1wg1a_          78 DAL   80 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.67  E-value=3.1e-17  Score=111.12  Aligned_cols=74  Identities=18%  Similarity=0.343  Sum_probs=66.8

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+||+  +|+++|+++|++||.|.+|.+.++      ++||||+|.+.++|.+|++.+ +..+.|++|+|.+++
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            45789999986  899999999999999999998754      679999999999999999987 589999999999998


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ++|
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

>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=99.67  E-value=1.1e-16  Score=110.31  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=67.5

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      ..++|||+|||+++++++|+++|++||.|..+.+..      ++|||||+|.++++|.+||..+ +..|.|++|.|.+++
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            346899999999999999999999999988777643      4789999999999999999987 588999999999988


Q ss_pred             eCC
Q psy1314         178 FNP  180 (275)
Q Consensus       178 ~~~  180 (275)
                      ++.
T Consensus        81 P~~   83 (86)
T d2cpda1          81 PVD   83 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=3e-16  Score=111.92  Aligned_cols=80  Identities=14%  Similarity=0.164  Sum_probs=70.0

Q ss_pred             CCCCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh---CCceecCee
Q psy1314          10 GPGRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA---GDHYIGNKK   86 (275)
Q Consensus        10 ~~~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~---~~~~~~g~~   86 (275)
                      .....++++|||+|||.++|+++|+++|++||+|++|.+.++      +++|||+|.+.++|++||+.   +...+.+++
T Consensus         9 ~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~   82 (104)
T d1wexa_           9 HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQ   82 (104)
T ss_dssp             CCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSB
T ss_pred             CCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEE
Confidence            345567889999999999999999999999999999999865      57999999999999999975   355788999


Q ss_pred             ecccccccc
Q psy1314          87 IDPKRVTKR   95 (275)
Q Consensus        87 i~v~~~~~~   95 (275)
                      |.|.++..+
T Consensus        83 l~v~~s~~~   91 (104)
T d1wexa_          83 AFFNYSTSK   91 (104)
T ss_dssp             CEEEECSSS
T ss_pred             EEEEEcCCC
Confidence            999988654

>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=2.2e-18  Score=120.01  Aligned_cols=78  Identities=18%  Similarity=0.349  Sum_probs=68.6

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEe-----eCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCeeecccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIK-----NDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKKIDPKR   91 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~-----~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~i~v~~   91 (275)
                      ++|||+|||.++|+++|+++|++||.|..+.+.     .+..+++++|||||+|.++++|++|+++++..+.|+.|.|+.
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            689999999999999999999999987766553     344677899999999999999999999889999999999986


Q ss_pred             ccc
Q psy1314          92 VTK   94 (275)
Q Consensus        92 ~~~   94 (275)
                      +..
T Consensus        82 ~k~   84 (90)
T d1u2fa_          82 PHD   84 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            543

>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=99.66  E-value=8.3e-17  Score=113.73  Aligned_cols=82  Identities=10%  Similarity=0.178  Sum_probs=70.8

Q ss_pred             CCCCCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH---hCCceecC
Q psy1314           9 AGPGRNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA---AGDHYIGN   84 (275)
Q Consensus         9 ~~~~~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~---~~~~~~~g   84 (275)
                      ..+.....++|||+|||.+ +|+++|.++|++||.|.+|.++.+      +++|||+|.+.++|.+|++   .++..+.|
T Consensus        11 ~~~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~g   84 (99)
T d1x4fa1          11 FDQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQG   84 (99)
T ss_dssp             CCCSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             cccCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECC
Confidence            3445567789999999986 899999999999999999999875      4799999999999999986   46778999


Q ss_pred             eeeccccccccc
Q psy1314          85 KKIDPKRVTKRV   96 (275)
Q Consensus        85 ~~i~v~~~~~~~   96 (275)
                      +.|.|+++..+.
T Consensus        85 r~l~V~~s~~~~   96 (99)
T d1x4fa1          85 RCVKVDLSEKYK   96 (99)
T ss_dssp             SCCEEEEECSCS
T ss_pred             EEEEEEEcCCcc
Confidence            999999886543

>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=99.66  E-value=5.1e-17  Score=113.13  Aligned_cols=80  Identities=18%  Similarity=0.351  Sum_probs=70.0

Q ss_pred             CcceeeecCCCCCCCHHHHHH----hcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEE
Q psy1314          99 LKCKIFVGGLTTEISEQDVRD----YFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDV  173 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~----~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v  173 (275)
                      ++++|||+|||+++++++|++    +|++||+|.+|.+..   ++.++|||||+|.+.++|.+|++.+ +..+.|++|.|
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            457899999999999999864    589999999998764   3567899999999999999999987 58899999999


Q ss_pred             EEeeeCCC
Q psy1314         174 KRVKFNPE  181 (275)
Q Consensus       174 ~~~~~~~~  181 (275)
                      .+++.+.+
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99987654

>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=99.66  E-value=1.1e-16  Score=108.26  Aligned_cols=75  Identities=20%  Similarity=0.348  Sum_probs=66.9

Q ss_pred             CCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccc
Q psy1314          13 RNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      +...++|||+||+  +|+++|+++|++||+|.+|.+.++      ++||||+|.+.++|.+|++. ++..+.+++|.|++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~   73 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNI   73 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEE
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999995  899999999999999999999765      57999999999999999975 67899999999999


Q ss_pred             cccc
Q psy1314          92 VTKR   95 (275)
Q Consensus        92 ~~~~   95 (275)
                      +.++
T Consensus        74 a~~~   77 (79)
T d2bz2a1          74 ARKQ   77 (79)
T ss_dssp             CCSS
T ss_pred             ecCC
Confidence            8654

>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=99.66  E-value=2.6e-17  Score=119.10  Aligned_cols=81  Identities=16%  Similarity=0.243  Sum_probs=72.4

Q ss_pred             CcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEEeee
Q psy1314          99 LKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKRVKF  178 (275)
Q Consensus        99 ~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~~~~  178 (275)
                      ..++|||+|||+++|+++|+++|+.+|.+..+.++.+..++.++|+|||+|.+.++|++|++..++.|.++.|.|..+..
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~~   96 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITK   96 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECH
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcCh
Confidence            45789999999999999999999999998876666677789999999999999999999998667899999999988765


Q ss_pred             C
Q psy1314         179 N  179 (275)
Q Consensus       179 ~  179 (275)
                      +
T Consensus        97 ~   97 (112)
T d1wela1          97 K   97 (112)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.66  E-value=1.2e-16  Score=112.58  Aligned_cols=77  Identities=22%  Similarity=0.403  Sum_probs=67.9

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCC--eEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICG--KEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g--~~i~v~  174 (275)
                      .+.++|||+|||+++++++|+++|++||+|..+++.++      ++||||+|.+.++|++|++.+ +..|.+  ++|+|.
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            34688999999999999999999999999999998754      679999999999999999987 477765  589999


Q ss_pred             EeeeCC
Q psy1314         175 RVKFNP  180 (275)
Q Consensus       175 ~~~~~~  180 (275)
                      +++..+
T Consensus        89 ~ak~~~   94 (97)
T d1whya_          89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             eCCCCC
Confidence            988654

>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=2.7e-16  Score=108.71  Aligned_cols=78  Identities=12%  Similarity=0.162  Sum_probs=69.8

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC---CceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP---KQVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~---~~~~~g~~i~v  173 (275)
                      .+++++|||+|||.++++++|+++|++||.|..+.+..+      +++|||+|.+.++|++|++.+   +..+.|++|.|
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            456789999999999999999999999999999998865      579999999999999999864   47899999999


Q ss_pred             EEeeeCC
Q psy1314         174 KRVKFNP  180 (275)
Q Consensus       174 ~~~~~~~  180 (275)
                      .+++.+.
T Consensus        79 ~~sk~~~   85 (88)
T d2cq1a1          79 QYSNHKE   85 (88)
T ss_dssp             EECSCSS
T ss_pred             EECCCCC
Confidence            9987654

>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=4.7e-16  Score=109.44  Aligned_cols=78  Identities=21%  Similarity=0.403  Sum_probs=67.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecC--eeec
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGN--KKID   88 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g--~~i~   88 (275)
                      ...++++|||+|||+++|+++|+++|++||+|++|++.++      ++||||+|.+.++|++|++. ++..|.+  ++|.
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~   86 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLR   86 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCE
T ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEE
Confidence            3456799999999999999999999999999999999865      46999999999999999976 5667765  5788


Q ss_pred             ccccccc
Q psy1314          89 PKRVTKR   95 (275)
Q Consensus        89 v~~~~~~   95 (275)
                      |+++...
T Consensus        87 v~~ak~~   93 (97)
T d1whya_          87 VDFAKSG   93 (97)
T ss_dssp             EEECCCC
T ss_pred             EEeCCCC
Confidence            8887643

>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=99.65  E-value=9.6e-17  Score=115.61  Aligned_cols=75  Identities=20%  Similarity=0.370  Sum_probs=67.4

Q ss_pred             cceeeecCCCC-CCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEee
Q psy1314         100 KCKIFVGGLTT-EISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVK  177 (275)
Q Consensus       100 ~~~l~V~~l~~-~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~  177 (275)
                      +++|||+|||+ .+|+++|+++|++||.|..|.|+.++     +|||||+|++.++|++||+.+ +..|.|+.|.|.+++
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            36899999965 59999999999999999999998773     789999999999999999987 588999999999986


Q ss_pred             eC
Q psy1314         178 FN  179 (275)
Q Consensus       178 ~~  179 (275)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.65  E-value=1.7e-16  Score=109.58  Aligned_cols=75  Identities=13%  Similarity=0.252  Sum_probs=63.7

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ..+++|||+|||++++++||+++|++|| +..+.+.      ++++||||+|.+.++|++||+. ++..+.+++|.|+++
T Consensus         3 s~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a   75 (88)
T d1wg1a_           3 SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee------ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4567899999999999999999999999 3334443      3578999999999999999975 688999999999998


Q ss_pred             ccc
Q psy1314          93 TKR   95 (275)
Q Consensus        93 ~~~   95 (275)
                      ..+
T Consensus        76 ~~~   78 (88)
T d1wg1a_          76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.64  E-value=1.3e-16  Score=110.32  Aligned_cols=77  Identities=19%  Similarity=0.303  Sum_probs=66.8

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-Ccee-CCeEEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVI-CGKEVDVKR  175 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~-~g~~i~v~~  175 (275)
                      +++++|||+|||.++++++|+++|++||.|..+.+...+    .+++|||+|++.++|.+|+..+ +..| +|++|+|.+
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 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSF   83 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec----ccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEe
Confidence            346789999999999999999999999999888776543    4779999999999999999887 4666 689999998


Q ss_pred             eee
Q psy1314         176 VKF  178 (275)
Q Consensus       176 ~~~  178 (275)
                      ++.
T Consensus        84 sk~   86 (88)
T d2adca2          84 SKS   86 (88)
T ss_dssp             CSS
T ss_pred             CCC
Confidence            865

>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=99.64  E-value=4e-16  Score=111.27  Aligned_cols=80  Identities=16%  Similarity=0.209  Sum_probs=70.1

Q ss_pred             CCCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC---CceeCCeEEEE
Q psy1314          97 NPLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP---KQVICGKEVDV  173 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~---~~~~~g~~i~v  173 (275)
                      ..++..|||+|||..+++++|+++|++||.|..+.+.++      +++|||+|++.++|++|++.+   ...+.+++|.|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v   85 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFF   85 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEE
Confidence            445678999999999999999999999999999998754      679999999999999999875   35788999999


Q ss_pred             EEeeeCCCC
Q psy1314         174 KRVKFNPET  182 (275)
Q Consensus       174 ~~~~~~~~~  182 (275)
                      .+++.+...
T Consensus        86 ~~s~~~~~~   94 (104)
T d1wexa_          86 NYSTSKRIT   94 (104)
T ss_dssp             EECSSSSCC
T ss_pred             EEcCCCccC
Confidence            999776543

>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=99.64  E-value=1.7e-16  Score=114.06  Aligned_cols=79  Identities=13%  Similarity=0.142  Sum_probs=67.3

Q ss_pred             CCCCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCcee--cCeeec
Q psy1314          12 GRNDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYI--GNKKID   88 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~--~g~~i~   88 (275)
                      .+.+..+|||+|||+++|+++|+++|++||.|++|.|+.++    ++|+|||+|.+.++|++||+. ++..+  .++.|.
T Consensus         3 ~~s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~   78 (108)
T d2adba1           3 GQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR   78 (108)
T ss_dssp             CCCCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCE
T ss_pred             CCCCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEE
Confidence            45677889999999999999999999999999999998764    479999999999999999986 45555  467777


Q ss_pred             cccccc
Q psy1314          89 PKRVTK   94 (275)
Q Consensus        89 v~~~~~   94 (275)
                      +.++..
T Consensus        79 v~~s~~   84 (108)
T d2adba1          79 IDFSKL   84 (108)
T ss_dssp             EEECSS
T ss_pred             EEecCC
Confidence            777654

>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=99.62  E-value=6.5e-16  Score=103.29  Aligned_cols=70  Identities=21%  Similarity=0.360  Sum_probs=61.4

Q ss_pred             eeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEeeeC
Q psy1314         103 IFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRVKFN  179 (275)
Q Consensus       103 l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~~~~  179 (275)
                      |||+|||+++++++|+++|++|| +..+.+.      +++|+|||+|.+.++|++|++.+ +..+.|++|.|.++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999998 5555543      35889999999999999999887 58999999999998654

>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=99.62  E-value=3.1e-16  Score=112.67  Aligned_cols=79  Identities=14%  Similarity=0.177  Sum_probs=68.2

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-Ccee--CCeEEEEE
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVI--CGKEVDVK  174 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~--~g~~i~v~  174 (275)
                      ....+|||+|||+++|+++|+++|++||.|..|.|..++    ++|+|||+|.++++|++||+.+ +..|  .+++|.|.
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            345789999999999999999999999999999998764    4899999999999999999988 4666  57788888


Q ss_pred             EeeeCC
Q psy1314         175 RVKFNP  180 (275)
Q Consensus       175 ~~~~~~  180 (275)
                      +++.+.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            876543

>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=99.61  E-value=1.3e-15  Score=101.79  Aligned_cols=69  Identities=16%  Similarity=0.353  Sum_probs=60.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHH-hCCceecCeeeccccccc
Q psy1314          19 LFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLA-AGDHYIGNKKIDPKRVTK   94 (275)
Q Consensus        19 l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~-~~~~~~~g~~i~v~~~~~   94 (275)
                      |||+|||+++++++|+++|++|| +..+.+.      +++|||||+|.+.++|++|++ +++..+.|++|.|+++..
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999998 5555543      457899999999999999997 578899999999999864

>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=99.61  E-value=1e-15  Score=105.74  Aligned_cols=78  Identities=13%  Similarity=0.141  Sum_probs=69.2

Q ss_pred             CCCCCCeEEEcCCCCC-CCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh---CCceecCeee
Q psy1314          12 GRNDERKLFVGGLHRN-TGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA---GDHYIGNKKI   87 (275)
Q Consensus        12 ~~~~~~~l~v~~Lp~~-~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~---~~~~~~g~~i   87 (275)
                      ..+++++|||+|||.. +|++||.++|++||+|.+|.++.++      ++|||+|.+.++|.+|++.   ++..+.|++|
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 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGKPV   77 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCceE
Confidence            4678899999999986 7899999999999999999998764      5899999999999999874   4668999999


Q ss_pred             cccccccc
Q psy1314          88 DPKRVTKR   95 (275)
Q Consensus        88 ~v~~~~~~   95 (275)
                      .|+++.+.
T Consensus        78 ~V~~s~~~   85 (89)
T d1x4da1          78 RVHLSQKY   85 (89)
T ss_dssp             EEEEECCC
T ss_pred             EEEECCCc
Confidence            99998653

>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=99.60  E-value=1.7e-15  Score=104.71  Aligned_cols=78  Identities=12%  Similarity=0.094  Sum_probs=68.3

Q ss_pred             CCCcceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC---CceeCCeEEE
Q psy1314          97 NPLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP---KQVICGKEVD  172 (275)
Q Consensus        97 ~~~~~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~---~~~~~g~~i~  172 (275)
                      .+.++.|||+|||.. +|++||.++|++||.|..|.++.+      +++|||+|++.++|.+|++.+   +..+.|++|.
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            445678999999986 789999999999999999999865      458999999999999999864   4689999999


Q ss_pred             EEEeeeCC
Q psy1314         173 VKRVKFNP  180 (275)
Q Consensus       173 v~~~~~~~  180 (275)
                      |.+++...
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99987543

>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=99.59  E-value=9.3e-16  Score=108.22  Aligned_cols=77  Identities=19%  Similarity=0.202  Sum_probs=67.5

Q ss_pred             CCcceeeecCCCCC-CCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc---CCceeCCeEEEE
Q psy1314          98 PLKCKIFVGGLTTE-ISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN---PKQVICGKEVDV  173 (275)
Q Consensus        98 ~~~~~l~V~~l~~~-~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~---~~~~~~g~~i~v  173 (275)
                      ...++|||+|||.+ +|+++|.++|++||.|.++.++.+      +++|||+|.+.++|.+|++.   .+..+.|++|.|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            34578999999985 899999999999999999999865      67999999999999999974   357899999999


Q ss_pred             EEeeeCC
Q psy1314         174 KRVKFNP  180 (275)
Q Consensus       174 ~~~~~~~  180 (275)
                      .+++.+.
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9997654

>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=99.56  E-value=2.3e-17  Score=114.69  Aligned_cols=77  Identities=21%  Similarity=0.429  Sum_probs=65.4

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEec-----cCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEE
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQP-----FDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR  175 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~-----~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~  175 (275)
                      ++|||+|||.++|+++|+++|+++|.|..+.+.     .+..++.++|||||+|.++++|++|++..+..+.|++|+|.+
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            579999999999999999999999987766554     244566789999999999999999997557999999999974


Q ss_pred             ee
Q psy1314         176 VK  177 (275)
Q Consensus       176 ~~  177 (275)
                      ++
T Consensus        82 ~k   83 (90)
T d1u2fa_          82 PH   83 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            33

>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=99.55  E-value=6.9e-15  Score=104.46  Aligned_cols=78  Identities=17%  Similarity=0.086  Sum_probs=67.9

Q ss_pred             CcceeeecCCCCCC-CH----HHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEE
Q psy1314          99 LKCKIFVGGLTTEI-SE----QDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVD  172 (275)
Q Consensus        99 ~~~~l~V~~l~~~~-~~----~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~  172 (275)
                      ..++|||+||+..+ ++    ++|+++|++||.|+.+.+++.      +++|||+|.+.++|.+|++.|+ ..|.|++|+
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            35789999999886 33    568999999999999998753      6799999999999999999995 899999999


Q ss_pred             EEEeeeCCCC
Q psy1314         173 VKRVKFNPET  182 (275)
Q Consensus       173 v~~~~~~~~~  182 (275)
                      |.++++....
T Consensus        78 v~~a~~~~~~   87 (104)
T d1weya_          78 LYFAQTLHIG   87 (104)
T ss_dssp             EECCCCSSCC
T ss_pred             EeecccCCCC
Confidence            9999877554

>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=1.1e-14  Score=103.33  Aligned_cols=79  Identities=8%  Similarity=0.009  Sum_probs=67.6

Q ss_pred             CCCCCeEEEcCCCCCC-C----HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-CceecCee
Q psy1314          13 RNDERKLFVGGLHRNT-G----EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYIGNKK   86 (275)
Q Consensus        13 ~~~~~~l~v~~Lp~~~-t----~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~~g~~   86 (275)
                      .....+|||+||+.++ +    +++|+++|++||+|+++++++.      +++|||+|.+.++|.+|++.+ +..|.+++
T Consensus         2 ~~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~   75 (104)
T d1weya_           2 SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKE   75 (104)
T ss_dssp             CSCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEE
T ss_pred             CCCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCE
Confidence            3567889999999875 3    3679999999999999999854      579999999999999999964 67999999


Q ss_pred             ecccccccccC
Q psy1314          87 IDPKRVTKRVN   97 (275)
Q Consensus        87 i~v~~~~~~~~   97 (275)
                      |.|.++..+..
T Consensus        76 l~v~~a~~~~~   86 (104)
T d1weya_          76 MKLYFAQTLHI   86 (104)
T ss_dssp             CEEECCCCSSC
T ss_pred             eEEeecccCCC
Confidence            99999876543

>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=99.48  E-value=2.9e-15  Score=106.43  Aligned_cols=75  Identities=13%  Similarity=0.251  Sum_probs=68.2

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeeccccc
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRV   92 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~   92 (275)
                      ..++|.+++.+++|++|+++|++||+|++|.|+++ .+++++|+|||+|.+.++|.+|++. +++++.|++|.|+.+
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            35788888889999999999999999999999877 6899999999999999999999985 788999999998865

>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=5.7e-15  Score=104.90  Aligned_cols=75  Identities=13%  Similarity=0.203  Sum_probs=67.9

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcC-CceeCCeEEEEEEe
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANP-KQVICGKEVDVKRV  176 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~-~~~~~g~~i~v~~~  176 (275)
                      ..++|.+++.++++++|+++|++||+|.+|.|+.+ .++.++|+|||+|.+.++|.+|++.+ +..++|++|.|.+.
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            35788888889999999999999999999999866 57889999999999999999999987 59999999999764

>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=99.45  E-value=7.7e-14  Score=98.41  Aligned_cols=66  Identities=11%  Similarity=0.233  Sum_probs=56.2

Q ss_pred             CCCCCCCeEEEcC--CCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhC-Ccee
Q psy1314          11 PGRNDERKLFVGG--LHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAG-DHYI   82 (275)
Q Consensus        11 ~~~~~~~~l~v~~--Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~-~~~~   82 (275)
                      ..+++.++|+|.|  ||.++|+++|+++|++||.|++|.++.+      ++||||+|.+.++|++|++.+ +..+
T Consensus        13 ~~~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             cCCCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            3456678899955  9999999999999999999999998865      469999999999999999864 3443

>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=99.43  E-value=8e-14  Score=100.50  Aligned_cols=73  Identities=16%  Similarity=0.137  Sum_probs=60.5

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCH-HHHHHHHhcCC-ceeCCeEEEEEEeee
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQ-NVAEQVLANPK-QVICGKEVDVKRVKF  178 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~-e~a~~Ai~~~~-~~~~g~~i~v~~~~~  178 (275)
                      ..+||+|||+.+|+++|+++|++||+|..|.|+.+      ++||||+|.++ ++|.+|+..++ ..+.++.+.|.+...
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            34599999999999999999999999999999865      78999999995 78888888874 666666666666554


Q ss_pred             C
Q psy1314         179 N  179 (275)
Q Consensus       179 ~  179 (275)
                      +
T Consensus        86 ~   86 (113)
T d1owxa_          86 E   86 (113)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.43  E-value=1.1e-13  Score=93.43  Aligned_cols=73  Identities=16%  Similarity=0.277  Sum_probs=60.7

Q ss_pred             CCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecCee-ecccccc
Q psy1314          15 DERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGNKK-IDPKRVT   93 (275)
Q Consensus        15 ~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g~~-i~v~~~~   93 (275)
                      +.+.|+|.+||++++++.| ++|++||+|.++++.++      ++||||+|.++++|++||++++..+.++. |.|.+..
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            4567999999999986555 57999999999987544      57999999999999999998899999874 4566654


Q ss_pred             c
Q psy1314          94 K   94 (275)
Q Consensus        94 ~   94 (275)
                      .
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=3.3e-13  Score=95.13  Aligned_cols=63  Identities=14%  Similarity=0.315  Sum_probs=54.7

Q ss_pred             CCcceeee--cCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-cee
Q psy1314          98 PLKCKIFV--GGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVI  166 (275)
Q Consensus        98 ~~~~~l~V--~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~  166 (275)
                      .+..+|+|  ++||.++|+++|+++|++||.|..|.+..+      ++||||+|.+.++|++|++.|+ ..|
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            34567788  559999999999999999999999998765      6799999999999999999985 555

>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=99.39  E-value=4.1e-13  Score=90.46  Aligned_cols=73  Identities=16%  Similarity=0.185  Sum_probs=60.9

Q ss_pred             cceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeE-EEEEEeee
Q psy1314         100 KCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKE-VDVKRVKF  178 (275)
Q Consensus       100 ~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~-i~v~~~~~  178 (275)
                      ++.|+|.++|++++++.| ++|++||+|.++++..      .++||||+|.++++|++||+..+..|+|+. |.|..+.+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~   76 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCID   76 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCC
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCC
Confidence            467999999999987666 5799999999998753      378999999999999999986578999975 56877665


Q ss_pred             C
Q psy1314         179 N  179 (275)
Q Consensus       179 ~  179 (275)
                      +
T Consensus        77 k   77 (81)
T d1wwha1          77 K   77 (81)
T ss_dssp             H
T ss_pred             h
Confidence            4

>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=99.39  E-value=3.1e-13  Score=97.38  Aligned_cols=73  Identities=15%  Similarity=0.151  Sum_probs=58.0

Q ss_pred             CCCCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccH-HHHHHHHHh-CCceecCeeecccc
Q psy1314          14 NDERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQ-KAVDDLLAA-GDHYIGNKKIDPKR   91 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~-e~a~~al~~-~~~~~~g~~i~v~~   91 (275)
                      ..-..+||+|||.++|+++|+++|++||+|.+|.|+.+      +|||||.|.++ ++|.+|+.. ++..+..+.+.+.+
T Consensus         9 ~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~   82 (113)
T d1owxa_           9 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTW   82 (113)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEE
T ss_pred             CCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEE
Confidence            33455799999999999999999999999999999865      58999999986 677777765 44566665555554


Q ss_pred             c
Q psy1314          92 V   92 (275)
Q Consensus        92 ~   92 (275)
                      .
T Consensus        83 ~   83 (113)
T d1owxa_          83 E   83 (113)
T ss_dssp             E
T ss_pred             e
Confidence            4

>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=99.33  E-value=2.1e-12  Score=90.55  Aligned_cols=81  Identities=14%  Similarity=0.297  Sum_probs=67.9

Q ss_pred             CCCCCCCeEEEcCC--CCCC---------CHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-C
Q psy1314          11 PGRNDERKLFVGGL--HRNT---------GEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-G   78 (275)
Q Consensus        11 ~~~~~~~~l~v~~L--p~~~---------t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~   78 (275)
                      +....+++|+|.||  |.++         .+++|++.|++||.|.+|.+..+    ..+|++||+|.++++|.+|++. +
T Consensus         3 ~~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~ln   78 (99)
T d2dita1           3 SRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLD   78 (99)
T ss_dssp             CCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHST
T ss_pred             CCCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhC
Confidence            45678899999999  6543         23789999999999999998765    3579999999999999999976 5


Q ss_pred             CceecCeeecccccccc
Q psy1314          79 DHYIGNKKIDPKRVTKR   95 (275)
Q Consensus        79 ~~~~~g~~i~v~~~~~~   95 (275)
                      +..+.+++|.++....+
T Consensus        79 g~~~~gr~i~v~~~~g~   95 (99)
T d2dita1          79 GRWFGGRQITAQAWDGT   95 (99)
T ss_dssp             TCEETTEECEEEECCSC
T ss_pred             CcEECCEEEEEEEeCCc
Confidence            77999999999987543

>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=99.31  E-value=2.4e-12  Score=90.26  Aligned_cols=80  Identities=14%  Similarity=0.219  Sum_probs=66.9

Q ss_pred             CCCcceeeecCC--CCCC---------CHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-c
Q psy1314          97 NPLKCKIFVGGL--TTEI---------SEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-Q  164 (275)
Q Consensus        97 ~~~~~~l~V~~l--~~~~---------~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~  164 (275)
                      ...+++|+|.||  |.++         .+++|++.|++||.|..|.+..+.    ++|++||+|.+.++|.+|+..++ .
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~----~~G~~fV~f~~~e~A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC----TTCEEEEECSCHHHHHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC----CccEEEEEECCHHHHHHHHHHhCCc
Confidence            345678999998  5432         236899999999999999987653    47899999999999999999985 8


Q ss_pred             eeCCeEEEEEEeeeCC
Q psy1314         165 VICGKEVDVKRVKFNP  180 (275)
Q Consensus       165 ~~~g~~i~v~~~~~~~  180 (275)
                      .++|++|.|.+...+.
T Consensus        81 ~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          81 WFGGRQITAQAWDGTT   96 (99)
T ss_dssp             EETTEECEEEECCSCC
T ss_pred             EECCEEEEEEEeCCcC
Confidence            9999999999987654

>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=99.21  E-value=5.4e-12  Score=89.30  Aligned_cols=81  Identities=20%  Similarity=0.221  Sum_probs=67.0

Q ss_pred             CCCCeEEEcCC--CCCC--------CHHHHHHHHhhcCCeeEEEEeeCCCCC--CcccEEEEEEccHHHHHHHHHh-CCc
Q psy1314          14 NDERKLFVGGL--HRNT--------GEKEINDYFSQYGEVESISIKNDPHTG--QSRGFAFVTFTTQKAVDDLLAA-GDH   80 (275)
Q Consensus        14 ~~~~~l~v~~L--p~~~--------t~~~l~~~f~~~G~v~~~~i~~~~~tg--~~~G~afV~f~~~e~a~~al~~-~~~   80 (275)
                      .++++|.|.||  |.++        ..++|++.|++||.|++|.|.+++.+.  ...|++||+|.+.++|.+|++. ++.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            46889999999  5544        346799999999999999998765543  4568999999999999999984 688


Q ss_pred             eecCeeeccccccc
Q psy1314          81 YIGNKKIDPKRVTK   94 (275)
Q Consensus        81 ~~~g~~i~v~~~~~   94 (275)
                      .+.||.|.+.....
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999887653

>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=99.17  E-value=8.4e-12  Score=88.27  Aligned_cols=80  Identities=18%  Similarity=0.190  Sum_probs=65.7

Q ss_pred             CcceeeecCC--CCCC--------CHHHHHHhcccCCCeEEEEeccCCCCC--CeeeEEEEEECCHHHHHHHHhcC-Cce
Q psy1314          99 LKCKIFVGGL--TTEI--------SEQDVRDYFSQYGSITEFQQPFDKSKN--MKKGFCFISFDDQNVAEQVLANP-KQV  165 (275)
Q Consensus        99 ~~~~l~V~~l--~~~~--------~~~~l~~~F~~~G~v~~v~i~~~~~~~--~~~G~afV~f~~~e~a~~Ai~~~-~~~  165 (275)
                      +++.|.|.||  |..+        ..+||++.|++||.|++|.|+++..+.  ...|++||+|.+.++|.+|++.| +..
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            4567888888  4443        236799999999999999998765543  34689999999999999999988 589


Q ss_pred             eCCeEEEEEEeee
Q psy1314         166 ICGKEVDVKRVKF  178 (275)
Q Consensus       166 ~~g~~i~v~~~~~  178 (275)
                      ++|+.|.+.++..
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999998764

>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=97.53  E-value=0.00011  Score=48.18  Aligned_cols=71  Identities=14%  Similarity=0.198  Sum_probs=56.2

Q ss_pred             CCCCeEEEcCCCCCCCH---------HHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHhCCceecC
Q psy1314          14 NDERKLFVGGLHRNTGE---------KEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAAGDHYIGN   84 (275)
Q Consensus        14 ~~~~~l~v~~Lp~~~t~---------~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~~~~~~~g   84 (275)
                      .+.-+|.|.=..++..+         .+|.+.|..||+|.-++++.+        ...|+|.+-+.|-+|+++++.++.+
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G   84 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKG   84 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETT
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcc
Confidence            44556666544333222         468888999999999999987        5889999999999999999999999


Q ss_pred             eeeccccc
Q psy1314          85 KKIDPKRV   92 (275)
Q Consensus        85 ~~i~v~~~   92 (275)
                      +.|.+...
T Consensus        85 ~~l~It~~   92 (95)
T d1ufwa_          85 RAVKISGP   92 (95)
T ss_dssp             EEEEEECC
T ss_pred             eEEEEecC
Confidence            99887654

>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=97.50  E-value=0.00027  Score=46.93  Aligned_cols=66  Identities=9%  Similarity=0.112  Sum_probs=51.9

Q ss_pred             CeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCC--cccEEEEEEccHHHHHHHHHh-CCcee
Q psy1314          17 RKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQ--SRGFAFVTFTTQKAVDDLLAA-GDHYI   82 (275)
Q Consensus        17 ~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~--~~G~afV~f~~~e~a~~al~~-~~~~~   82 (275)
                      ++|.|+.||+.+||+++.+.+...+++.......-+.+-+  .---|||.|.+.++.....+. .++.+
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            5799999999999999999999999888877776544332  123599999999999888775 34443

>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=97.44  E-value=0.0003  Score=46.86  Aligned_cols=61  Identities=20%  Similarity=0.367  Sum_probs=49.3

Q ss_pred             CCCCCCC-CCeEEEcCCCCCCCHHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh
Q psy1314           9 AGPGRND-ERKLFVGGLHRNTGEKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA   77 (275)
Q Consensus         9 ~~~~~~~-~~~l~v~~Lp~~~t~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~   77 (275)
                      +++++.+ ...||.-.+|.++...||.++|+.||.| .|..+.+.       .|||...+.|+|+.++..
T Consensus         7 ~G~d~~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIddT-------Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_           7 GGPDLQPKRDHVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDDT-------SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCSCCCCCCCSEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEETT-------EEEEECSCHHHHHHHHHH
T ss_pred             CCCCCCCCcceeEEEeCCcccchhHHHHHhcCCCce-EEEEecCc-------eEEEEecCHHHHHHHHHH
Confidence            3444444 4569999999999999999999999988 46666653       799999999999888764

>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=97.28  E-value=0.00022  Score=46.69  Aligned_cols=53  Identities=19%  Similarity=0.307  Sum_probs=47.2

Q ss_pred             HHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCCceeCCeEEEEEE
Q psy1314         115 QDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPKQVICGKEVDVKR  175 (275)
Q Consensus       115 ~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~~~~~g~~i~v~~  175 (275)
                      .+|.+.|.+||+|.-|+++.+        --.|+|.+-++|.+|+.+...+++|+.|+|..
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKVKGRAVKISG   91 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEETTEEEEEEC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEEcceEEEEec
Confidence            467788889999999999876        37999999999999999999999999999863

>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=96.98  E-value=0.0017  Score=40.27  Aligned_cols=60  Identities=12%  Similarity=0.115  Sum_probs=49.8

Q ss_pred             HHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhcCC-ceeCCeEEEEEEee
Q psy1314         115 QDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLANPK-QVICGKEVDVKRVK  177 (275)
Q Consensus       115 ~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~~~-~~~~g~~i~v~~~~  177 (275)
                      +.|.+.|.+++.|..+.|....+ +  .-.|-|...+.++|.-|+..+. ..|..++|.|..+.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~d-g--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTD-Y--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCS-T--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEeccC-C--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            45667889999999999876533 2  2259999999999999999985 89999999998875

>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=96.54  E-value=0.0034  Score=41.44  Aligned_cols=62  Identities=10%  Similarity=0.132  Sum_probs=49.8

Q ss_pred             ceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCe--eeEEEEEECCHHHHHHHHhcC
Q psy1314         101 CKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMK--KGFCFISFDDQNVAEQVLANP  162 (275)
Q Consensus       101 ~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~--~G~afV~f~~~e~a~~Ai~~~  162 (275)
                      .+|.|+.||+.+|++++.+.+...+++........+.+...  -.-|+|.|.+.+++....+..
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f   65 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRF   65 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHH
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHc
Confidence            47899999999999999999999998888777655443221  234899999999998888774

>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=96.51  E-value=0.0078  Score=37.20  Aligned_cols=61  Identities=21%  Similarity=0.226  Sum_probs=48.4

Q ss_pred             HHHHHHHHhhcCCeeEEEEeeCCCCCCcccEEEEEEccHHHHHHHHHh-CCceecCeeecccccc
Q psy1314          30 EKEINDYFSQYGEVESISIKNDPHTGQSRGFAFVTFTTQKAVDDLLAA-GDHYIGNKKIDPKRVT   93 (275)
Q Consensus        30 ~~~l~~~f~~~G~v~~~~i~~~~~tg~~~G~afV~f~~~e~a~~al~~-~~~~~~g~~i~v~~~~   93 (275)
                      .+.|.+.|.++++|.++.+... ..+..  .|-|...+.++|.-|++. +..++..++|.|..+.
T Consensus        10 qq~L~~~f~~h~~V~sv~l~~~-~dg~~--~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          10 QQLLQEAFARHGKVKSVELSPH-TDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHHSCEEEEEECSC-CSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHHhheeEEEEEEEec-cCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            3556678899999999998654 23333  689999999999999986 5679999999887653

>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=95.51  E-value=0.021  Score=37.75  Aligned_cols=56  Identities=18%  Similarity=0.266  Sum_probs=44.6

Q ss_pred             CCcceeeecCCCCCCCHHHHHHhcccCCCeEEEEeccCCCCCCeeeEEEEEECCHHHHHHHHhc
Q psy1314          98 PLKCKIFVGGLTTEISEQDVRDYFSQYGSITEFQQPFDKSKNMKKGFCFISFDDQNVAEQVLAN  161 (275)
Q Consensus        98 ~~~~~l~V~~l~~~~~~~~l~~~F~~~G~v~~v~i~~~~~~~~~~G~afV~f~~~e~a~~Ai~~  161 (275)
                      +....||.-.+|..+...||.++|++||.|.-..| -|  |     -|||...+.|+|+.+++.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswI-dd--T-----Sa~V~L~~~e~~~~v~~~   68 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWI-DD--T-----SAFVSLSQPEQVQIAVNT   68 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEE-ET--T-----EEEEECSCHHHHHHHHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceEEEEe-cC--c-----eEEEEecCHHHHHHHHHH
Confidence            34456888899999999999999999998654444 22  2     499999999999888765