Citrus Sinensis ID: 022814

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-
Protein Sequence
MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEEcccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEccHHHHccccEEcccEEEEEEEccccccHHHHHHHHHHHHHccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHccccccccHHHHcccccEEEEEcccccccHHHHHHHHHHHccEEEEEEEEccccccEEEEEEEEEcccccccccEEEcccEEEEcccccccccccHcHHHHHHHHHHccccccccccccccccccccccccHHcccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccHHHHccccccccccccccccHHHccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mnpltqvkriqhinskeadlgisddaswhakykdsayvyvggipfdlteGDLLAVFAQCGEIvdvnlvrdkgtgkprgfAFVAYEDQRNNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERgvcrafqrgectrgdgckfshneqraantgggpqdrssrwghekfegfswgkndsssratgsgrvalegnpnqsdrreekrsirhdhrekpredhgrredkrsrrhsdnnefearsredhyrrdekrpkrhesesylredqdrrggdksstgrgdssshrhrer
Flexible Loop (DISEMBL)
mnpltqvkriqhinskeadlgisDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYedqrnnlngaqilgrtirvdhvakykkkeeedeetrqrmreergvcrafqrgectrgdgckfshneqraantgggpqdrssrWGHEKFEgfswgkndsssratgsgrvalegnpnqsdrreekrsirhdhrekpredhgrredkrsrrhsdnnefearsredhyrrdekrpkrhesesylredqdrrggdksstgrgdssshrhrer
Low Complexity Region (SEG)
MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVDHVAkykkkeeedeetrqrmreerGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER
Disordered region (IsUnstruct)
*******************LGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVDHVAK***************************************************************************************************************************************************************************************
Disordered Region (DISOPRED)
*****QV************************YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVD*******************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVDHVAK*****************ERGVCRAFQRGECTRGDGCKFSHNE****************WGHEKFEGFSWG**********SGRVALE************************************************************************************************
Disordered Region (DISPRO)
*NPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVDHVAKYKK****D*E*RQRM**ERGVCRA***************************************************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRTIRVDHxxxxxxxxxxxxxxxxxxxxxRGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER
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	291	2.2.26 [Sep-21-2011]
Q9SD61	352	Zinc finger CCCH domain-c	yes	no	0.587	0.485	0.764	4e-76
Q10B98	312	Zinc finger CCCH domain-c	yes	no	0.587	0.548	0.713	3e-63
Q9Y388	322	RNA-binding motif protein	yes	no	0.415	0.375	0.569	7e-40
B0BN49	328	RNA-binding motif protein	yes	no	0.443	0.393	0.536	9e-40
Q8R0F5	326	RNA-binding motif protein	yes	no	0.443	0.395	0.529	4e-39
O94290	217	U2 snRNP component ist3 O	yes	no	0.384	0.516	0.483	7e-28
P40565	148	U2 snRNP component IST3 O	yes	no	0.340	0.668	0.5	6e-22
Q8HXM1	572	Cleavage stimulation fact	no	no	0.264	0.134	0.445	2e-12
P33240	577	Cleavage stimulation fact	no	no	0.264	0.133	0.445	3e-12
Q5RDA3	577	Cleavage stimulation fact	no	no	0.264	0.133	0.445	3e-12

>sp|Q9SD61|C3H42_ARATH Zinc finger CCCH domain-containing protein 42 OS=Arabidopsis thaliana GN=At3g47120 PE=2 SV=1

 Score =  285 bits (728), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 136/178 (76%), Positives = 156/178 (87%), Gaps = 7/178 (3%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLTQVK +Q IN++E+DLGISD+ASWHAKYK+SAYVYVGGIPFDLTEGDLLAVF+Q G
Sbjct: 1   MNPLTQVKNLQKINARESDLGISDEASWHAKYKNSAYVYVGGIPFDLTEGDLLAVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNL+RDKGTGK +GFAF+AYEDQR      +NLNGA +LGRTI+VDH   YKK EE
Sbjct: 61  EIVDVNLIRDKGTGKSKGFAFLAYEDQRSTILAVDNLNGALVLGRTIKVDHCGAYKKHEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEK 171
           EDEETR++ RE RGVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSS+W H+K
Sbjct: 121 EDEETRRQNREARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSKWDHDK 178

Arabidopsis thaliana (taxid: 3702)

>sp|Q10B98|C3H25_ORYSJ Zinc finger CCCH domain-containing protein 25 OS=Oryza sativa subsp. japonica GN=Os03g0826400 PE=2 SV=1

 Score =  242 bits (617), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 127/178 (71%), Positives = 149/178 (83%), Gaps = 7/178 (3%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLTQVKR Q IN KEA LGI +D SWHAK+KDSAYV+VGGIP+DLTEGDLLAVFAQ G
Sbjct: 1   MNPLTQVKRTQVINQKEALLGIGEDGSWHAKFKDSAYVFVGGIPYDLTEGDLLAVFAQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           E+VDVNLVRDKGTGK +GFAF+AYEDQR      +NLNGA++LGR +RVDHV+KYKKKEE
Sbjct: 61  EVVDVNLVRDKGTGKSKGFAFLAYEDQRSTILAVDNLNGAKVLGRIVRVDHVSKYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRS-SRWGHEK 171
           EDEE  Q+ RE RGVC AFQ+GEC RG  C++SH+EQR ANTG G ++ S +RW H++
Sbjct: 121 EDEEELQKKREARGVCYAFQKGECNRGASCRYSHDEQRNANTGWGSKEESKARWEHDR 178

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9Y388|RBMX2_HUMAN RNA-binding motif protein, X-linked 2 OS=Homo sapiens GN=RBMX2 PE=1 SV=2

 Score =  164 bits (415), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 74/130 (56%), Positives = 99/130 (76%), Gaps = 9/130 (6%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT+VK I  +N +E  LG++D  SWH++YKDSA++++GG+P++LTEGD++ VF+Q G
Sbjct: 1   MNPLTKVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKY---KK 111
           EIV++NLVRDK TGK +GF F+ YEDQR      +N NG +I GRTIRVDHV+ Y   K 
Sbjct: 61  EIVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVSNYRAPKD 120

Query: 112 KEEEDEETRQ 121
            EE D+ TRQ
Sbjct: 121 SEEIDDVTRQ 130

Homo sapiens (taxid: 9606)

>sp|B0BN49|RBMX2_RAT RNA-binding motif protein, X-linked 2 OS=Rattus norvegicus GN=Rbmx2 PE=2 SV=1

 Score =  164 bits (414), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 73/136 (53%), Positives = 102/136 (75%), Gaps = 7/136 (5%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT+VK I  +N +E  LG+++  SWH++YKDSA++++GG+P++LTEGD++ VF+Q G
Sbjct: 1   MNPLTKVKLINELNEREVQLGVAEKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIV++NLVRDK TGK +GF F+ YEDQR      +N NG +I GRTIRVDHVA Y+  +E
Sbjct: 61  EIVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVANYRAPQE 120

Query: 115 -EDEETRQRMREERGV 129
            ED +   R  +E+G 
Sbjct: 121 SEDVDDVTRELQEKGC 136

Rattus norvegicus (taxid: 10116)

>sp|Q8R0F5|RBMX2_MOUSE RNA-binding motif protein, X-linked 2 OS=Mus musculus GN=Rbmx2 PE=1 SV=1

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 72/136 (52%), Positives = 101/136 (74%), Gaps = 7/136 (5%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT+VK I  +N +E  LG+++  SWH++YK SA+++VGG+P++LTEGD++ VF+Q G
Sbjct: 1   MNPLTKVKLINELNEREVQLGVAEKVSWHSEYKHSAWIFVGGLPYELTEGDIICVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIV++NLVRDK TGK +GF F+ YEDQR      +N NG +I GRTIRVDHV+ Y+  +E
Sbjct: 61  EIVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVSNYRAPQE 120

Query: 115 -EDEETRQRMREERGV 129
            ED +   R  +E+G 
Sbjct: 121 SEDVDDVTRELQEKGC 136

Mus musculus (taxid: 10090)

>sp|O94290|IST3_SCHPO U2 snRNP component ist3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cwf29 PE=1 SV=1

 Score =  124 bits (311), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 58/120 (48%), Positives = 82/120 (68%), Gaps = 8/120 (6%)

Query: 4   LTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV 63
           +  +++I+ +N +E D   S  +SWH  Y DSAY+Y+G + FDL E D+L VF++ GE V
Sbjct: 1   MNSIRQIERLNEQELDKPFS--SSWHQDYSDSAYIYIGNLDFDLNEDDILCVFSEFGEPV 58

Query: 64  DVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEEEDE 117
           D+NLVRDK TGK +GFAF+ YEDQR      +N+   ++L R +RVDHVA YK  ++E E
Sbjct: 59  DINLVRDKETGKSKGFAFLKYEDQRSTVLAVDNMTNVKLLDRLVRVDHVASYKVPQKEKE 118

Required for pre-mRNA splicing and spliceosome assembly.

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

>sp|P40565|IST3_YEAST U2 snRNP component IST3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=IST3 PE=1 SV=1

 Score =  104 bits (260), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 53/106 (50%), Positives = 74/106 (69%), Gaps = 7/106 (6%)

Query: 7   VKRIQHINSKEADLGI-SDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDV 65
           + +IQ IN KE   GI S   SWH +YKD+AY+Y+G +  +LTEGD+L VF++ G  VDV
Sbjct: 1   MNKIQQINDKELQSGILSPHQSWHNEYKDNAYIYIGNLNRELTEGDILTVFSEYGVPVDV 60

Query: 66  NLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDH 105
            L RD+ TG+ +GFA++ YEDQR      +NLNG +I GR +++DH
Sbjct: 61  ILSRDENTGESQGFAYLKYEDQRSTILAVDNLNGFKIGGRALKIDH 106

Required for pre-mRNA splicing and spliceosome assembly. As part of the pre-mRNA retention and splicing (RES) complex, required for nuclear pre-mRNA retention and efficient splicing. Required for MER1-activated splicing.

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

>sp|Q8HXM1|CSTF2_BOVIN Cleavage stimulation factor subunit 2 OS=Bos taurus GN=CSTF2 PE=2 SV=1

 Score = 73.2 bits (178), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 37/83 (44%), Positives = 51/83 (61%), Gaps = 6/83 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ        NL
Sbjct: 18  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 77

Query: 92  NGAQILGRTIRVDHVAKYKKKEE 114
           NG +  GR +RVD+ A  K KEE
Sbjct: 78  NGREFSGRALRVDNAASEKNKEE 100

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.

Bos taurus (taxid: 9913)

>sp|P33240|CSTF2_HUMAN Cleavage stimulation factor subunit 2 OS=Homo sapiens GN=CSTF2 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/83 (44%), Positives = 51/83 (61%), Gaps = 6/83 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ        NL
Sbjct: 18  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 77

Query: 92  NGAQILGRTIRVDHVAKYKKKEE 114
           NG +  GR +RVD+ A  K KEE
Sbjct: 78  NGREFSGRALRVDNAASEKNKEE 100

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.

Homo sapiens (taxid: 9606)

>sp|Q5RDA3|CSTF2_PONAB Cleavage stimulation factor subunit 2 OS=Pongo abelii GN=CSTF2 PE=2 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 37/83 (44%), Positives = 51/83 (61%), Gaps = 6/83 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ        NL
Sbjct: 18  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 77

Query: 92  NGAQILGRTIRVDHVAKYKKKEE 114
           NG +  GR +RVD+ A  K KEE
Sbjct: 78  NGREFSGRALRVDNAASEKNKEE 100

One of the multiple factors required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs. This subunit is directly involved in the binding to pre-mRNAs.

Pongo abelii (taxid: 9601)

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	291
224104290	243	predicted protein [Populus trichocarpa]	0.790	0.946	0.706	8e-83
297819328	316	hypothetical protein ARALYDRAFT_905943 [	0.810	0.746	0.606	7e-76
15232729	352	RNA-binding motif protein, X-linked 2 [A	0.587	0.485	0.764	2e-74
297745915	375	unnamed protein product [Vitis vinifera]	0.927	0.72	0.606	3e-74
225434618	429	PREDICTED: uncharacterized protein LOC10	0.910	0.617	0.545	4e-74
449460375	395	PREDICTED: zinc finger CCCH domain-conta	0.896	0.660	0.567	4e-73
356551855	354	PREDICTED: zinc finger CCCH domain-conta	0.924	0.759	0.546	1e-72
147840589	737	hypothetical protein VITISV_032469 [Viti	0.927	0.366	0.569	3e-71
357490653	393	RNA binding domain protein [Medicago tru	0.862	0.638	0.606	3e-71
356498939	235	PREDICTED: zinc finger CCCH domain-conta	0.711	0.880	0.663	2e-68

>gi|224104290|ref|XP_002313385.1| predicted protein [Populus trichocarpa] gi|222849793|gb|EEE87340.1| predicted protein [Populus trichocarpa]

 Score =  313 bits (801), Expect = 8e-83,   Method: Compositional matrix adjust.
 Identities = 173/245 (70%), Positives = 193/245 (78%), Gaps = 15/245 (6%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKRIQ+INSKEA LGIS++ASWHAKYKDSAYV+VGGIPFDLTEGDLLAVFAQ G
Sbjct: 1   MNPLTLVKRIQNINSKEAALGISEEASWHAKYKDSAYVFVGGIPFDLTEGDLLAVFAQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           E+VD NLVRDKGTGK +GFAF+AYEDQR      +NLNGAQ+LGR IRVDHV KYKKKEE
Sbjct: 61  EVVDANLVRDKGTGKSKGFAFIAYEDQRSTNLAVDNLNGAQVLGRIIRVDHVTKYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEG 174
           EDEET Q+ RE RGVC AFQRGEC RG GC+FSH+EQRAANTG G QD+SSRWGHE F+G
Sbjct: 121 EDEETAQQKREARGVCHAFQRGECNRGAGCRFSHDEQRAANTGWGAQDKSSRWGHEMFDG 180

Query: 175 FSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHRE---KPREDHGRREDKRSR 231
                    S    S  +  E +P Q+DRREEKRS  HD  E   KPRED+ RREDK+ R
Sbjct: 181 ------PKKSEERSSYNMPSESHPKQNDRREEKRSRWHDDNEIVQKPREDYNRREDKKLR 234

Query: 232 RHSDN 236
           R  D+
Sbjct: 235 RLEDD 239

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297819328|ref|XP_002877547.1| hypothetical protein ARALYDRAFT_905943 [Arabidopsis lyrata subsp. lyrata] gi|297323385|gb|EFH53806.1| hypothetical protein ARALYDRAFT_905943 [Arabidopsis lyrata subsp. lyrata]

 Score =  290 bits (741), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 160/264 (60%), Positives = 190/264 (71%), Gaps = 28/264 (10%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLTQVK +Q IN++E+DLGIS++ASWHAKYK+SAYVYVG IPFDLTEGDLLAVF+Q G
Sbjct: 1   MNPLTQVKNLQKINARESDLGISEEASWHAKYKNSAYVYVGCIPFDLTEGDLLAVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNL+RDKGTGK +GFAF+AYEDQR      +NLNGA +LGRTI+VDH  +YKK EE
Sbjct: 61  EIVDVNLIRDKGTGKSKGFAFLAYEDQRSTVLAVDNLNGALVLGRTIKVDHCREYKKHEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEKFE 173
           EDEETR++ RE RGVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSSRW H+KF 
Sbjct: 121 EDEETRRQNREARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSRWDHDKFN 180

Query: 174 G-------------FSWGKNDSSSRATGSGRVALEGNPNQSDRRE-EKRSIR----HDHR 215
           G             F     + S R  G G  A  G P + +R E E    R    +D R
Sbjct: 181 GAKKGGTSFGHRGDFKSDAEEKSYRGKGDGD-AWYGRPKERERVEREDMGPRSRDAYDMR 239

Query: 216 EKPREDHGRREDKRSRRHSDNNEF 239
           E+ R   G  +D RSR H+  N++
Sbjct: 240 EQKRS--GPYDDSRSRSHNAGNDY 261

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15232729|ref|NP_190296.1| RNA-binding motif protein, X-linked 2 [Arabidopsis thaliana] gi|75337070|sp|Q9SD61.1|C3H42_ARATH RecName: Full=Zinc finger CCCH domain-containing protein 42; Short=AtC3H42 gi|6522593|emb|CAB61958.1| putative RNA binding protein [Arabidopsis thaliana] gi|27311733|gb|AAO00832.1| putative RNA-binding protein [Arabidopsis thaliana] gi|34098859|gb|AAQ56812.1| At3g47120 [Arabidopsis thaliana] gi|332644724|gb|AEE78245.1| RNA-binding motif protein, X-linked 2 [Arabidopsis thaliana]

 Score =  285 bits (728), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 136/178 (76%), Positives = 156/178 (87%), Gaps = 7/178 (3%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLTQVK +Q IN++E+DLGISD+ASWHAKYK+SAYVYVGGIPFDLTEGDLLAVF+Q G
Sbjct: 1   MNPLTQVKNLQKINARESDLGISDEASWHAKYKNSAYVYVGGIPFDLTEGDLLAVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNL+RDKGTGK +GFAF+AYEDQR      +NLNGA +LGRTI+VDH   YKK EE
Sbjct: 61  EIVDVNLIRDKGTGKSKGFAFLAYEDQRSTILAVDNLNGALVLGRTIKVDHCGAYKKHEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEK 171
           EDEETR++ RE RGVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSS+W H+K
Sbjct: 121 EDEETRRQNREARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSKWDHDK 178

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297745915|emb|CBI15971.3| unnamed protein product [Vitis vinifera]

 Score =  284 bits (727), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 177/292 (60%), Positives = 206/292 (70%), Gaps = 22/292 (7%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKRIQ INS+EA LGIS+ ASWHAKYK+SAYV+VGGIPFDLTEGDLLAVF+Q G
Sbjct: 1   MNPLTLVKRIQKINSQEAALGISESASWHAKYKESAYVFVGGIPFDLTEGDLLAVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNLVRDKGTGK +GFAFVAYEDQR      +NLNGAQILGR IRVDHV+ YKKKEE
Sbjct: 61  EIVDVNLVRDKGTGKSKGFAFVAYEDQRSTNLAVDNLNGAQILGRIIRVDHVSNYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEG 174
           EDEET ++ RE RGVCRAFQRGEC RG GCKFSH+EQRA+NTG G +D+SSRWGH+KF+G
Sbjct: 121 EDEETERQKREARGVCRAFQRGECNRGAGCKFSHDEQRASNTGWGSEDKSSRWGHDKFQG 180

Query: 175 FSWGKNDSSSRATGSGRVALEGNPNQSDR--REEKRSIRHDHREKPREDHGRREDKRSR- 231
            +  K+D    +  + RV  E    +  R   ++ RS R    E  RE H RR +   R 
Sbjct: 181 ST--KSDGRPNSIPTNRVH-EPTVGEGHRFGNKDARSSRTKGSEGGRESHHRRSELDIRD 237

Query: 232 -------RHSDNNEFEARSREDHYRR-DEKRPKRHESESYLREDQDRRGGDK 275
                  R  +  E E   +ED  RR  E+R  R +S     ED DRRG D+
Sbjct: 238 QDGRGLERQMEQKEKELNYKEDQDRRTTERRSGRPDSNPG--EDHDRRGEDQ 287

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225434618|ref|XP_002279321.1| PREDICTED: uncharacterized protein LOC100246760 [Vitis vinifera]

 Score =  284 bits (726), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 184/337 (54%), Positives = 212/337 (62%), Gaps = 72/337 (21%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKRIQ INS+EA LGIS+ ASWHAKYK+SAYV+VGGIPFDLTEGDLLAVF+Q G
Sbjct: 1   MNPLTLVKRIQKINSQEAALGISESASWHAKYKESAYVFVGGIPFDLTEGDLLAVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNLVRDKGTGK +GFAFVAYEDQR      +NLNGAQILGR IRVDHV+ YKKKEE
Sbjct: 61  EIVDVNLVRDKGTGKSKGFAFVAYEDQRSTNLAVDNLNGAQILGRIIRVDHVSNYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKF-- 172
           EDEET ++ RE RGVCRAFQRGEC RG GCKFSH+EQRA+NTG G +D+SSRWGH+KF  
Sbjct: 121 EDEETERQKREARGVCRAFQRGECNRGAGCKFSHDEQRASNTGWGSEDKSSRWGHDKFQG 180

Query: 173 ----------------------EGFSWGKNDS-SSRATGS--GRVA-------------- 193
                                 EG  +G  D+ SSR  GS  GR +              
Sbjct: 181 STKSDGRPNSIPTNRVHEPTVGEGHRFGNKDARSSRTKGSEGGRESHHRRSELDIRDQDG 240

Query: 194 -------------LEGNPNQSDRREEKRSIRHDHREKPREDHGRR--------EDKRSRR 232
                        L    +Q  R  E+RS R D    P EDH RR         ++RSRR
Sbjct: 241 RGLERQMEQKEKELNYKEDQDRRTTERRSGRPD--SNPGEDHDRRGEDQDIRATERRSRR 298

Query: 233 HSDN--NEFEARSREDHYRRDEKRPKRHESESYLRED 267
           H  N   + + R  +   R  E+R +RH+ ES  RED
Sbjct: 299 HDSNPSEDHDRRGEDQDIRATERRSRRHDFESNPRED 335

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460375|ref|XP_004147921.1| PREDICTED: zinc finger CCCH domain-containing protein 25-like [Cucumis sativus]

 Score =  280 bits (717), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 173/305 (56%), Positives = 211/305 (69%), Gaps = 44/305 (14%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKRIQ INS+EA LGIS++ASWHAKYKDSAYV+VGGIP+DLTEGDLLAVFAQ G
Sbjct: 1   MNPLTLVKRIQKINSQEAALGISEEASWHAKYKDSAYVFVGGIPYDLTEGDLLAVFAQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNL+RDKGTGK +G+AFVAYEDQR      +NLNGAQILGR +RVDHV+KYKKKEE
Sbjct: 61  EIVDVNLIRDKGTGKSKGYAFVAYEDQRSTNLAVDNLNGAQILGRIVRVDHVSKYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTG-GGPQDRSSRWGHEKFE 173
           EDEE  Q+ RE RGVCRAFQRGECTRG GCKFSH+EQRAA+TG G  +D SS+WGH+KF+
Sbjct: 121 EDEEEEQKKREARGVCRAFQRGECTRGAGCKFSHDEQRAADTGWGAAEDASSKWGHDKFD 180

Query: 174 GFSWGKNDSSSRATG--------------SGRVALEGNPNQSDRREEKRSIRHDHREKPR 219
             S   +D    A G              SG +  E  P   D  +E          K R
Sbjct: 181 --SRKNHDKELHAKGRKTSDNLGRHPRETSGSLRQENRPRGWDDSKESEL-------KSR 231

Query: 220 EDHGRREDKRSRRHSDNNEFEARSREDHY--------------RRDEKRPKRHESESYLR 265
           EDHG +++KRSRR+  +   + +S +D Y              R+DEKR ++H+++  ++
Sbjct: 232 EDHGGKDEKRSRRYDLDGNSDPKSGDDQYKGEEKRSSRNHDDNRKDEKRSRKHDNDDEMK 291

Query: 266 EDQDR 270
            + DR
Sbjct: 292 LEDDR 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356551855|ref|XP_003544288.1| PREDICTED: zinc finger CCCH domain-containing protein 42-like [Glycine max]

 Score =  278 bits (712), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 181/331 (54%), Positives = 216/331 (65%), Gaps = 62/331 (18%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKR Q+IN++EA LGI + ASWH KYKDSAYV+VGGIPFDLTEGDLLAVFAQ G
Sbjct: 1   MNPLTLVKRTQNINAREAALGIGEQASWHTKYKDSAYVFVGGIPFDLTEGDLLAVFAQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           E+VDVNLVRDKGTGK +GFAF+AYEDQR      +NLNGAQ+LGR IRVDHV KYKKKEE
Sbjct: 61  EVVDVNLVRDKGTGKSKGFAFLAYEDQRSTNLAVDNLNGAQVLGRIIRVDHVDKYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEG 174
           EDEET ++ RE RGVCRAFQRGECTRG  CKFSH+EQRAANTG G ++   +WGH+KF+G
Sbjct: 121 EDEETERQKREARGVCRAFQRGECTRGASCKFSHDEQRAANTGWGREEDKPKWGHDKFDG 180

Query: 175 FS----WGKN-----------DSSSRATGSGRVALEGNPNQSDR---------------- 203
                  G N           DS SRA  +    L+  P +SDR                
Sbjct: 181 PKKERRSGNNQSNHIAETRDRDSFSRARNND-AELDNQPKRSDRKEMTKREYRYKREEKG 239

Query: 204 ------------------REEKRSIRHDHRE-KPRE-DHGRREDKRSRRHSDNNEFEARS 243
                             REEKRSI+ D  E +P+  D   REDKRSRR  DN++  ++S
Sbjct: 240 SRRDDYDGMKLEPKDHHLREEKRSIKPDDVEVEPKSRDSDIREDKRSRRR-DNDDIVSKS 298

Query: 244 REDHYRRDEKRPKRH---ESESYLREDQDRR 271
           RE H   ++++ ++H   ES    RED DR+
Sbjct: 299 REPHGYSEDRKSRKHSEGESAPKPREDYDRK 329

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147840589|emb|CAN72715.1| hypothetical protein VITISV_032469 [Vitis vinifera]

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 177/311 (56%), Positives = 206/311 (66%), Gaps = 41/311 (13%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKRIQ INS+EA LGIS+ ASWHAKYK+SAYV+VGGIPFDLTEGDLLAVF+Q G
Sbjct: 1   MNPLTLVKRIQKINSQEAALGISESASWHAKYKESAYVFVGGIPFDLTEGDLLAVFSQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EIVDVNLVRDKGTGK +GFAFVAYEDQR      +NLNGAQILGR IRVDHV+ YKKKEE
Sbjct: 61  EIVDVNLVRDKGTGKSKGFAFVAYEDQRSTNLAVDNLNGAQILGRIIRVDHVSNYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQ-------------------RAAN 155
           EDEET ++ RE RGVCRAFQRGEC RG GCKFSH+EQ                   RA+N
Sbjct: 121 EDEETERQKREARGVCRAFQRGECNRGAGCKFSHDEQDLTFSWLSKSWRLVLQGLERASN 180

Query: 156 TGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDR--REEKRSIRHD 213
           TG G +D+SSRWGH+KF+G +  K+D    +  + RV  E    +  R   ++ RS R  
Sbjct: 181 TGWGSEDKSSRWGHDKFQGST--KSDGRPNSIPTNRVH-EPTVGEGHRFGNKDARSSRTK 237

Query: 214 HREKPREDHGRREDKRSR--------RHSDNNEFEARSREDHYRR-DEKRPKRHESESYL 264
             E  RE H RR +   R        R  +  E E   +ED  RR  E+R  R +S    
Sbjct: 238 GSEGGRESHHRRSELDIRDQDGRGLERQMEQKEKELNYKEDQDRRTTERRSGRPDSNP-- 295

Query: 265 REDQDRRGGDK 275
            ED DRRG D+
Sbjct: 296 GEDHDRRGEDQ 306

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357490653|ref|XP_003615614.1| RNA binding domain protein [Medicago truncatula] gi|355516949|gb|AES98572.1| RNA binding domain protein [Medicago truncatula]

 Score =  274 bits (701), Expect = 3e-71,   Method: Compositional matrix adjust.
 Identities = 168/277 (60%), Positives = 200/277 (72%), Gaps = 26/277 (9%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKRIQ INS+EA L IS+DASWH KYKDSAYV+VGGIPFD TEGD++AVFAQ G
Sbjct: 1   MNPLTLVKRIQQINSREAALNISEDASWHTKYKDSAYVFVGGIPFDFTEGDVIAVFAQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           E+VD+NLVRDKGTGK +GFAF+AYEDQR      +NLNGAQ+ GR IRVDHV KYKK EE
Sbjct: 61  EVVDINLVRDKGTGKSKGFAFIAYEDQRSTNLAVDNLNGAQVSGRIIRVDHVDKYKKMEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEG 174
           EDEE  ++ RE RGVCRAFQRGECTRG GCKFSH+EQRAANTG G  +  ++  ++K++G
Sbjct: 121 EDEEEAKQKREARGVCRAFQRGECTRGAGCKFSHDEQRAANTGWG-DNGIAKGDNDKYDG 179

Query: 175 FS----WGKN-----------DSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREK-- 217
                 +G N           DS SRA G+G + L+    +SDRREEK   R D      
Sbjct: 180 PKKERRYGNNQPDRIPETRDRDSRSRAHGNG-MELDNPSKRSDRREEKMLRRQDGDGNFV 238

Query: 218 PREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKR 254
            RE+  RRE+KR R + D +EFE   RED +RR+EKR
Sbjct: 239 GRENTSRREEKRPRDYKD-DEFEQWPREDRHRREEKR 274

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356498939|ref|XP_003518303.1| PREDICTED: zinc finger CCCH domain-containing protein 42-like [Glycine max]

 Score =  265 bits (676), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 152/229 (66%), Positives = 172/229 (75%), Gaps = 22/229 (9%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
           MNPLT VKR Q+IN++EA LGI + ASWH KYKDSAYV+VGGIPFDLTEGDLLAVFAQ G
Sbjct: 1   MNPLTLVKRTQNINAREAALGIGEQASWHTKYKDSAYVFVGGIPFDLTEGDLLAVFAQYG 60

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           E+VDVNLVRDKGTGK +GFAF+AYEDQR      +NLNGAQ+LGR IRVDHV KYKKKEE
Sbjct: 61  EVVDVNLVRDKGTGKSKGFAFLAYEDQRSTNLAVDNLNGAQVLGRIIRVDHVDKYKKKEE 120

Query: 115 EDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEG 174
           EDEET ++ RE RGVCRAFQRGECTRG  CKFSH+EQRAANTG G ++   +WGH+KFEG
Sbjct: 121 EDEETERQKREARGVCRAFQRGECTRGASCKFSHDEQRAANTGWGREEDKPKWGHDKFEG 180

Query: 175 FS----WGKN-----------DSSSRATGSGRVALEGNPNQSDRREEKR 208
                  G N           DS +RA       L+  P +SDRRE KR
Sbjct: 181 PKKERRSGNNQSNHIPETRDRDSRTRARNFD-AELDNQPKKSDRRETKR 228

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	291
TAIR|locus:2075676	352	AT3G47120 [Arabidopsis thalian	0.948	0.784	0.483	8.8e-63
MGI|MGI:1919414	326	Rbmx2 "RNA binding motif prote	0.367	0.328	0.575	1.4e-44
UNIPROTKB|G5E5I0	338	RBMX2 "Uncharacterized protein	0.367	0.316	0.575	1.6e-43
RGD|1562693	328	Rbmx2 "RNA binding motif prote	0.367	0.326	0.584	3.2e-43
UNIPROTKB|J9P250	341	RBMX2 "Uncharacterized protein	0.367	0.313	0.584	2.8e-42
UNIPROTKB|F1LMQ9	327	Rbmx2 "RNA-binding motif prote	0.364	0.324	0.571	3.6e-42
UNIPROTKB|F1PRG0	326	RBMX2 "Uncharacterized protein	0.364	0.325	0.571	5.2e-41
ZFIN|ZDB-GENE-050626-88	450	rbmx2 "RNA binding motif prote	0.367	0.237	0.592	6.6e-41
UNIPROTKB|G3X6K3	330	LOC534630 "Uncharacterized pro	0.367	0.324	0.566	8.4e-41
ASPGD|ASPL0000074275	279	AN4665 [Emericella nidulans (t	0.350	0.365	0.527	2.8e-38

TAIR|locus:2075676 AT3G47120 [Arabidopsis thaliana (taxid:3702)]

 Score = 641 (230.7 bits), Expect = 8.8e-63, P = 8.8e-63
 Identities = 144/298 (48%), Positives = 171/298 (57%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLTQVK +Q IN++E+DLGISD+ASWHAKYK+SAYVYVGGIPFDLTEGDLLAVF+Q G
Sbjct:     1 MNPLTQVKNLQKINARESDLGISDEASWHAKYKNSAYVYVGGIPFDLTEGDLLAVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAXXXXXXX 114
             EIVDVNL+RDKGTGK +GFAF+AYEDQR+      NLNGA +LGRTI+VDH         
Sbjct:    61 EIVDVNLIRDKGTGKSKGFAFLAYEDQRSTILAVDNLNGALVLGRTIKVDHCGAYKKHEE 120

Query:   115 XXXXXXXXXXXXXGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG-PQDRSSRWGHEKFE 173
                          GVCRAFQRGECTRGD CKFSH+E+RAANTG G  +DRSS+W H+K  
Sbjct:   121 EDEETRRQNREARGVCRAFQRGECTRGDSCKFSHDEKRAANTGWGHEEDRSSKWDHDK-- 178

Query:   174 GFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRH 233
                      +    G  R    G   + D  +      HD +       G  ED+ S+  
Sbjct:   179 ---------NREGRGVCRAFQRGECTRGDSCK----FSHDEKRAATTGWGHEEDRSSKWD 225

Query:   234 SDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRHRER 291
              D      +       R + +P   E     R D D   G      R D      R R
Sbjct:   226 QDKLNGAKKGGTSFGNRGDFKPDVEEKSYRGRGDGDASYGRPKERERVDREDMGPRSR 283

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:1919414 Rbmx2 "RNA binding motif protein, X-linked 2" [Mus musculus (taxid:10090)]

 Score = 360 (131.8 bits), Expect = 1.4e-44, Sum P(2) = 1.4e-44
 Identities = 65/113 (57%), Positives = 89/113 (78%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLT+VK I  +N +E  LG+++  SWH++YK SA+++VGG+P++LTEGD++ VF+Q G
Sbjct:     1 MNPLTKVKLINELNEREVQLGVAEKVSWHSEYKHSAWIFVGGLPYELTEGDIICVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             EIV++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHV+
Sbjct:    61 EIVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVS 113

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003674 "molecular_function" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|G5E5I0 RBMX2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 363 (132.8 bits), Expect = 1.6e-43, Sum P(2) = 1.6e-43
 Identities = 65/113 (57%), Positives = 90/113 (79%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLT+VK I  +N +E +LG+++  SWH +YKDSA++++GG+P++LTEGD++ VF+Q G
Sbjct:     1 MNPLTKVKLINELNEREVELGVAEKVSWHNEYKDSAWIFLGGLPYELTEGDIICVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             EIV++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHV+
Sbjct:    61 EIVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVS 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

RGD|1562693 Rbmx2 "RNA binding motif protein, X-linked 2" [Rattus norvegicus (taxid:10116)]

 Score = 367 (134.2 bits), Expect = 3.2e-43, Sum P(2) = 3.2e-43
 Identities = 66/113 (58%), Positives = 90/113 (79%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLT+VK I  +N +E  LG+++  SWH++YKDSA++++GG+P++LTEGD++ VF+Q G
Sbjct:     1 MNPLTKVKLINELNEREVQLGVAEKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             EIV++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHVA
Sbjct:    61 EIVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVA 113

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

UNIPROTKB|J9P250 RBMX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 368 (134.6 bits), Expect = 2.8e-42, Sum P(2) = 2.8e-42
 Identities = 66/113 (58%), Positives = 90/113 (79%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLT+VK I  +N +E  LG++D  SWH++YKDSA++++GG+P++LTEGD++ VF+Q G
Sbjct:     1 MNPLTKVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             EIV++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHV+
Sbjct:    61 EIVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVS 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1LMQ9 Rbmx2 "RNA-binding motif protein, X-linked 2" [Rattus norvegicus (taxid:10116)]

 Score = 357 (130.7 bits), Expect = 3.6e-42, Sum P(2) = 3.6e-42
 Identities = 64/112 (57%), Positives = 89/112 (79%)

Query:     2 NPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGE 61
             +PLT+VK I  +N +E  LG+++  SWH++YKDSA++++GG+P++LTEGD++ VF+Q GE
Sbjct:     1 SPLTKVKLINELNEREVQLGVAEKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGE 60

Query:    62 IVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             IV++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHVA
Sbjct:    61 IVNINLVRDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVA 112

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F1PRG0 RBMX2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 358 (131.1 bits), Expect = 5.2e-41, Sum P(2) = 5.2e-41
 Identities = 64/112 (57%), Positives = 89/112 (79%)

Query:     2 NPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGE 61
             +PLT+VK I  +N +E  LG++D  SWH++YKDSA++++GG+P++LTEGD++ VF+Q GE
Sbjct:     1 SPLTKVKLINELNEREVQLGVADKVSWHSEYKDSAWIFLGGLPYELTEGDIICVFSQYGE 60

Query:    62 IVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             IV++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHV+
Sbjct:    61 IVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVS 112

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ZFIN|ZDB-GENE-050626-88 rbmx2 "RNA binding motif protein, X-linked 2" [Danio rerio (taxid:7955)]

 Score = 360 (131.8 bits), Expect = 6.6e-41, Sum P(2) = 6.6e-41
 Identities = 67/113 (59%), Positives = 87/113 (76%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLT+VK I  +N +EA LGI +  SWH+ YK+SA+V++GG P++LTEGD++ VF+Q G
Sbjct:     1 MNPLTKVKLINELNEREAQLGIKETVSWHSVYKNSAWVFIGGFPYELTEGDIICVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             EI ++NLVRDK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHVA
Sbjct:    61 EIANINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIKGRTIRVDHVA 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|G3X6K3 LOC534630 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 351 (128.6 bits), Expect = 8.4e-41, Sum P(2) = 8.4e-41
 Identities = 64/113 (56%), Positives = 87/113 (76%)

Query:     1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
             MNPLT+VK I  +N +E  LG+ +  SWH +YKDSA++++GG+P++LTEGD++ VF+Q G
Sbjct:     1 MNPLTKVKLINELNEREVQLGVPEKVSWHNEYKDSAWIFLGGLPYELTEGDIICVFSQYG 60

Query:    61 EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA 107
             EIV++NLV DK TGK +GF F+ YEDQR+      N NG +I GRTIRVDHV+
Sbjct:    61 EIVNINLVWDKKTGKSKGFCFLCYEDQRSTVLAVDNFNGIKIKGRTIRVDHVS 113

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

ASPGD|ASPL0000074275 AN4665 [Emericella nidulans (taxid:162425)]

 Score = 327 (120.2 bits), Expect = 2.8e-38, Sum P(2) = 2.8e-38
 Identities = 57/108 (52%), Positives = 82/108 (75%)

Query:     4 LTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV 63
             +  ++++Q +N +E +  +  +ASWHA Y+D+AY+Y+GG+PFDL+EGD++ +F+Q GE V
Sbjct:     1 MNNIRQVQALNKRELEHAVPPEASWHADYRDTAYIYIGGLPFDLSEGDIVTIFSQYGEPV 60

Query:    64 DVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH 105
              +NLVRDK TGK RGFAF+ YEDQR+      NL GA +LGR +RVDH
Sbjct:    61 HINLVRDKETGKSRGFAFLKYEDQRSTDLAVDNLGGATVLGRVLRVDH 108

GO:0008150 "biological_process" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q10B98	C3H25_ORYSJ	No assigned EC number	0.7134	0.5876	0.5480	yes	no
Q9SD61	C3H42_ARATH	No assigned EC number	0.7640	0.5876	0.4857	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	estExt_Genewise1_v1.C_LG_IX3799	hypothetical protein (243 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.VIII.2127.1	hypothetical protein (133 aa)			•						0.458
	gw1.XV.2574.1	hypothetical protein (203 aa)			•						0.454
	eugene3.00050125	hypothetical protein (218 aa)			•						0.445
	estExt_fgenesh4_pg.C_LG_VII0461	hypothetical protein (218 aa)			•						0.440
	gw1.232.53.1	hypothetical protein (203 aa)			•						0.437

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	291
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	4e-51
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-21
smart00360	73	smart00360, RRM, RNA recognition motif	5e-21
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	8e-18
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-16
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-16
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	7e-16
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	2e-15
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	8e-14
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-13
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	8e-13
cd12401	76	cd12401, RRM_eIF4H, RNA recognition motif in eukar	1e-12
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	2e-12
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	7e-12
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	1e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	1e-11
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	1e-11
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	1e-11
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	1e-11
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-11
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-11
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	3e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	4e-11
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	9e-11
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	1e-10
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	1e-10
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-10
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	3e-10
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	3e-10
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	3e-10
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	4e-10
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-10
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	6e-10
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	6e-10
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	1e-09
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-09
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-09
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	2e-09
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-09
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-09
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	3e-09
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-09
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	6e-09
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	6e-09
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	7e-09
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	8e-09
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-09
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-08
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	1e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	2e-08
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	2e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-08
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	2e-08
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	2e-08
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-08
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	4e-08
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-08
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	5e-08
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	5e-08
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-08
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	6e-08
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	7e-08
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	7e-08
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	8e-08
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	1e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	1e-07
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-07
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-07
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-07
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-07
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	1e-07
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-07
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-07
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	2e-07
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-07
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	3e-07
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-07
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	4e-07
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	4e-07
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-07
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	4e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	5e-07
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	5e-07
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	5e-07
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	6e-07
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	7e-07
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	8e-07
cd12534	83	cd12534, RRM_SARFH, RNA recognition motif in Droso	8e-07
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	9e-07
cd12482	79	cd12482, RRM1_hnRNPR, RNA recognition motif 1 in v	9e-07
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	9e-07
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	1e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	1e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	1e-06
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	2e-06
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	2e-06
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	2e-06
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	2e-06
cd12484	78	cd12484, RRM1_RBM46, RNA recognition motif 1 found	2e-06
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	2e-06
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	2e-06
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	2e-06
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	2e-06
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	3e-06
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	3e-06
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-06
cd12483	79	cd12483, RRM1_hnRNPQ, RNA recognition motif 1 in v	4e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	5e-06
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	5e-06
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-06
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	7e-06
TIGR01659	346	TIGR01659, sex-lethal, sex-lethal family splicing	7e-06
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	8e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	8e-06
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	8e-06
cd12402	77	cd12402, RRM_eIF4B, RNA recognition motif in eukar	9e-06
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-05
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	1e-05
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	1e-05
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-05
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	2e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	2e-05
cd12273	71	cd12273, RRM1_NEFsp, RNA recognition motif 1 in ve	2e-05
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-05
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	3e-05
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	4e-05
cd12446	84	cd12446, RRM_RBM25, RNA recognition motif in eukar	4e-05
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	5e-05
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	5e-05
cd12524	77	cd12524, RRM1_MEI2_like, RNA recognition motif 1 i	5e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-05
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	6e-05
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	6e-05
cd12241	77	cd12241, RRM_SF3B14, RNA recognition motif found i	6e-05
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	8e-05
cd12315	77	cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1	8e-05
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	8e-05
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	8e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	9e-05
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	1e-04
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-04
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	1e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	1e-04
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	1e-04
cd12533	84	cd12533, RRM_EWS, RNA recognition motif in vertebr	1e-04
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	2e-04
cd12280	81	cd12280, RRM_FET, RNA recognition motif in the FET	2e-04
cd12250	82	cd12250, RRM2_hnRNPR_like, RNA recognition motif 2	2e-04
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	2e-04
smart00356	27	smart00356, ZnF_C3H1, zinc finger	2e-04
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	2e-04
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	2e-04
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	2e-04
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-04
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	2e-04
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	3e-04
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	3e-04
cd12599	72	cd12599, RRM1_SF2_plant_like, RNA recognition moti	3e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-04
cd12773	84	cd12773, RRM2_HuR, RNA recognition motif 2 in vert	3e-04
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	3e-04
cd12223	84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	4e-04
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	4e-04
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	4e-04
cd12776	81	cd12776, RRM2_HuC, RNA recognition motif 2 in vert	4e-04
cd12338	72	cd12338, RRM1_SRSF1_like, RNA recognition motif 1	4e-04
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	5e-04
cd12358	73	cd12358, RRM1_VICKZ, RNA recognition motif 1 in th	5e-04
PRK12678	672	PRK12678, PRK12678, transcription termination fact	6e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	6e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	6e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	8e-04
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	8e-04
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	8e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	9e-04
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	9e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.001
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.001
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	0.001
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12672	82	cd12672, RRM_DAZL, RNA recognition motif in verteb	0.001
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	0.001
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
PRK12678	672	PRK12678, PRK12678, transcription termination fact	0.002
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	0.002
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	0.002
cd12598	72	cd12598, RRM1_SRSF9, RNA recognition motif 1 in ve	0.002
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.002
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	0.002
PRK10811	1068	PRK10811, rne, ribonuclease E; Reviewed	0.002
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	0.003
cd12247	72	cd12247, RRM2_U1A_like, RNA recognition motif 2 in	0.003
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	0.003
cd12224	74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	0.003
cd12561	81	cd12561, RRM1_RBM5_like, RNA recognition motif 1 i	0.003
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.004
cd12281	92	cd12281, RRM1_TatSF1_like, RNA recognition motif 1	0.004

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

 Score =  162 bits (413), Expect = 4e-51
 Identities = 61/89 (68%), Positives = 75/89 (84%), Gaps = 6/89 (6%)

Query: 27  SWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           SWH +YKDSAY+Y+GG+P++LTEGD+L VF+Q GEIVD+NLVRDK TGK +GFAF+AYED
Sbjct: 1   SWHDQYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLVRDKKTGKSKGFAFLAYED 60

Query: 87  QR------NNLNGAQILGRTIRVDHVAKY 109
           QR      +NLNG ++LGRTIRVDHV  Y
Sbjct: 61  QRSTILAVDNLNGIKLLGRTIRVDHVRNY 89

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|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 = 84.6 bits (210), Expect = 4e-21
 Identities = 32/74 (43%), Positives = 45/74 (60%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           V+VG IP+D TE  L+ +F++ G +V   LV D+ TGKP+G+ F  +ED         NL
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 92  NGAQILGRTIRVDH 105
           NG +  GR +RVD 
Sbjct: 61  NGYEFNGRALRVDF 74

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|214636 smart00360, RRM, RNA recognition motif

 Score = 84.2 bits (209), Expect = 5e-21
 Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +P D TE +L  +F++ G++  V LVRDK TGK +GFAFV +E +         L
Sbjct: 2   LFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEAL 61

Query: 92  NGAQILGRTIRV 103
           NG ++ GR ++V
Sbjct: 62  NGKELDGRPLKV 73

Length = 73

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

 Score = 75.7 bits (187), Expect = 8e-18
 Identities = 29/71 (40%), Positives = 45/71 (63%), Gaps = 7/71 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +P D TE DL  +F++ G I  + +VRD+ TG+ +GFAFV +ED+         L
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDE-TGRSKGFAFVEFEDEEDAEKALEAL 59

Query: 92  NGAQILGRTIR 102
           NG ++ GR +R
Sbjct: 60  NGKELGGRELR 70

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

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

 Score = 74.2 bits (183), Expect = 3e-17
 Identities = 29/72 (40%), Positives = 43/72 (59%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YVGG+  ++ E  L A F   G+I D+ +  D  T K RGFAFV +E+  +      N+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM 60

Query: 92  NGAQILGRTIRV 103
           N +++ GRTIRV
Sbjct: 61  NESELFGRTIRV 72

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

>gnl|CDD|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 = 72.3 bits (178), Expect = 2e-16
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+    TE +L A+F++ G + +V L++D  TG+ RGF FV +E          +L
Sbjct: 4   LFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDL 63

Query: 92  NGAQILGRTIRVDH 105
           NG ++ GR I+V+ 
Sbjct: 64  NGKELEGRVIKVEK 77

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

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

 Score = 71.6 bits (176), Expect = 3e-16
 Identities = 31/73 (42%), Positives = 44/73 (60%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +P D TE DL  +F++ GEI  V +VRDK  GK +GFAFV +E           L
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDK-DGKSKGFAFVEFESPEDAEKALEAL 59

Query: 92  NGAQILGRTIRVD 104
           NG ++ GR ++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|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 = 70.6 bits (173), Expect = 7e-16
 Identities = 32/74 (43%), Positives = 47/74 (63%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ        NL
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNL 60

Query: 92  NGAQILGRTIRVDH 105
           NG ++ GR +RVD+
Sbjct: 61  NGYELNGRQLRVDN 74

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

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN 92
           YVG +P+++TE DL  +F Q GE+    ++ D+ TG+ RGF FV  E           LN
Sbjct: 3   YVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLN 62

Query: 93  GAQILGRTIRV 103
           G    GRT+ V
Sbjct: 63  GTDFGGRTLTV 73

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

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

 Score = 65.0 bits (159), Expect = 8e-14
 Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 6/71 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY---EDQRN---NLN 92
           YVG + F++TE DL  +F   GEI  V L RD  TG+ +G+ F+ +   ED +     LN
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 93  GAQILGRTIRV 103
           G ++ GR I+V
Sbjct: 62  GFELAGRPIKV 72

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

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

 Score = 63.3 bits (155), Expect = 3e-13
 Identities = 28/71 (39%), Positives = 44/71 (61%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           V+VG +PFD+ E +L   F  CG++  V +VRD+ TG  +GF +V ++ + +      LN
Sbjct: 2   VFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKLN 61

Query: 93  GAQILGRTIRV 103
           G ++ GR IRV
Sbjct: 62  GIKLKGRKIRV 72

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

 Score = 62.3 bits (152), Expect = 8e-13
 Identities = 28/72 (38%), Positives = 43/72 (59%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY---EDQRN---NL 91
           VYV  +PF LT  DL  +F++ G++V V +V+DK T K +G AF+ +   ED       L
Sbjct: 4   VYVSNLPFSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKAL 63

Query: 92  NGAQILGRTIRV 103
           N  ++ GRT++ 
Sbjct: 64  NNKELFGRTLKC 75

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|240847 cd12401, RRM_eIF4H, RNA recognition motif in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins

 Score = 61.6 bits (150), Expect = 1e-12
 Identities = 28/71 (39%), Positives = 41/71 (57%), Gaps = 6/71 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNG 93
           +VG +PF+  +GDL A+F     +  V LVRDK T K +GF +V +ED  +       +G
Sbjct: 5   FVGNLPFNTVQGDLDAIFKDL-SVKSVRLVRDKETDKFKGFCYVEFEDVESLKEALEYDG 63

Query: 94  AQILGRTIRVD 104
           A    R++RVD
Sbjct: 64  ALFDDRSLRVD 74

This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. . Length = 76

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ--RNN---LN 92
           ++VG + +  T  +L   F  CG I  + ++ DK TG+P+GFA++ + D+    N   LN
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALLLN 61

Query: 93  GAQILGRTIRV 103
            ++  GR I+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|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 = 59.6 bits (145), Expect = 7e-12
 Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 12/75 (16%)

Query: 38  VYVGGIPFDLTEG---DLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           +++GG+P  L+E    +LL  F   G++   NLV+D  TG  +G+AF  Y D        
Sbjct: 3   IFIGGLPNYLSEDQVKELLESF---GKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAI 59

Query: 89  NNLNGAQILGRTIRV 103
             LNG Q+  + + V
Sbjct: 60  AGLNGMQLGDKKLTV 74

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

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 26/71 (36%), Positives = 44/71 (61%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ-----RNNLN 92
           VYVGGIP+  TE ++ + F+ CGEI +++L+    TG+ RG AF+ ++ +        L+
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 93  GAQILGRTIRV 103
           G  + GR ++V
Sbjct: 61  GEDMGGRFLKV 71

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

 Score = 58.9 bits (143), Expect = 1e-11
 Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG + FD  E  +   F + GEI  V L  D  +G+P+GF +V +  Q       + L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 92  NGAQILGRTIRVD 104
            G  +LGR +R+D
Sbjct: 61  GGTDLLGRPVRLD 73

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

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

 Score = 59.2 bits (144), Expect = 1e-11
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN 92
           +V  + +D TE  L   F + G I  + LVRDK TGKPRG+AF+ +E +R+        +
Sbjct: 5   FVARLNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYAD 64

Query: 93  GAQILGRTIRVD 104
           G +I GR + VD
Sbjct: 65  GKKIDGRRVLVD 76

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|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 = 20/49 (40%), Positives = 33/49 (67%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          ++VGG+P+  T+  L   F+Q GEI +  ++ D+ TGK RG+ FV ++D
Sbjct: 3  IFVGGLPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKD 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|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 58.8 bits (143), Expect = 1e-11
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 6/70 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLN 92
           ++G +   + E  + + FA+CGE+  V ++R+K TGK  G+ FV +           +LN
Sbjct: 3   WMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLN 62

Query: 93  GAQILGRTIR 102
           G  I     R
Sbjct: 63  GKPIPNTQQR 72

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

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 7/67 (10%)

Query: 44  PFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNLNGAQIL 97
           PF  TE DL  +F+  G + +V + R    GK +GFAFV +      E     +NG +I 
Sbjct: 8   PFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKIK 66

Query: 98  GRTIRVD 104
           GR + VD
Sbjct: 67  GRPVAVD 73

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

 Score = 58.0 bits (141), Expect = 2e-11
 Identities = 25/49 (51%), Positives = 34/49 (69%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          ++VGG+  D+TE DL   F+Q G +  V +V DK TGK RGFAFV ++D
Sbjct: 2  LFVGGLKEDVTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDD 50

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

 Score = 57.9 bits (141), Expect = 3e-11
 Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           +YVG + F  TE  +  +F++CG+I  + +  D+ T  P GF FV Y  +         L
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIKRIIMGLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 92  NGAQILGRTIRVD 104
           NG ++  R IRVD
Sbjct: 61  NGTKLDDRIIRVD 73

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

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

 Score = 57.7 bits (140), Expect = 3e-11
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVA---YEDQRN---NL 91
           ++V  +P D  E  L  +F+  G + +V ++RD  T K +G+ FV    YE+  +   +L
Sbjct: 4   IFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIASL 63

Query: 92  NGAQILGRTIRV 103
           NG ++ GR ++V
Sbjct: 64  NGYRLGGRVLQV 75

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

 Score = 57.2 bits (139), Expect = 4e-11
 Identities = 20/49 (40%), Positives = 32/49 (65%)

Query: 39 YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++GG+ +D TE  L   F++ GE+VD  +++D  TG+ RGF FV + D 
Sbjct: 2  FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADP 50

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|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 = 56.8 bits (137), Expect = 9e-11
 Identities = 30/77 (38%), Positives = 45/77 (58%), Gaps = 6/77 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNL 91
           +++GG+ FD  E  L  VF++ G+I +V +V+D+ T + RGF FV +E      D    +
Sbjct: 3   LFIGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAM 62

Query: 92  NGAQILGRTIRVDHVAK 108
           NG  + GR IRVD   K
Sbjct: 63  NGKSVDGRQIRVDQAGK 79

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

 Score = 56.6 bits (137), Expect = 1e-10
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 43  IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQI 96
           +P D+T+ +L ++F   G I    +VRD+ TG+  G+ FV Y D+       N LNG +I
Sbjct: 8   LPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEI 67

Query: 97  LGRTIRV 103
             + ++V
Sbjct: 68  RNKRLKV 74

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

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

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 8/71 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           +YV  +P  +TE DL   F+  G++  V LVR+K   +PRGFAFV +            L
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNK--DRPRGFAFVEFASPEDAEAALKKL 58

Query: 92  NGAQILGRTIR 102
           NG  + GRT+R
Sbjct: 59  NGLVLDGRTLR 69

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

>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 = 55.8 bits (135), Expect = 1e-10
 Identities = 21/50 (42%), Positives = 35/50 (70%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGG+P D+TE +    F+Q G++VD  L++D  TG+ RGF FV ++ +
Sbjct: 2  IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSE 51

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

 Score = 59.6 bits (143), Expect = 3e-10
 Identities = 36/122 (29%), Positives = 62/122 (50%), Gaps = 9/122 (7%)

Query: 16  KEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGK 75
           +E         S     +++  ++VG +P+D+TE DL  +F + G +  V LVRD+ TGK
Sbjct: 96  EELFRSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGK 155

Query: 76  PRGFAFVAYEDQRN------NLNGAQILGRTIRVD---HVAKYKKKEEEDEETRQRMREE 126
            RGFAFV +E + +       LNG ++ GR +RV      ++ + +   + +     +  
Sbjct: 156 SRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLS 215

Query: 127 RG 128
           RG
Sbjct: 216 RG 217

Length = 306

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

 Score = 55.3 bits (133), Expect = 3e-10
 Identities = 28/66 (42%), Positives = 35/66 (53%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQ 95
             +YV  +P  LTE +L  +F   G IV  NL+RDK TG PRG AFV Y+ +        
Sbjct: 1   TNLYVTNLPRQLTEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAIS 60

Query: 96  ILGRTI 101
            L  TI
Sbjct: 61  SLNGTI 66

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

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

 Score = 55.1 bits (133), Expect = 3e-10
 Identities = 28/75 (37%), Positives = 39/75 (52%), Gaps = 12/75 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE---------DQR 88
           VYVG I F+L E  +   F+  G I  +++  D  T K +GFAFV YE         +Q 
Sbjct: 3   VYVGSISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQ- 61

Query: 89  NNLNGAQILGRTIRV 103
             +NG  + GR I+V
Sbjct: 62  --MNGVMLGGRNIKV 74

This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 76

>gnl|CDD|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 = 55.0 bits (133), Expect = 4e-10
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 6/67 (8%)

Query: 43  IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQI 96
           +P + T+ DL  +FA  G ++   +  DK TG+ + F FV+Y++          +NG Q+
Sbjct: 6   LPNEFTDQDLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQV 65

Query: 97  LGRTIRV 103
            G+ ++V
Sbjct: 66  GGKRLKV 72

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|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 = 54.5 bits (132), Expect = 5e-10
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 6/66 (9%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
          ++VG +P   TE D+ A+F + G I +V ++RDK TG+ +G AFV +  +         L
Sbjct: 2  LFVGQLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEAL 61

Query: 92 NGAQIL 97
          +G   +
Sbjct: 62 HGKVTM 67

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

 Score = 54.7 bits (132), Expect = 6e-10
 Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 7/72 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+PF +T+ +L  +F + G +  V LV ++  GKP+G A+V YE++         +
Sbjct: 5   LFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRS-GKPKGLAYVEYENESSASQAVLKM 63

Query: 92  NGAQILGRTIRV 103
           +G +I  +TI V
Sbjct: 64  DGTEIKEKTISV 75

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

 Score = 54.3 bits (131), Expect = 6e-10
 Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 37  YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY---EDQRN---N 90
           +++VG +  ++    L A FA  GEI D  +V+D  TGK +G+ FV++   ED  N   +
Sbjct: 1   HIFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQS 60

Query: 91  LNGAQILGRTIR 102
           +NG  + GR IR
Sbjct: 61  MNGQWLGGRAIR 72

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------L 91
           VYVG +   +TE  L  +F Q G +V+V++ +D+ T   +G+ FV +  + +       +
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIM 60

Query: 92  NGAQILGRTIRV 103
           N  ++ G+ IRV
Sbjct: 61  NMIKLYGKPIRV 72

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

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

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 7/79 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY---EDQR---NNL 91
           ++V  +P+D T+  L   F++ G I    +V+DKG+ K RGF +V +   ED +      
Sbjct: 2   LFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEK 61

Query: 92  NGAQILGRTIRVDHVAKYK 110
              +  GR I V+  AK K
Sbjct: 62  KKTKFGGRKIHVE-FAKKK 79

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

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

 Score = 53.1 bits (128), Expect = 1e-09
 Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILG 98
           +V  +PF  TE +L  +F   GEI +V+L  DK T + +GFAFV++    + +     L 
Sbjct: 3   FVRNLPFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELD 62

Query: 99  RTI---RVDHV 106
            +I   R+ HV
Sbjct: 63  GSIFQGRLLHV 73

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

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           V+VG IP DL E +L+ +F + G I ++ L+ D   G  RG+AFV Y ++         L
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFS-GLNRGYAFVTYTNKEAAQRAVKQL 62

Query: 92  NGAQI-LGRTIRV 103
           +  +I  G+ + V
Sbjct: 63  HNYEIRPGKRLGV 75

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

 Score = 52.8 bits (127), Expect = 2e-09
 Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 6/69 (8%)

Query: 43  IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQI 96
           +P ++T+ ++ ++F+  GEI    L+RDK TG+  G+ FV Y D        N LNG ++
Sbjct: 9   LPQNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRL 68

Query: 97  LGRTIRVDH 105
             +TI+V +
Sbjct: 69  QNKTIKVSY 77

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

 Score = 52.7 bits (127), Expect = 2e-09
 Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLN 92
            VG +P + T+     + +  G +    LV  + TG+ +G+ FV Y  +      +N L+
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 93  GAQILGRTIRVD 104
           G QI GR ++VD
Sbjct: 63  GKQIGGRKLQVD 74

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

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 22/52 (42%), Positives = 31/52 (59%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
          VYV  +P + T   L AVF++ G +V V+L R K TG  +GFAF+ +E    
Sbjct: 2  VYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKGFAFIEFETPEE 53

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

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 10/81 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           VYV  +  D+ +  L  +F + G+I    +++D   GK +GF FV +E+          L
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEEL 62

Query: 92  NGAQILGRTIRVDHVAKYKKK 112
           NG ++ G+ +   +V + +KK
Sbjct: 63  NGKEVNGKKL---YVGRAQKK 80

This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 80

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

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 31/71 (43%), Positives = 40/71 (56%), Gaps = 6/71 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNLNG 93
           V G+    TE DL  VF++ G I  V +V D+ TG+ RGF FV +E        +  LNG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKERLNG 63

Query: 94  AQILGRTIRVD 104
            +I GR IRVD
Sbjct: 64  MEIDGRRIRVD 74

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

 Score = 51.6 bits (124), Expect = 6e-09
 Identities = 27/72 (37%), Positives = 38/72 (52%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VG +P+D T  DLLA F   G    V L+ DK TGK +G AFV ++          L+
Sbjct: 3   LFVGNLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKALKLH 62

Query: 93  GAQILGRTIRVD 104
              + GR I V+
Sbjct: 63  HTLLKGRKINVE 74

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

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

 Score = 51.2 bits (123), Expect = 7e-09
 Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           VY+G + +D+TE D+   F    EI  V L  DK TG+ +GF  V + D+ +      L+
Sbjct: 2   VYIGNLAWDITEDDVREFFK-GCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKLD 60

Query: 93  GAQILGRTIRVD 104
           G  + GR IR+ 
Sbjct: 61  GTVLCGRPIRIA 72

The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. . Length = 72

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

 Score = 51.2 bits (123), Expect = 8e-09
 Identities = 21/73 (28%), Positives = 39/73 (53%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG + + + +  L A F + G +V   ++ D+ TG+ RGF +V +E           +
Sbjct: 2   LFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAM 61

Query: 92  NGAQILGRTIRVD 104
           +G ++ GR I VD
Sbjct: 62  DGKELDGRPINVD 74

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

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

 Score = 51.2 bits (123), Expect = 8e-09
 Identities = 19/50 (38%), Positives = 33/50 (66%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGG+P ++TE DL   F+Q G + +V ++ D    +PRGF F+ +E +
Sbjct: 5  IFVGGLPPNVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESE 54

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

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 8/72 (11%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------ 89
           A +YV G+P  +T+ +L A+F+  G I+   ++ D  TG  RG  F+ + D+R       
Sbjct: 1   ANLYVSGLPKTMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRF-DKRIEAERAI 59

Query: 90  -NLNGAQILGRT 100
             LNG    G T
Sbjct: 60  KALNGTIPPGAT 71

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

 Score = 50.7 bits (122), Expect = 1e-08
 Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL---VRDKGTGKPRGFAFVAYEDQRN----- 89
           +YV  + F L E DL  +F++ GE+  + +     +K      GFAFV ++D  +     
Sbjct: 3   IYVRNLDFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL 62

Query: 90  NLNGAQILGRTIRV 103
            LNG ++ GR I V
Sbjct: 63  QLNGTELGGRKISV 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|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 9/72 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YVG +   +TE  L  +F+Q G I    L+R+ G   P  +AFV Y D R+       +
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHG-NDP--YAFVEYYDHRSAAAALQTM 57

Query: 92  NGAQILGRTIRV 103
           NG  ILG+ I+V
Sbjct: 58  NGRLILGQEIKV 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|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YV  +  DL+E D+ +VF   G+I   +L  D  TGK +G+ F+ YE+ ++      ++
Sbjct: 3   IYVASVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASM 62

Query: 92  NGAQILGRTIRV 103
           N   + G+ +RV
Sbjct: 63  NLFDLGGQQLRV 74

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

 Score = 50.2 bits (121), Expect = 2e-08
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNL 91
           ++VG +  ++ +  L  +F+  G + DV+L  D+    PRG+A+V +      E    ++
Sbjct: 1   LHVGKLTRNVNKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHM 60

Query: 92  NGAQILGRTIRV 103
           +G QI G+ + V
Sbjct: 61  DGGQIDGQEVTV 72

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

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 12/72 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VYVG +P  LTE +L   F+  G I +V + +DK      G+AFV ++           +
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDK------GYAFVRFDTHEAAATAIVAV 56

Query: 92  NGAQILGRTIRV 103
           NG  I G+T++ 
Sbjct: 57  NGTSINGQTVKC 68

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

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

 Score = 49.9 bits (120), Expect = 2e-08
 Identities = 20/49 (40%), Positives = 29/49 (59%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          VY+G +P    E +L   F+Q G +  + L R K TGK +G+AFV +E 
Sbjct: 2  VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFES 50

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 19/50 (38%), Positives = 35/50 (70%), Gaps = 1/50 (2%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          V+V  + + + E +L  +F++CGEI DV LV++   GK +G+A+V +E++
Sbjct: 2  VFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENE 50

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VG + +   + DL   F +CGE+VDV + +D   G+ +GF  V +  +         +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDD-DGRSKGFGHVEFATEEGAQKALEKS 60

Query: 93  GAQILGRTIRVD 104
           G ++LGR IRVD
Sbjct: 61  GEELLGREIRVD 72

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

 Score = 53.7 bits (129), Expect = 4e-08
 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 6/79 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------L 91
           +YVG + F++TE +L  +F   G+I DV L RD  TG+ +GF F+ + D          +
Sbjct: 189 LYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM 248

Query: 92  NGAQILGRTIRVDHVAKYK 110
           NG ++ GR I+V +     
Sbjct: 249 NGFELAGRPIKVGYAQDST 267

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

 Score = 49.5 bits (119), Expect = 4e-08
 Identities = 30/78 (38%), Positives = 39/78 (50%), Gaps = 11/78 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAY---EDQ----- 87
           + + G+    TE D+L   +      I DV L+RDK TG  RGFAFV +   ED      
Sbjct: 5   LILRGLDLLTTEEDILQALSAIASVPIKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMD 64

Query: 88  -RNNLNGAQILGRTIRVD 104
             NNL+   I GR +RV 
Sbjct: 65  ALNNLDPFVIDGRVVRVS 82

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

 Score = 49.3 bits (118), Expect = 4e-08
 Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 6/76 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           ++  ++V  +P+   E DL  +F++ GE+ +V++  DK +GK +GFA+V + D  +    
Sbjct: 1   ETGRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKA 60

Query: 90  --NLNGAQILGRTIRV 103
              L+G    GR I +
Sbjct: 61  YKELDGKVFQGRLIHI 76

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

 Score = 48.8 bits (117), Expect = 5e-08
 Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 6/71 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNG 93
           V  + +  T  DL  VF + GE+ DV + RD+ T + RGFAFV + D+R+       ++G
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDG 62

Query: 94  AQILGRTIRVD 104
            ++ GR +RV 
Sbjct: 63  KELDGRELRVQ 73

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

 Score = 48.9 bits (117), Expect = 5e-08
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +   +TE  L  +F Q G +  V + +D   GKP+ FAFV ++ +         L
Sbjct: 4   LFVGNLDARVTEEILYELFLQAGPLEGVKIPKDP-NGKPKSFAFVTFKHEVSVPYAIQLL 62

Query: 92  NGAQILGRTIRVD 104
           NG ++ GR +R+ 
Sbjct: 63  NGIRLFGRELRIK 75

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

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

 Score = 49.0 bits (117), Expect = 6e-08
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 5/69 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN----LNG 93
           ++VGG+ ++ T+  L   F+Q GE+VD  +++DK T + RGF FV ++D          G
Sbjct: 2   LFVGGLSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGG 61

Query: 94  AQIL-GRTI 101
              L GRTI
Sbjct: 62  PHTLDGRTI 70

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|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 = 48.9 bits (117), Expect = 6e-08
 Identities = 26/73 (35%), Positives = 36/73 (49%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGGI   L+E DL   F+ CGE+  V L  D        FAFV + D  +     NL+
Sbjct: 3   IHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGD--RQHSARFAFVEFADAESALSALNLS 60

Query: 93  GAQILGRTIRVDH 105
           G  + G  +RV  
Sbjct: 61  GTLLGGHPLRVSP 73

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

 Score = 48.9 bits (117), Expect = 7e-08
 Identities = 22/54 (40%), Positives = 35/54 (64%)

Query: 31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          K  D+  ++VG IP +L E DL  +F Q G+I ++ +++DK TG  +G AF+ Y
Sbjct: 1  KDDDAIKLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLKDKYTGMHKGCAFLTY 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|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 11/78 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ---------- 87
           V++  +PFD TE +L  +F+Q GE+    +V+DK TG  +G AFV ++ +          
Sbjct: 3   VFIRNLPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAA 62

Query: 88  -RNNLNGAQILGRTIRVD 104
                +G  + GR + V 
Sbjct: 63  DNAEDSGLSLDGRRLIVT 80

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

 Score = 48.4 bits (116), Expect = 8e-08
 Identities = 21/71 (29%), Positives = 41/71 (57%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           V+V  +   + E DL   F++ G++ DV ++RD+ + + +G A+V + D+ +      L 
Sbjct: 2   VFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLALGLT 61

Query: 93  GAQILGRTIRV 103
           G ++LG+ I V
Sbjct: 62  GQRLLGQPIMV 72

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

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

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 23/71 (32%), Positives = 39/71 (54%), Gaps = 6/71 (8%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
           A +YV G+P  +T+ +L  +F+Q G I+   ++RD+ TG  RG  F+ +      E+   
Sbjct: 1   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIK 60

Query: 90  NLNGAQILGRT 100
            LNG +  G +
Sbjct: 61  GLNGQKPEGAS 71

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

 Score = 48.4 bits (115), Expect = 1e-07
 Identities = 21/49 (42%), Positives = 32/49 (65%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          ++VGG+  D+ EGDL   F+Q G +    ++ DK TGK RGF FV +++
Sbjct: 2  LFVGGLKGDVGEGDLTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQN 50

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

 Score = 48.2 bits (115), Expect = 1e-07
 Identities = 23/62 (37%), Positives = 35/62 (56%), Gaps = 3/62 (4%)

Query: 40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV---AYEDQRNNLNGAQI 96
          V G+P+  TE DL   F+  GE++ V + +D  TG+ +GF FV    YEDQ   L+   +
Sbjct: 4  VLGLPWKTTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHM 63

Query: 97 LG 98
          + 
Sbjct: 64 ID 65

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

 Score = 47.9 bits (115), Expect = 1e-07
 Identities = 19/41 (46%), Positives = 23/41 (56%)

Query: 46 DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          D  E DL  +F   G I  V L +DK TG+ RGFAFV +  
Sbjct: 10 DADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHT 50

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 9/76 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG---TGKPRGFAFVAYEDQ------R 88
           +++G +   LTE  LL +F++ G+I   + +  K     G+PRG+ FV +E +       
Sbjct: 2   LWIGNLDSRLTEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKAL 61

Query: 89  NNLNGAQILGRTIRVD 104
            +LNG   LG+ + V 
Sbjct: 62  KSLNGKTALGKKLVVR 77

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

 Score = 48.0 bits (115), Expect = 1e-07
 Identities = 26/73 (35%), Positives = 44/73 (60%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  +  E D+   FA+ GEI +++L  D+ TG  +G+A + YE ++        L
Sbjct: 9   IFVTGVHEEAQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGL 68

Query: 92  NGAQILGRTIRVD 104
           NG ++LG+TI VD
Sbjct: 69  NGKELLGQTISVD 81

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

 Score = 48.2 bits (114), Expect = 1e-07
 Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNG 93
           V  +P ++T+ +L ++F   GEI    LVRDK TG+  G+ FV Y D +      N LNG
Sbjct: 9   VNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 68

Query: 94  AQILGRTIRVDH 105
            ++  +TI+V +
Sbjct: 69  LRLQTKTIKVSY 80

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

 Score = 52.0 bits (124), Expect = 2e-07
 Identities = 29/72 (40%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           VYVG I F+L E  +   F   G I  +N+  D  TGK +GFAFV YE           +
Sbjct: 110 VYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQM 169

Query: 92  NGAQILGRTIRV 103
           NG  + GR I+V
Sbjct: 170 NGQMLGGRNIKV 181

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 18/42 (42%), Positives = 27/42 (64%)

Query: 43 IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          IP   TE DL   F + G+I  V++V+DK TG+ +GF +V +
Sbjct: 8  IPKSYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

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

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

 Score = 47.2 bits (112), Expect = 2e-07
 Identities = 17/49 (34%), Positives = 31/49 (63%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +++GG+ ++ T+  L   F Q GE+ D  ++RD  TG+ RGF F+ ++ 
Sbjct: 1  MFIGGLNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKK 49

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

 Score = 47.2 bits (113), Expect = 2e-07
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 11/74 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VYVG +    T+ +L   F + G +  V + R      P GFAFV +ED R+       L
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVAR-----NPPGFAFVEFEDPRDAEDAVRAL 56

Query: 92  NGAQILGRTIRVDH 105
           +G +I G  +RV+ 
Sbjct: 57  DGRRICGNRVRVEL 70

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

 Score = 47.4 bits (113), Expect = 2e-07
 Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 6/80 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YV  +       DL  +F + G IVDV +  D  T +PRGFA+V +ED R+       L
Sbjct: 3   LYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYL 62

Query: 92  NGAQILGRTIRVDHVAKYKK 111
           +  + LGR I +      +K
Sbjct: 63  DRTRFLGREIEIQFAQGDRK 82

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

 Score = 47.0 bits (111), Expect = 3e-07
 Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 6/72 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNG 93
           V  +P ++T+ +  ++F   GEI    LVRDK TG+  G+ FV Y D +      N LNG
Sbjct: 7   VNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNG 66

Query: 94  AQILGRTIRVDH 105
            ++  +TI+V +
Sbjct: 67  LRLQTKTIKVSY 78

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

 Score = 50.3 bits (120), Expect = 4e-07
 Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 6/67 (8%)

Query: 43  IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQI 96
           +P  +T+ ++ ++F   GEI    LVRDK TG+  G+ FV Y          N+LNG ++
Sbjct: 11  LPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRL 70

Query: 97  LGRTIRV 103
             +TI+V
Sbjct: 71  QNKTIKV 77

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

 Score = 46.7 bits (111), Expect = 4e-07
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 3/70 (4%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR---NNLNGA 94
           ++VG + F+ TE +L A F + G I  V ++  + +GK +GFAFV +E+     N L G 
Sbjct: 1   LFVGNLSFETTEDELRAHFGRVGRIRRVRMMTFEDSGKCKGFAFVDFEEIEFATNALKGK 60

Query: 95  QILGRTIRVD 104
            + GR +RV+
Sbjct: 61  HLNGRALRVE 70

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

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNL------ 91
           ++VG +    TE  L  VF++ G+I  + LVRD  TG  +G+AFV YE +R+ L      
Sbjct: 6   LFVGRLSLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDA 65

Query: 92  NGAQILGRTIRVD 104
           +   I G  I VD
Sbjct: 66  HKLVIDGSEIFVD 78

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

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

 Score = 46.6 bits (111), Expect = 4e-07
 Identities = 20/51 (39%), Positives = 33/51 (64%)

Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          +S  +++  + +  TE DL  +F++ G + +V+L  DK T KP+GFAFV Y
Sbjct: 1  ESGRLFIRNLAYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTY 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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 46.4 bits (110), Expect = 4e-07
 Identities = 25/72 (34%), Positives = 41/72 (56%), Gaps = 7/72 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
           VYVG + +  T  +L A F+ CG I  V ++ DK +G P+G+A++ +   R+++  A  L
Sbjct: 2   VYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEF-ATRDSVEAAVAL 60

Query: 98  ------GRTIRV 103
                 GR I+V
Sbjct: 61  DESSFRGRVIKV 72

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

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 20/52 (38%), Positives = 33/52 (63%), Gaps = 1/52 (1%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
          ++VGGIP D TE +L   F++ G + DV ++ D+  G  +G+ FV +E Q +
Sbjct: 5  IFVGGIPPDTTEEELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQED 55

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

 Score = 46.3 bits (109), Expect = 5e-07
 Identities = 26/72 (36%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNG 93
           V  +P ++T+ +  ++F   GEI    LVRDK TG+  G+ FV Y D        N LNG
Sbjct: 8   VNYLPQNMTQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNG 67

Query: 94  AQILGRTIRVDH 105
            ++  +TI+V +
Sbjct: 68  LKLQTKTIKVSY 79

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

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

 Score = 46.1 bits (109), Expect = 5e-07
 Identities = 31/72 (43%), Positives = 44/72 (61%), Gaps = 6/72 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE---DQRNNL---NG 93
           V G+    TE DL  VF++ G +  VN+V D+ TG+ RGFAFV +E   D +  +   NG
Sbjct: 4   VFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEHANG 63

Query: 94  AQILGRTIRVDH 105
            ++ GR IRVD+
Sbjct: 64  MELDGRRIRVDY 75

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

 Score = 45.8 bits (109), Expect = 6e-07
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGG+  + TE  +   F + G IV++ L  DK T K RGF F+ ++ +
Sbjct: 2  IFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSE 51

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

 Score = 45.8 bits (109), Expect = 7e-07
 Identities = 17/49 (34%), Positives = 30/49 (61%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +++GG+ ++ T+  L   F+Q GEI D  +++D  T + RGF FV +  
Sbjct: 2  LFIGGLSYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFAS 50

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

 Score = 45.3 bits (108), Expect = 8e-07
 Identities = 20/72 (27%), Positives = 35/72 (48%), Gaps = 7/72 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V  +PF +T  DL  +F +CG ++  ++  D   G+ +GF  V +E            
Sbjct: 1   IFVRNLPFSVTWQDLKDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMF 59

Query: 92  NGAQILGRTIRV 103
           NG  + GR + V
Sbjct: 60  NGYDLEGRELEV 71

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

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

 Score = 45.9 bits (109), Expect = 8e-07
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 14/80 (17%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEI-VD-------VNLVRDKGTGKPRGFAFVAYEDQR- 88
           V+V  +P + TE DL   F   G I +D       + L +DK TG+P+G A V Y+D   
Sbjct: 1   VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDTGEPKGEATVTYDDPHA 60

Query: 89  -----NNLNGAQILGRTIRV 103
                   N    +G TI+V
Sbjct: 61  ASAAIEWFNNKDFMGNTIKV 80

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

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

 Score = 45.6 bits (108), Expect = 9e-07
 Identities = 14/49 (28%), Positives = 27/49 (55%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +Y+G +P    E +L   F+Q G + +V + R K TG  + + F+ + +
Sbjct: 2  IYIGHLPHGFLEKELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLN 50

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

 Score = 45.7 bits (108), Expect = 9e-07
 Identities = 20/47 (42%), Positives = 32/47 (68%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          V+VG IP DL E +L+ +F + G I D+ L+ D  +G+ RG+AF+ +
Sbjct: 4  VFVGKIPRDLYEDELVPLFEKAGPIWDLRLMMDPLSGQNRGYAFITF 50

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

 Score = 47.3 bits (112), Expect = 9e-07
 Identities = 24/76 (31%), Positives = 44/76 (57%), Gaps = 6/76 (7%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           S  +++GG+ +   +  L   FA  G++VD  ++ D+ TG+ RGF FV + D+       
Sbjct: 34  STKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI 93

Query: 89  NNLNGAQILGRTIRVD 104
           + ++G ++ GR IRV+
Sbjct: 94  SEMDGKELNGRHIRVN 109

Length = 144

>gnl|CDD|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.5 bits (107), Expect = 1e-06
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 37  YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNN 90
           +V+VG +  ++T  D+ A FA  G I D  +V+D  TGK +G+ FV++      E+    
Sbjct: 3   HVFVGDLSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 62

Query: 91  LNGAQILGRTIRVD 104
           + G  + GR IR +
Sbjct: 63  MGGQWLGGRQIRTN 76

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

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 21/49 (42%), Positives = 33/49 (67%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          ++VGG+ +D T+ DL   F++ GE+VD  +  D  TG+ RGF FV ++D
Sbjct: 1  MFVGGLSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKD 49

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

 Score = 44.8 bits (107), Expect = 1e-06
 Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLN 92
           YVG +  D+TE  L  +F+  G ++ + + RD  T +  G+A+V +++        + LN
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 93  GAQILGRTIRV 103
              I G+ IR+
Sbjct: 63  FDVIKGKPIRI 73

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

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

 Score = 44.6 bits (105), Expect = 2e-06
 Identities = 20/49 (40%), Positives = 33/49 (67%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +++GG+ +D T+ DL   F++ GE+VD  L  D  TG+ RGF FV +++
Sbjct: 1  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKE 49

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

 Score = 44.9 bits (107), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 7/74 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV---AYEDQ----RNN 90
           ++VGG+   +TE DL   F++ G + DV +++ K  G  RGFA++     E Q    ++ 
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKKKDAGPDRGFAYIDLRTSEAQLKKCKST 61

Query: 91  LNGAQILGRTIRVD 104
           LNG +  G  ++++
Sbjct: 62  LNGTKWKGSVLKIE 75

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 10/75 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLV-RDKGTGKPRGFAFVAYEDQ------RNN 90
           ++V  IPF   + DL  +F Q G I+DV ++  ++G+   +GF FV + +       R  
Sbjct: 3   LHVSNIPFRFRDPDLRQMFGQFGPILDVEIIFNERGS---KGFGFVTFANSADADRAREK 59

Query: 91  LNGAQILGRTIRVDH 105
           L+G  + GR I V++
Sbjct: 60  LHGTVVEGRKIEVNN 74

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 6/74 (8%)

Query: 37  YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------N 90
           +V+VG +  ++T  D+ + FA  G+I D  +V+D  TGK +G+ FV++ ++ +      +
Sbjct: 3   HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 62

Query: 91  LNGAQILGRTIRVD 104
           + G  + GR IR +
Sbjct: 63  MGGQWLGGRQIRTN 76

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

 Score = 44.7 bits (106), Expect = 2e-06
 Identities = 18/53 (33%), Positives = 31/53 (58%)

Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          DS  ++VG +P D+TE +L   F + G +++V +    G G+   F FV ++D
Sbjct: 2  DSHQLFVGNLPHDITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDD 54

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|240928 cd12484, RRM1_RBM46, RNA recognition motif 1 found in vertebrate RNA-binding protein 46 (RBM46)

 Score = 44.5 bits (105), Expect = 2e-06
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
          V+VG IP D+ E +L+ +F + G+I +  L+ +  +G+ RG+AFV Y  +       +IL
Sbjct: 4  VFVGKIPRDMYEDELVPLFERAGKIYEFRLMMEF-SGENRGYAFVMYTTKEEAQLAIRIL 62

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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           VYVG + +  T  +L A F  CG +  V ++ DK +G P+GFA++ + D+ +      L+
Sbjct: 2   VYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTALALD 61

Query: 93  GAQILGRTIRV 103
            +   GR I+V
Sbjct: 62  ESLFRGRQIKV 72

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

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 16/48 (33%), Positives = 28/48 (58%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
          VY+ G+P + T+ DL  +    G+I+    + DK T K +G+ FV ++
Sbjct: 3  VYIRGLPPNTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFD 50

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

 Score = 44.2 bits (104), Expect = 2e-06
 Identities = 22/50 (44%), Positives = 32/50 (64%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D 
Sbjct: 3  IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 52

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

 Score = 44.9 bits (106), Expect = 2e-06
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN---LNGA 94
           ++V  +P+D TE  L   F++ G +     V DK TG+ +G  FV ++DQ      L  A
Sbjct: 4   LFVRNLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLKNA 63

Query: 95  QILGRT 100
              G T
Sbjct: 64  PAAGST 69

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

 Score = 44.0 bits (104), Expect = 3e-06
 Identities = 20/48 (41%), Positives = 31/48 (64%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
          ++VGG+  + TE D+   F+Q G++ D  L+ DK T + RGF FV +E
Sbjct: 2  IFVGGLSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFE 49

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

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 6/72 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLNG 93
           V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E+       +   NG
Sbjct: 14  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 73

Query: 94  AQILGRTIRVDH 105
            ++ GR IRVD 
Sbjct: 74  MELDGRRIRVDF 85

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 6/63 (9%)

Query: 48  TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI 101
           T+ DL  +F++ G+I    ++RDK TG    +AF+ +E + +       ++   I  R I
Sbjct: 16  TDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRRI 75

Query: 102 RVD 104
            VD
Sbjct: 76  HVD 78

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

 Score = 43.8 bits (103), Expect = 4e-06
 Identities = 21/47 (44%), Positives = 31/47 (65%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          ++VG IP DL E +L+ +F + G I D+ L+ D  TG  RG+AFV +
Sbjct: 4  IFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVTF 50

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

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 7/74 (9%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN----- 90
             + V  + +D+TE DL  +F + GE+  V +  D+ +G+  G A V +E + +      
Sbjct: 1   TRLRVSNLHYDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIK 59

Query: 91  -LNGAQILGRTIRV 103
             NG  + G+ ++V
Sbjct: 60  QFNGVLLDGQPMQV 73

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

 Score = 43.4 bits (102), Expect = 5e-06
 Identities = 23/72 (31%), Positives = 41/72 (56%), Gaps = 7/72 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +   +TE  +  +F Q G ++ V + +DK  GKP+ FAFV ++ +       N L
Sbjct: 4   LFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDK-DGKPKQFAFVNFKHEVSVPYAMNLL 62

Query: 92  NGAQILGRTIRV 103
           NG ++ GR + +
Sbjct: 63  NGIKLYGRPLNI 74

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

 Score = 47.1 bits (112), Expect = 6e-06
 Identities = 28/97 (28%), Positives = 52/97 (53%), Gaps = 8/97 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YV  +   + E  L  +FA+ GEI    +++D  +G+ RGFAFV +E   +       +
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEM 239

Query: 92  NGAQI-LGRTIRVDHVAKYKKKEEEDEETRQRMREER 127
           NG +I L +  +  +V + +K+ E + E R++  E +
Sbjct: 240 NGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQ 276

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

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

 Score = 42.6 bits (101), Expect = 7e-06
 Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 5/49 (10%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          V+VG +  D+TE DL   F+Q GE+ DV + +       R FAFV + D
Sbjct: 3  VFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKP-----FRAFAFVTFAD 46

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|233515 TIGR01659, sex-lethal, sex-lethal family splicing factor

 Score = 46.5 bits (110), Expect = 7e-06
 Identities = 21/47 (44%), Positives = 31/47 (65%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
           +YV  +P  +T+  L  +F + G+IV  N++RDK TG PRG AFV +
Sbjct: 196 LYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRF 242

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|240836 cd12390, RRM3_RAVER, RNA recognition motif 3 in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins

 Score = 43.4 bits (103), Expect = 8e-06
 Identities = 24/72 (33%), Positives = 35/72 (48%), Gaps = 8/72 (11%)

Query: 39  YVGGIPFDLTEGDLL-AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNL 91
           +V  +P    +  +L  +F+Q G+     L      G+PRGFAFV Y      E+ +  L
Sbjct: 6   FVDRLPKTFRDVSILRKLFSQVGKPTFCQLAIAPN-GQPRGFAFVEYATAEDAEEAQQAL 64

Query: 92  NGAQILGRTIRV 103
           NG  + G  IRV
Sbjct: 65  NGHSLQGSPIRV 76

This subfamily corresponds to the RRM3 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 = 92

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

 Score = 43.2 bits (101), Expect = 8e-06
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)

Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNLNG 93
           V  +P ++T+ +L ++F+  GE+    L+RDK  G   G+ FV Y      E   N LNG
Sbjct: 6   VNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNG 65

Query: 94  AQILGRTIRVDH 105
            ++  +TI+V +
Sbjct: 66  LRLQSKTIKVSY 77

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|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 42.1 bits (100), Expect = 8e-06
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 11/59 (18%)

Query: 52  LLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD 104
           L  +F+  G +  + L++ K      GFAFV +  +         LNG    GR +RVD
Sbjct: 1   LYKLFSPFGNVEKIKLLKKKP-----GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

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

>gnl|CDD|240848 cd12402, RRM_eIF4B, RNA recognition motif in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins

 Score = 42.8 bits (101), Expect = 9e-06
 Identities = 26/72 (36%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG-TGKPRGFAFVAYED-----QRNNLN 92
           Y+G +P+D+TE D+   F     +  V L R+ G  G+ RGF +  +ED     Q  +LN
Sbjct: 5   YLGNLPYDVTEEDIKEFFRGL-NVSSVRLPREPGDPGRLRGFGYAEFEDRDSLLQALSLN 63

Query: 93  GAQILGRTIRVD 104
              +  R IRVD
Sbjct: 64  DESLKNRRIRVD 75

This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. . Length = 77

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 26/69 (37%), Positives = 38/69 (55%), Gaps = 6/69 (8%)

Query: 43  IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY---ED-QR--NNLNGAQI 96
           +P  LT+ +  ++F   G + +  +VRDK TG   GF FV Y   ED QR    LNG Q+
Sbjct: 8   LPQTLTDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQL 67

Query: 97  LGRTIRVDH 105
             + I+V +
Sbjct: 68  QNKRIKVAY 76

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

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

 Score = 42.3 bits (99), Expect = 1e-05
 Identities = 18/49 (36%), Positives = 31/49 (63%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          ++VGG+ +D ++ DL   F + GE+ D  +  D  TG+ RGF F+ ++D
Sbjct: 2  MFVGGLSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKD 50

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

 Score = 42.2 bits (99), Expect = 1e-05
 Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 10/75 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
           V+VG + F+  E  L  VF +CG I  V +VRD  T   +GFA+V ++D+ N +  A +L
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDE-NAVEKALLL 60

Query: 98  ---------GRTIRV 103
                     R +RV
Sbjct: 61  NEKKFPPMLPRELRV 75

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 9/84 (10%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDKGTGKPRGFAFVAYED------QR 88
           A +++G +  ++ E  L   F+  G I+    ++RD  TG  +GFAF++Y+         
Sbjct: 2   ANLFIGNLDPEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAI 61

Query: 89  NNLNGAQILGRTIRVDHVAKYKKK 112
             +NG  +  R I V +   +KK 
Sbjct: 62  EAMNGQYLCNRPITVSYA--FKKD 83

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

 Score = 45.4 bits (107), Expect = 2e-05
 Identities = 17/49 (34%), Positives = 26/49 (53%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           +YV  +  DL+E D+ +VF   GEIV   L R       +G+ F+ Y +
Sbjct: 207 IYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNN 255

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 8/76 (10%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           D   ++VG +  D+T+ +L   F++ G+I++VNL+  K       FAF+ +E ++     
Sbjct: 2   DKYSIFVGQLSPDVTKEELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARA 59

Query: 90  --NLNGAQILGRTIRV 103
             + N + +  +T+ V
Sbjct: 60  VESENHSMLKNKTMHV 75

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

 Score = 41.5 bits (97), Expect = 2e-05
 Identities = 17/49 (34%), Positives = 32/49 (65%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +++GG+ +D ++ DL    ++ GE++D  +  D  TG+ RGF FV ++D
Sbjct: 2  MFIGGLSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKD 50

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

 Score = 41.3 bits (97), Expect = 2e-05
 Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 10/72 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VY G  P      D+  +F  CG +  V ++    +   +  AF+ +E+          L
Sbjct: 2   VYAGPFPTSFCLSDVKRLFETCGPVRKVTML----SRTVQPHAFITFENLEAAQLAIETL 57

Query: 92  NGAQILGRTIRV 103
           NGA + G  I+V
Sbjct: 58  NGASVDGNCIKV 69

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

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

 Score = 41.1 bits (97), Expect = 2e-05
 Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 12/71 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V+VGG+   +TE +L ++F   GEIV V +   KG G      FV +  +         L
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCG------FVQFVHRAAAEAAIQQL 57

Query: 92  NGAQILGRTIR 102
            G  I G  IR
Sbjct: 58  QGTIIGGSRIR 68

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 9/74 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT-GKPRGFAFVAYEDQRN-----NL 91
           +YVG +    T   LL  F+Q GE   V  VR  G   +P  +AFV + +Q +      L
Sbjct: 7   IYVGNLDPTTTADQLLEFFSQAGE---VKYVRMAGDETQPTRYAFVEFAEQTSVINALKL 63

Query: 92  NGAQILGRTIRVDH 105
           NGA   GR ++V+H
Sbjct: 64  NGAMFGGRPLKVNH 77

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

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLN 92
          ++VGGI F   E DL   F+Q G + +V +V D+  G  +G+ FV +E Q +   
Sbjct: 5  IFVGGIDFKTNENDLRKFFSQYGTVKEVKIVNDR-AGVSKGYGFVTFETQEDAQK 58

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|240892 cd12446, RRM_RBM25, RNA recognition motif in eukaryotic RNA-binding protein 25 and similar proteins

 Score = 41.1 bits (97), Expect = 4e-05
 Identities = 18/60 (30%), Positives = 33/60 (55%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
          V+VG IP  +++  +  +  +CG+++    V+D  TGK + F F  +ED    L   ++L
Sbjct: 3  VFVGNIPEGVSDDFIRKLLEKCGKVLSWKRVKDPSTGKLKAFGFCEFEDPEGALRALRLL 62

This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. . Length = 84

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

 Score = 43.8 bits (103), Expect = 5e-05
 Identities = 17/53 (32%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR 88
           A +YV G+P  +T+ +L ++F+  G+I+   ++ D  TG  +G  F+ + D+R
Sbjct: 90  ANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRF-DKR 141

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

 Score = 40.6 bits (95), Expect = 5e-05
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +  ++T+  L A F+      D  ++ D  +G+ RG+ FV++  Q+      N +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 92  NGAQILGRTIRVD 104
           NG  +  R IR +
Sbjct: 62  NGKWLGSRPIRCN 74

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|240840 cd12394, RRM1_RBM34, RNA recognition motif 1 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 40.7 bits (96), Expect = 5e-05
 Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 22/89 (24%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDV---NLVRDKGTGKPRGF--------------A 80
           V+VG +P    + DL  +F Q G I  V   ++   +     +                A
Sbjct: 3   VFVGNLPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNA 62

Query: 81  FVAYEDQRN-----NLNGAQILGRTIRVD 104
           +V ++++ +      LNG +  G  IRVD
Sbjct: 63  YVVFKEEESAEKALKLNGTEFEGHHIRVD 91

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

 Score = 40.3 bits (95), Expect = 5e-05
 Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 11/71 (15%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLN 92
           +V  I  ++ + +L A+F Q G+I  +         K RGF  V+Y D R        L 
Sbjct: 5   FVRNINSNVEDEELRALFEQFGDIRTLY-----TACKHRGFIMVSYYDIRAARRAKRALQ 59

Query: 93  GAQILGRTIRV 103
           G ++ GR + +
Sbjct: 60  GTELGGRKLDI 70

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

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 14/73 (19%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------- 90
           ++VG +P D+TE +   +F++ GE+ +V L ++K      GF F+   D R N       
Sbjct: 4   LFVGNLPNDITEEEFKELFSKYGEVSEVFLNKEK------GFGFIRL-DTRTNAEKAKAE 56

Query: 91  LNGAQILGRTIRV 103
           L+G    GR +RV
Sbjct: 57  LDGIMRKGRQLRV 69

This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. . Length = 71

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

 Score = 40.4 bits (94), Expect = 6e-05
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGG+  + T  D+   F Q G++ D  L+ DK T + RGF FV +E +
Sbjct: 2  IFVGGLSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

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|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 = 40.2 bits (95), Expect = 6e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 37  YVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDKGTGKPRGFAFVAYEDQRN-----N 90
            V + G+PF  TE D+   F+      D +++V D   G+P G A+V +    +      
Sbjct: 1   VVRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVYDDD-GRPTGEAYVEFASPEDARRALR 59

Query: 91  LNGAQILGRTIRV 103
            +  ++ GR I V
Sbjct: 60  KHNNKMGGRYIEV 72

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

 Score = 40.3 bits (95), Expect = 6e-05
 Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 9/72 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE---DQRN---NL 91
           +YV  +PF ++  +L  +F + G I  + +   K T   RG AFV YE   D +N   +L
Sbjct: 5   LYVRNLPFKISSEELYDLFGKYGAIRQIRIGNTKET---RGTAFVVYEDIYDAKNACDHL 61

Query: 92  NGAQILGRTIRV 103
           +G  +  R + V
Sbjct: 62  SGFNVANRYLVV 73

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|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 8/73 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YVG +  D+TE  +L +F+Q G      ++ D     P  + FV + + R+       +
Sbjct: 2   LYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDP--YCFVEFFEHRHAAASLAAM 59

Query: 92  NGAQILGRTIRVD 104
           NG +I+G+ ++V+
Sbjct: 60  NGRKIMGKEVKVN 72

This subgroup corresponds to the RRM1 of 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 functions 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|240761 cd12315, RRM1_RBM19_MRD1, RNA recognition motif 1 in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 8/72 (11%)

Query: 40  VGGIPFDLTEGDLLAVFAQC-GEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLN 92
           V  +P  LTE +L   F++  GEI DV L+R +  GK R  AF+ Y+ +      ++  N
Sbjct: 5   VKNLPASLTEAELKEHFSKHGGEITDVKLLRTED-GKSRRIAFIGYKTEEEAQKAKDYFN 63

Query: 93  GAQILGRTIRVD 104
              I    I V+
Sbjct: 64  NTYINTSKISVE 75

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

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

 Score = 39.9 bits (93), Expect = 8e-05
 Identities = 16/47 (34%), Positives = 31/47 (65%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          ++VG +P  +TE ++  +F + G +++V +++DK TG  +G  FV Y
Sbjct: 2  LFVGSVPRTITEQEVRPMFEEHGNVLEVAIIKDKRTGHQQGCCFVKY 48

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

 Score = 40.0 bits (93), Expect = 8e-05
 Identities = 21/50 (42%), Positives = 28/50 (56%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          V+VGG+  D TE  +   F   GEI ++ L  D  T + RGF FV Y D+
Sbjct: 2  VFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDE 51

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

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGGI  D  E  L   F + G+I  + ++ D+ +GK RGF FV ++D 
Sbjct: 3  LFVGGIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDH 52

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

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 20/50 (40%), Positives = 31/50 (62%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGGI  D  E  L   F + G+I  + ++ D+ +GK RGFAFV ++D 
Sbjct: 3  IFVGGIKEDTEEYHLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDH 52

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|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 = 39.6 bits (93), Expect = 1e-04
 Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 12/76 (15%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           S  +++G +   +TE DL  +F + GEI  ++++       PRG A+V  E ++      
Sbjct: 2   STTLWIGHLSKKVTEEDLKNLFEEYGEIQSIDMI------PPRGCAYVCMETRQDAHRAL 55

Query: 89  NNLNGAQILGRTIRVD 104
             L   ++ G+ I+V 
Sbjct: 56  QKLRNVKLAGKKIKVA 71

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

 Score = 39.7 bits (93), Expect = 1e-04
 Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 9/76 (11%)

Query: 38  VYVGGIPFDLTEGD----LLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           ++V G    L E D    L   F+ CGEI  V++  D+ TG  +GFA++ ++        
Sbjct: 2   IFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEKA 61

Query: 90  -NLNGAQILGRTIRVD 104
             L+G+ + G  + VD
Sbjct: 62  LELDGSDLGGGNLVVD 77

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|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 32/138 (23%), Positives = 43/138 (31%), Gaps = 11/138 (7%)

Query: 113 EEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKF 172
             E  E  +R    R   R  ++ E  RG+        +      G  +DR  R   E+ 
Sbjct: 160 AAERTEEEERDERRRRGDREDRQAEAERGER-----GRREERGRDGDDRDRRDR--REQG 212

Query: 173 EGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRR 232
           +              G  R     +    D RE++     D  E      GRR   R RR
Sbjct: 213 DRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRR 272

Query: 233 HSDN----NEFEARSRED 246
                   NE E   RED
Sbjct: 273 GRRGGDGGNEREPELRED 290

Length = 672

>gnl|CDD|240929 cd12485, RRM1_RBM47, RNA recognition motif 1 found in vertebrate RNA-binding protein 47 (RBM47)

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 22/47 (46%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          V+VG IP D+ E +L+ VF   G I ++ L+ D   GK RG+AFV Y
Sbjct: 4  VFVGKIPRDVYEDELVPVFESVGRIYEMRLMMDF-DGKNRGYAFVMY 49

This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

>gnl|CDD|240977 cd12533, RRM_EWS, RNA recognition motif in vertebrate Ewing Sarcoma Protein (EWS)

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 8/57 (14%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIV--------DVNLVRDKGTGKPRGFAFVAYED 86
          +YV G+  ++T  +L   F  CG +          VN+  DK TGKP+G A V+YED
Sbjct: 3  IYVQGLNDNVTLEELADFFKHCGVVKINKRTGQPMVNIYTDKETGKPKGDATVSYED 59

This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. . Length = 84

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

 Score = 39.0 bits (92), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 11/59 (18%)

Query: 52  LLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED-------QRNNLNGAQILGRTIRV 103
           L A+F+Q G ++D+   +   T K RG AFV ++D        R  L G     + +R+
Sbjct: 20  LYALFSQFGPVLDIVASK---TLKMRGQAFVVFKDVESATNALR-ALQGFPFYDKPMRI 74

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

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

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 15/80 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVD--------VNLVRDKGTGKPRGFAFVAYEDQR- 88
           +Y+ G+P D+TE  L  +F   G I          + +  DK T +P+G A V Y+D   
Sbjct: 1   IYISGLPDDVTEDSLAELFGGIGIIKRDKRTWPPMIKIYTDKET-EPKGEATVTYDDPSA 59

Query: 89  -----NNLNGAQILGRTIRV 103
                   NG +  G  I+V
Sbjct: 60  AQAAIEWFNGYEFRGNKIKV 79

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|240696 cd12250, RRM2_hnRNPR_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 39 YVGGIPFDLTEGDLLAVFAQCGE-IVDVNLVRD-KGTGKPRGFAFVAYEDQRN 89
          +VGGIP   T+ ++L  F++  E +VDV + R      K RGFAFV YE  R 
Sbjct: 5  FVGGIPKTKTKEEILEEFSKVTEGVVDVIVYRSPDDKNKNRGFAFVEYESHRA 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|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q family

 Score = 42.3 bits (99), Expect = 2e-04
 Identities = 36/99 (36%), Positives = 53/99 (53%), Gaps = 19/99 (19%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY----EDQR--NNL 91
           V+VG IP DL E +L+ +F + G I ++ L+ D  +G+ RG+AFV +    E +     L
Sbjct: 61  VFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDF-SGQNRGYAFVTFCGKEEAKEAVKLL 119

Query: 92  NGAQI-----LGRTIRVDH-------VAKYKKKEEEDEE 118
           N  +I     LG  I VD+       + K KK+EE  EE
Sbjct: 120 NNYEIRPGRLLGVCISVDNCRLFVGGIPKNKKREEILEE 158

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|214632 smart00356, ZnF_C3H1, zinc finger

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 12/22 (54%), Positives = 16/22 (72%)

Query: 129 VCRAFQRGECTRGDGCKFSHNE 150
           +C+ F+RG C RGD CKF+H  
Sbjct: 6   LCKFFKRGYCPRGDRCKFAHPL 27

Length = 27

>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 = 39.0 bits (91), Expect = 2e-04
 Identities = 18/56 (32%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP--RGFAFVAYEDQRNNL 91
          ++VG IP   +E DL  +F Q G +  +N++RD+    P  +G  FV +  ++  L
Sbjct: 4  MFVGQIPRSWSEKDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKAAL 59

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

 Score = 38.8 bits (90), Expect = 2e-04
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 7/72 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN------L 91
           ++VG +   + E  L  +F Q G +  V + +DK  GKP+ F FV ++   +       L
Sbjct: 4   LFVGNLECRVREEILYELFLQAGPLTKVTICKDK-EGKPKSFGFVCFKHSESVPYAIALL 62

Query: 92  NGAQILGRTIRV 103
           NG ++ GR I+V
Sbjct: 63  NGIRLYGRPIKV 74

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

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

 Score = 38.9 bits (90), Expect = 2e-04
 Identities = 18/47 (38%), Positives = 29/47 (61%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          +++GG+ F+ T+  L + F Q G + D  ++RD  T + RGF FV Y
Sbjct: 5  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY 51

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|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 22/77 (28%), Positives = 34/77 (44%), Gaps = 7/77 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIV-DVNLVRDKGTGKPRGFAFV--AYEDQR----NN 90
           ++VG +  D+T+  L   F      V    +V D  TG+ +G+ FV    ED+R      
Sbjct: 4   IFVGDLAPDVTDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTE 63

Query: 91  LNGAQILGRTIRVDHVA 107
           +NG     R +RV    
Sbjct: 64  MNGVYCSSRPMRVSPAT 80

This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. . Length = 80

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

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           ++V  + F +T+ DL   F+    I    +V D  TG+ RG+ FV +            L
Sbjct: 2   LFVRNLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKL 61

Query: 92  NGAQILGRTIRVD 104
              ++ GR +R+D
Sbjct: 62  KNKKLHGRILRLD 74

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|240905 cd12459, RRM1_CID8_like, RNA recognition motif 1 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 7/71 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ---RNNLN-G 93
           VYV  I   +TE  L A+F+ CG++VD  +  D        FAF+ + D+   R  L+  
Sbjct: 5   VYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGD--PNSVLRFAFIEFTDEEGARAALSLS 62

Query: 94  AQILGR-TIRV 103
             +LG   +RV
Sbjct: 63  GTMLGFYPVRV 73

This subgroup corresponds to the RRM1 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 = 80

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

 Score = 38.5 bits (90), Expect = 3e-04
 Identities = 17/40 (42%), Positives = 25/40 (62%)

Query: 46 DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
           +TE DL   FA  GEI D+ +V+DK T + +G A+V + 
Sbjct: 13 SVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFA 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|241043 cd12599, RRM1_SF2_plant_like, RNA recognition motif 1 in plant pre-mRNA-splicing factor SF2 and similar proteins

 Score = 38.2 bits (89), Expect = 3e-04
 Identities = 21/52 (40%), Positives = 34/52 (65%), Gaps = 3/52 (5%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
          VYVG +P D+ E ++  +F + G IVD++L   K   +P G+AF+ +ED R+
Sbjct: 2  VYVGNLPGDIREREVEDLFYKYGPIVDIDL---KLPPRPPGYAFIEFEDARD 50

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 24/59 (40%), Positives = 33/59 (55%), Gaps = 6/59 (10%)

Query: 51  DLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV 103
           DL   F + G IVDV +  D  T +PRGFA++ +ED R+      NLN   + GR I +
Sbjct: 16  DLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEI 74

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

 Score = 38.5 bits (89), Expect = 3e-04
 Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 6/64 (9%)

Query: 36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
          A +Y+ G+P  +T+ D+  +F++ G I++  ++ D+ TG  RG AF+ +      E+   
Sbjct: 1  ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQATGLSRGVAFIRFDKRSEAEEAIT 60

Query: 90 NLNG 93
          + NG
Sbjct: 61 SFNG 64

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|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 38.6 bits (89), Expect = 3e-04
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 8/73 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YVG +  D+TE  +L +F+Q G      ++ +  +  P  + FV + + R+       +
Sbjct: 2   LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP--YCFVEFYEHRDAAAALAAM 59

Query: 92  NGAQILGRTIRVD 104
           NG +ILG+ ++V+
Sbjct: 60  NGRKILGKEVKVN 72

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and 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 = 81

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 9/75 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLV---RDKGTGKPRGFAFVAY------EDQR 88
           +YVG +   +TE  L   F + G +  V ++    ++   + R   FVA+      E   
Sbjct: 4   LYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAERAL 63

Query: 89  NNLNGAQILGRTIRV 103
           + L+G  ++G  +++
Sbjct: 64  DELDGKDVMGYELKL 78

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

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

 Score = 38.4 bits (90), Expect = 4e-04
 Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 11/75 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPR-----GFAFVAYEDQRN--- 89
           ++V  + F  TE  L   F +CG +  V + + K    P      G+ FV ++ +     
Sbjct: 3   LFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQK 62

Query: 90  ---NLNGAQILGRTI 101
               L G  + G  +
Sbjct: 63  ALKRLQGTVLDGHAL 77

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

 Score = 38.2 bits (88), Expect = 4e-04
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 6/71 (8%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
           A +YV G+P  +T+ +L  +F+Q G I+   ++ D+ TG  RG  F+ +      E+   
Sbjct: 3   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 62

Query: 90  NLNGAQILGRT 100
            LNG +  G  
Sbjct: 63  GLNGQKPSGAA 73

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

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

 Score = 38.4 bits (89), Expect = 4e-04
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +Y DS  ++VG +P D+ E +L   F   G +V++ +      GK   F FV ++D
Sbjct: 1  RYPDSHQLFVGNLPHDIDESELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDD 56

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

 Score = 38.1 bits (88), Expect = 4e-04
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 8/72 (11%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN----- 90
           A +YV G+P  +++ ++  +F+Q G I+   ++ D+ TG  RG  F+ + D+R       
Sbjct: 2   ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILVDQVTGISRGVGFIRF-DKRIEAEEAI 60

Query: 91  --LNGAQILGRT 100
             LNG + LG  
Sbjct: 61  KGLNGQKPLGAA 72

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

 Score = 37.8 bits (88), Expect = 4e-04
 Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
          +YVG +P D+ E D+  +F + G I  ++L   K   +   FAFV +ED R+
Sbjct: 2  IYVGNLPGDIRERDIEDLFYKYGPIKAIDL---KNRRRGPPFAFVEFEDPRD 50

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

 Score = 38.2 bits (88), Expect = 5e-04
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 6/71 (8%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRN 89
           A +YV G+P  +T+ +L  +F+Q G I+   ++ D+ TG  RG  F+ +      E+   
Sbjct: 6   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 65

Query: 90  NLNGAQILGRT 100
            LNG +  G T
Sbjct: 66  GLNGQKPPGAT 76

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|240804 cd12358, RRM1_VICKZ, RNA recognition motif 1 in the VICKZ family proteins

 Score = 37.4 bits (87), Expect = 5e-04
 Identities = 24/73 (32%), Positives = 33/73 (45%), Gaps = 12/73 (16%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN 92
           Y+G +  D+ E DL  +F +    V   LV      K  G+AFV   DQ         LN
Sbjct: 2   YIGNLSSDVNESDLRQLFEEHKIPVSSVLV------KKGGYAFVDCPDQSWADKAIEKLN 55

Query: 93  GAQILGRTIRVDH 105
           G  + G+ I V+H
Sbjct: 56  GKILQGKVIEVEH 68

Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. Length = 73

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 40.7 bits (96), Expect = 6e-04
 Identities = 36/182 (19%), Positives = 57/182 (31%), Gaps = 13/182 (7%)

Query: 112 KEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEK 171
                E  + R R ERG   A +      G+G +    E RA       ++         
Sbjct: 118 AASAPEAAQARERRERGE-AARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRG 176

Query: 172 FEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSR 231
                  + +   R     R     + ++ DRRE+        R    +  GRR  +  R
Sbjct: 177 DREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRR 236

Query: 232 RHSDNNEFEARSREDHYRRDEK---RPKRHESESYLREDQDRRGGDKSSTGRGDSSSHRH 288
               ++  E R   D    + +   R +R         D+DRRG        G+      
Sbjct: 237 DARGDDNREDRGDRDGDDGEGRGGRRGRR-------FRDRDRRGRR--GGDGGNEREPEL 287

Query: 289 RE 290
           RE
Sbjct: 288 RE 289

Length = 672

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

 Score = 37.3 bits (87), Expect = 6e-04
 Identities = 15/50 (30%), Positives = 30/50 (60%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VG +P+ +   +L   F+Q G++   N+  DK TG  +G+ FV++  +
Sbjct: 2  LFVGNLPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSR 51

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

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

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          + V  +P  +TE  L   F   GE+ DV ++R +  GK R F FV ++ +
Sbjct: 3  IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTR-DGKSRRFGFVGFKSE 51

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

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

 Score = 40.6 bits (95), Expect = 6e-04
 Identities = 21/91 (23%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 201 SDRREEKRSIRHDHREKPRE--DHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRH 258
           S+R   +   R   R++ R   +   RED R R     +    RS      R  +   R 
Sbjct: 21  SERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDSRSPRSLRYSSVRRSRDRPRR 80

Query: 259 ESESYLREDQDRRGGDKSSTGRGDSSSHRHR 289
            S S    +Q RR     S         + R
Sbjct: 81  RSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111

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

 Score = 40.3 bits (94), Expect = 8e-04
 Identities = 30/96 (31%), Positives = 36/96 (37%), Gaps = 7/96 (7%)

Query: 203 RREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDE----KRPKRH 258
           R EE    R   R + R+    R  +RSR  S   +   RSRE  YR D     +R    
Sbjct: 1   RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60

Query: 259 ESESYLREDQDRRGGD---KSSTGRGDSSSHRHRER 291
            S   LR    RR  D   + S        HR R R
Sbjct: 61  RSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLR 96

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

 Score = 37.4 bits (86), Expect = 8e-04
 Identities = 16/47 (34%), Positives = 29/47 (61%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          +++GG+ F+ TE  L   + Q G++ D  ++RD  + + RGF FV +
Sbjct: 5  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 51

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

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 28/72 (38%), Positives = 38/72 (52%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           ++V  I  D    DL   F + G IVDV +  D  T +PRGFA+V +ED R+      NL
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYVQFEDVRDAEDALHNL 62

Query: 92  NGAQILGRTIRV 103
           +   I GR I +
Sbjct: 63  DRKWICGRQIEI 74

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|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 = 36.8 bits (86), Expect = 9e-04
 Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 43  IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQILGRT 100
           +PF+ T+ +L  +F+  G++  V L + K  G  RGFAFV +  ++   N  + L  T
Sbjct: 8   VPFEATKKELRELFSPFGQVKSVRLPK-KFDGSHRGFAFVEFVTKQEAQNAMEALKST 64

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

 Score = 36.9 bits (85), Expect = 9e-04
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          +++GG+ +  T+  L   F Q GE+ +  ++RD  T + RGF FV + DQ
Sbjct: 3  MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52

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

 Score = 39.5 bits (92), Expect = 0.001
 Identities = 19/72 (26%), Positives = 37/72 (51%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVA---YEDQRN---NL 91
           ++V  +  D  E  L  +F   G + +V ++RD  T + +G+ FV+   Y++      +L
Sbjct: 272 IFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSL 331

Query: 92  NGAQILGRTIRV 103
           NG  +  R ++V
Sbjct: 332 NGYTLGNRVLQV 343

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

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 32/189 (16%), Positives = 66/189 (34%), Gaps = 18/189 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV  +   +T+  L  +F++CGEI    ++ D+  G  RGF FV + +          +
Sbjct: 288 LYVKNLDDTVTDEKLRELFSECGEITSAKVMLDE-KGVSRGFGFVCFSNPEEANRAVTEM 346

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQ 151
           +G  + G+ +   +VA  ++KE+     + +  + +   R    G    G     +  + 
Sbjct: 347 HGRMLGGKPL---YVALAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGG-----AMGQP 398

Query: 152 RAANTGGGPQDRSS--RWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRS 209
                G   Q       W                 R  G   +     P+++ +   ++ 
Sbjct: 399 PYYGQGPQQQFNGQPLGWPRMSMMPTP-MGPGGPLRPNGLAPMNAVRAPSRNAQNAAQKP 457

Query: 210 IRHDHREKP 218
                   P
Sbjct: 458 PMQPVMYPP 466

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

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 18/48 (37%), Positives = 28/48 (58%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
          ++VGG+  +    D+   F Q G++ D  L+ DK T + RGF FV +E
Sbjct: 6  IFVGGLSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFE 53

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +  D ++ +L A+F   G ++   ++R         FAFV    +         L
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQ--------FAFVHLRGEAAADRAIEEL 54

Query: 92  NGAQILGRTIRVDH 105
           NG ++ GR + V+H
Sbjct: 55  NGRELHGRKLVVEH 68

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

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 7/68 (10%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGE-IVDVNLVRDKGTGKPRGFAFVAYEDQRN------N 90
          +++G +   + E  +   FA  GE ++ V ++R+K TG P G+ FV + D+         
Sbjct: 2  LWMGDLEPYMDENFIKRAFASMGETVLSVKIIRNKLTGGPAGYCFVEFADEATAERCLHK 61

Query: 91 LNGAQILG 98
          LNG  I G
Sbjct: 62 LNGKPIPG 69

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 17/50 (34%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          V+VGGI   + E ++ + FA+ G + +V ++ D+ TG  +G+ FV++ D 
Sbjct: 8  VFVGGIDIRMDETEIRSFFAKYGSVKEVKIITDR-TGVSKGYGFVSFYDD 56

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 17/47 (36%), Positives = 28/47 (59%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          +++GG+ F+ T+  L   F + G + D  ++RD  T + RGF FV Y
Sbjct: 5  LFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTY 51

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

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 8/75 (10%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN----- 90
           A +YVG +  D+TE  L  +F   G ++ V + RD  T +  G+ +V +     +     
Sbjct: 1   ASLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNF-QNPADAERAL 59

Query: 91  --LNGAQILGRTIRV 103
             +N  ++ G+ IR+
Sbjct: 60  ETMNFKRLGGKPIRI 74

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

>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional

 Score = 38.7 bits (91), Expect = 0.002
 Identities = 22/143 (15%), Positives = 42/143 (29%), Gaps = 6/143 (4%)

Query: 149 NEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKR 208
               AA     P+   +R   E+ E    G    +             +  +    EE+ 
Sbjct: 111 AAAAAAEAASAPEAAQARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERD 170

Query: 209 SIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQ 268
             R     + R+    R ++  R     +  +   R+   + D +  +        R+  
Sbjct: 171 ERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGR------RDGG 224

Query: 269 DRRGGDKSSTGRGDSSSHRHRER 291
           DRRG  +    R         +R
Sbjct: 225 DRRGRRRRRDRRDARGDDNREDR 247

Length = 672

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 7/59 (11%)

Query: 52  LLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD 104
           L  +F + G++ +  + R +G GK  GFAFV  + ++N      N NG +I GR + VD
Sbjct: 18  LKKIFGRYGKVREATIPRKRG-GKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAVD 75

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

>gnl|CDD|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 36.3 bits (84), Expect = 0.002
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR 88
          V++G IP D+ E  L+ +F   G + +  L+    +G  RGFA+  Y D+R
Sbjct: 4  VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTF-SGLNRGFAYAKYSDRR 53

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that 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. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 21/52 (40%), Positives = 30/52 (57%), Gaps = 3/52 (5%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
          +YVG +P D+ E DL  +F + G I D+ L   +G      FAFV +ED R+
Sbjct: 2  IYVGNLPSDVREKDLEDLFYKYGRIRDIELKNRRGLVP---FAFVRFEDPRD 50

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 24/71 (33%), Positives = 32/71 (45%), Gaps = 12/71 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VYVG IP   T+ DL+ +F   G I++     D      RGFAFV  +           L
Sbjct: 3   VYVGNIPPYTTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQL 56

Query: 92  NGAQILGRTIR 102
            G  + GR +R
Sbjct: 57  QGFPVHGRPLR 67

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 16/49 (32%), Positives = 29/49 (59%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          +++GG+ +  +   L   F++ GEI +  ++RD  T + RGF FV + D
Sbjct: 2  MFIGGLSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFAD 50

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|236766 PRK10811, rne, ribonuclease E; Reviewed

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 9/83 (10%)

Query: 192 VALEGNPNQSDRREEKRSIRHDHREKPREDHGRREDKRSRRHSDNNEFEARSREDHYRRD 251
              E    +++ + E++  R   R+  R D   R D R  R           RE    R+
Sbjct: 587 KPQEQPAPKAEAKPERQQDRRKPRQNNRRDRNERRDTRDNRT---------RREGRENRE 637

Query: 252 EKRPKRHESESYLREDQDRRGGD 274
           E R  R +++    E ++ +  +
Sbjct: 638 ENRRNRRQAQQQTAETRESQQAE 660

Length = 1068

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

 Score = 38.7 bits (90), Expect = 0.003
 Identities = 16/49 (32%), Positives = 28/49 (57%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           +Y+G +P  L E  +  +    G++   NL++D  TG  +G+AF  Y+D
Sbjct: 298 IYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKD 346

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|240693 cd12247, RRM2_U1A_like, RNA recognition motif 2 in the U1A/U2B"/SNF protein family

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 12/63 (19%)

Query: 42 GIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLNGAQ 95
           +P + T+  L  +F Q     +V LV        RG AFV +E +         L G +
Sbjct: 9  NLPEETTKEMLEMLFNQFPGFKEVRLV------PRRGIAFVEFETEEQATVALQALQGFK 62

Query: 96 ILG 98
          I  
Sbjct: 63 ITP 65

This subfamily corresponds to the RRM2 of U1A/U2B"/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. . Length = 72

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VY+G +P+   E D+   F   G I ++NL          GF FV +ED R+       L
Sbjct: 2   VYIGRLPYRARERDVERFFKGYGRIREINL--------KNGFGFVEFEDPRDADDAVYEL 53

Query: 92  NGAQILGRTIRVDH 105
           NG ++ G  + V+H
Sbjct: 54  NGKELCGERVIVEH 67

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 6/46 (13%)

Query: 39 YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          YVGG+   +TE DL   F Q GEI  + +V  +        AFV +
Sbjct: 5  YVGGLGERVTEKDLRDHFYQFGEIRSITVVPRQQC------AFVTF 44

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|241005 cd12561, RRM1_RBM5_like, RNA recognition motif 1 in RNA-binding protein 5 (RBM5) and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFV 82
          + + G+P  +TE D+       G E  DV L+R K TG  RGFAFV
Sbjct: 5  IMLRGLPLSVTEEDIRNALVSHGVEPKDVRLMRRKTTGASRGFAFV 50

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

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YVG +   +TE  L  +F   G + +V ++ DK   K   + FV Y    +       L
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNN-KGVNYGFVEYHQSHDAEIALQTL 59

Query: 92  NGAQILGRTIRVD 104
           NG QI    IRV+
Sbjct: 60  NGRQIENNEIRVN 72

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 35.6 bits (83), Expect = 0.004
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 8/56 (14%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNG 93
          VYV G+P D+T  + + VF++CG I       D  TGKP+      Y D+  NL G
Sbjct: 4  VYVSGLPLDITVEEFVEVFSKCGII-----KEDPETGKPK---IKLYRDENGNLKG 51

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	291
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.92
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.91
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.81
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.75
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.74
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.73
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.7
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.69
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.64
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.62
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.61
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.61
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.59
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.59
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.58
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.56
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.56
PLN03120	260	nucleic acid binding protein; Provisional	99.54
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.52
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.51
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.5
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.49
PLN03121	243	nucleic acid binding protein; Provisional	99.48
KOG0122	270	consensus Translation initiation factor 3, subunit	99.48
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.47
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.46
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.46
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.45
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.45
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.43
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.42
PLN03213	759	repressor of silencing 3; Provisional	99.42
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.42
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.39
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.37
smart00362	72	RRM_2 RNA recognition motif.	99.37
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.34
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.34
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.33
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.32
smart00360	71	RRM RNA recognition motif.	99.31
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.31
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.3
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.28
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.27
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.27
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.26
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.26
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.25
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.23
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.22
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.21
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.21
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.21
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.16
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.15
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.14
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.14
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.13
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.13
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.06
smart00361	70	RRM_1 RNA recognition motif.	99.04
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.97
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	98.96
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.95
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.94
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.92
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.87
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.84
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.81
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.81
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.8
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.74
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.7
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.69
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.67
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.62
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.6
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.51
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.44
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.41
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.41
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.4
KOG0226	290	consensus RNA-binding proteins [General function p	98.38
KOG0151	877	consensus Predicted splicing regulator, contains R	98.16
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.13
KOG4210	285	consensus Nuclear localization sequence binding pr	98.05
KOG4660	549	consensus Protein Mei2, essential for commitment t	97.95
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.93
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.93
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.88
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.77
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.53
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.49
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.45
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.4
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.38
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.35
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.35
KOG2314	698	consensus Translation initiation factor 3, subunit	97.18
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.03
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	97.03
KOG3152	278	consensus TBP-binding protein, activator of basal	97.02
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.0
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.96
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.9
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	96.48
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	96.4
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.29
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.26
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.19
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	96.11
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.06
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.99
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	95.96
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	95.95
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	95.76
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	95.67
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	95.66
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	95.58
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.48
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	95.3
KOG4210	285	consensus Nuclear localization sequence binding pr	95.08
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	94.97
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	94.95
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	94.92
KOG1548	382	consensus Transcription elongation factor TAT-SF1	94.58
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	93.97
KOG2135	526	consensus Proteins containing the RNA recognition	93.81
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	93.66
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	93.51
KOG1996	378	consensus mRNA splicing factor [RNA processing and	92.58
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	92.53
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.32
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	91.72
KOG4660	549	consensus Protein Mei2, essential for commitment t	91.59
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	91.32
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	88.65
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	85.82
KOG0226	290	consensus RNA-binding proteins [General function p	81.32
smart00596	69	PRE_C2HC PRE_C2HC domain.	80.6

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.92  E-value=5.5e-25  Score=195.29  Aligned_cols=109  Identities=23%  Similarity=0.356  Sum_probs=103.6

Q ss_pred             cHHHHHHHhhhchhhhccCCCCCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEE
Q 022814            3 PLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV   82 (291)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV   82 (291)
                      .++.+.+..++.+++..|+|+++++.+...||.++||||.|+|+||+++|+-||+.||+|.+|.||+|..||.+..||||
T Consensus       207 el~e~~~e~ea~~~A~iLEmvGDlpdAd~~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFi  286 (479)
T KOG0415|consen  207 ELEEVLAEKEAKAQAVILEMVGDLPDADVKPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFI  286 (479)
T ss_pred             HHHHHHHHHHHHhhHhHHHHhcCCcccccCCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeee
Confidence            46778888899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEcChhh------hcCCceeCCeEEEEeccCCccc
Q 022814           83 AYEDQRN------NLNGAQILGRTIRVDHVAKYKK  111 (291)
Q Consensus        83 ~F~~~~~------~lng~~i~gr~i~V~~a~~~~~  111 (291)
                      +|++.++      +|++++|+++.|+|+|+++..+
T Consensus       287 EFen~escE~AyFKMdNvLIDDrRIHVDFSQSVsk  321 (479)
T KOG0415|consen  287 EFENKESCEQAYFKMDNVLIDDRRIHVDFSQSVSK  321 (479)
T ss_pred             eecchhhHHHHHhhhcceeeccceEEeehhhhhhh
Confidence            9999988      9999999999999999987654

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.91  E-value=1.3e-24  Score=177.10  Aligned_cols=113  Identities=68%  Similarity=1.197  Sum_probs=109.0

Q ss_pred             CCcHHHHHHHhhhchhhhccCCCCCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEE
Q 022814            1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA   80 (291)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~a   80 (291)
                      ||+++.|+.+++++++++.++.....+|++.+.++.-|||||||+.+||.+|..+|++||+|+.|.|++|+.||+|+|||
T Consensus         1 mnplt~vk~i~~lne~Elq~g~~~~~SWH~~YkdsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFa   80 (219)
T KOG0126|consen    1 MNPLTNVKNIQKLNERELQLGIADKKSWHQEYKDSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFA   80 (219)
T ss_pred             CchhHHHHHHHHhhHHhhccccccccchhhhcccceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcChhh------hcCCceeCCeEEEEeccCCccccc
Q 022814           81 FVAYEDQRN------NLNGAQILGRTIRVDHVAKYKKKE  113 (291)
Q Consensus        81 FV~F~~~~~------~lng~~i~gr~i~V~~a~~~~~~~  113 (291)
                      |+.|+++-+      .|||+.|.|+.|+|++.....+..
T Consensus        81 FLcYEDQRSTILAVDN~NGiki~gRtirVDHv~~Yk~pk  119 (219)
T KOG0126|consen   81 FLCYEDQRSTILAVDNLNGIKILGRTIRVDHVSNYKKPK  119 (219)
T ss_pred             EEEecCccceEEEEeccCCceecceeEEeeecccccCCc
Confidence            999999988      899999999999999988776654

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=99.81  E-value=8.4e-19  Score=153.07  Aligned_cols=79  Identities=35%  Similarity=0.571  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...|.+||||+.||+.|+|..|+..|+.||+|+.|.||.|+.||+++|||||+|++..+      ..+|++|+|+.|.|+
T Consensus        97 ~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   97 IGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             cCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            45788999999999999999999999999999999999999999999999999999877      789999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      +....
T Consensus       177 vERgR  181 (335)
T KOG0113|consen  177 VERGR  181 (335)
T ss_pred             ecccc
Confidence            87543

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.75  E-value=1.3e-17  Score=135.85  Aligned_cols=81  Identities=30%  Similarity=0.640  Sum_probs=74.5

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ......++|||+|||+.+|+++|+++|++||.|..|.|+.++.|++++|||||+|.+.++      .||+..|+|+.|+|
T Consensus        29 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V  108 (144)
T PLN03134         29 SLRLMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRV  108 (144)
T ss_pred             cccCCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            335668899999999999999999999999999999999999999999999999999887      68999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus       109 ~~a~~~~  115 (144)
T PLN03134        109 NPANDRP  115 (144)
T ss_pred             EeCCcCC
Confidence            9986543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.74  E-value=3.3e-18  Score=158.11  Aligned_cols=134  Identities=19%  Similarity=0.291  Sum_probs=100.3

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ......++|||+|||+.+|+++|+++|+.||+|+.|.|+.|..|++++|||||+|.+.++      .||++.|.+++|+|
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            345678999999999999999999999999999999999999999999999999999887      79999999999999


Q ss_pred             eccCCccccchhHHH---HHHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccC
Q 022814          104 DHVAKYKKKEEEDEE---TRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEG  174 (291)
Q Consensus       104 ~~a~~~~~~~~~~~~---~~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~  174 (291)
                      .++.+.........-   .......+..|...|.  .+|.+..|.+..+..++.         .++|+||.|..
T Consensus       182 ~~a~p~~~~~~~~~lfV~nLp~~vtee~L~~~F~--~fG~V~~v~i~~d~~tg~---------~kG~aFV~F~~  244 (346)
T TIGR01659       182 SYARPGGESIKDTNLYVTNLPRTITDDQLDTIFG--KYGQIVQKNILRDKLTGT---------PRGVAFVRFNK  244 (346)
T ss_pred             ecccccccccccceeEEeCCCCcccHHHHHHHHH--hcCCEEEEEEeecCCCCc---------cceEEEEEECC
Confidence            998654321110000   0000012233444443  466788888888877776         44667777754

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

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.73  E-value=8.1e-18  Score=163.91  Aligned_cols=134  Identities=25%  Similarity=0.428  Sum_probs=101.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ....++|||+|||+.+++++|+.+|++||.|..|.|+.|+.||+++|||||+|.+.++      .|||..|+|+.|.|..
T Consensus       104 ~~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~r  183 (612)
T TIGR01645       104 LAIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  183 (612)
T ss_pred             hcCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecc
Confidence            4567899999999999999999999999999999999999999999999999999987      6999999999999987


Q ss_pred             cCCccccchhHHHH----HHhh----------hhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCC
Q 022814          106 VAKYKKKEEEDEET----RQRM----------REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEK  171 (291)
Q Consensus       106 a~~~~~~~~~~~~~----~~~~----------~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~  171 (291)
                      ..............    ....          -....+...|.  .||.+..|.+..+..++.         .+||||+.
T Consensus       184 p~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs--~FG~I~svrl~~D~~tgk---------sKGfGFVe  252 (612)
T TIGR01645       184 PSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFE--AFGEIVKCQLARAPTGRG---------HKGYGFIE  252 (612)
T ss_pred             cccccccccccccccccccccceEEeecCCCCCCHHHHHHHHh--hcCCeeEEEEEecCCCCC---------cCCeEEEE
Confidence            65432211100000    0000          01223333443  478899999999888766         56788888


Q ss_pred             ccCCC
Q 022814          172 FEGFS  176 (291)
Q Consensus       172 ~~~~~  176 (291)
                      |....
T Consensus       253 Fe~~e  257 (612)
T TIGR01645       253 YNNLQ  257 (612)
T ss_pred             ECCHH
Confidence            87644

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=99.70  E-value=3.3e-17  Score=152.09  Aligned_cols=132  Identities=21%  Similarity=0.323  Sum_probs=94.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +.++|||+|||+.+|+++|+++|++||+|..|.|+.++.+|+++|||||+|.+.++      .|||..|.|+.|.|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            46899999999999999999999999999999999999999999999999999887      799999999999999986


Q ss_pred             CccccchhHHH---HHHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          108 KYKKKEEEDEE---TRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       108 ~~~~~~~~~~~---~~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      +.........-   .....-....+...|.  .+|.+..+.+..+..++.         .+||||+.|....
T Consensus        82 ~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~--~~G~i~~~~~~~~~~~~~---------~~g~~fv~f~~~~  142 (352)
T TIGR01661        82 PSSDSIKGANLYVSGLPKTMTQHELESIFS--PFGQIITSRILSDNVTGL---------SKGVGFIRFDKRD  142 (352)
T ss_pred             ccccccccceEEECCccccCCHHHHHHHHh--ccCCEEEEEEEecCCCCC---------cCcEEEEEECCHH
Confidence            54321100000   0000001111222222  345566677776665554         4567777765433

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.69  E-value=2.9e-17  Score=146.92  Aligned_cols=131  Identities=28%  Similarity=0.474  Sum_probs=106.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .-.|.||||.|.+.+.|+.|+..|.+||+|++|.|..|+.|++.+|||||+|+-++.      .|||.+++|+.|+|...
T Consensus       111 aiMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrP  190 (544)
T KOG0124|consen  111 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRP  190 (544)
T ss_pred             HHhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCC
Confidence            457899999999999999999999999999999999999999999999999999987      89999999999999977


Q ss_pred             CCccccchhH----HHHHHhhh-------------hhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCC
Q 022814          107 AKYKKKEEED----EETRQRMR-------------EERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGH  169 (291)
Q Consensus       107 ~~~~~~~~~~----~~~~~~~~-------------~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~  169 (291)
                      ....+.....    ++.+....             +.++++++|+.     +..|.++++++.+.         ++||||
T Consensus       191 sNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~-----I~~C~LAr~pt~~~---------HkGyGf  256 (544)
T KOG0124|consen  191 SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGE-----IVKCQLARAPTGRG---------HKGYGF  256 (544)
T ss_pred             CCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcc-----eeeEEeeccCCCCC---------ccceee
Confidence            6655443322    22222222             46777777654     99999999999888         455667


Q ss_pred             CCccCCCC
Q 022814          170 EKFEGFSW  177 (291)
Q Consensus       170 ~~~~~~~~  177 (291)
                      .+|.+...
T Consensus       257 iEy~n~qs  264 (544)
T KOG0124|consen  257 IEYNNLQS  264 (544)
T ss_pred             EEeccccc
Confidence            77766543

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.64  E-value=1.1e-15  Score=141.97  Aligned_cols=76  Identities=24%  Similarity=0.425  Sum_probs=71.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      +.+|||+|||+.|++++|.++|++||.|..|.|+.|..||.++|||||+|.+.++      +|||..|+|+.|.|.|+.+
T Consensus       269 ~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~  348 (352)
T TIGR01661       269 GYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTN  348 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccC
Confidence            4479999999999999999999999999999999999999999999999999886      8999999999999999876


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus       349 ~~  350 (352)
T TIGR01661       349 KA  350 (352)
T ss_pred             CC
Confidence            54

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.62  E-value=9.2e-16  Score=147.43  Aligned_cols=134  Identities=21%  Similarity=0.382  Sum_probs=98.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|+++|||||+|.+.++     .|+|..|.|++|.|.+
T Consensus        85 ~~~~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~  164 (457)
T TIGR01622        85 AERDDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQS  164 (457)
T ss_pred             cccCCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEee
Confidence            34567899999999999999999999999999999999999999999999999999887     8999999999999988


Q ss_pred             cCCccccchhHHHHHH---------------hhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCC
Q 022814          106 VAKYKKKEEEDEETRQ---------------RMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHE  170 (291)
Q Consensus       106 a~~~~~~~~~~~~~~~---------------~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~  170 (291)
                      +...............               ..-.+..+...|  ..+|.+..|.+..+..++.         ..||+||
T Consensus       165 ~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f--~~~G~i~~v~~~~d~~~g~---------~~g~afV  233 (457)
T TIGR01622       165 SQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIF--EPFGDIEDVQLHRDPETGR---------SKGFGFI  233 (457)
T ss_pred             cchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHH--HhcCCeEEEEEEEcCCCCc---------cceEEEE
Confidence            6543222111000000               000122233333  2466788888888877665         4566677


Q ss_pred             CccCC
Q 022814          171 KFEGF  175 (291)
Q Consensus       171 ~~~~~  175 (291)
                      .|...
T Consensus       234 ~f~~~  238 (457)
T TIGR01622       234 QFHDA  238 (457)
T ss_pred             EECCH
Confidence            76553

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.

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.61  E-value=1e-15  Score=130.07  Aligned_cols=75  Identities=28%  Similarity=0.543  Sum_probs=68.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      -.++||||+|+|.|+.+.|..+|++||+|++..||.|+.||+|+|||||+|.+.++     +-..-.|+|+...|++|.-
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            35789999999999999999999999999999999999999999999999999998     3344679999999988754

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.61  E-value=6.8e-16  Score=119.47  Aligned_cols=77  Identities=32%  Similarity=0.615  Sum_probs=71.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ....++|||||||++.|+|++|.++|++||+|..|.|-.|+.+..+.|||||+|...++      -++|..|+.++|.|+
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            45678999999999999999999999999999999999999999999999999998776      789999999999999


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      |..
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            875

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.59  E-value=1.7e-14  Score=117.55  Aligned_cols=72  Identities=35%  Similarity=0.580  Sum_probs=66.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      +-.++||||||+..+++.+|+.+|..||+|..|+|...+     .|||||||+++-+      .|+|..|+|..|.|+++
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            457899999999999999999999999999999999876     8999999998765      99999999999999988


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus        83 ~G~   85 (195)
T KOG0107|consen   83 TGR   85 (195)
T ss_pred             cCC
Confidence            643

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

Probab=99.59  E-value=2.4e-15  Score=148.32  Aligned_cols=128  Identities=21%  Similarity=0.400  Sum_probs=94.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCcc
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKYK  110 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~~  110 (291)
                      +|||||||+.+||++|.++|++||+|.+|.|++|..|++++|||||+|.+.++      .||+..|.|++|.|.|+....
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            79999999999999999999999999999999999999999999999999887      789999999999999875432


Q ss_pred             ccchhHH-HHH----HhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          111 KKEEEDE-ETR----QRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       111 ~~~~~~~-~~~----~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      ....... ...    ...-.+..+...|.  .+|.+..|.+..+. .+.         .+|||||.|....
T Consensus        82 ~~~~~~~~~vfV~nLp~~~~~~~L~~~F~--~~G~i~~~~i~~~~-~g~---------skg~afV~F~~~e  140 (562)
T TIGR01628        82 SLRRSGVGNIFVKNLDKSVDNKALFDTFS--KFGNILSCKVATDE-NGK---------SRGYGFVHFEKEE  140 (562)
T ss_pred             cccccCCCceEEcCCCccCCHHHHHHHHH--hcCCcceeEeeecC-CCC---------cccEEEEEECCHH
Confidence            1110000 000    00012233444443  36778888888764 233         4577888886543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PF00076 RRM_1: RNA recognition motif

Probab=99.58  E-value=8.7e-15  Score=103.52  Aligned_cols=64  Identities=44%  Similarity=0.872  Sum_probs=60.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      |||+|||+.+|+++|..+|++||.|..|.|+.+ .++.+.|||||+|.+.++      .|+|..|+|+.|+
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            899999999999999999999999999999998 589999999999999887      6999999999885

(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 ....

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.56  E-value=2.2e-14  Score=139.61  Aligned_cols=76  Identities=26%  Similarity=0.560  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...++|||+|||+.+|+++|.++|+.||.|..|.|+.+..||.++|||||+|.+.++      .|||+.|+|+.|.|.++
T Consensus       293 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a  372 (509)
T TIGR01642       293 DSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRA  372 (509)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            446899999999999999999999999999999999999999999999999999876      79999999999999998


Q ss_pred             CC
Q 022814          107 AK  108 (291)
Q Consensus       107 ~~  108 (291)
                      ..
T Consensus       373 ~~  374 (509)
T TIGR01642       373 CV  374 (509)
T ss_pred             cc
Confidence            54

Members of this subfamily are found in plants, metazoa and fungi.

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.56  E-value=2.1e-14  Score=119.75  Aligned_cols=77  Identities=32%  Similarity=0.579  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ......+|-|.||.+-|+.++|..+|++||.|.+|.|+.|..|++++|||||-|....+      +|+|.+|+|+.|.|+
T Consensus         9 dv~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq   88 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQ   88 (256)
T ss_pred             CcccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeeh
Confidence            34557899999999999999999999999999999999999999999999999987554      999999999999998


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      +|.
T Consensus        89 ~ar   91 (256)
T KOG4207|consen   89 MAR   91 (256)
T ss_pred             hhh
Confidence            875

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.54  E-value=3.3e-14  Score=124.49  Aligned_cols=72  Identities=24%  Similarity=0.445  Sum_probs=66.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCCc
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~~  109 (291)
                      .++|||+|||+.+|+++|+++|+.||+|..|.|+.+..   ++|||||+|.++++     .|||..|+|+.|.|..+...
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            57999999999999999999999999999999998853   57999999999887     89999999999999998644

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.52  E-value=6.2e-14  Score=129.73  Aligned_cols=78  Identities=32%  Similarity=0.559  Sum_probs=70.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEEEe
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIRVD  104 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~V~  104 (291)
                      ...++|||+|||+.||+++|+++|++||+|+.|.|+.++.||+++|||||+|.+.++      +||++.|.+  ++|.|.
T Consensus       191 ~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~  270 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVR  270 (346)
T ss_pred             cccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEE
Confidence            346789999999999999999999999999999999999999999999999999887      799999876  789999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++....
T Consensus       271 ~a~~~~  276 (346)
T TIGR01659       271 LAEEHG  276 (346)
T ss_pred             ECCccc
Confidence            886543

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

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.51  E-value=3.9e-14  Score=138.31  Aligned_cols=76  Identities=28%  Similarity=0.486  Sum_probs=71.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ..++|||+|||+.+++++|+.+|+.||.|..|.|+.++.+|.++|||||+|.+.++      .||++.|+|+.|.|.++.
T Consensus       203 ~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       203 KFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             ccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            45799999999999999999999999999999999999899999999999999887      899999999999999887


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      ..
T Consensus       283 ~p  284 (612)
T TIGR01645       283 TP  284 (612)
T ss_pred             CC
Confidence            53

In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.50  E-value=6.8e-14  Score=136.33  Aligned_cols=73  Identities=36%  Similarity=0.594  Sum_probs=66.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEEEecc
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIRVDHV  106 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~V~~a  106 (291)
                      ..++|||+|||++++|++|.++|++||.|..|.|++| .+|+++|||||+|.+.++      .||+..|. ++.|.|..+
T Consensus        57 ~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S  135 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCIS  135 (578)
T ss_pred             CCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCcccccccc
Confidence            3589999999999999999999999999999999999 699999999999999887      78998885 788777765


Q ss_pred             C
Q 022814          107 A  107 (291)
Q Consensus       107 ~  107 (291)
                      .
T Consensus       136 ~  136 (578)
T TIGR01648       136 V  136 (578)
T ss_pred             c
Confidence            4

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.

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.49  E-value=5.6e-14  Score=135.09  Aligned_cols=77  Identities=35%  Similarity=0.684  Sum_probs=72.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      +...+|||+|||+.+|+++|.++|++||.|..|.|+.+..+|+++|||||+|.+.++      .|||..|.|++|.|.++
T Consensus       184 p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a  263 (457)
T TIGR01622       184 PNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYA  263 (457)
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEc
Confidence            447899999999999999999999999999999999999899999999999999887      79999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus       264 ~~~  266 (457)
T TIGR01622       264 QDS  266 (457)
T ss_pred             cCC
Confidence            743

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.

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.48  E-value=1.8e-13  Score=118.16  Aligned_cols=73  Identities=23%  Similarity=0.393  Sum_probs=66.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      +...||||+||++.+|+++|+++|+.||+|.+|.|+.+.   ...|||||+|.++++     .|+|..|.+++|.|....
T Consensus         3 ~~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~---et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          3 PGGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSG---EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CCceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCC---CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            346799999999999999999999999999999999984   556899999999887     999999999999998765


Q ss_pred             C
Q 022814          108 K  108 (291)
Q Consensus       108 ~  108 (291)
                      .
T Consensus        80 ~   80 (243)
T PLN03121         80 Q   80 (243)
T ss_pred             c
Confidence            3

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.48  E-value=1.3e-13  Score=117.89  Aligned_cols=80  Identities=36%  Similarity=0.522  Sum_probs=74.6

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ..-.++++|=|.||+.+++|++|+++|.+||.|..|.|++|+.||.++|||||+|.+.++      .|||+-++.-.|.|
T Consensus       184 R~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrv  263 (270)
T KOG0122|consen  184 RERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRV  263 (270)
T ss_pred             ccCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEE
Confidence            344678999999999999999999999999999999999999999999999999999887      89999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .|+.|.
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            999764

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.47  E-value=6.5e-14  Score=127.95  Aligned_cols=131  Identities=24%  Similarity=0.426  Sum_probs=93.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCC-ceeCC--eEEEE
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNG-AQILG--RTIRV  103 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng-~~i~g--r~i~V  103 (291)
                      .+.-+||||.||..|+|.+|+.+|++||.|.+|.|++|+.|+.++|||||.|.+.++      +|++ +.|-|  .+|.|
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            445689999999999999999999999999999999999999999999999999877      5555 44544  78899


Q ss_pred             eccCCccccchhHHHH----HHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          104 DHVAKYKKKEEEDEET----RQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       104 ~~a~~~~~~~~~~~~~----~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      .+|.............    ...+-.+..+.+.|..  +|.+..|.+.+|... .         .+|++||.|..+
T Consensus       112 k~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~--fG~Ied~~ilrd~~~-~---------sRGcaFV~fstk  175 (510)
T KOG0144|consen  112 KYADGERERIVEERKLFVGMLSKQCTENEVREIFSR--FGHIEDCYILRDPDG-L---------SRGCAFVKFSTK  175 (510)
T ss_pred             cccchhhhccccchhhhhhhccccccHHHHHHHHHh--hCccchhhheecccc-c---------ccceeEEEEehH
Confidence            8887654432111111    1111123344444443  556777777776542 2         567778877654

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=2.3e-13  Score=124.90  Aligned_cols=76  Identities=32%  Similarity=0.545  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEEEe
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIRVD  104 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~V~  104 (291)
                      .+-.+-||||.||.++.|++|..+|++.|+|-.+.|++|+.+|.++|||||+|.+.+.      .||+++|- |+.|.|.
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc  159 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVC  159 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEE
Confidence            3557999999999999999999999999999999999999999999999999999887      89999885 7888887


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      .+.
T Consensus       160 ~Sv  162 (506)
T KOG0117|consen  160 VSV  162 (506)
T ss_pred             Eee
Confidence            664

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=1.2e-13  Score=119.02  Aligned_cols=77  Identities=32%  Similarity=0.563  Sum_probs=72.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ..+.|.|..||..+|+++|+.+|+..|+|++|+|++|+.||++.||+||.|.++++      .|||..|..+.|+|.+|.
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            34689999999999999999999999999999999999999999999999999887      899999999999999997


Q ss_pred             Ccc
Q 022814          108 KYK  110 (291)
Q Consensus       108 ~~~  110 (291)
                      |..
T Consensus       120 PSs  122 (360)
T KOG0145|consen  120 PSS  122 (360)
T ss_pred             CCh
Confidence            754

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.45  E-value=3.7e-13  Score=95.70  Aligned_cols=64  Identities=41%  Similarity=0.778  Sum_probs=57.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      |||+|||+.+++++|.++|+.||.|..|.++.++. +.++|+|||+|.++++      .+++..|+|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999986 9999999999999987      6677999999874

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 ....

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.45  E-value=5.7e-14  Score=115.12  Aligned_cols=75  Identities=29%  Similarity=0.587  Sum_probs=71.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ....|||||||+..++++.|.++|-++|+|+.|+|+.|..|....|||||+|.++++      -||.+.|.|++|+|..+
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            446899999999999999999999999999999999999999999999999999887      78999999999999988


Q ss_pred             C
Q 022814          107 A  107 (291)
Q Consensus       107 ~  107 (291)
                      .
T Consensus        87 s   87 (203)
T KOG0131|consen   87 S   87 (203)
T ss_pred             c
Confidence            7

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.43  E-value=8.6e-14  Score=120.44  Aligned_cols=76  Identities=30%  Similarity=0.603  Sum_probs=71.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      ..-||||-|.+.++-++|++.|.+||+|.+++||+|..|++++|||||.|...++      .|||+-|+++.|.-+||..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            3469999999999999999999999999999999999999999999999998776      9999999999999999976


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      +.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            55

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

Probab=99.42  E-value=7.5e-13  Score=130.58  Aligned_cols=132  Identities=26%  Similarity=0.476  Sum_probs=97.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC----CeEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL----GRTI  101 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~----gr~i  101 (291)
                      ....++|||+|||+.+|+++|+++|+.||.|..|.|+.+. +|.++|||||+|.+.++      .|+|..|.    |..|
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 LKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDG-SGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKL  253 (562)
T ss_pred             ccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCcEecccccceee
Confidence            3456789999999999999999999999999999999986 79999999999999887      79999999    9999


Q ss_pred             EEeccCCccccchhHHHHHHhhh---------------------hhhccccccccCCCCCCCceeEeecCCCCCCCCCCC
Q 022814          102 RVDHVAKYKKKEEEDEETRQRMR---------------------EERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGP  160 (291)
Q Consensus       102 ~V~~a~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~  160 (291)
                      .|..+..................                     ....+...|.  .+|.+..|.+..+ .++.      
T Consensus       254 ~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~--~~G~i~~~~i~~d-~~g~------  324 (562)
T TIGR01628       254 YVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFS--ECGEITSAKVMLD-EKGV------  324 (562)
T ss_pred             EeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHH--hcCCeEEEEEEEC-CCCC------
Confidence            99888665443221111111000                     1222333333  4778888988887 3444      


Q ss_pred             CCCCCCCCCCCccCCC
Q 022814          161 QDRSSRWGHEKFEGFS  176 (291)
Q Consensus       161 ~~~~~g~g~~~~~~~~  176 (291)
                         .+|||||.|....
T Consensus       325 ---~~g~gfV~f~~~~  337 (562)
T TIGR01628       325 ---SRGFGFVCFSNPE  337 (562)
T ss_pred             ---cCCeEEEEeCCHH
Confidence               5678888887643

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>PLN03213 repressor of silencing 3; Provisional

Probab=99.42  E-value=3.8e-13  Score=124.79  Aligned_cols=72  Identities=26%  Similarity=0.533  Sum_probs=64.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcCh--hh------hcCCceeCCeEEEEec
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ--RN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~--~~------~lng~~i~gr~i~V~~  105 (291)
                      ...+||||||++.+|+++|..+|+.||.|..|.||+.  ||  +|||||+|...  .+      .|||..+.|+.|+|..
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRE--TG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNK   84 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRT--KG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEK   84 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecc--cC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEee
Confidence            4578999999999999999999999999999999944  67  99999999986  22      8999999999999999


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      |.+.
T Consensus        85 AKP~   88 (759)
T PLN03213         85 AKEH   88 (759)
T ss_pred             ccHH
Confidence            8653

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=99.42  E-value=1.2e-13  Score=116.31  Aligned_cols=82  Identities=37%  Similarity=0.599  Sum_probs=76.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      .....+|||||+|...++|.-|...|-+||.|+.|.|+.|..+++.+|||||+|...++      .||+.+|.|+.|.|+
T Consensus         6 ~a~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN   85 (298)
T KOG0111|consen    6 MANQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVN   85 (298)
T ss_pred             ccccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEe
Confidence            34567899999999999999999999999999999999999999999999999998887      899999999999999


Q ss_pred             ccCCcccc
Q 022814          105 HVAKYKKK  112 (291)
Q Consensus       105 ~a~~~~~~  112 (291)
                      +|.|...+
T Consensus        86 ~AkP~kik   93 (298)
T KOG0111|consen   86 LAKPEKIK   93 (298)
T ss_pred             ecCCcccc
Confidence            99887654

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=99.39  E-value=1.1e-12  Score=115.12  Aligned_cols=74  Identities=43%  Similarity=0.829  Sum_probs=70.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      ..+|||+|||+.+|+++|.++|.+||.|..|.|+.+..+|.++|||||+|.+.++      .|++..|.|++|.|..+..
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            6999999999999999999999999999999999998899999999999999987      8999999999999999753

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.37  E-value=1.3e-12  Score=115.82  Aligned_cols=73  Identities=30%  Similarity=0.627  Sum_probs=67.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      -.+.|+|.|||+...+-||..+|++||.|.+|.||.+.  --|||||||+|++.++      +|+|..|.|++|.|+.+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNE--RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNE--RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEecc--CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            35799999999999999999999999999999999874  5689999999999987      999999999999999886


Q ss_pred             C
Q 022814          108 K  108 (291)
Q Consensus       108 ~  108 (291)
                      .
T Consensus       173 a  173 (376)
T KOG0125|consen  173 A  173 (376)
T ss_pred             h
Confidence            5

>smart00362 RRM_2 RNA recognition motif

Probab=99.37  E-value=3.5e-12  Score=89.33  Aligned_cols=66  Identities=42%  Similarity=0.832  Sum_probs=60.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      +|||+|||+.+++++|..+|.+||.|..|.++.+.  +.+.|+|||+|.+.++      .|++..|.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            59999999999999999999999999999999876  7889999999999877      789999999998873

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.34  E-value=2.8e-12  Score=111.13  Aligned_cols=75  Identities=31%  Similarity=0.558  Sum_probs=68.8

Q ss_pred             cccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           28 WHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        28 ~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      .++..+++++||||||+..+||+.|+..|++||.|.+|+|..+      +|||||-|++.|+      .||+.+|.|..+
T Consensus       157 ~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~V  230 (321)
T KOG0148|consen  157 YNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLV  230 (321)
T ss_pred             hccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEE
Confidence            3456789999999999999999999999999999999999988      6899999999998      899999999999


Q ss_pred             EEeccCC
Q 022814          102 RVDHVAK  108 (291)
Q Consensus       102 ~V~~a~~  108 (291)
                      ++-|-..
T Consensus       231 kCsWGKe  237 (321)
T KOG0148|consen  231 RCSWGKE  237 (321)
T ss_pred             EEecccc
Confidence            9988653

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.34  E-value=2e-12  Score=125.87  Aligned_cols=70  Identities=21%  Similarity=0.458  Sum_probs=57.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcC------------CCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQC------------GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGA   94 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~------------G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~   94 (291)
                      .....+|||||||+.||+++|.++|.+|            +.|..|.+      +..+|||||+|.+.++     +|||+
T Consensus       172 ~~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~------~~~kg~afVeF~~~e~A~~Al~l~g~  245 (509)
T TIGR01642       172 TRQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNI------NKEKNFAFLEFRTVEEATFAMALDSI  245 (509)
T ss_pred             CccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEE------CCCCCEEEEEeCCHHHHhhhhcCCCe
Confidence            3456899999999999999999999975            23333333      4558999999999887     89999


Q ss_pred             eeCCeEEEEeccC
Q 022814           95 QILGRTIRVDHVA  107 (291)
Q Consensus        95 ~i~gr~i~V~~a~  107 (291)
                      .|.|.+|.|....
T Consensus       246 ~~~g~~l~v~r~~  258 (509)
T TIGR01642       246 IYSNVFLKIRRPH  258 (509)
T ss_pred             EeeCceeEecCcc
Confidence            9999999997543

Members of this subfamily are found in plants, metazoa and fungi.

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=99.33  E-value=2.5e-12  Score=121.16  Aligned_cols=76  Identities=41%  Similarity=0.809  Sum_probs=72.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ++|||||||+.+++++|..+|+..|.|.+++++.|+.||+++||||++|.+.+.      .|||.++.|++|+|.++...
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            899999999999999999999999999999999999999999999999999776      89999999999999998765


Q ss_pred             cc
Q 022814          110 KK  111 (291)
Q Consensus       110 ~~  111 (291)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            54

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=99.32  E-value=1.9e-12  Score=101.36  Aligned_cols=79  Identities=34%  Similarity=0.588  Sum_probs=72.4

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      ++.....=.|||.++...+||++|.+.|..||+|+.|.|..|.-||..+|||+|+|++.+.      +|||..|.|..|.
T Consensus        66 PqrSVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   66 PQRSVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             CccceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            3445556689999999999999999999999999999999999999999999999999876      8999999999999


Q ss_pred             EeccC
Q 022814          103 VDHVA  107 (291)
Q Consensus       103 V~~a~  107 (291)
                      |+|+.
T Consensus       146 VDw~F  150 (170)
T KOG0130|consen  146 VDWCF  150 (170)
T ss_pred             EEEEE
Confidence            99874

>smart00360 RRM RNA recognition motif

Probab=99.31  E-value=8.6e-12  Score=86.94  Aligned_cols=65  Identities=48%  Similarity=0.863  Sum_probs=60.2

Q ss_pred             EcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           40 VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        40 VgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      |+|||+.+++++|..+|.+||.|..|.|+.++.++.++|||||+|.+.++      .|++..|.++.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            68999999999999999999999999999988789999999999999887      788899999998873

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.31  E-value=1.2e-11  Score=101.72  Aligned_cols=72  Identities=32%  Similarity=0.596  Sum_probs=63.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...++|||||||..+.+.+|+++|.+||.|..|.|..-+   -+.+||||+|+++-+      .-+|..++|+.|.|.|+
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~---g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP---GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC---CCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            357899999999999999999999999999999886432   356799999998766      67889999999999988


Q ss_pred             C
Q 022814          107 A  107 (291)
Q Consensus       107 ~  107 (291)
                      .
T Consensus        81 r   81 (241)
T KOG0105|consen   81 R   81 (241)
T ss_pred             c
Confidence            5

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.30  E-value=1.2e-12  Score=107.32  Aligned_cols=103  Identities=25%  Similarity=0.447  Sum_probs=84.0

Q ss_pred             CCcHHHHHHHhhhchhhhccCCCCCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceE
Q 022814            1 MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDKGTGKPRGF   79 (291)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~-i~i~~d~~tg~s~G~   79 (291)
                      ||++.++++++..+... +.        +........|||+||.+.+.|..|.++|+.||.|.. ..|+++..||.++||
T Consensus        71 ln~VkLYgrpIrv~kas-~~--------~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~  141 (203)
T KOG0131|consen   71 LNMVKLYGRPIRVNKAS-AH--------QKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGF  141 (203)
T ss_pred             HHHHHhcCceeEEEecc-cc--------cccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCC
Confidence            46666777666665443 11        223455689999999999999999999999999865 488999999999999


Q ss_pred             EEEEEcChhh------hcCCceeCCeEEEEeccCCcccc
Q 022814           80 AFVAYEDQRN------NLNGAQILGRTIRVDHVAKYKKK  112 (291)
Q Consensus        80 aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~~~~  112 (291)
                      |||.|.+.++      +|||+.++.++|.|.++.....+
T Consensus       142 g~i~~~sfeasd~ai~s~ngq~l~nr~itv~ya~k~~~k  180 (203)
T KOG0131|consen  142 GFINYASFEASDAAIGSMNGQYLCNRPITVSYAFKKDTK  180 (203)
T ss_pred             eEEechhHHHHHHHHHHhccchhcCCceEEEEEEecCCC
Confidence            9999999887      99999999999999998655444

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.28  E-value=1.2e-11  Score=119.88  Aligned_cols=70  Identities=23%  Similarity=0.305  Sum_probs=63.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--------hcCCceeCCeEEEEec
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--------~lng~~i~gr~i~V~~  105 (291)
                      |+.+|||+|||+.+++++|.++|++||.|..|.|+.+      +|||||+|.+.++        .+++..|.|++|.|.+
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            5789999999999999999999999999999999854      5899999999887        2578999999999999


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      +...
T Consensus        75 s~~~   78 (481)
T TIGR01649        75 STSQ   78 (481)
T ss_pred             cCCc
Confidence            8643

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).

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.27  E-value=1.5e-11  Score=115.56  Aligned_cols=78  Identities=33%  Similarity=0.567  Sum_probs=69.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----------hcCC-ceeCCeEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----------NLNG-AQILGRTI  101 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----------~lng-~~i~gr~i  101 (291)
                      ...||||.|||+.+|++.|.+.|++||+|.++.|+.++.||.++|.|||.|.++.+           +-.| ++|+|+.|
T Consensus       291 ~~~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~L  370 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLL  370 (678)
T ss_pred             ccceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEE
Confidence            34899999999999999999999999999999999999999999999999999887           1334 88999999


Q ss_pred             EEeccCCccc
Q 022814          102 RVDHVAKYKK  111 (291)
Q Consensus       102 ~V~~a~~~~~  111 (291)
                      .|..+.....
T Consensus       371 kv~~Av~Rke  380 (678)
T KOG0127|consen  371 KVTLAVTRKE  380 (678)
T ss_pred             eeeeccchHH
Confidence            9998865543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.27  E-value=4.9e-12  Score=114.48  Aligned_cols=77  Identities=30%  Similarity=0.623  Sum_probs=69.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      ..++||||+|+|.|+++.|.++|++||+|..|.|++|+.|+.++||+||+|++.+.     ...-+.|+++.|.+..+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            67899999999999999999999999999999999999999999999999998776     3345778999999888766


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        85 r~   86 (311)
T KOG4205|consen   85 RE   86 (311)
T ss_pred             cc
Confidence            54

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.26  E-value=3.6e-11  Score=112.12  Aligned_cols=135  Identities=19%  Similarity=0.399  Sum_probs=95.7

Q ss_pred             CCCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee
Q 022814           23 SDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI   96 (291)
Q Consensus        23 ~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i   96 (291)
                      +--.+|.+..+..  |||.||+++++...|.++|+.||+|++|+|+.+. .| ++|| ||+|++.++      .|||.++
T Consensus        66 ~~rim~s~rd~~~--~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll  140 (369)
T KOG0123|consen   66 PIRIMWSQRDPSL--VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLL  140 (369)
T ss_pred             EEEeehhccCCce--eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCccc
Confidence            3334555544333  9999999999999999999999999999999997 45 9999 999999887      8999999


Q ss_pred             CCeEEEEeccCCccccchhHHHHHHhhhh-----------hhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCC
Q 022814           97 LGRTIRVDHVAKYKKKEEEDEETRQRMRE-----------ERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSS  165 (291)
Q Consensus        97 ~gr~i~V~~a~~~~~~~~~~~~~~~~~~~-----------~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~  165 (291)
                      .++.|.|..........+...+.......           ...+...|  ...|.+.++.+..+....          ..
T Consensus       141 ~~kki~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f--~~~g~i~s~~v~~~~~g~----------~~  208 (369)
T KOG0123|consen  141 NGKKIYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLF--SAYGSITSVAVMRDSIGK----------SK  208 (369)
T ss_pred             CCCeeEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhh--cccCcceEEEEeecCCCC----------CC
Confidence            99999999887665544333321111110           11222222  335567777766655432          45


Q ss_pred             CCCCCCccC
Q 022814          166 RWGHEKFEG  174 (291)
Q Consensus       166 g~g~~~~~~  174 (291)
                      +||++.|..
T Consensus       209 ~~gfv~f~~  217 (369)
T KOG0123|consen  209 GFGFVNFEN  217 (369)
T ss_pred             CccceeecC
Confidence            788888876

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.26  E-value=2e-11  Score=118.33  Aligned_cols=73  Identities=21%  Similarity=0.409  Sum_probs=65.9

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           32 YKDSAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        32 ~~~~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      .+++++|||+|||+ .+|+++|.++|+.||.|..|.|+.++     +|||||+|.+.++      .|||..|.|++|.|.
T Consensus       272 ~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~  346 (481)
T TIGR01649       272 GGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVC  346 (481)
T ss_pred             CCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEE
Confidence            35778999999998 69999999999999999999999874     6999999999887      799999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++...
T Consensus       347 ~s~~~  351 (481)
T TIGR01649       347 PSKQQ  351 (481)
T ss_pred             Ecccc
Confidence            87543

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).

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.25  E-value=4.8e-12  Score=119.06  Aligned_cols=78  Identities=33%  Similarity=0.664  Sum_probs=71.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .|...||||||.+++++++|..+|++||.|..|.++.|..||.++|||||+|.+.+.      .|||.+|.|+.|+|...
T Consensus       276 ~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v  355 (549)
T KOG0147|consen  276 GPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVV  355 (549)
T ss_pred             cchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEe
Confidence            455559999999999999999999999999999999999999999999999999887      89999999999999877


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      ....
T Consensus       356 ~~r~  359 (549)
T KOG0147|consen  356 TERV  359 (549)
T ss_pred             eeec
Confidence            5543

>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=99.23  E-value=6.6e-11  Score=83.20  Aligned_cols=68  Identities=46%  Similarity=0.855  Sum_probs=61.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      +|||+|||+.+++++|..+|..||.|..+.++.++.+ .+.|+|||+|.+.++      .+++..+.++.|.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999988744 789999999999887      7889999999998863

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).

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.22  E-value=7.6e-12  Score=114.60  Aligned_cols=82  Identities=27%  Similarity=0.487  Sum_probs=71.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCc-eeC--CeEEEE
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGA-QIL--GRTIRV  103 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~-~i~--gr~i~V  103 (291)
                      +...+||||-|+..+||.+|+++|++||.|++|.|++|. .+.++|||||.|.+.+.      +|||. .+.  ..+|.|
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            457899999999999999999999999999999999998 79999999999999876      88884 444  479999


Q ss_pred             eccCCccccchh
Q 022814          104 DHVAKYKKKEEE  115 (291)
Q Consensus       104 ~~a~~~~~~~~~  115 (291)
                      .||...+.+..+
T Consensus       201 kFADtqkdk~~~  212 (510)
T KOG0144|consen  201 KFADTQKDKDGK  212 (510)
T ss_pred             EecccCCCchHH
Confidence            999887666543

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.21  E-value=6.9e-11  Score=88.56  Aligned_cols=75  Identities=27%  Similarity=0.473  Sum_probs=66.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .+..|||+|||+.+|.+++.++|.+||.|..|.|-..+   ..+|-|||.|++..+      .|+|..++++.+.|-+-+
T Consensus        17 vnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k---~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq   93 (124)
T KOG0114|consen   17 VNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTK---ETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQ   93 (124)
T ss_pred             hheeEEEecCCccccHHHHHHHhhcccceEEEEecCcc---CcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecC
Confidence            35789999999999999999999999999999997654   458999999999876      899999999999999887


Q ss_pred             Cccc
Q 022814          108 KYKK  111 (291)
Q Consensus       108 ~~~~  111 (291)
                      +...
T Consensus        94 ~~~~   97 (124)
T KOG0114|consen   94 PEDA   97 (124)
T ss_pred             HHHH
Confidence            6543

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.21  E-value=5.4e-11  Score=116.19  Aligned_cols=70  Identities=29%  Similarity=0.480  Sum_probs=63.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcC--CCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQC--GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~--G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ...+|||+||++.+++++|+++|++|  |+|+.|.++        ++||||+|.+.++      +||+.+|+|+.|.|.+
T Consensus       232 ~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~--------rgfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~  303 (578)
T TIGR01648       232 KVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKI--------RDYAFVHFEDREDAVKAMDELNGKELEGSEIEVTL  303 (578)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEee--------cCeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45789999999999999999999999  999999876        3599999999887      7999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus       304 Akp~~~  309 (578)
T TIGR01648       304 AKPVDK  309 (578)
T ss_pred             ccCCCc
Confidence            977543

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.

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.21  E-value=3e-11  Score=113.57  Aligned_cols=77  Identities=31%  Similarity=0.592  Sum_probs=68.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +.-.|+|.||||.+.+.+|+.+|+.||.|..|.|++.+. |+-+|||||.|....+      .||+.+|+|++|-|+||.
T Consensus       116 ~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~d-gklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV  194 (678)
T KOG0127|consen  116 PKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKD-GKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAV  194 (678)
T ss_pred             ccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCC-CCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeec
Confidence            356899999999999999999999999999999998774 5555999999998776      899999999999999997


Q ss_pred             Cccc
Q 022814          108 KYKK  111 (291)
Q Consensus       108 ~~~~  111 (291)
                      +...
T Consensus       195 ~Kd~  198 (678)
T KOG0127|consen  195 DKDT  198 (678)
T ss_pred             cccc
Confidence            6543

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.16  E-value=9.8e-11  Score=101.15  Aligned_cols=73  Identities=27%  Similarity=0.463  Sum_probs=68.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .=.|||-||.+++.|.-|-.+|++||.|..|+|++|..|.+++|||||++.+-++      .|||..++++.|.|.|-.
T Consensus       278 g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFKt  356 (360)
T KOG0145|consen  278 GWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFKT  356 (360)
T ss_pred             eeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEec
Confidence            3489999999999999999999999999999999999999999999999998765      899999999999998754

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=99.15  E-value=8.2e-11  Score=98.58  Aligned_cols=81  Identities=26%  Similarity=0.484  Sum_probs=73.4

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQC-GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~-G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      .+.......+||..||..+-+.+|..+|.+| |.|..+.+.+++.||.++|||||+|++.+.      +||+++|.++.|
T Consensus        43 ~p~~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL  122 (214)
T KOG4208|consen   43 KPEQEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLL  122 (214)
T ss_pred             CCccCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhhee
Confidence            3445667889999999999999999999998 788888888999999999999999999886      999999999999


Q ss_pred             EEeccCCc
Q 022814          102 RVDHVAKY  109 (291)
Q Consensus       102 ~V~~a~~~  109 (291)
                      .|.+..+.
T Consensus       123 ~c~vmppe  130 (214)
T KOG4208|consen  123 ECHVMPPE  130 (214)
T ss_pred             eeEEeCch
Confidence            99998766

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.14  E-value=3.1e-11  Score=104.53  Aligned_cols=79  Identities=20%  Similarity=0.451  Sum_probs=73.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..++.|.|||-.||.+.++.+|..+|-+||.|++.+|..|..|.++++|+||.|.++.+      +|||+.|+-+.|+|.
T Consensus       281 eGPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQ  360 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQ  360 (371)
T ss_pred             cCCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhh
Confidence            45789999999999999999999999999999999999999999999999999999887      999999999999998


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      +-.++
T Consensus       361 LKRPk  365 (371)
T KOG0146|consen  361 LKRPK  365 (371)
T ss_pred             hcCcc
Confidence            76544

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.14  E-value=4.7e-11  Score=111.32  Aligned_cols=119  Identities=24%  Similarity=0.397  Sum_probs=90.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ..||||   +.+|+..|.++|+++|+|++|.|++|. |  +.|||||.|.++.+      +||...|.|++|.|.|++..
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            469999   899999999999999999999999998 6  99999999999987      89999999999999999765


Q ss_pred             cccchhHHHHHHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          110 KKKEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      ....-..  .....-+...+...|.  .+|.+.+|+++.+...           .+|| ||.|....
T Consensus        76 ~~~~~i~--nl~~~~~~~~~~d~f~--~~g~ilS~kv~~~~~g-----------~kg~-FV~f~~e~  126 (369)
T KOG0123|consen   76 PSLVFIK--NLDESIDNKSLYDTFS--EFGNILSCKVATDENG-----------SKGY-FVQFESEE  126 (369)
T ss_pred             Cceeeec--CCCcccCcHHHHHHHH--hhcCeeEEEEEEcCCC-----------ceee-EEEeCCHH
Confidence            4431000  0000001223333332  4778999999998654           5678 99987644

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.13  E-value=7.1e-11  Score=108.71  Aligned_cols=70  Identities=29%  Similarity=0.471  Sum_probs=65.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ..|||.||+.+|||+.|+++|++||.|..|..++|        ||||.|.+.++      .|||++|+|..|.|.+|.+.
T Consensus       260 KvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~  331 (506)
T KOG0117|consen  260 KVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPV  331 (506)
T ss_pred             eeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEecCCh
Confidence            68999999999999999999999999999998877        99999999988      89999999999999999887


Q ss_pred             cccc
Q 022814          110 KKKE  113 (291)
Q Consensus       110 ~~~~  113 (291)
                      .++.
T Consensus       332 ~k~k  335 (506)
T KOG0117|consen  332 DKKK  335 (506)
T ss_pred             hhhc
Confidence            6544

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.13  E-value=7.3e-11  Score=103.40  Aligned_cols=68  Identities=29%  Similarity=0.622  Sum_probs=61.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      .+|||||||..+++.+|+.+|++||+|++|.||++        ||||..++...      .|+|..|+|..|.|+.+.++
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            47999999999999999999999999999999966        99999988765      79999999999999998776


Q ss_pred             cc
Q 022814          110 KK  111 (291)
Q Consensus       110 ~~  111 (291)
                      .+
T Consensus        75 sk   76 (346)
T KOG0109|consen   75 SK   76 (346)
T ss_pred             CC
Confidence            43

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.06  E-value=3.3e-10  Score=109.56  Aligned_cols=73  Identities=22%  Similarity=0.461  Sum_probs=64.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT---GKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~t---g~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++|||.||++.+|.++|..+|...|.|.+|.|...+..   -.|.|||||+|.+.++      +|+|+.|+|+.|.|.+
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            344999999999999999999999999999988765421   2467999999999997      8999999999999999


Q ss_pred             cC
Q 022814          106 VA  107 (291)
Q Consensus       106 a~  107 (291)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            97

>smart00361 RRM_1 RNA recognition motif

Probab=99.04  E-value=9.1e-10  Score=78.48  Aligned_cols=55  Identities=27%  Similarity=0.524  Sum_probs=49.2

Q ss_pred             HHHHHHHHh----cCCCeeEEE-EeecCCC--CCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           49 EGDLLAVFA----QCGEIVDVN-LVRDKGT--GKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        49 e~~L~~~F~----~~G~I~~i~-i~~d~~t--g~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      +++|.++|+    +||.|..|. |+.++.+  +.++|||||+|.+.++      .|||..|+|+.|.+
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            578999998    999999995 7777666  9999999999999987      79999999999986

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.97  E-value=1.4e-09  Score=97.44  Aligned_cols=77  Identities=22%  Similarity=0.375  Sum_probs=68.2

Q ss_pred             cccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-------hcCCceeCC
Q 022814           26 ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-------NLNGAQILG   98 (291)
Q Consensus        26 ~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-------~lng~~i~g   98 (291)
                      ..|.+......||||++|...++|.+|.+.|.+||+|.+|.|+..      +++|||+|.+..+       .+|-..|+|
T Consensus       219 ~lepPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G  292 (377)
T KOG0153|consen  219 TLEPPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVING  292 (377)
T ss_pred             ccCCCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecc
Confidence            355566667789999999999999999999999999999998765      4699999999887       778889999


Q ss_pred             eEEEEeccCC
Q 022814           99 RTIRVDHVAK  108 (291)
Q Consensus        99 r~i~V~~a~~  108 (291)
                      ..|+|.|..+
T Consensus       293 ~Rl~i~Wg~~  302 (377)
T KOG0153|consen  293 FRLKIKWGRP  302 (377)
T ss_pred             eEEEEEeCCC
Confidence            9999999987

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=98.96  E-value=6.1e-10  Score=97.69  Aligned_cols=72  Identities=26%  Similarity=0.494  Sum_probs=65.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      +....++||||||.+.++..+|+..|++||+|..|.|+.|        |+||.|.-.++      .||+.++.|++++|+
T Consensus        74 Ksk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq  145 (346)
T KOG0109|consen   74 KSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQ  145 (346)
T ss_pred             cCCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeee
Confidence            4668899999999999999999999999999999999965        99999998776      899999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus       146 ~stsrl  151 (346)
T KOG0109|consen  146 LSTSRL  151 (346)
T ss_pred             eecccc
Confidence            987654

>PF13893 RRM_5: RNA recognition motif

Probab=98.95  E-value=2.5e-09  Score=72.63  Aligned_cols=50  Identities=36%  Similarity=0.741  Sum_probs=44.3

Q ss_pred             HHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           52 LLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        52 L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      |..+|++||+|..|.+....     .++|||+|.+.++      .|||..|+|++|+|.+|
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            68899999999999997654     6899999999887      79999999999999875

(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 ....

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.94  E-value=1.9e-09  Score=97.81  Aligned_cols=79  Identities=30%  Similarity=0.558  Sum_probs=72.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      ...+||||+||+.+++++|+++|.+||.|..+.|+.|..+..++||+||+|.+.++     ....+.|+++.+.|..|.+
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            46699999999999999999999999999999999999999999999999999888     5666889999999999987


Q ss_pred             cccc
Q 022814          109 YKKK  112 (291)
Q Consensus       109 ~~~~  112 (291)
                      ....
T Consensus       176 k~~~  179 (311)
T KOG4205|consen  176 KEVM  179 (311)
T ss_pred             hhhc
Confidence            7554

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.92  E-value=7.2e-10  Score=99.87  Aligned_cols=75  Identities=29%  Similarity=0.520  Sum_probs=69.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...+.|||..+.++.+|++|+.+|+.||+|++|.|.+++.++..+||+||+|.+..+      .||-+.|+|..|.|..+
T Consensus       208 k~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~  287 (544)
T KOG0124|consen  208 KKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKC  287 (544)
T ss_pred             HhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccc
Confidence            346899999999999999999999999999999999999889999999999998765      89999999999999866


Q ss_pred             C
Q 022814          107 A  107 (291)
Q Consensus       107 ~  107 (291)
                      .
T Consensus       288 v  288 (544)
T KOG0124|consen  288 V  288 (544)
T ss_pred             c
Confidence            4

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.87  E-value=5.2e-09  Score=89.05  Aligned_cols=77  Identities=23%  Similarity=0.487  Sum_probs=67.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHH----HHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLA----VFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~----~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      ..++.||||.||+.-+..++|+.    +|++||.|..|.+..   |.+.+|-|||.|.+.++      +|+|..+.|+++
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            34566999999999999998887    999999999887654   67899999999999765      999999999999


Q ss_pred             EEeccCCccc
Q 022814          102 RVDHVAKYKK  111 (291)
Q Consensus       102 ~V~~a~~~~~  111 (291)
                      .|.+|.....
T Consensus        83 riqyA~s~sd   92 (221)
T KOG4206|consen   83 RIQYAKSDSD   92 (221)
T ss_pred             heecccCccc
Confidence            9999976543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.84  E-value=2.7e-08  Score=91.68  Aligned_cols=76  Identities=32%  Similarity=0.498  Sum_probs=68.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFA-QCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~-~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      .......+||.|||+++.+.+|+++|. +.|+|++|.|..|. +|+++|||.|+|.+++.      .||-+.+.|++|.|
T Consensus        40 ~~~r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~v  118 (608)
T KOG4212|consen   40 VAARDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVV  118 (608)
T ss_pred             cccccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEE
Confidence            344566799999999999999999996 68999999999997 89999999999999987      89999999999999


Q ss_pred             eccC
Q 022814          104 DHVA  107 (291)
Q Consensus       104 ~~a~  107 (291)
                      +-..
T Consensus       119 KEd~  122 (608)
T KOG4212|consen  119 KEDH  122 (608)
T ss_pred             eccC
Confidence            7553

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.81  E-value=3.6e-08  Score=92.73  Aligned_cols=74  Identities=28%  Similarity=0.431  Sum_probs=61.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ....+|||.|||+++++++|+++|.+||.|+...|..-...++..+||||+|.+.++     ..+-..|+++.|.|.--
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            345679999999999999999999999999988776543345555999999999887     55578899999999643

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.81  E-value=6.8e-09  Score=101.39  Aligned_cols=76  Identities=30%  Similarity=0.511  Sum_probs=67.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ...++|||||.|+..++|.+|..+|+.||+|.+|.|+-.      +|||||.+....+      +|+.+.|.++.|+|.|
T Consensus       418 sV~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~W  491 (894)
T KOG0132|consen  418 SVCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAW  491 (894)
T ss_pred             eEeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEee
Confidence            345789999999999999999999999999999998765      7899999988665      8999999999999999


Q ss_pred             cCCccccc
Q 022814          106 VAKYKKKE  113 (291)
Q Consensus       106 a~~~~~~~  113 (291)
                      +.....+.
T Consensus       492 a~g~G~ks  499 (894)
T KOG0132|consen  492 AVGKGPKS  499 (894)
T ss_pred             eccCCcch
Confidence            98776554

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.80  E-value=6.8e-09  Score=90.75  Aligned_cols=77  Identities=34%  Similarity=0.568  Sum_probs=71.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      +...+...+||+|+.+.+|.++|+..|+.||.|..|.|+.|..+|+++|||||+|.+.+.     .||+..|.+..|.|.
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            456788999999999999999999999999999999999999999999999999999887     889999999999997


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      +.
T Consensus       176 ~~  177 (231)
T KOG4209|consen  176 LK  177 (231)
T ss_pred             ee
Confidence            65

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=98.74  E-value=2.9e-09  Score=100.51  Aligned_cols=125  Identities=18%  Similarity=0.323  Sum_probs=93.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      -+-.|||+-.|+..+++-+|.++|+.+|+|..|.||.|..++.++|.|||+|.+..+     +|.|+.+.|.+|.|..++
T Consensus       177 Rd~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  177 RDQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             HhHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccH
Confidence            345799999999999999999999999999999999999999999999999999887     999999999999999876


Q ss_pred             CccccchhHHHHHHhhh-----------------hhhccccccccCCCCCCCceeEeecCCCCCCCCCC
Q 022814          108 KYKKKEEEDEETRQRMR-----------------EERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGG  159 (291)
Q Consensus       108 ~~~~~~~~~~~~~~~~~-----------------~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g  159 (291)
                      ..+...+...+....+.                 .+..+...  ...+|.+.-+.+..|..+|.++|||
T Consensus       257 aeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~i--fepfg~Ie~v~l~~d~~tG~skgfG  323 (549)
T KOG0147|consen  257 AEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGI--FEPFGKIENVQLTKDSETGRSKGFG  323 (549)
T ss_pred             HHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhh--ccCcccceeeeeccccccccccCcc
Confidence            55544222221111110                 00001111  2356667777778887788855554

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.70  E-value=3.3e-08  Score=86.46  Aligned_cols=79  Identities=25%  Similarity=0.503  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..-+.+|+|.|||+.+++++|+++|..||.+..+.|.+++ +|.+.|.|-|.|...++      .+|++.|+|++|+|..
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            3445889999999999999999999999999999998888 89999999999999855      8999999999999988


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus       159 i~~~~~  164 (243)
T KOG0533|consen  159 ISSPSQ  164 (243)
T ss_pred             ecCccc
Confidence            765543

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.69  E-value=3.3e-08  Score=93.71  Aligned_cols=77  Identities=21%  Similarity=0.406  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .....|||.+|...|...+|+.||++||.|+-..|+++.-+.-.++|+||++.+...      .|+-++|.|+.|.|..+
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEka  482 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKA  482 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeec
Confidence            446799999999999999999999999999999999998788889999999998776      78889999999999988


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus       483 KNE  485 (940)
T KOG4661|consen  483 KNE  485 (940)
T ss_pred             ccC
Confidence            654

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.67  E-value=7.5e-09  Score=87.58  Aligned_cols=76  Identities=16%  Similarity=0.213  Sum_probs=67.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .+...||||+||...++|+-|.++|-+.|+|..|.|+.++ .+..+ ||||+|.++.+      .|||..+.+.+|.|.+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~-d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~   83 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQ-DQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTL   83 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCc-cCCCc-eeeeecccccchhhhhhhcccchhccchhhccc
Confidence            4557899999999999999999999999999999998877 56677 99999999887      8899999999999987


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      -...
T Consensus        84 r~G~   87 (267)
T KOG4454|consen   84 RCGN   87 (267)
T ss_pred             ccCC
Confidence            6544

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.62  E-value=3.2e-08  Score=96.09  Aligned_cols=80  Identities=26%  Similarity=0.536  Sum_probs=71.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ..++|+|.|||+.++..+|+.+|+.||.|.+|.|+.-...+.++|||||+|-++..      +|..+.|.|+.|.+.|+.
T Consensus       612 ~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~  691 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAK  691 (725)
T ss_pred             ccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhc
Confidence            36799999999999999999999999999999999876567789999999999766      677899999999999998


Q ss_pred             Cccccc
Q 022814          108 KYKKKE  113 (291)
Q Consensus       108 ~~~~~~  113 (291)
                      ......
T Consensus       692 ~d~~~e  697 (725)
T KOG0110|consen  692 SDNTME  697 (725)
T ss_pred             cchHHH
Confidence            766543

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.60  E-value=4.4e-08  Score=85.22  Aligned_cols=77  Identities=25%  Similarity=0.478  Sum_probs=64.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCce-eC--CeEEEEe
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQ-IL--GRTIRVD  104 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~-i~--gr~i~V~  104 (291)
                      +..+||||-|+..-.|++++.+|..||.|.+|.|.+.. .|.++|||||.|.+..+      .|+|.. +-  ...|.|+
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVVK   96 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVVK   96 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEEE
Confidence            67899999999999999999999999999999999887 79999999999998766      566632 32  3678888


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++...+.
T Consensus        97 ~ADTdkE  103 (371)
T KOG0146|consen   97 FADTDKE  103 (371)
T ss_pred             eccchHH
Confidence            8865443

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.51  E-value=5.8e-07  Score=67.86  Aligned_cols=72  Identities=19%  Similarity=0.269  Sum_probs=62.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhc--CCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC----CeEEEE
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQ--CGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL----GRTIRV  103 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~--~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~----gr~i~V  103 (291)
                      +||.|.|||...|.++|.+++..  .|....+.|+.|..++-+.|||||.|.+++.      .++|..+.    .+.+.|
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            68999999999999999999865  4788999999999999999999999999987      88888775    455666


Q ss_pred             eccC
Q 022814          104 DHVA  107 (291)
Q Consensus       104 ~~a~  107 (291)
                      .+|.
T Consensus        82 ~yAr   85 (97)
T PF04059_consen   82 SYAR   85 (97)
T ss_pred             ehhH
Confidence            6653

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.44  E-value=7.5e-07  Score=80.18  Aligned_cols=80  Identities=31%  Similarity=0.635  Sum_probs=67.3

Q ss_pred             cccCCCC-CCEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEEcChhh------hcC
Q 022814           28 WHAKYKD-SAYVYVGGIPFDLTEGDLLAVFAQCGEIV--------DVNLVRDKGTGKPRGFAFVAYEDQRN------NLN   92 (291)
Q Consensus        28 ~~~~~~~-~~~lfVgnL~~~~te~~L~~~F~~~G~I~--------~i~i~~d~~tg~s~G~aFV~F~~~~~------~ln   92 (291)
                      |....+. ++.|||.|||..+|.+++.++|++||.|.        .|.|.++. .|+.+|=|.|.|...++      .|+
T Consensus       126 ~~~~~~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilD  204 (382)
T KOG1548|consen  126 WFNPEPKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILD  204 (382)
T ss_pred             ccCcccccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhC
Confidence            4433333 45599999999999999999999999874        46777777 59999999999999888      899


Q ss_pred             CceeCCeEEEEeccCC
Q 022814           93 GAQILGRTIRVDHVAK  108 (291)
Q Consensus        93 g~~i~gr~i~V~~a~~  108 (291)
                      +..|.|+.|.|..|+-
T Consensus       205 e~~~rg~~~rVerAkf  220 (382)
T KOG1548|consen  205 EDELRGKKLRVERAKF  220 (382)
T ss_pred             cccccCcEEEEehhhh
Confidence            9999999999998843

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.41  E-value=2.5e-07  Score=88.30  Aligned_cols=80  Identities=30%  Similarity=0.529  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ....+.|||++||..+++.++.++...||.+....++.+..+|.++||||.+|.++..      .|||..+++..|.|..
T Consensus       286 ~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~  365 (500)
T KOG0120|consen  286 PDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQR  365 (500)
T ss_pred             ccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeeh
Confidence            3456899999999999999999999999999999999999999999999999998765      8999999999999998


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      |.....
T Consensus       366 A~~g~~  371 (500)
T KOG0120|consen  366 AIVGAS  371 (500)
T ss_pred             hhccch
Confidence            865443

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.41  E-value=4.1e-07  Score=84.06  Aligned_cols=71  Identities=24%  Similarity=0.494  Sum_probs=62.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      .....|+|||.|||+++|+..|++-|..||.|.++.|+.   .|+++|  .|.|.++++      .|||..|+|+.|.|.
T Consensus       532 aarKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~  606 (608)
T KOG4212|consen  532 AARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVT  606 (608)
T ss_pred             ccccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeee
Confidence            446678999999999999999999999999999999843   588888  888888876      899999999999998


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      +.
T Consensus       607 y~  608 (608)
T KOG4212|consen  607 YF  608 (608)
T ss_pred             eC
Confidence            63

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.40  E-value=3.6e-07  Score=78.42  Aligned_cols=65  Identities=34%  Similarity=0.727  Sum_probs=57.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      ..||||+||+.+.+.+|+.+|..||.|..|.|.        .||+||+|.+.-+      .||+..|++-.+.|.++..
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~   72 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARG   72 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecccc
Confidence            469999999999999999999999999999875        5699999999776      8999999998888888764

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.38  E-value=3.7e-07  Score=79.04  Aligned_cols=78  Identities=23%  Similarity=0.496  Sum_probs=70.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+.-.||.|-|.-.++++.|-..|.+|-.-....+++++-||+++||+||.|.+..+      +|||..++.++|++..+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            355799999999999999999999999888888999999999999999999999988      99999999999998876


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      ....
T Consensus       268 ~wke  271 (290)
T KOG0226|consen  268 EWKE  271 (290)
T ss_pred             hHHh
Confidence            5443

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.16  E-value=3.6e-06  Score=82.04  Aligned_cols=75  Identities=20%  Similarity=0.419  Sum_probs=64.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC---CCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG---TGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~---tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      .|..+.|||+||++.++++.|...|+.||+|..|.|+....   .....-||||.|-+..+      .|+|+.|....++
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            45568999999999999999999999999999999876542   23456799999988775      8999999999999


Q ss_pred             Eecc
Q 022814          103 VDHV  106 (291)
Q Consensus       103 V~~a  106 (291)
                      +.|+
T Consensus       251 ~gWg  254 (877)
T KOG0151|consen  251 LGWG  254 (877)
T ss_pred             eccc
Confidence            9887

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.13  E-value=9.4e-06  Score=69.23  Aligned_cols=79  Identities=20%  Similarity=0.346  Sum_probs=62.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeec-CCCCCcceEEEEEEcChhh------hcCCceeC---CeEEE
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRD-KGTGKPRGFAFVAYEDQRN------NLNGAQIL---GRTIR  102 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d-~~tg~s~G~aFV~F~~~~~------~lng~~i~---gr~i~  102 (291)
                      ..-+||||.+||.++..-+|..+|-.|--.+.+.|... +....++-+|||+|.+...      +|||+.++   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            34689999999999999999999999866666666543 3223456799999999776      89999997   68899


Q ss_pred             EeccCCccc
Q 022814          103 VDHVAKYKK  111 (291)
Q Consensus       103 V~~a~~~~~  111 (291)
                      |+++....+
T Consensus       112 iElAKSNtK  120 (284)
T KOG1457|consen  112 IELAKSNTK  120 (284)
T ss_pred             eeehhcCcc
Confidence            999876544

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.05  E-value=2.1e-06  Score=77.62  Aligned_cols=77  Identities=34%  Similarity=0.587  Sum_probs=67.8

Q ss_pred             CCCEEE-EcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh---hcC--CceeCCeEEEEeccC
Q 022814           34 DSAYVY-VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NLN--GAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lf-VgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~ln--g~~i~gr~i~V~~a~  107 (291)
                      +..++| |++|++.+++++|...|..+|.|..+.++.+..++.++|||||.|.....   +|+  ...|.++++.|....
T Consensus       183 ~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  262 (285)
T KOG4210|consen  183 PSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDE  262 (285)
T ss_pred             ccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCC
Confidence            445566 99999999999999999999999999999999999999999999999877   555  788999999998876


Q ss_pred             Ccc
Q 022814          108 KYK  110 (291)
Q Consensus       108 ~~~  110 (291)
                      +..
T Consensus       263 ~~~  265 (285)
T KOG4210|consen  263 PRP  265 (285)
T ss_pred             CCc
Confidence            543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=97.95  E-value=4.6e-06  Score=79.39  Aligned_cols=67  Identities=30%  Similarity=0.530  Sum_probs=58.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      +..+..+|||-|||..+++++|..+|+.||+|..|.....     ..|.+||+|-+.-+      +|++..|.|+.|+
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~-----~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN-----KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             ccCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc-----cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3566789999999999999999999999999999766444     48999999998665      8899999998887

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.93  E-value=2.9e-05  Score=73.05  Aligned_cols=73  Identities=26%  Similarity=0.514  Sum_probs=60.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      ....|=+.+|||++|+++|.++|+.|+ |..+.+++.  +|++.|-|||+|.++++     +.+-..+..+.|.|-.+..
T Consensus         9 ~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    9 TAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             cceEEEecCCCccccHHHHHHHHhcCc-eeEEEEecc--CCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCC
Confidence            344566889999999999999999995 777666654  79999999999999988     6677888899999987744


Q ss_pred             c
Q 022814          109 Y  109 (291)
Q Consensus       109 ~  109 (291)
                      .
T Consensus        86 ~   86 (510)
T KOG4211|consen   86 A   86 (510)
T ss_pred             c
Confidence            3

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.93  E-value=8.9e-06  Score=73.81  Aligned_cols=78  Identities=35%  Similarity=0.561  Sum_probs=67.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEEcChhh------hcCCcee
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV--------DVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI   96 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~--------~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i   96 (291)
                      ......+|||-+||..+++++|.++|.+||.|.        .|.|-+++.|+.++|-|.|+|.+..+      -+++..+
T Consensus        62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf  141 (351)
T KOG1995|consen   62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDF  141 (351)
T ss_pred             cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccc
Confidence            356678999999999999999999999999884        56778899999999999999999876      6788888


Q ss_pred             CCeEEEEeccCC
Q 022814           97 LGRTIRVDHVAK  108 (291)
Q Consensus        97 ~gr~i~V~~a~~  108 (291)
                      .+..|+|-++..
T Consensus       142 ~gn~ikvs~a~~  153 (351)
T KOG1995|consen  142 CGNTIKVSLAER  153 (351)
T ss_pred             cCCCchhhhhhh
Confidence            898888877753

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.88  E-value=3.4e-05  Score=69.71  Aligned_cols=69  Identities=23%  Similarity=0.465  Sum_probs=57.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G--~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      -.+|||||-|.||+++|.+.+...|  .|..+++..+..+|+++|||+|...+..+      .|.-.+|.|..-.|.
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            3799999999999999999988766  46777778888899999999999988666      566677888766654

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=97.77  E-value=0.00011  Score=62.86  Aligned_cols=72  Identities=21%  Similarity=0.385  Sum_probs=60.0

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIR  102 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~  102 (291)
                      ...++..+||+.|||..++.+.|..+|.+|.--..|.++...     .+.|||+|.+...      ++.+..|- ...+.
T Consensus       141 ~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~  215 (221)
T KOG4206|consen  141 QMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQ  215 (221)
T ss_pred             cCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEE
Confidence            446888999999999999999999999999988999888765     7899999998654      66666665 66777


Q ss_pred             Eecc
Q 022814          103 VDHV  106 (291)
Q Consensus       103 V~~a  106 (291)
                      |.++
T Consensus       216 i~~a  219 (221)
T KOG4206|consen  216 ITFA  219 (221)
T ss_pred             eccc
Confidence            7665

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.53  E-value=6.3e-05  Score=64.27  Aligned_cols=52  Identities=13%  Similarity=0.289  Sum_probs=40.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      .+.||||.||.+++||++|+.+|+.|--..-++|-. + .|  ...|||+|++.+.
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~-~-~g--~~vaf~~~~~~~~  260 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA-R-GG--MPVAFADFEEIEQ  260 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec-C-CC--cceEeecHHHHHH
Confidence            467999999999999999999999996554444432 1 22  4589999998776

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.49  E-value=0.00029  Score=65.05  Aligned_cols=70  Identities=20%  Similarity=0.426  Sum_probs=62.5

Q ss_pred             CCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           35 SAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        35 ~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +++|.|.||+.. +|.+.|-.+|+-||.|..|.|..++     +--|.|.|.+...      .|+|+.|.|++|+|.++.
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nk-----kd~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SK  371 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNK-----KDNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSK  371 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecC-----CcceeeeecchhHHHHHHHHhhcceecCceEEEeecc
Confidence            588999999885 8999999999999999999999887     3579999999765      899999999999999986


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      ..
T Consensus       372 H~  373 (492)
T KOG1190|consen  372 HT  373 (492)
T ss_pred             Cc
Confidence            54

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.45  E-value=0.00032  Score=66.61  Aligned_cols=61  Identities=25%  Similarity=0.429  Sum_probs=56.3

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFA-QCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~-~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      .+...+..|||||+||--++.++|-.||. -||.|..+-|=+|+.-+.++|-|=|+|.+..+
T Consensus       364 sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqs  425 (520)
T KOG0129|consen  364 NQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQA  425 (520)
T ss_pred             CcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHH
Confidence            34567889999999999999999999999 69999999999998889999999999999988

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.40  E-value=0.00039  Score=65.64  Aligned_cols=73  Identities=34%  Similarity=0.513  Sum_probs=58.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceEEEEEEcChhh---hcC--CceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDKGTGKPRGFAFVAYEDQRN---NLN--GAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~-i~i~~d~~tg~s~G~aFV~F~~~~~---~ln--g~~i~gr~i~V~~a~  107 (291)
                      +..+|=+.+||+.||+++|.++|+..=.|.. |.|+.+. .+.+.|-|||.|++++.   +|.  -..|+.+.|.|..+.
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            4568889999999999999999997643333 5566666 68899999999999998   444  467888999997664

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.38  E-value=0.00062  Score=61.54  Aligned_cols=75  Identities=21%  Similarity=0.461  Sum_probs=55.5

Q ss_pred             CCCCEEEEcCCCCCCCHHH----H--HHHHhcCCCeeEEEEeecCCC-CCcceEE--EEEEcChhh------hcCCceeC
Q 022814           33 KDSAYVYVGGIPFDLTEGD----L--LAVFAQCGEIVDVNLVRDKGT-GKPRGFA--FVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~----L--~~~F~~~G~I~~i~i~~d~~t-g~s~G~a--FV~F~~~~~------~lng~~i~   97 (291)
                      ...+-+||-+||+.+..++    |  .++|++||.|..|.|.+-..+ ....+.+  ||+|...++      +.+|..++
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~D  191 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLD  191 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhcccccc
Confidence            3456789999998766655    3  389999999998877543211 1222333  999999887      89999999


Q ss_pred             CeEEEEeccC
Q 022814           98 GRTIRVDHVA  107 (291)
Q Consensus        98 gr~i~V~~a~  107 (291)
                      |+.|+..+-.
T Consensus       192 Gr~lkatYGT  201 (480)
T COG5175         192 GRVLKATYGT  201 (480)
T ss_pred             CceEeeecCc
Confidence            9999987753

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.35  E-value=1.7e-05  Score=72.67  Aligned_cols=59  Identities=10%  Similarity=0.008  Sum_probs=47.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQIL   97 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~   97 (291)
                      ..||+|++|+..|...+|.++|..+|+|....+..    |...-||-|+|..+.+     .++|..+.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~as----k~~s~~c~~sf~~qts~~halr~~gre~k  214 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTAS----KSRSSSCSHSFRKQTSSKHALRSHGRERK  214 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhhc----cCCCcchhhhHhhhhhHHHHHHhcchhhh
Confidence            36899999999999999999999999998887753    4446688899998877     45555444

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=97.35  E-value=0.00025  Score=67.31  Aligned_cols=71  Identities=30%  Similarity=0.540  Sum_probs=50.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC--C-CCCcce---EEEEEEcChhh---hcCCceeCCeEEEEec
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK--G-TGKPRG---FAFVAYEDQRN---NLNGAQILGRTIRVDH  105 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~--~-tg~s~G---~aFV~F~~~~~---~lng~~i~gr~i~V~~  105 (291)
                      +++||||+||+.++|+.|...|..||.+. |.++...  . --.++|   |+|+.|+++.+   .|+....+...+.++.
T Consensus       259 S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~~~~~~yf~v  337 (520)
T KOG0129|consen  259 SRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSEGEGNYYFKV  337 (520)
T ss_pred             ccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhhcccceEEEE
Confidence            57999999999999999999999999864 5555211  1 123566   99999999887   4444444444444443


Q ss_pred             c
Q 022814          106 V  106 (291)
Q Consensus       106 a  106 (291)
                      +
T Consensus       338 s  338 (520)
T KOG0129|consen  338 S  338 (520)
T ss_pred             e
Confidence            3

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.18  E-value=0.00094  Score=64.11  Aligned_cols=75  Identities=29%  Similarity=0.468  Sum_probs=58.4

Q ss_pred             CCCEEEEcCCCCCCCH--H----HHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeE
Q 022814           34 DSAYVYVGGIPFDLTE--G----DLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRT  100 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te--~----~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~  100 (291)
                      -...|+|.|+|..-..  +    -|..+|+++|+|+.+.++.+..+| ++||.|++|.+..+      .|||+.|+ .+.
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            3578999999864322  2    344789999999999999888655 99999999999876      89999887 567


Q ss_pred             EEEeccCCc
Q 022814          101 IRVDHVAKY  109 (291)
Q Consensus       101 i~V~~a~~~  109 (291)
                      +.|......
T Consensus       136 f~v~~f~d~  144 (698)
T KOG2314|consen  136 FFVRLFKDF  144 (698)
T ss_pred             EEeehhhhH
Confidence            777655433

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=97.03  E-value=0.0004  Score=59.80  Aligned_cols=62  Identities=31%  Similarity=0.530  Sum_probs=53.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ..+.|+|-+|+..+.+.+|.++|+++|.+....+        ..++|||+|.++++      .|++..|.++.|.|
T Consensus        98 s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~  165 (216)
T KOG0106|consen   98 THFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISV  165 (216)
T ss_pred             ccceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeee
Confidence            3568889999999999999999999999954433        36799999999987      89999999999999

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=97.03  E-value=0.0016  Score=59.99  Aligned_cols=71  Identities=17%  Similarity=0.280  Sum_probs=57.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC---CCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK---GTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~---~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      .|-|.||.+++|.+++..+|.-.|+|..+.|....   .-....-.|||-|.+...     .|.++.+-++.|.|-.+.
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~   87 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYG   87 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecC
Confidence            79999999999999999999999999999886532   223456689999999876     777777777777776543

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.02  E-value=0.0004  Score=60.54  Aligned_cols=67  Identities=25%  Similarity=0.372  Sum_probs=54.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC--------CCcceE----EEEEEcChhh------hcCCce
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT--------GKPRGF----AFVAYEDQRN------NLNGAQ   95 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~t--------g~s~G~----aFV~F~~~~~------~lng~~   95 (291)
                      ..-.||+++||+.+...-|++||+.||+|-.|.|.....+        |.+..+    |+|+|.+...      .||+..
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            4578999999999999999999999999999998776544        344443    5688987654      899999


Q ss_pred             eCCeE
Q 022814           96 ILGRT  100 (291)
Q Consensus        96 i~gr~  100 (291)
                      |+|+.
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            99864

>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=97.00  E-value=0.0015  Score=50.22  Aligned_cols=64  Identities=17%  Similarity=0.335  Sum_probs=37.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--------hcC---CceeCCeEEEEe
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--------NLN---GAQILGRTIRVD  104 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--------~ln---g~~i~gr~i~V~  104 (291)
                      +.|+|.+|+..++-++|+++|++||.|.+|.+....      --|||-|.++++        ...   +..|.+..+.+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            568898999999999999999999999999887642      279999999865        222   455666655554


Q ss_pred             c
Q 022814          105 H  105 (291)
Q Consensus       105 ~  105 (291)
                      .
T Consensus        76 v   76 (105)
T PF08777_consen   76 V   76 (105)
T ss_dssp             -
T ss_pred             E
Confidence            3

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.96  E-value=0.00053  Score=63.75  Aligned_cols=59  Identities=20%  Similarity=0.374  Sum_probs=48.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeec---CCC--CC--------cceEEEEEEcChhh
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRD---KGT--GK--------PRGFAFVAYEDQRN   89 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d---~~t--g~--------s~G~aFV~F~~~~~   89 (291)
                      ...+..||.|+|||.+-.-+.|.+||+.||.|..|.|+..   +.+  +.        .+-||||+|...+.
T Consensus       227 eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~  298 (484)
T KOG1855|consen  227 EELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEA  298 (484)
T ss_pred             cccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHH
Confidence            3457899999999999888999999999999999999876   222  22        24589999998776

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.90  E-value=0.00044  Score=69.15  Aligned_cols=75  Identities=24%  Similarity=0.361  Sum_probs=64.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      ...|||.|+|+..|.+.|+.+|..+|.++++.++..+ .|+++|.|||.|.++.+      .++...+.-..+.|..+.+
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r-~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            5689999999999999999999999999999988887 79999999999999876      5666666677778877766


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus       815 ~~  816 (881)
T KOG0128|consen  815 ER  816 (881)
T ss_pred             cc
Confidence            43

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=96.48  E-value=0.0088  Score=55.57  Aligned_cols=81  Identities=21%  Similarity=0.279  Sum_probs=61.2

Q ss_pred             CCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC
Q 022814           24 DDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        24 ~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~   97 (291)
                      +......-+||+.+|.+.|||++++|++|+++|..-|-.......    -++.+-+|++.+.+.+.      .|+.+.++
T Consensus       403 gsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkf----f~kd~kmal~q~~sveeA~~ali~~hnh~lg  478 (492)
T KOG1190|consen  403 GSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKF----FQKDRKMALPQLESVEEAIQALIDLHNHYLG  478 (492)
T ss_pred             ccccccccCCchhheeeccCCcccchhHHHHhhhcCCceEEeeee----cCCCcceeecccCChhHhhhhccccccccCC
Confidence            333444467899999999999999999999999988765444322    23345699999999887      67777777


Q ss_pred             C-eEEEEeccCC
Q 022814           98 G-RTIRVDHVAK  108 (291)
Q Consensus        98 g-r~i~V~~a~~  108 (291)
                      . ..|.|.|+..
T Consensus       479 en~hlRvSFSks  490 (492)
T KOG1190|consen  479 ENHHLRVSFSKS  490 (492)
T ss_pred             CCceEEEEeecc
Confidence            5 4889988753

>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=96.40  E-value=0.0089  Score=43.64  Aligned_cols=63  Identities=22%  Similarity=0.535  Sum_probs=40.7

Q ss_pred             CEEEEcCCCCCCCHHHHH----HHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           36 AYVYVGGIPFDLTEGDLL----AVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~----~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..|||.|||.......|.    .++..|| .|..|.          .+-|+|-|.+++.      -|+|-.+.|..|.|.
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            469999999988876655    5556775 566551          3689999999987      799999999999999


Q ss_pred             ccCC
Q 022814          105 HVAK  108 (291)
Q Consensus       105 ~a~~  108 (291)
                      +...
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.

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.29  E-value=0.012  Score=58.07  Aligned_cols=71  Identities=25%  Similarity=0.452  Sum_probs=58.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      +++|-|.|+|+.++-++|.++|..|-.+-.-.+++-...|.+.|-|.|.|++++.      .|++..|..+.|.|.+
T Consensus       867 p~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  867 PRVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            4488899999999999999999999766433333434479999999999999887      7899999999988864

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.26  E-value=0.017  Score=46.71  Aligned_cols=73  Identities=30%  Similarity=0.394  Sum_probs=48.6

Q ss_pred             CCCCCCEEEEcCCCC------CCCH---HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCcee
Q 022814           31 KYKDSAYVYVGGIPF------DLTE---GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQI   96 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~------~~te---~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i   96 (291)
                      ..||..||.|.-+.+      ...+   .+|...|..||+|.-|+++-+        .-+|+|.+-.+     .|+|..|
T Consensus        23 ~GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~dg~~v   94 (146)
T PF08952_consen   23 QGPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSLDGIQV   94 (146)
T ss_dssp             ---TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHGCCSEE
T ss_pred             cCCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHccCCcEE
Confidence            457888888866651      2322   267788999999988888754        57999999876     8999999


Q ss_pred             CCeEEEEeccCCccc
Q 022814           97 LGRTIRVDHVAKYKK  111 (291)
Q Consensus        97 ~gr~i~V~~a~~~~~  111 (291)
                      +|+.|+|..-.+...
T Consensus        95 ~g~~l~i~LKtpdW~  109 (146)
T PF08952_consen   95 NGRTLKIRLKTPDWL  109 (146)
T ss_dssp             TTEEEEEEE------
T ss_pred             CCEEEEEEeCCccHH
Confidence            999999998766544

; PDB: 1UFW_A 2DNR_A.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.19  E-value=0.0026  Score=61.50  Aligned_cols=70  Identities=19%  Similarity=0.298  Sum_probs=57.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee---CCeEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFA-QCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI---LGRTI  101 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~-~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i---~gr~i  101 (291)
                      ..+++.|||.||-.-+|.-+|++++. .+|.|...+|  |+    .+..|||.|.+.+.      +|+|+.+   +.+.|
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~Wm--Dk----IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L  514 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWM--DK----IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHL  514 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhccCchHHHHH--HH----hhcceeEecccHHHHHHHHHHHhccccCCCCCcee
Confidence            45678999999999999999999999 5777777733  22    36689999999776      9999887   46788


Q ss_pred             EEeccC
Q 022814          102 RVDHVA  107 (291)
Q Consensus       102 ~V~~a~  107 (291)
                      .|.|..
T Consensus       515 ~adf~~  520 (718)
T KOG2416|consen  515 IADFVR  520 (718)
T ss_pred             Eeeecc
Confidence            888875

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=96.11  E-value=0.018  Score=52.94  Aligned_cols=71  Identities=21%  Similarity=0.332  Sum_probs=63.2

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           32 YKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..+.+.+.|-+|... +.-+.|-.+|..||.|..|++++.+     .|-|.|++.+..+      .||+..+-|..|.|.
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~  358 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVC  358 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEe
Confidence            467889999999886 6668999999999999999999876     7899999999887      899999999999998


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      ++.
T Consensus       359 ~Sk  361 (494)
T KOG1456|consen  359 VSK  361 (494)
T ss_pred             ecc
Confidence            874

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.06  E-value=0.0086  Score=60.55  Aligned_cols=77  Identities=23%  Similarity=0.353  Sum_probs=63.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~  102 (291)
                      +..+.+.|||++|.+++....|..+|..||.|..|.+-.    |  .-||||.|++...      .|-|..|++  +.|.
T Consensus       451 kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----g--q~yayi~yes~~~aq~a~~~~rgap~G~P~~r~r  524 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----G--QPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLR  524 (975)
T ss_pred             ccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----C--CcceeeecccCccchhhHHHHhcCcCCCCCcccc
Confidence            556788999999999999999999999999998876532    2  3499999998776      788888886  7799


Q ss_pred             EeccCCccccc
Q 022814          103 VDHVAKYKKKE  113 (291)
Q Consensus       103 V~~a~~~~~~~  113 (291)
                      |.++......+
T Consensus       525 vdla~~~~~~P  535 (975)
T KOG0112|consen  525 VDLASPPGATP  535 (975)
T ss_pred             cccccCCCCCh
Confidence            99997665443

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=95.99  E-value=0.02  Score=38.19  Aligned_cols=47  Identities=30%  Similarity=0.675  Sum_probs=36.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      +.|-|.+.++... +.|...|..||+|..+.+..      ..-+.||.|.+..+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~   48 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASFGEIVDIYVPE------STNWMYLKYKSRKD   48 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhcCCEEEEEcCC------CCcEEEEEECCHHH
Confidence            5678888887776 44556899999999998872      24589999998765

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=95.96  E-value=0.00053  Score=68.61  Aligned_cols=64  Identities=23%  Similarity=0.396  Sum_probs=53.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILG   98 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~g   98 (291)
                      .+++||.||++.+.+.+|...|..+|.|..+.|.....+++.+|+|||+|..++.     +++-..+.|
T Consensus       667 ~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            3689999999999999999999999999888877666689999999999999876     444444444

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=95.95  E-value=0.0068  Score=53.06  Aligned_cols=77  Identities=22%  Similarity=0.273  Sum_probs=60.9

Q ss_pred             hhchhhhccCCCCCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           12 HINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      ++.++++........++.-.+.....|||-||+..++-+.|...|+.||+|....++.|. .+++.+-++|+|...-.
T Consensus         8 e~ak~eLd~~~~~~~~lr~rfa~~a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~-r~k~t~eg~v~~~~k~~   84 (275)
T KOG0115|consen    8 EIAKRELDGRFPKGRSLRVRFAMHAELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDD-RGKPTREGIVEFAKKPN   84 (275)
T ss_pred             HHHHHhcCCCCCCCCceEEEeeccceEEEEecchhhhhHHHHHhhhhcCccchheeeecc-cccccccchhhhhcchh
Confidence            333445555555555555566666899999999999999999999999999887777765 68999999999998655

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=95.76  E-value=0.013  Score=54.16  Aligned_cols=72  Identities=24%  Similarity=0.394  Sum_probs=56.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCC-eeE--EEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGE-IVD--VNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~-I~~--i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ....|-+.+||+.++.++|..+|..|.. |..  |+|+.+. .|.+.|-|||+|.+.+.      .-+.+....+.|.|-
T Consensus       279 ~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvf  357 (508)
T KOG1365|consen  279 SKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVF  357 (508)
T ss_pred             CCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEe
Confidence            3567889999999999999999999864 444  7787775 79999999999999887      223334457777775


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      .+
T Consensus       358 p~  359 (508)
T KOG1365|consen  358 PC  359 (508)
T ss_pred             ec
Confidence            44

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=95.67  E-value=0.037  Score=40.36  Aligned_cols=48  Identities=23%  Similarity=0.423  Sum_probs=36.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      .-.+.+||. +|..+...+|..+|+.||.|. |.++-|.       -|||.....+.
T Consensus         7 ~RdHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~   54 (87)
T PF08675_consen    7 SRDHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQ   54 (87)
T ss_dssp             SGCCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHH
T ss_pred             CcceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHH
Confidence            345677786 999999999999999999975 6777765       79999998876

; 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.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=95.66  E-value=0.0074  Score=56.29  Aligned_cols=70  Identities=30%  Similarity=0.490  Sum_probs=52.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCe-eEEEEeecCCCCCcceEEEEEEcChhh------hcCC-ceeCCeEEEEeccC
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEI-VDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNG-AQILGRTIRVDHVA  107 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I-~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng-~~i~gr~i~V~~a~  107 (291)
                      ++||||||.+.++..+|..+|...-.- ..-.|+       ..|||||.+.+...      .++| +++.|..+.|.++.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv   74 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSV   74 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchh
Confidence            579999999999999999999764111 111122       25899999998776      6677 57889999999887


Q ss_pred             Ccccc
Q 022814          108 KYKKK  112 (291)
Q Consensus       108 ~~~~~  112 (291)
                      +.++.
T Consensus        75 ~kkqr   79 (584)
T KOG2193|consen   75 PKKQR   79 (584)
T ss_pred             hHHHH
Confidence            66544

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=95.58  E-value=0.014  Score=57.67  Aligned_cols=77  Identities=26%  Similarity=0.237  Sum_probs=60.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~-i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...+|||-.||..|++.++.++|...-.|++ |.|..-+ +++-.+.|||+|..+++      .-.-+.++.+.|.|+-+
T Consensus       433 ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  433 AGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ccceEEeccCCccccccchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            4579999999999999999999998766666 7777666 78899999999999666      22335677888999876


Q ss_pred             CCccc
Q 022814          107 AKYKK  111 (291)
Q Consensus       107 ~~~~~  111 (291)
                      .....
T Consensus       512 ~~~~m  516 (944)
T KOG4307|consen  512 ADYAM  516 (944)
T ss_pred             hhHHH
Confidence            54433

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.48  E-value=0.0049  Score=62.26  Aligned_cols=74  Identities=19%  Similarity=0.376  Sum_probs=58.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .-.+.|||+|||+..+++.+|.-+|..+|.|..|.|-+.. -++-.-||||.|.+...      .|.+..|..-.+.+.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~-~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~gl  447 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPH-IKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGL  447 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCC-CCcccchhhhhhhccccCcccchhhcCCccccCcccccc
Confidence            3456899999999999999999999999999999887654 35556699999988766      6777777655555554


Q ss_pred             c
Q 022814          106 V  106 (291)
Q Consensus       106 a  106 (291)
                      .
T Consensus       448 G  448 (975)
T KOG0112|consen  448 G  448 (975)
T ss_pred             c
Confidence            4

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=95.30  E-value=0.04  Score=50.75  Aligned_cols=73  Identities=25%  Similarity=0.286  Sum_probs=58.2

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--------hcCCceeCCeE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--------NLNGAQILGRT  100 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--------~lng~~i~gr~  100 (291)
                      ..+.+++-.|.|.+|-..++|.+|.+.++.||.|..+.++..      +-.|.|+|++.+.        +-|...|.|..
T Consensus        25 phk~~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~------~r~alvefedi~~akn~Vnfaa~n~i~i~gq~   98 (494)
T KOG1456|consen   25 PHKPNPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPH------KRQALVEFEDIEGAKNCVNFAADNQIYIAGQQ   98 (494)
T ss_pred             CCCCCCCceEEEeccccccchhHHHHHHhcCCceEEEEeccc------cceeeeeeccccchhhheehhccCcccccCch
Confidence            345677889999999999999999999999999998876644      3479999997765        44556677777


Q ss_pred             EEEeccC
Q 022814          101 IRVDHVA  107 (291)
Q Consensus       101 i~V~~a~  107 (291)
                      -.++++.
T Consensus        99 Al~NySt  105 (494)
T KOG1456|consen   99 ALFNYST  105 (494)
T ss_pred             hhcccch
Confidence            7777663

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=95.08  E-value=0.01  Score=53.79  Aligned_cols=77  Identities=16%  Similarity=0.163  Sum_probs=62.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCc-eeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGA-QILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~-~i~gr~i~V~~a~  107 (291)
                      ..+++||++|.+.+.+.++..+|..+|.+..+.+........++||++|.|...+.     +|.+. .+.+..+...+..
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            47899999999999999999999999999888888777789999999999999887     55653 5556665555544


Q ss_pred             Ccc
Q 022814          108 KYK  110 (291)
Q Consensus       108 ~~~  110 (291)
                      ...
T Consensus       167 ~~~  169 (285)
T KOG4210|consen  167 RRG  169 (285)
T ss_pred             ccc
Confidence            433

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=94.97  E-value=0.058  Score=52.16  Aligned_cols=54  Identities=22%  Similarity=0.333  Sum_probs=43.9

Q ss_pred             HHHhcCCCeeEEEEeecCCC---CCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           54 AVFAQCGEIVDVNLVRDKGT---GKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        54 ~~F~~~G~I~~i~i~~d~~t---g~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .-+++||.|..|.|+++..+   .-..|.-||+|.+.++      +|+|..+.++.|...+..
T Consensus       428 ~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyd  490 (500)
T KOG0120|consen  428 TECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYD  490 (500)
T ss_pred             HHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecC
Confidence            44668999999999987323   3456788999999887      999999999999887764

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=94.95  E-value=0.014  Score=51.17  Aligned_cols=85  Identities=26%  Similarity=0.555  Sum_probs=63.4

Q ss_pred             HHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCccccchhHHHHHHhh
Q 022814           51 DLLAVFA-QCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRM  123 (291)
Q Consensus        51 ~L~~~F~-~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~~~~~~~~~~~~~~~  123 (291)
                      +|...|+ +||+|..+.|..+- .-.-.|-+||.|...++      .||+--|.|++|...++.-.--            
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT~~------------  150 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVTDF------------  150 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcCch------------
Confidence            3444445 89999998766543 44568899999998877      8999999999999988753221            


Q ss_pred             hhhhccccccccCCCCCCCceeEeecC
Q 022814          124 REERGVCRAFQRGECTRGDGCKFSHNE  150 (291)
Q Consensus       124 ~~~~~~~~~f~~~~~g~~~~~~~~~d~  150 (291)
                        ....|..|-.+.|..+..|.|++-.
T Consensus       151 --rea~C~~~e~~~C~rG~~CnFmH~k  175 (260)
T KOG2202|consen  151 --REAICGQFERTECSRGGACNFMHVK  175 (260)
T ss_pred             --hhhhhcccccccCCCCCcCcchhhh
Confidence              2245788888888888888887754

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=94.92  E-value=0.012  Score=57.68  Aligned_cols=73  Identities=14%  Similarity=0.173  Sum_probs=58.8

Q ss_pred             CCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC
Q 022814           24 DDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        24 ~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~   97 (291)
                      ...+..+..++.-++||+||...+..+-+..++..||-|.+|..+.         |||.+|..+..      .+.-..|+
T Consensus        29 p~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~   99 (668)
T KOG2253|consen   29 PIQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNID   99 (668)
T ss_pred             CCcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCC
Confidence            3445555678889999999999999999999999999998886553         99999998876      56666777


Q ss_pred             CeEEEEec
Q 022814           98 GRTIRVDH  105 (291)
Q Consensus        98 gr~i~V~~  105 (291)
                      |..+.+..
T Consensus       100 ~~kl~~~~  107 (668)
T KOG2253|consen  100 DQKLIENV  107 (668)
T ss_pred             cchhhccc
Confidence            77766654

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=94.58  E-value=0.31  Score=44.69  Aligned_cols=73  Identities=15%  Similarity=0.261  Sum_probs=55.7

Q ss_pred             CCCCCEEEEcCCCC----CCC-------HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCc
Q 022814           32 YKDSAYVYVGGIPF----DLT-------EGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGA   94 (291)
Q Consensus        32 ~~~~~~lfVgnL~~----~~t-------e~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~   94 (291)
                      ....+||.|.||=.    ..+       +++|.+-.++||.|..|.|.-    ..+.|.+-|.|.+.+.      .|+|-
T Consensus       262 ~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR  337 (382)
T KOG1548|consen  262 ARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGR  337 (382)
T ss_pred             ccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCe
Confidence            45567888888832    333       345556678999999987752    3568999999999886      89999


Q ss_pred             eeCCeEEEEeccCC
Q 022814           95 QILGRTIRVDHVAK  108 (291)
Q Consensus        95 ~i~gr~i~V~~a~~  108 (291)
                      .++|+.|.......
T Consensus       338 ~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  338 WFDGRQLTASIWDG  351 (382)
T ss_pred             eecceEEEEEEeCC
Confidence            99999998876543

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=93.97  E-value=0.13  Score=43.15  Aligned_cols=49  Identities=24%  Similarity=0.377  Sum_probs=44.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      ....|.|.+||++.++.+|++.+-+.|.|....|.+|       |++.|+|...++
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eD  162 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKED  162 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhh
Confidence            3458899999999999999999999999999998887       389999998887

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.81  E-value=0.054  Score=51.37  Aligned_cols=69  Identities=26%  Similarity=0.340  Sum_probs=55.4

Q ss_pred             CCCEEEEcCCCCCCCH-HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTE-GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te-~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      +.+.|-+-..|+.+.. ++|...|.+||+|..|.|-..      .-.|.|+|.+...     +..+..|+++.|+|-|..
T Consensus       371 dhs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whn  444 (526)
T KOG2135|consen  371 DHSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHN  444 (526)
T ss_pred             ccchhhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhccccceecCceeEEEEec
Confidence            4456666666776544 899999999999999987544      4479999998765     788899999999999987


Q ss_pred             C
Q 022814          108 K  108 (291)
Q Consensus       108 ~  108 (291)
                      +
T Consensus       445 p  445 (526)
T KOG2135|consen  445 P  445 (526)
T ss_pred             C
Confidence            7

>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=93.66  E-value=0.29  Score=37.20  Aligned_cols=71  Identities=20%  Similarity=0.360  Sum_probs=44.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEE-EeecC------CCCCcceEEEEEEcChhh-----hcCCceeCCeE-E
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVN-LVRDK------GTGKPRGFAFVAYEDQRN-----NLNGAQILGRT-I  101 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~-i~~d~------~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~-i  101 (291)
                      .+.|.|=+.|+. ....|...|++||+|.... +..+.      .......+-.|+|.++.+     .-||..|.|.. |
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            455777788887 4578889999999998774 11110      011234588999999887     67999998854 4


Q ss_pred             EEecc
Q 022814          102 RVDHV  106 (291)
Q Consensus       102 ~V~~a  106 (291)
                      -|.+.
T Consensus        85 GV~~~   89 (100)
T PF05172_consen   85 GVKPC   89 (100)
T ss_dssp             EEEE-
T ss_pred             EEEEc
Confidence            46554

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.

>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=93.51  E-value=0.083  Score=44.42  Aligned_cols=76  Identities=13%  Similarity=0.205  Sum_probs=44.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhc-CCCe---eEEEEeecCCC--CCcceEEEEEEcChhh------hcCCceeCC--
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQ-CGEI---VDVNLVRDKGT--GKPRGFAFVAYEDQRN------NLNGAQILG--   98 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~-~G~I---~~i~i~~d~~t--g~s~G~aFV~F~~~~~------~lng~~i~g--   98 (291)
                      ....+|.|.+||+.+|++++.+.+.. ++..   ..+.-.....+  -....-|||.|.+.++      .++|+.+.+  
T Consensus         5 ~~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    5 KEGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             ----EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             ccCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            34568999999999999999987776 6655   34432222211  1234568999999887      788876643  


Q ss_pred             ---eEEEEeccCC
Q 022814           99 ---RTIRVDHVAK  108 (291)
Q Consensus        99 ---r~i~V~~a~~  108 (291)
                         ....|.+|.-
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence               3445666643

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.

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=92.58  E-value=0.28  Score=43.96  Aligned_cols=58  Identities=17%  Similarity=0.223  Sum_probs=44.4

Q ss_pred             HHHHHHHhcCCCeeEEEEeecCCCCCcc-eEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           50 GDLLAVFAQCGEIVDVNLVRDKGTGKPR-GFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        50 ~~L~~~F~~~G~I~~i~i~~d~~tg~s~-G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +++++..++||.|..|.|...+..-... ---||+|+..++      .|||..|+|+.+...|-.
T Consensus       301 de~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  301 DETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            4666778899999999887665222222 246999999887      899999999999887754

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=92.53  E-value=0.43  Score=44.36  Aligned_cols=66  Identities=30%  Similarity=0.473  Sum_probs=47.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhc---C-CCeeEEEEeecCCCCCcceEEEEEEcChhh---h--cCCceeCCeEEEE
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQ---C-GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---N--LNGAQILGRTIRV  103 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~---~-G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~--lng~~i~gr~i~V  103 (291)
                      .|-+.+||+++|+.++.++|.+   . |....|.++..+ .|+..|-|||.|..++.   +  -+-..|+-+.|.|
T Consensus       163 ivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rp-dgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIEl  237 (508)
T KOG1365|consen  163 IVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRP-DGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIEL  237 (508)
T ss_pred             EEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECC-CCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHH
Confidence            4456799999999999999963   2 345566666655 79999999999999887   2  2334455555544

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.32  E-value=0.05  Score=49.51  Aligned_cols=73  Identities=25%  Similarity=0.491  Sum_probs=52.2

Q ss_pred             CCEEEEcCCCCCCCHHHHH---HHHhcCCCeeEEEEeecCC--CCC-cceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           35 SAYVYVGGIPFDLTEGDLL---AVFAQCGEIVDVNLVRDKG--TGK-PRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~---~~F~~~G~I~~i~i~~d~~--tg~-s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      .+-+||-+|++....+.+.   ++|.+||.|..|.+..+..  .+. ...-++|+|...++      ..+|+.++|+.|+
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            3678899999876555443   6899999999998887662  111 11237999998665      6788888888866


Q ss_pred             EeccC
Q 022814          103 VDHVA  107 (291)
Q Consensus       103 V~~a~  107 (291)
                      +.+..
T Consensus       157 a~~gt  161 (327)
T KOG2068|consen  157 ASLGT  161 (327)
T ss_pred             HhhCC
Confidence            65543

>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=91.72  E-value=0.75  Score=32.70  Aligned_cols=61  Identities=23%  Similarity=0.519  Sum_probs=34.6

Q ss_pred             EEEEcCCCC--CCCHHHHHHHHhcCC-----CeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           37 YVYVGGIPF--DLTEGDLLAVFAQCG-----EIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        37 ~lfVgnL~~--~~te~~L~~~F~~~G-----~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      +||| |+-.  .++..+|..++...+     .|-.|.|...        |+||+-....+     +|++..+.|++|.|.
T Consensus         2 rl~i-n~Gr~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~~~a~~v~~~l~~~~~~gk~v~ve   72 (74)
T PF03880_consen    2 RLFI-NVGRKDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPEEVAEKVLEALNGKKIKGKKVRVE   72 (74)
T ss_dssp             EEEE-S-SGGGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-TT-HHHHHHHHTT--SSS----EE
T ss_pred             EEEE-EcccccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECHHHHHHHHHHhcCCCCCCeeEEEE
Confidence            4565 3332  578889999998764     4556766543        89999988765     899999999999997


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      .|
T Consensus        73 ~A   74 (74)
T PF03880_consen   73 RA   74 (74)
T ss_dssp             E-
T ss_pred             EC
Confidence            54

; PDB: 2G0C_A 3MOJ_B.

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=91.59  E-value=0.18  Score=48.72  Aligned_cols=74  Identities=19%  Similarity=0.182  Sum_probs=53.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhc-CCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC----CeEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQ-CGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL----GRTIR  102 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~-~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~----gr~i~  102 (291)
                      +-+++-|.|+|-..|-..|.+.-++ .|.-..+.|+.|..+..+.|||||.|.++++      +.||+.++    .+.+.
T Consensus       387 ~rtt~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~  466 (549)
T KOG4660|consen  387 PRTTLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIAS  466 (549)
T ss_pred             chhhhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeee
Confidence            3456666677766666665555433 6888889999999999999999999999998      88887654    23445


Q ss_pred             EeccC
Q 022814          103 VDHVA  107 (291)
Q Consensus       103 V~~a~  107 (291)
                      |.+|.
T Consensus       467 itYAr  471 (549)
T KOG4660|consen  467 ITYAR  471 (549)
T ss_pred             eehhh
Confidence            55553

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=91.32  E-value=0.99  Score=36.42  Aligned_cols=71  Identities=20%  Similarity=0.249  Sum_probs=49.8

Q ss_pred             CCCCCCEEEEcCCCCCCCH-HHHHHH---HhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh---hcCCc--eeCCeEE
Q 022814           31 KYKDSAYVYVGGIPFDLTE-GDLLAV---FAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NLNGA--QILGRTI  101 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te-~~L~~~---F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~lng~--~i~gr~i  101 (291)
                      +.+|..||.|.=|..++.. ++|+.+   ++.||+|.+|.+.-       +.-|.|.|.+..+   +++.+  ..-|..+
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s~~pgtm~  154 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQSRAPGTMF  154 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcCCCCCceE
Confidence            4688999999988777554 566654   57899999997753       4479999999877   33322  3456666


Q ss_pred             EEeccCC
Q 022814          102 RVDHVAK  108 (291)
Q Consensus       102 ~V~~a~~  108 (291)
                      .+.|-+.
T Consensus       155 qCsWqqr  161 (166)
T PF15023_consen  155 QCSWQQR  161 (166)
T ss_pred             Eeecccc
Confidence            6665543

>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=88.65  E-value=2.8  Score=32.35  Aligned_cols=71  Identities=23%  Similarity=0.296  Sum_probs=47.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC---eEEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQC-GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG---RTIRV  103 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~-G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g---r~i~V  103 (291)
                      ....+.+...|+.++-+.|..+.+.+ ..|..+.|++|.  ..++=.+.|.|.++.+      .+||..+..   -.++|
T Consensus        12 ~~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chv   89 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHV   89 (110)
T ss_pred             CceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEE
Confidence            34455555555556666776555555 467888999874  3366688999999887      889987753   33444


Q ss_pred             ecc
Q 022814          104 DHV  106 (291)
Q Consensus       104 ~~a  106 (291)
                      -+.
T Consensus        90 vfV   92 (110)
T PF07576_consen   90 VFV   92 (110)
T ss_pred             EEE
Confidence            443

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=85.82  E-value=3.3  Score=28.53  Aligned_cols=47  Identities=19%  Similarity=0.377  Sum_probs=37.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcC---CCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQC---GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~---G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      +.+|+|.++. +++.++|+.+|..|   .....|.++-|.       -|-|.|.+.+.
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~   54 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEET   54 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHH
Confidence            4679999997 68889999999998   235678888886       68888888765

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=81.32  E-value=0.48  Score=41.73  Aligned_cols=73  Identities=18%  Similarity=0.234  Sum_probs=49.2

Q ss_pred             CEEEEcCCCCCCCHHH-H--HHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           36 AYVYVGGIPFDLTEGD-L--LAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~-L--~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      -.+|++++-..+..+- |  ...|+.+-.+....++.+. -+...+++|+.|....+      .-+++.|+-.+|++.-.
T Consensus        97 f~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~-p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~g  175 (290)
T KOG0226|consen   97 FRPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDR-PQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAG  175 (290)
T ss_pred             ccccccccccccCCCCCCcchhhhccchhhhhhhhhhcC-CCccCcccccCcchhhhhhhhccccccccccCcceeeccc
Confidence            3556667666555544 3  6778877777777777765 57789999999987665      55666777666665544


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      +..
T Consensus       176 tsw  178 (290)
T KOG0226|consen  176 TSW  178 (290)
T ss_pred             ccc
Confidence            433

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=80.60  E-value=5.4  Score=28.03  Aligned_cols=57  Identities=16%  Similarity=0.236  Sum_probs=45.5

Q ss_pred             HHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh---hcCCceeCCeEEEEecc
Q 022814           50 GDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        50 ~~L~~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~lng~~i~gr~i~V~~a  106 (291)
                      .+|++.|...| ++..|..+....+..+.-+-||+......   .|+=+.|++..|.|.-.
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~Il~ik~Lg~~~V~VEr~   62 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKEILNIKTLGGQRVTVERP   62 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcceEeehhhCCeeEEEecC
Confidence            46888888888 68888888887778888899999887654   66777889999888654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	291
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-12
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		3e-09
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		7e-08
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		4e-07
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		9e-07
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		1e-06
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		1e-06
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		1e-06
3mdf_A	85	Crystal Structure Of The Rrm Domain Of Cyclophilin		2e-06
2ku7_A	140	Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric		2e-06
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-06
3lpy_A	79	Crystal Structure Of The Rrm Domain Of Cyp33 Length		2e-06
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		2e-06
2kyx_A	83	Solution Structure Of The Rrm Domain Of Cyp33 Lengt		2e-06
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-06
1sxl_A	97	Resonance Assignments And Solution Structure Of The		2e-06
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-06
3sxl_A	184	Sex-Lethal Rna Recognition Domains 1 And 2 From Dro		3e-06
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		3e-06
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		3e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		4e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-06
1b7f_A	168	Sxl-Lethal ProteinRNA COMPLEX Length = 168		4e-06
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		5e-06
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		6e-06
1hl6_A	165	A Novel Mode Of Rbd-Protein Recognition In The Y14-		9e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		1e-05
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		1e-05
3pgw_S	437	Crystal Structure Of Human U1 Snrnp Length = 437		1e-05
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		1e-05
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		1e-05
2dng_A	103	Solution Structure Of Rna Binding Domain In Eukaryo		1e-05
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		1e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		1e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		2e-05
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-05
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-05
1oo0_B	110	Crystal Structure Of The Drosophila Mago Nashi-Y14		2e-05
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		6e-05
2dgp_A	106	Solution Structure Of The N-Terminal Rna Binding Do		8e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		8e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		9e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		2e-04
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		2e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		2e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		2e-04
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		2e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-04
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		3e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		3e-04
1h2t_Z	156	Structure Of The Human Nuclear Cap-Binding-Complex		3e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		3e-04
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		4e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		4e-04
2dnm_A	103	Solution Structure Of Rna Binding Domain In Srp46 S		5e-04
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		5e-04
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		6e-04
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		8e-04

>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 = 68.2 bits (165), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 33/76 (43%), Positives = 47/76 (61%), Gaps = 6/76 (7%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ        NL
Sbjct: 11  VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 92  NGAQILGRTIRVDHVA 107
           NG +  GR +RVD+ A
Sbjct: 71  NGREFSGRALRVDNAA 86

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 58.9 bits (141), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 45/78 (57%), Gaps = 6/78 (7%)
Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQ 87
           D   ++VGG+ FD  E  L  VF++ G+I +V +V+D+ T + RGF FV +E      D 
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 88  RNNLNGAQILGRTIRVDH 105
              +NG  + GR IRVD 
Sbjct: 71  MMAMNGKSVDGRQIRVDQ 88

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/71 (36%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VYV  +PF LT  DL  +F++ G++V V +++DK T K +G AF+ + D+ +       +
Sbjct: 19  VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 92  NGAQILGRTIR 102
           N  Q+ GR I+
Sbjct: 79  NNKQLFGRVIK 89

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 54.3 bits (129), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 6/79 (7%)
Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------R 88
           S+ +YVG + F++TE  L  +F   G+I ++ L++D  TG+ +G+ F+ + D        
Sbjct: 5   SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 89  NNLNGAQILGRTIRVDHVA 107
             LNG ++ GR +RV HV 
Sbjct: 65  EQLNGFELAGRPMRVGHVT 83

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 6/76 (7%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           +YVG + F++TE  L  +F   G I  + L+ D  TG+ +G+ F+ + D          L
Sbjct: 29  LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 92  NGAQILGRTIRVDHVA 107
           NG ++ GR ++V HV 
Sbjct: 89  NGFELAGRPMKVGHVT 104

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 50.8 bits (120), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VY+G IP+D TE  +L + +  G ++++ ++ D  TG+ +G+AF+ + D  +      NL
Sbjct: 6   VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 92  NGAQILGRTIRVDH 105
           NG Q+  R ++  +
Sbjct: 66  NGYQLGSRFLKCGY 79

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 44/72 (61%), Gaps = 7/72 (9%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
           VYVG + +  T  DL A F+ CG I  + ++ DK +G P+G+A++ +  +RN+++ A  +
Sbjct: 39  VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAVAM 97
Query: 98  ------GRTIRV 103
                 GRTI+V
Sbjct: 98  DETVFRGRTIKV 109

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----- 89
           S  VY+G IP+D TE  +L + +  G ++++ ++ D  TG+ +G+AF+ + D  +     
Sbjct: 4   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 90  -NLNGAQILGRTIR 102
            NLNG Q+  R ++
Sbjct: 64  RNLNGYQLGSRFLK 77

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/74 (32%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----- 89
           S  VY+G IP+D TE  +L + +  G ++++ ++ D  TG+ +G+AF+ + D  +     
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 90  -NLNGAQILGRTIR 102
            NLNG Q+  R ++
Sbjct: 62  RNLNGYQLGSRFLK 75

>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33 Length = 85

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E         +N+
Sbjct: 10  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 92  NGAQILGRTIRVD 104
           N +++ GRTIRV+
Sbjct: 70  NESELFGRTIRVN 82

>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein Length = 140

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E         +N+
Sbjct: 66  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 92  NGAQILGRTIRVD 104
           N +++ GRTIRV+
Sbjct: 126 NESELFGRTIRVN 138

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 46/75 (61%), Gaps = 7/75 (9%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE---DQRN---NL 91
           +++GG+  +  E  L AVF + G I +V L++D+ T K RGFAF+ +E   D +N   ++
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 92  NGAQILGRTIRVDHV 106
           NG  + G+ I+V+  
Sbjct: 69  NGKSLHGKAIKVEQA 83

>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33 Length = 79

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E         +N+
Sbjct: 5   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 92  NGAQILGRTIRVD 104
           N +++ GRTIRV+
Sbjct: 65  NESELFGRTIRVN 77

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E         +N+
Sbjct: 15  LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 92  NGAQILGRTIRVD 104
           N +++ GRTIRV+
Sbjct: 75  NESELFGRTIRVN 87

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNLNG 93
           V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E      + +   NG
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 94  AQILGRTIRVDH 105
            ++ GR IRVD 
Sbjct: 80  MELDGRRIRVDF 91

>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33 Length = 83

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/73 (38%), Positives = 43/73 (58%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E         +N+
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 92  NGAQILGRTIRVD 104
           N +++ GRTIRV+
Sbjct: 68  NESELFGRTIRVN 80

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 37  YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNN 90
           +V+VG +  ++T  D+ A FA  G I D  +V+D  TGK +G+ FV++      E+    
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 91  LNGAQILGRTIRVD 104
           + G  + GR IR +
Sbjct: 77  MGGQWLGGRQIRTN 90

>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second Rna-Binding Domain Of Sex-Lethal Determined By Multidimensional Heteronuclear Magnetic Resonance Spectroscopy Length = 97

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          +YV  +P  +T+  L  +F + G IV  N++RDK TG+PRG AFV Y
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 62

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 42/71 (59%), Gaps = 5/71 (7%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGGIP +  E +L   F + G + +V ++ D    +PRGF F+ +ED+++     N++
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
Query: 93  GAQILGRTIRV 103
              I+G+ + V
Sbjct: 73  FHDIMGKKVEV 83

>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila Melanogaster Length = 184

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
           +YV  +P  +T+  L  +F + G IV  N++RDK TG+PRG AFV Y
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 149

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 5/71 (7%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR-----NNLN 92
           +YVG + +  T   +  +F+Q G++ +V L+ D+ T KP+GF FV  +++        L+
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63
Query: 93  GAQILGRTIRV 103
               +GRTIRV
Sbjct: 64  NTDFMGRTIRV 74

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +P ++T+ +  ++F   GEI    LVRDK TG+  G+ FV Y D +      N L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64
Query: 92  NGAQILGRTIRVDH 105
           NG ++  +TI+V +
Sbjct: 65  NGLRLQTKTIKVSY 78

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNLNG 93
           V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E      + +   NG
Sbjct: 17  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 94  AQILGRTIRVDH 105
            ++ GR IRVD 
Sbjct: 77  MELDGRRIRVDF 88

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 6/71 (8%)
Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNLNG 93
           V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E+       +   NG
Sbjct: 51  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 94  AQILGRTIRVD 104
            ++ GR IRVD
Sbjct: 111 MELDGRRIRVD 121

>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX Length = 168

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/47 (46%), Positives = 31/47 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
           +YV  +P  +T+  L  +F + G IV  N++RDK TG+PRG AFV Y
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 138

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +P ++T+ +  ++F   G+I    LVRDK TG+  G+ FV Y D        N L
Sbjct: 7   LIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTL 66
Query: 92  NGAQILGRTIRVDH 105
           NG ++  +TI+V +
Sbjct: 67  NGLKLQTKTIKVSY 80

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 36/53 (67%)
Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
          K+S  +++GG+ +D TE +L   F + G + D+ +++D  TG+ RGF F+++E
Sbjct: 1  KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53

>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago Complex Length = 165

Iteration: 1
 Score = 47.4 bits (111), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           ++V  I  +  E ++   F   GEI +++L  D+ TG  +G+A V YE  +        L
Sbjct: 75  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 92  NGAQILGRTIRVD 104
           NGA+I+G+TI+VD
Sbjct: 135 NGAEIMGQTIQVD 147

>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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 154

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 156

>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp Length = 437

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           ++V  + +D TE  L   F   G I  +++V  K +GKPRG+AF+ YE +R+      + 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 92  NGAQILGRTIRVD 104
           +G +I GR + VD
Sbjct: 165 DGKKIDGRRVLVD 177

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           ++V  + +D TE  L   F   G I  +++V  K +GKPRG+AF+ YE +R+      + 
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 92  NGAQILGRTIRVD 104
           +G +I GR + VD
Sbjct: 165 DGKKIDGRRVLVD 177

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 6/74 (8%)
Query: 37  YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNN 90
           +V+VG +  ++T  D+ + FA  G+I D  +V+D  TGK +G+ FV++      E+   +
Sbjct: 17  HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 91  LNGAQILGRTIRVD 104
           + G  + GR IR +
Sbjct: 77  MGGQWLGGRQIRTN 90

>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic Translation Initiation Factor 4h Length = 103

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 44/72 (61%), Gaps = 8/72 (11%)
Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNL------N 92
           YVG +PF+  +GD+ A+F     I  V LVRDK T K +GF +V + D+ ++L      +
Sbjct: 19  YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEF-DEVDSLKEALTYD 76
Query: 93  GAQILGRTIRVD 104
           GA +  R++RVD
Sbjct: 77  GALLGDRSLRVD 88

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNG 93
           V  +P ++T+ +  ++F   G+I    LVRDK TG+  G+ FV Y D        N LNG
Sbjct: 9   VNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
Query: 94  AQILGRTIRVDH 105
            ++  +TI+V +
Sbjct: 69  LKLQTKTIKVSY 80

>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 = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 33/53 (62%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          D+   +VGG+ +D ++ DL   F + GE+VD  +  D  TG+ RGF F+ ++D
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKD 62

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 41/70 (58%), Gaps = 6/70 (8%)
Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNLNG 93
           V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E+       +   NG
Sbjct: 20  VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 94  AQILGRTIRV 103
            ++ GR IRV
Sbjct: 80  MELDGRRIRV 89

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 155

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D
Sbjct: 100 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 148

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 46.6 bits (109), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D
Sbjct: 105 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD 153

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNL 91
           + V  +P ++T+ +L ++F+  GE+    L+RDK  G   G+ FV Y      E   N L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 92  NGAQILGRTIRVDH 105
           NG ++  +TI+V +
Sbjct: 65  NGLRLQSKTIKVSY 78

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 6/74 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNL 91
           + V  +P ++T+ +L ++F+  GE+    L+RDK  G   G+ FV Y      E   N L
Sbjct: 5   LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 92  NGAQILGRTIRVDH 105
           NG ++  +TI+V +
Sbjct: 65  NGLRLQSKTIKVSY 78

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
           ++VGG+ +  T+  L + F+Q GE+VD  +++DK T + RGF FV ++D   N  G  + 
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP--NCVGTVLA 76
Query: 98  GRTIRVD 104
            R   +D
Sbjct: 77  SRPHTLD 83

>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex Length = 110

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           ++V  I  +  E ++   F   GEI +++L  D+ TG  +G+A V YE  +        L
Sbjct: 29  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 92  NGAQILGRTIRVD 104
           NGA+I+G+TI+VD
Sbjct: 89  NGAEIMGQTIQVD 101

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/52 (38%), Positives = 34/52 (65%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
          +++GG+ +D T+ DL   F++ GE+VD  L  D  TG+ RGF FV +++  +
Sbjct: 2  MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES 53

>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 = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 39/64 (60%)
Query: 34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNG 93
          D+  +++G IP +L E DL  +F + G+I ++ +++D+ TG  +G AF+ Y ++ + L  
Sbjct: 12 DAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Query: 94 AQIL 97
             L
Sbjct: 72 QSAL 75

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 40  VGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------EDQRNNLNG 93
           V  +P ++T+ +L ++F+  GE+    L+RDK  G   G+ FV Y      E   N LNG
Sbjct: 9   VNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNG 68
Query: 94  AQILGRTIRVDH 105
            ++  +TI+V +
Sbjct: 69  LRLQSKTIKVSY 80

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +P + T+ +L ++F+  GE+    L+RDK  G   G+ FV Y   +      N L
Sbjct: 22  LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 92  NGAQILGRTIRVDH 105
           NG ++  +TI+V +
Sbjct: 82  NGLRLQSKTIKVSY 95

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           D+  +YVG + +  T  +L A F  CG +  V ++ DK +G P+GFA++ + D+ +    
Sbjct: 5   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 90  -NLNGAQILGRTIRV 103
             L+ +   GR I+V
Sbjct: 65  LALDESLFRGRQIKV 79

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           D+  +YVG + +  T  +L A F  CG +  V ++ DK +G P+GFA++ + D+ +    
Sbjct: 4   DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 90  -NLNGAQILGRTIRV 103
             L+ +   GR I+V
Sbjct: 64  LALDESLFRGRQIKV 78

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+  V YE  +        L
Sbjct: 25  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 92  NGAQILGRTIRVD 104
           NG  ++G+ I VD
Sbjct: 85  NGQDLMGQPISVD 97

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+  V YE  +        L
Sbjct: 26  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 92  NGAQILGRTIRVD 104
           NG  ++G+ I VD
Sbjct: 86  NGQDLMGQPISVD 98

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 44/75 (58%), Gaps = 6/75 (8%)
Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN----- 90
           A VYVGG+   ++E  L  +F Q G +V+ ++ +D+ TG+ +G+ FV +  + +      
Sbjct: 16  ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 91  -LNGAQILGRTIRVD 104
            ++  ++ G+ IRV+
Sbjct: 76  IMDMIKLYGKPIRVN 90

>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 = 42.7 bits (99), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+  V YE  +        L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92  NGAQILGRTIRVD 104
           NG  ++G+ I VD
Sbjct: 70  NGQDLMGQPISVD 82

>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 = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 6/72 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE------DQRNNL 91
           +YV  +  DL++ D+ +VF   G+I    L RD  TGK +G+ F+ YE      D  +++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 92  NGAQILGRTIRV 103
           N   + G+ +RV
Sbjct: 188 NLFDLGGQYLRV 199

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+  V YE  +        L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92  NGAQILGRTIRVD 104
           NG  ++G+ I VD
Sbjct: 70  NGQDLMGQPISVD 82

>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 = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+  V YE  +        L
Sbjct: 12  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 92  NGAQILGRTIRVD 104
           NG  ++G+ I VD
Sbjct: 72  NGQDLMGQPISVD 84

>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 = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY------ED 86
           K S  +YVG + F  TE  +  +F++ G+I  + +  DK      GF FV Y      E+
Sbjct: 37  KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 96
Query: 87  QRNNLNGAQILGRTIRVD 104
               +NG ++  R IR D
Sbjct: 97  AMRYINGTRLDDRIIRTD 114

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           ++V  IPF   + DL  +F Q G+I+DV ++ ++   K  GF FV +E+       R  L
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREKL 89
Query: 92  NGAQILGRTIRVDH 105
           +G  + GR I V++
Sbjct: 90  HGTVVEGRKIEVNN 103

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 36/72 (50%), Gaps = 6/72 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNL 91
           VYVG I ++L E  +   FA  G I  +++  D  T K +GFAFV YE           +
Sbjct: 16  VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 92  NGAQILGRTIRV 103
           N   + GR I+V
Sbjct: 76  NSVMLGGRNIKV 87

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           ++V  IPF   + DL  +F Q G+I+DV ++ ++   K  GF FV +E+       R  L
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSK--GFGFVTFENSADADRAREKL 75
Query: 92  NGAQILGRTIRVDH 105
           +G  + GR I V++
Sbjct: 76  HGTVVEGRKIEVNN 89

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+  V YE  +        L
Sbjct: 10  LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 92  NGAQILGRTIRVD 104
           NG  ++G+ I VD
Sbjct: 70  NGQDLMGQPISVD 82

>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing Factor Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 55  VFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV 103
           VF + G + DV + R+  T  PRGFAFV + D+R+       ++GA++ GR +RV
Sbjct: 33  VFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV 87

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAY 84
          +++GG+ F+ TE  L   + Q G++ D  ++RD  + + RGF FV +
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 33 KDSAY--VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          KD+ +  ++VGG+P+  T+  L   F   G+I +  ++ D+ TGK RG+ FV   D
Sbjct: 13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 68

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          ++VGG+  + T  D+   F Q G++ D  L+ DK T + RGF FV +E +
Sbjct: 2  IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESE 51

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	291
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	7e-33
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	1e-32
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-32
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	7e-32
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	7e-29
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	1e-27
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	3e-27
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	9e-25
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-24
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	3e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-22
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	6e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	8e-22
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	2e-13
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	1e-21
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-21
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-14
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-21
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-21
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-20
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	2e-20
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-20
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-20
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-20
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	4e-20
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-20
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	5e-20
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	6e-20
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	6e-20
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-20
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	1e-19
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	1e-19
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	2e-19
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	3e-19
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	3e-19
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-19
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	7e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	8e-19
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-15
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-18
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	1e-12
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-09
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-18
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	2e-18
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	3e-18
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-18
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	4e-18
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	5e-18
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-18
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-14
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	9e-18
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	9e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	9e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-17
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-17
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	3e-17
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-17
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	6e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	7e-17
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-15
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	7e-17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	7e-17
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	1e-16
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	1e-16
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	1e-16
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-16
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	2e-16
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-11
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	3e-16
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-13
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	4e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-16
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-15
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	7e-16
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-16
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	9e-14
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	7e-16
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	9e-16
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	1e-15
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	1e-15
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-15
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-15
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	2e-15
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-15
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-15
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-15
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	6e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	7e-15
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-14
2dis_A	109	Unnamed protein product; structural genomics, RRM	8e-15
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	9e-15
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	9e-15
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	1e-14
2div_A	99	TRNA selenocysteine associated protein; structural	1e-14
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	1e-14
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-14
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-14
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	3e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-14
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-14
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-14
1x5o_A	114	RNA binding motif, single-stranded interacting pro	7e-14
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	8e-14
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-14
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-13
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-13
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-13
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	5e-12
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-13
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-13
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	2e-13
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-13
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-13
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-13
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	4e-13
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	8e-13
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	9e-13
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-12
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-12
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	2e-12
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	2e-12
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-12
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	8e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	4e-12
1x5p_A	97	Negative elongation factor E; structure genomics,	6e-12
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	7e-12
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	9e-12
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	1e-11
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-11
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	2e-11
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-06
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-11
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	4e-11
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	4e-11
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	5e-11
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	6e-11
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-11
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	7e-11
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	1e-10
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-10
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-10
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-10
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-10
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	4e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-10
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	7e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	8e-10
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	9e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	1e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-09
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-09
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-09
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	7e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	9e-09
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-08
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	1e-08
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-08
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-08
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	4e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	7e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	1e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-07
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	4e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	6e-06
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	4e-05
2rhk_C	72	Cleavage and polyadenylation specificity factor su	4e-05
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	6e-05
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	7e-05
2rpp_A	89	Muscleblind-like protein 2; zinc finger domain, C3	1e-04
2d9n_A	77	Cleavage and polyadenylation specificity factor, 3	1e-04
3d2n_A	83	Muscleblind-like protein 1; tandem zinc finger dom	3e-04
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-04
3d2q_A	70	Muscleblind-like protein 1; tandem zinc finger dom	7e-04

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score =  115 bits (291), Expect = 7e-33
 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 6/104 (5%)

Query: 13  INSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG 72
           +      +    D     +  +   ++V G+  + TE D+   FA+ GEI +++L  D+ 
Sbjct: 1   MREDYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRR 60

Query: 73  TGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYK 110
           TG  +G+  V YE  +        LNG  ++G+ I VD      
Sbjct: 61  TGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104

>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 =  115 bits (289), Expect = 1e-32
 Identities = 38/97 (39%), Positives = 53/97 (54%), Gaps = 6/97 (6%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR- 88
           A  +    V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 89  -----NNLNGAQILGRTIRVDHVAKYKKKEEEDEETR 120
                 NLNG +  GR +RVD+ A  K KEE      
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEELKSLGT 99

>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 =  113 bits (285), Expect = 4e-32
 Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 6/93 (6%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           S  VY+G IP+D TE  +L + +  G ++++ ++ D  TG+ +G+AF+ + D        
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61

Query: 89  NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQ 121
            NLNG Q+  R ++  + +         E    
Sbjct: 62  RNLNGYQLGSRFLKCGYSSNSDISGVSLEHHHH 94

>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 =  112 bits (283), Expect = 7e-32
 Identities = 26/86 (30%), Positives = 43/86 (50%), Gaps = 6/86 (6%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
                     + VYV  +PF LT  DL  +F++ G++V V +++DK T K +G AF+ + 
Sbjct: 7   GMSGGLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFL 66

Query: 86  DQR------NNLNGAQILGRTIRVDH 105
           D+         +N  Q+ GR I+   
Sbjct: 67  DKDSAQNCTRAINNKQLFGRVIKASI 92

>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 =  105 bits (264), Expect = 7e-29
 Identities = 30/112 (26%), Positives = 54/112 (48%), Gaps = 14/112 (12%)

Query: 6   QVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDV 65
             +R+++ +  E + G         +  +   ++V  I  +  E ++   F   GEI ++
Sbjct: 4   SYERVRNEDDDELEPG-------PQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 56

Query: 66  NLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKK 111
           +L  D+ TG  +G+A V YE  +        LNGA+I+G+TI+VD     K 
Sbjct: 57  HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW-CFVKG 107

>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 =  102 bits (257), Expect = 1e-27
 Identities = 29/111 (26%), Positives = 51/111 (45%), Gaps = 6/111 (5%)

Query: 20  LGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGF 79
           +    D     +  +   ++V G+  + TE D+   FA+ GEI +++L  D+ TG  +G+
Sbjct: 7   VEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGY 66

Query: 80  AFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
             V YE  +        LNG  ++G+ I VD        + +    R+R R
Sbjct: 67  TLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKGKRRGGRRRSR 117

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score =  102 bits (256), Expect = 3e-27
 Identities = 31/108 (28%), Positives = 49/108 (45%), Gaps = 6/108 (5%)

Query: 3   PLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEI 62
           P +      +   +  D G                +YVGG+  ++ +  L A F   G+I
Sbjct: 31  PESVAYTCVNCTERHVDGGSGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDI 90

Query: 63  VDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVD 104
            D+ +  D  T K RGFAFV +E         +N+N +++ GRTIRV+
Sbjct: 91  TDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN 138

>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 = 96.4 bits (240), Expect = 9e-25
 Identities = 31/128 (24%), Positives = 56/128 (43%), Gaps = 6/128 (4%)

Query: 1   MNPLTQVKRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG 60
               +  +   H   +  +    +      +  +   ++V  I  +  E ++   F   G
Sbjct: 38  FGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYG 97

Query: 61  EIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
           EI +++L  D+ TG  +G+A V YE  +        LNGA+I+G+TI+VD       K  
Sbjct: 98  EIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRV 157

Query: 115 EDEETRQR 122
           +  E R+R
Sbjct: 158 KKSEKRRR 165

>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 = 93.5 bits (233), Expect = 2e-24
 Identities = 23/95 (24%), Positives = 41/95 (43%), Gaps = 14/95 (14%)

Query: 25  DASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD--------VNLVRDKGTGKP 76
               H  + D+  ++V G+  ++T   +   F Q G I          +NL  D+ TGK 
Sbjct: 3   HHHHHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKL 62

Query: 77  RGFAFVAYEDQR------NNLNGAQILGRTIRVDH 105
           +G A V+++D        +  +G +  G  I+V  
Sbjct: 63  KGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSF 97

>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 = 90.3 bits (225), Expect = 3e-23
 Identities = 27/79 (34%), Positives = 46/79 (58%), Gaps = 6/79 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
            S+ +YVG + F++TE  L  +F   G+I ++ L++D  TG+ +G+ F+ + D       
Sbjct: 4   GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63

Query: 89  -NNLNGAQILGRTIRVDHV 106
              LNG ++ GR +RV HV
Sbjct: 64  LEQLNGFELAGRPMRVGHV 82

>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 = 88.4 bits (220), Expect = 1e-22
 Identities = 28/77 (36%), Positives = 43/77 (55%), Gaps = 6/77 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
               +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E        
Sbjct: 6   TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 65

Query: 89  -NNLNGAQILGRTIRVD 104
            +N+N +++ GRTIRV+
Sbjct: 66  IDNMNESELFGRTIRVN 82

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 86.9 bits (216), Expect = 6e-22
 Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 10/91 (10%)

Query: 23  SDDASWHAKYK---DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGF 79
           S  +S   +Y    +   +++ G+PF  T+ +L  +    G + D+ LV ++  GKP+G 
Sbjct: 2   SSGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGL 60

Query: 80  AFVAYEDQR------NNLNGAQILGRTIRVD 104
           A+V YE++         ++G  I    I+V 
Sbjct: 61  AYVEYENESQASQAVMKMDGMTIKENIIKVA 91

>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 = 86.4 bits (215), Expect = 8e-22
 Identities = 24/77 (31%), Positives = 42/77 (54%), Gaps = 5/77 (6%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--- 89
            D+  +YVG + +  T  +L A F  CG +  V ++ DK +G P+GFA++ + D+ +   
Sbjct: 4   ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 90  --NLNGAQILGRTIRVD 104
              L+ +   GR I+V 
Sbjct: 64  SLALDESLFRGRQIKVI 80

>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 = 88.1 bits (219), Expect = 1e-21
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++GG+P  L +  +  +    G +   NLV+D  TG  +G+AF  Y D          L
Sbjct: 97  LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156

Query: 92  NGAQILGRTIRVDH 105
           NG Q+  + + V  
Sbjct: 157 NGMQLGDKKLLVQR 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 = 66.1 bits (162), Expect = 2e-13
 Identities = 16/87 (18%), Positives = 33/87 (37%), Gaps = 10/87 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL-----VRDKGTGKPRGFAFVAYEDQRN--- 89
           +YVG IPF +TE  ++  F     +  +       V      + + FAF+ +        
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 90  --NLNGAQILGRTIRVDHVAKYKKKEE 114
               +G    G+++++     Y+    
Sbjct: 67  AMAFDGIIFQGQSLKIRRPHDYQPLPG 93

>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 = 88.0 bits (218), Expect = 1e-21
 Identities = 28/107 (26%), Positives = 48/107 (44%), Gaps = 7/107 (6%)

Query: 14  NSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT 73
                    S     H   +    + V  + +  +   L  VF + G + DV + RD+ T
Sbjct: 49  TKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 108

Query: 74  GKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEE 114
            + RGFAFV + D+R      + ++GA + GR +RV   A+Y +  +
Sbjct: 109 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM-ARYGRPPD 154

>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 = 86.1 bits (214), Expect = 1e-21
 Identities = 28/93 (30%), Positives = 46/93 (49%), Gaps = 7/93 (7%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
            S          + V  + +  +   L  VF + G + DV + R+  T  PRGFAFV + 
Sbjct: 4   GSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFH 63

Query: 86  DQR------NNLNGAQILGRTIRVDHVAKYKKK 112
           D+R        ++GA++ GR +RV  VA+Y ++
Sbjct: 64  DRRDAQDAEAAMDGAELDGRELRVQ-VARYGRR 95

>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 = 87.0 bits (216), Expect = 6e-21
 Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 6/77 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++GG+P  L +  +  +    G +   NLV+D  TG  +G+AF  Y D          L
Sbjct: 117 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 176

Query: 92  NGAQILGRTIRVDHVAK 108
           NG Q+  + + V   + 
Sbjct: 177 NGMQLGDKKLLVQRASV 193

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 69.7 bits (171), Expect = 2e-14
 Identities = 17/101 (16%), Positives = 35/101 (34%), Gaps = 10/101 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL-----VRDKGTGKPRGFAFVAYEDQRN--- 89
           +YVG IPF +TE  ++  F     +  +       V      + + FAF+ +        
Sbjct: 7   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 66

Query: 90  --NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
               +G    G+++++     Y+      E     +     
Sbjct: 67  AMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVS 107

>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 = 84.3 bits (209), Expect = 7e-21
 Identities = 25/89 (28%), Positives = 47/89 (52%), Gaps = 9/89 (10%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
            S   K  D+  +++G IP +L E DL  +F + G+I ++ +++D+ TG  +G AF+ Y 
Sbjct: 4   GSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYC 63

Query: 86  DQR------NNLNGAQIL---GRTIRVDH 105
           ++       + L+  + L    R I+V  
Sbjct: 64  ERESALKAQSALHEQKTLPGMNRPIQVKP 92

>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 = 83.8 bits (208), Expect = 9e-21
 Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 6/79 (7%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR---- 88
                +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E       
Sbjct: 10  TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 69

Query: 89  --NNLNGAQILGRTIRVDH 105
             +N+N +++ GRTIRV+ 
Sbjct: 70  AIDNMNESELFGRTIRVNL 88

>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 = 83.1 bits (206), Expect = 2e-20
 Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 7/90 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
             A VYVGG+   ++E  L  +F Q G +V+ ++ +D+ TG+ +G+ FV +  +      
Sbjct: 14  QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYA 73

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDE 117
              ++  ++ G+ IRV+  A    K     
Sbjct: 74  IKIMDMIKLYGKPIRVNK-ASAHNKNLSGP 102

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 84.4 bits (209), Expect = 2e-20
 Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  IP  + E  L  +F + G I  V +V D+ T + RG+ FV ++           L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 92  NGAQILGRTIRVDH 105
           NG  IL + ++V  
Sbjct: 105 NGFNILNKRLKVAL 118

>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 = 83.2 bits (206), Expect = 2e-20
 Identities = 30/110 (27%), Positives = 47/110 (42%), Gaps = 15/110 (13%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEI--------VDVNLVRDKG 72
           G S  +    +  D++ +YV G+   +T  DL   F QCG +          +++  DK 
Sbjct: 1   GSSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKE 60

Query: 73  TGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEEED 116
           TGKP+G A V+YED           +G    G  ++V   A+ K      
Sbjct: 61  TGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSL-ARKKPPMNSG 109

>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 = 82.7 bits (205), Expect = 3e-20
 Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 6/103 (5%)

Query: 10  IQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVR 69
           + H +   + +  +   +          +YVG + F++TE  L  +F   G I  + L+ 
Sbjct: 1   MGHHHHHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60

Query: 70  DKGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRVDHV 106
           D  TG+ +G+ F+ + D          LNG ++ GR ++V HV
Sbjct: 61  DSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV 103

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 82.8 bits (205), Expect = 3e-20
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 6/87 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V    +  ++ E  L  +  + GE+ +V ++    T K  G A V +   R       NL
Sbjct: 9   VTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNL 68

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEE 118
           +   ++G  I      K +++ +  E 
Sbjct: 69  HLTSVMGNIIHAQLDIKGQQRMKYYEL 95

>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 = 81.9 bits (203), Expect = 4e-20
 Identities = 24/86 (27%), Positives = 40/86 (46%), Gaps = 7/86 (8%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
             + A+ +    V+VG +   + E  L  +F Q G +  V + +D+  GKP+ F FV ++
Sbjct: 7   GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFK 65

Query: 86  DQR------NNLNGAQILGRTIRVDH 105
                      LNG ++ GR I V  
Sbjct: 66  HPESVSYAIALLNGIRLYGRPINVSG 91

>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 = 81.9 bits (203), Expect = 5e-20
 Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 7/97 (7%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +  + +  D+A + V  +  D  E DL  +F   G I  + L +DK TG+ +GFA
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFA 60

Query: 81  FVAYEDQR------NNLNGAQILGRTIRVDHVAKYKK 111
           F+++  +         ++G       + V+  AK   
Sbjct: 61  FISFHRREDAARAIAGVSGFGYDHLILNVE-WAKPST 96

>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 = 81.9 bits (203), Expect = 5e-20
 Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 7/90 (7%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR---- 88
             S  ++V  + +  +E DL  +F+  G + +++   D  T KP+GFAFV +        
Sbjct: 6   SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVK 65

Query: 89  --NNLNGAQILGRTIRVDHVAKYKKKEEED 116
               ++G    GR + V   +  KK+  + 
Sbjct: 66  AYAEVDGQVFQGRMLHVLP-STIKKEASQS 94

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 81.5 bits (202), Expect = 6e-20
 Identities = 29/84 (34%), Positives = 50/84 (59%), Gaps = 7/84 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
            YVG +PF+  +GD+ A+F     I  V LVRDK T K +GF +V +++  +       +
Sbjct: 18  AYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYD 76

Query: 93  GAQILGRTIRVDHVAKYKKKEEED 116
           GA +  R++RVD +A+ +K+++  
Sbjct: 77  GALLGDRSLRVD-IAEGRKQDKSG 99

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 81.5 bits (202), Expect = 6e-20
 Identities = 28/74 (37%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E+           
Sbjct: 18  LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77

Query: 92  NGAQILGRTIRVDH 105
           NG ++ GR IRV  
Sbjct: 78  NGMELDGRRIRVSG 91

>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 = 80.7 bits (200), Expect = 9e-20
 Identities = 16/76 (21%), Positives = 41/76 (53%), Gaps = 7/76 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG-TGKPRGFAFVAYEDQR------NN 90
           V++G +  ++T+  ++ +F+  G+I  +++  ++      +G+A+V +E+         +
Sbjct: 7   VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66

Query: 91  LNGAQILGRTIRVDHV 106
           ++G QI G+ I    V
Sbjct: 67  MDGGQIDGQEITATAV 82

>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 = 82.6 bits (205), Expect = 1e-19
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 6/84 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +P D+T+ +L A+F   G I    ++RD  TG   G+AFV +  +         L
Sbjct: 6   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65

Query: 92  NGAQILGRTIRVDHVAKYKKKEEE 115
           NG  +  + ++V +     +  ++
Sbjct: 66  NGITVRNKRLKVSYARPGGESIKD 89

>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 = 70.7 bits (174), Expect = 4e-15
 Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 8/74 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV  +P  +T+  L  +F + G IV  N++RDK TG+PRG AFV Y  +       + L
Sbjct: 92  LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151

Query: 92  NGAQILGRT--IRV 103
           N     G +  + V
Sbjct: 152 NNVIPEGGSQPLSV 165

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 81.3 bits (201), Expect = 1e-19
 Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 5/79 (6%)

Query: 31  KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN- 89
           K  D   VYVG + +  T  DL A F+ CG I  + ++ DK +G P+G+A++ + ++ + 
Sbjct: 32  KEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSV 91

Query: 90  ----NLNGAQILGRTIRVD 104
                ++     GRTI+V 
Sbjct: 92  DAAVAMDETVFRGRTIKVL 110

>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 = 79.9 bits (198), Expect = 2e-19
 Identities = 25/89 (28%), Positives = 45/89 (50%), Gaps = 8/89 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR-----NNLN 92
           +YVG + +  T   +  +F+Q G++ +V L+ D+ T KP+GF FV  +++        L+
Sbjct: 4   IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLD 63

Query: 93  GAQILGRTIRVDHVAKYKKKEEEDEETRQ 121
               +GRTIRV    +   K+  +     
Sbjct: 64  NTDFMGRTIRVT---EANPKKSLEHHHHH 89

>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 = 80.0 bits (198), Expect = 3e-19
 Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 6/78 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           D   ++VGG+ FD  E  L  VF++ G+I +V +V+D+ T + RGF FV +E+       
Sbjct: 11  DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70

Query: 89  -NNLNGAQILGRTIRVDH 105
              +NG  + GR IRVD 
Sbjct: 71  MMAMNGKSVDGRQIRVDQ 88

>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 = 80.4 bits (199), Expect = 3e-19
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 5/78 (6%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--- 89
           +D+  V+   +   +   DL   F+  G++ DV ++ D+ + + +G A+V + + ++   
Sbjct: 23  RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 82

Query: 90  --NLNGAQILGRTIRVDH 105
              L G ++LG  I V  
Sbjct: 83  AIGLTGQRLLGVPIIVQA 100

>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 = 78.7 bits (195), Expect = 5e-19
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 6/76 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
            S+ +Y+ G+    T+ DL+ +    G+IV    + DK T K +G+ FV ++        
Sbjct: 4   GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKA 63

Query: 89  -NNLNGAQILGRTIRV 103
              L  + +  +  + 
Sbjct: 64  VTALKASGVQAQMAKQ 79

>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 = 79.3 bits (196), Expect = 7e-19
 Identities = 24/102 (23%), Positives = 50/102 (49%), Gaps = 13/102 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +Y+  +P+ +T  ++  +F + G I     +R   T + RG A+V YED        ++L
Sbjct: 11  LYIRNLPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67

Query: 92  NGAQILGRTIRVDHVAKYKKKEEED----EETRQRMREERGV 129
           +G  +  R + V +    +  ++ D    EE  + ++E+ G+
Sbjct: 68  SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGI 109

>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 = 80.7 bits (200), Expect = 8e-19
 Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 6/75 (8%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
              + V  +P ++T+ +  ++F   GEI    LVRDK TG+  G+ FV Y D +      
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 89  NNLNGAQILGRTIRV 103
           N LNG ++  +TI+V
Sbjct: 62  NTLNGLRLQTKTIKV 76

>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 = 69.9 bits (172), Expect = 7e-15
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 8/78 (10%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
             A +YV G+P  +T+ +L  +F+Q G I+   ++ D+ TG  RG  F+ ++ +      
Sbjct: 87  RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA 146

Query: 89  -NNLNGAQILGRT--IRV 103
              LNG +  G T  I V
Sbjct: 147 IKGLNGQKPSGATEPITV 164

>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 = 83.1 bits (206), Expect = 1e-18
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 6/94 (6%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ----- 87
              A + V  +P  LT+     +    G +    LV  + TG+ +G+ F  Y  +     
Sbjct: 93  PTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR 152

Query: 88  -RNNLNGAQILGRTIRVDHVAKYKKKEEEDEETR 120
            +++L G  +  RT+ V      +          
Sbjct: 153 AKSDLLGKPLGPRTLYVHWTDAGQLTPALLHSRC 186

>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 = 65.4 bits (160), Expect = 1e-12
 Identities = 15/98 (15%), Positives = 30/98 (30%), Gaps = 12/98 (12%)

Query: 38  VYVGGIPFDLTEGDLL-AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNN 90
           + V  +P    + D L    +         L   +  G+ +GFA + YE        +  
Sbjct: 187 LCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQ 245

Query: 91  LNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
            +G  + G  +RV     +             +   + 
Sbjct: 246 ADGLSLGGSHLRVS----FCAPGPPGRSMLAALIAAQA 279

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 56.1 bits (136), Expect = 2e-09
 Identities = 13/99 (13%), Positives = 38/99 (38%), Gaps = 16/99 (16%)

Query: 11  QHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRD 70
             ++ +E    +        ++++   + + G+P D+T  ++  + +          ++ 
Sbjct: 1   HMLDPEEIRKRLEHTE---RQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-------LKY 50

Query: 71  KGTGKPRGFAFVAYEDQR------NNLNGAQILGRTIRV 103
               K +G AFV   +        N  + +++  R + V
Sbjct: 51  CFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSV 89

>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 = 78.5 bits (194), Expect = 1e-18
 Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 10/97 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++GG+  +  E  L AVF + G I +V L++D+ T K RGFAF+ +E+         ++
Sbjct: 10  LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
           NG  + G+ I+V+     KK   +    R+     R 
Sbjct: 69  NGKSLHGKAIKVEQA---KKPSFQSGGRRRPPASSRN 102

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 81.2 bits (201), Expect = 2e-18
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV  +  DL++ D+ +VF   G+I    L RD  TGK +G+ F+ YE  +      +++
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187

Query: 92  NGAQILGRTIRVDHVAK 108
           N   + G+ +RV     
Sbjct: 188 NLFDLGGQYLRVGKAVT 204

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 80.1 bits (198), Expect = 3e-18
 Identities = 27/98 (27%), Positives = 44/98 (44%), Gaps = 6/98 (6%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
             + VYVG I ++L E  +   FA  G I  +++  D  T K +GFAFV YE        
Sbjct: 27  IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMRE 125
              +N   + GR I+V   +   + +   ++  +  R 
Sbjct: 87  LEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARA 124

>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 = 77.2 bits (191), Expect = 2e-18
 Identities = 16/77 (20%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           +  ++VG +  ++ +  L   F      +  +++ D  TG  RG+ FV++  Q       
Sbjct: 1   TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60

Query: 89  NNLNGAQILGRTIRVDH 105
           +++ G  + GR +R++ 
Sbjct: 61  DSMQGQDLNGRPLRINW 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 = 77.9 bits (192), Expect = 4e-18
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 7/85 (8%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
               + V  + +  +   L  VF + G + DV + RD+ T + RGFAFV + D+R     
Sbjct: 46  GMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDA 105

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKK 112
            + ++GA + GR +RV   A+Y + 
Sbjct: 106 MDAMDGAVLDGRELRVQM-ARYGRP 129

>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 = 77.0 bits (190), Expect = 5e-18
 Identities = 22/97 (22%), Positives = 37/97 (38%), Gaps = 12/97 (12%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +   +   +   V++  + FD  E  L  V  Q G++  V +V    T   +G A
Sbjct: 1   GSSGSSGLPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCA 60

Query: 81  FVAYEDQ------------RNNLNGAQILGRTIRVDH 105
           F  +  Q                 G ++ GR ++VD 
Sbjct: 61  FAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDL 97

>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 = 78.3 bits (194), Expect = 5e-18
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGGI  D+   +    F+Q G I+D  L+ DK TG+ RGF FV Y+            
Sbjct: 90  IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNK 149

Query: 93  GAQILGRTIRVD 104
                 R I + 
Sbjct: 150 FIDFKDRKIEIK 161

>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 = 67.9 bits (167), Expect = 4e-14
 Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 14/81 (17%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------ 86
           K+S  +++GG+ +D TE +L   F + G + D+ +++D  TG+ RGF F+++E       
Sbjct: 1   KESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60

Query: 87  ---QRNNLNGAQILGRTIRVD 104
               ++ L+     G+ I   
Sbjct: 61  VVKTQHILD-----GKVIDPK 76

>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 = 75.3 bits (186), Expect = 9e-18
 Identities = 23/74 (31%), Positives = 39/74 (52%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V+VG +  ++T   + A FA  G I D  +V+D  TGK +G+ FV++ ++         +
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68

Query: 92  NGAQILGRTIRVDH 105
            G  + GR IR + 
Sbjct: 69  GGQWLGGRQIRTNW 82

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 76.1 bits (188), Expect = 9e-18
 Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 8/85 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG-TGKPRGFAFVAYEDQRN-----NL 91
            ++G +P+D+TE  +   F     I  V L R+     + +GF +  +ED  +     +L
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 76

Query: 92  NGAQILGRTIRVDHVAKYKKKEEED 116
           N   +  + IRVD VA   + ++  
Sbjct: 77  NEESLGNKRIRVD-VADQAQDKDSG 100

>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 = 75.7 bits (187), Expect = 9e-18
 Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 8/77 (10%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
               +YVG +  D+TE  +L +F+Q G      ++ +  +     + FV + + R     
Sbjct: 14  QPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAA 71

Query: 89  -NNLNGAQILGRTIRVD 104
              +NG +ILG+ ++V+
Sbjct: 72  LAAMNGRKILGKEVKVN 88

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 75.9 bits (187), Expect = 1e-17
 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++  +P + T+ DL + F   G ++   +  DK T   + F FV++++          +
Sbjct: 43  LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102

Query: 92  NGAQILGRTIRV 103
           NG Q+  + ++V
Sbjct: 103 NGFQVGTKRLKV 114

>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 = 75.0 bits (185), Expect = 2e-17
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT-GKPRGFAFVAYEDQRN-----NL 91
            ++G +P+D+TE  +   F     I  V L R+     + +GF +  +ED  +     +L
Sbjct: 22  AFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSL 80

Query: 92  NGAQILGRTIRVD 104
           N   +  R IRVD
Sbjct: 81  NEESLGNRRIRVD 93

>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 = 75.1 bits (185), Expect = 3e-17
 Identities = 27/97 (27%), Positives = 48/97 (49%), Gaps = 9/97 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V+VG +  ++T  D+ A FA  G I D  +V+D  TGK +G+ FV++ ++         +
Sbjct: 18  VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
            G  + GR IR +      +K    + T +   ++ G
Sbjct: 78  GGQWLGGRQIRTNWA---TRKPPAPKSTYESNTKQSG 111

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 74.3 bits (183), Expect = 3e-17
 Identities = 20/73 (27%), Positives = 28/73 (38%), Gaps = 12/73 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
            Y+G IP   TE DL+ +F   G I+D     +K      G  F+ Y+           L
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEK------GCCFIKYDTHEQAAVCIVAL 83

Query: 92  NGAQILGRTIRVD 104
                 GR +R  
Sbjct: 84  ANFPFQGRNLRTG 96

>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 = 74.4 bits (183), Expect = 6e-17
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 6/78 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
            +  + V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E+       
Sbjct: 45  PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 104

Query: 89  -NNLNGAQILGRTIRVDH 105
               NG ++ GR IRVD 
Sbjct: 105 KERANGMELDGRRIRVDF 122

>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 = 76.5 bits (189), Expect = 7e-17
 Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVG +  D+TE  L   F+  G I+ + + RD  T +  G+A+V ++         + +
Sbjct: 18  LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77

Query: 92  NGAQILGRTIRVD 104
           N   I G+ +R+ 
Sbjct: 78  NFDVIKGKPVRIM 90

>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 = 71.2 bits (175), Expect = 5e-15
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 8/93 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++  +   +    L   F+  G I+   +V D      +G+ FV +E Q         +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKM 163

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
           NG  +  R + V      K++E E     +   
Sbjct: 164 NGMLLNDRKVFVGRFKSRKEREAELGARAKEFY 196

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 74.0 bits (182), Expect = 7e-17
 Identities = 24/110 (21%), Positives = 43/110 (39%), Gaps = 15/110 (13%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEI--------VDVNLVRDKGTGKPRGFAFVAY 84
            D+  ++V G+  ++T   +   F Q G I          +NL  D+ TGK +G A V++
Sbjct: 5   SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSF 64

Query: 85  EDQR------NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
           +D        +  +G +  G  I+V   A  +          +   E   
Sbjct: 65  DDPPSAKAAIDWFDGKEFSGNPIKVSF-ATRRADFNRGGGNGRGGLEHHH 113

>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 = 73.9 bits (182), Expect = 7e-17
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 10/84 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++  +P +  + DLL +F   G +V   +  DK T   + F FV+Y++         ++
Sbjct: 28  LFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSM 87

Query: 92  NGAQILGRTIRVDHVAKYKKKEEE 115
           NG QI  + ++V    + K+ + +
Sbjct: 88  NGFQIGMKRLKV----QLKRSKND 107

>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 = 73.1 bits (180), Expect = 1e-16
 Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 8/92 (8%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK-GTGKPRGF 79
           G S  +    K + ++ + V  IPF   + ++  +F+  GE+  V L +   GTG  RGF
Sbjct: 1   GSSGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGF 60

Query: 80  AFVAYEDQR------NNL-NGAQILGRTIRVD 104
            FV +  ++      N L +   + GR + ++
Sbjct: 61  GFVDFITKQDAKKAFNALCHSTHLYGRRLVLE 92

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 72.8 bits (179), Expect = 1e-16
 Identities = 18/93 (19%), Positives = 42/93 (45%), Gaps = 13/93 (13%)

Query: 37  YVYVGGIP------FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR-- 88
           Y+ V G P        + +  L ++F++ G++V++    D+ TGK +GF FV        
Sbjct: 8   YIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDA 67

Query: 89  ----NNLNGAQILGR-TIRVDHVAKYKKKEEED 116
                + +G ++  +  + +  +   ++   +D
Sbjct: 68  KKIIKSFHGKRLDLKHRLFLYTMKDVERYNSDD 100

>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 = 72.7 bits (179), Expect = 1e-16
 Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 24  DDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVA 83
           +D    ++      +++G +  + +  +L    ++     D+  V D  TG  R F +V 
Sbjct: 6   EDPVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVD 64

Query: 84  YEDQRN-----NLNGAQILGRTIRVD 104
           +E   +      L G ++ G  I+++
Sbjct: 65  FESAEDLEKALELTGLKVFGNEIKLE 90

>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 = 72.3 bits (178), Expect = 2e-16
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 11/83 (13%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR- 88
            K + +  +    + F++TE +L  VF    EI           GK +G A++ ++ +  
Sbjct: 11  KKVRAARTLLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEAD 65

Query: 89  -----NNLNGAQILGRTIRVDHV 106
                    GA+I GR++ + + 
Sbjct: 66  AEKNLEEKQGAEIDGRSVSLYYT 88

>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 = 72.7 bits (179), Expect = 2e-16
 Identities = 20/80 (25%), Positives = 42/80 (52%), Gaps = 7/80 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +Y+  +   +TE DL+++FA+  E     +     TG+ RG AF+ + ++       + +
Sbjct: 28  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87

Query: 92  NGAQILGRTIRVDHVAKYKK 111
           NG ++ G+ + ++   K KK
Sbjct: 88  NGYKLYGKILVIEF-GKNKK 106

>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 = 73.7 bits (181), Expect = 2e-16
 Identities = 30/112 (26%), Positives = 46/112 (41%), Gaps = 13/112 (11%)

Query: 23  SDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV 82
            D+       K S  +YVG + F  TE  +  +F++ G+I  + +  DK      GF FV
Sbjct: 27  GDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFV 86

Query: 83  AYEDQR------NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
            Y  +         +NG ++  R IR D        +   +E RQ  R   G
Sbjct: 87  EYYSRADAENAMRYINGTRLDDRIIRTD-------WDAGFKEGRQYGRGRSG 131

>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 = 76.2 bits (188), Expect = 3e-16
 Identities = 14/90 (15%), Positives = 31/90 (34%), Gaps = 6/90 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           +++   P   T+ ++  +      +     +        R FA++    +         L
Sbjct: 120 LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 179

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQ 121
           NG +I G T+        +K +  D  T +
Sbjct: 180 NGLKIEGYTLVTKVSNPLEKSKRTDSATLE 209

>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 = 62.7 bits (153), Expect = 2e-11
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 7/74 (9%)

Query: 38  VYVGGIPFDLT-EGDLLAVFAQCGEIVDVNLVRD-KGTGKPRGFAFVAYEDQRN-----N 90
           + +  +  +L  E  L   F   G I  +N+    K        AF+ +E++ +      
Sbjct: 213 IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 272

Query: 91  LNGAQILGRTIRVD 104
           +N + +  R I V 
Sbjct: 273 MNRSLLGNREISVS 286

>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 = 61.5 bits (150), Expect = 3e-11
 Identities = 14/77 (18%), Positives = 26/77 (33%), Gaps = 9/77 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V V  +P    +  +   F  CG I+ V++       K   FA + +             
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADS--LKKNFRFARIEFARYDGALAAITKT 101

Query: 92  NGAQILGRTIRVDHVAK 108
           +   +    I V H+ +
Sbjct: 102 HK-VVGQNEIIVSHLTE 117

>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 = 74.3 bits (183), Expect = 3e-16
 Identities = 28/96 (29%), Positives = 43/96 (44%), Gaps = 12/96 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D  +        
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 166

Query: 93  GAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
              + G    V       +K    +E       +RG
Sbjct: 167 YHTVNGHNCEV-------RKALSKQEMASASSSQRG 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 = 66.5 bits (163), Expect = 2e-13
 Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ F+ T+  L + F Q G + D  ++RD  T + RGF FV Y          N  
Sbjct: 16  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 75

Query: 93  GAQILGRTIRVD 104
             ++ GR +   
Sbjct: 76  PHKVDGRVVEPK 87

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 71.1 bits (175), Expect = 4e-16
 Identities = 15/76 (19%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQR------N 89
           +Y+G + +  T+ DL       G  +I+++    ++  G+ +GFA V    +       +
Sbjct: 4   LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 63

Query: 90  NLNGAQILGRTIRVDH 105
            L   ++ G+   V  
Sbjct: 64  LLPKRELHGQNPVVTP 79

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 72.9 bits (180), Expect = 6e-16
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVG +   +TE  L   F   G I ++ ++ DK   K   +AFV Y            L
Sbjct: 3   LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61

Query: 92  NGAQILGRTIRVD 104
           NG QI    ++++
Sbjct: 62  NGKQIENNIVKIN 74

>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 = 70.2 bits (173), Expect = 5e-15
 Identities = 17/77 (22%), Positives = 38/77 (49%), Gaps = 6/77 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           D+  ++VG +  ++ +  L   F      +  +++ D  TG  RG+ FV++  Q      
Sbjct: 86  DTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNA 145

Query: 89  -NNLNGAQILGRTIRVD 104
            +++ G  + GR +R++
Sbjct: 146 MDSMQGQDLNGRPLRIN 162

>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 = 70.7 bits (174), Expect = 7e-16
 Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 8/88 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED----QRNNLNG 93
           V+VGGI   + E ++ + FA+ G + +V ++ D+ TG  +G+ FV++ +    Q+   + 
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70

Query: 94  AQILGRTIRVDHVAKYKKKEEEDEETRQ 121
               G+ ++   +    +K+       Q
Sbjct: 71  INFHGKKLK---LGPAIRKQNLSTYHVQ 95

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 69.8 bits (172), Expect = 7e-16
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGG+  + T  D+   F Q G++ D  L+ DK T + RGF FV +E +        ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 93  GAQILGRTIRVD 104
             +I  + +   
Sbjct: 62  FHEINNKMVECK 73

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 72.6 bits (179), Expect = 7e-16
 Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 9/88 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP--RGFAFVAYEDQR------N 89
           ++VG +P   +E DL  +F Q G + ++N++RD+    P  +G  FV +  ++      N
Sbjct: 6   MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65

Query: 90  NLNGAQILGRTIRVDHVAKYKKKEEEDE 117
            L+  ++L        + K    E+ + 
Sbjct: 66  ALHNMKVLPGMHHPIQM-KPADSEKNNA 92

>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 = 66.9 bits (164), Expect = 9e-14
 Identities = 18/75 (24%), Positives = 34/75 (45%), Gaps = 10/75 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           +++G I    TE D+  +F+  G+I +  ++R    G  RG AFV +  +         +
Sbjct: 98  LFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAM 156

Query: 92  NGAQIL---GRTIRV 103
           + AQ +      + V
Sbjct: 157 HQAQTMEGCSSPMVV 171

>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 = 70.8 bits (174), Expect = 7e-16
 Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 10/78 (12%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           +S  + +  + +  TE  L  VF +   I     V     GK +G+AF+ +         
Sbjct: 14  ESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEA 69

Query: 89  -NNLNGAQILGRTIRVDH 105
            N+ N  +I GR IR++ 
Sbjct: 70  LNSCNKREIEGRAIRLEL 87

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 70.3 bits (173), Expect = 9e-16
 Identities = 22/72 (30%), Positives = 42/72 (58%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGGIP +  E +L   F + G + +V ++ D    +PRGF F+ +ED+++     N++
Sbjct: 13  IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72

Query: 93  GAQILGRTIRVD 104
              I+G+ + V 
Sbjct: 73  FHDIMGKKVEVK 84

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 70.0 bits (172), Expect = 1e-15
 Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 12/88 (13%)

Query: 29  HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYED 86
           H  +     + +  I        ++   +      + ++ L++DK T + RGFAFV    
Sbjct: 3   HHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSS 62

Query: 87  QR------NNLNGAQ----ILGRTIRVD 104
                     L        I G+TI VD
Sbjct: 63  AMDASQLLQILQSLHPPLKIDGKTIGVD 90

>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 = 70.4 bits (173), Expect = 1e-15
 Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 11/98 (11%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
            S  +++  +   +    L   F+  G I+   +V D+   K  G+ FV +E Q      
Sbjct: 4   GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSK--GYGFVHFETQEAAERA 61

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMRE 125
              +NG  +  R + V     +K ++E + E   R +E
Sbjct: 62  IEKMNGMLLNDRKVFVGR---FKSRKEREAELGARAKE 96

>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 = 70.0 bits (172), Expect = 1e-15
 Identities = 21/81 (25%), Positives = 35/81 (43%), Gaps = 9/81 (11%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR- 88
           A+ + S  ++V G+  D TE  L   F      V   +V D+ TG  +GF FV +  +  
Sbjct: 10  ARSQPSKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEED 66

Query: 89  -----NNLNGAQILGRTIRVD 104
                  +   +I G  + +D
Sbjct: 67  AKAAKEAMEDGEIDGNKVTLD 87

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 69.7 bits (171), Expect = 2e-15
 Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 12/72 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           VY GGI   LT+  +   F+  G+I+++ +  +K      G++FV +    +      ++
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSV 81

Query: 92  NGAQILGRTIRV 103
           NG  I G  ++ 
Sbjct: 82  NGTTIEGHVVKC 93

>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 = 69.6 bits (171), Expect = 2e-15
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 8/74 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           ++V  IPF   + DL  +F Q G+I+DV ++ ++     +GF FV +E+       R  L
Sbjct: 18  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 75

Query: 92  NGAQILGRTIRVDH 105
           +G  + GR I V++
Sbjct: 76  HGTVVEGRKIEVNN 89

>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 = 68.7 bits (169), Expect = 2e-15
 Identities = 16/49 (32%), Positives = 26/49 (53%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
          ++VGG+  D  E  +   F   GE+  + L  D  T K RGF F+ +++
Sbjct: 2  IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKE 50

>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 = 68.8 bits (169), Expect = 4e-15
 Identities = 19/73 (26%), Positives = 37/73 (50%), Gaps = 12/73 (16%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           ++VG +P D+TE ++  +F + G+  +V + +DK      GF F+  E +         L
Sbjct: 18  LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK------GFGFIRLETRTLAEIAKVEL 71

Query: 92  NGAQILGRTIRVD 104
           +   + G+ +RV 
Sbjct: 72  DNMPLRGKQLRVR 84

>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 = 6e-15
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V  +PFD T   L   F +CG ++  ++  +   GK +G   V +E           +
Sbjct: 11  IFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMM 68

Query: 92  NGAQILGRTIRV 103
           NG ++ GR I V
Sbjct: 69  NGMKLSGREIDV 80

>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 = 68.1 bits (167), Expect = 6e-15
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +PF ++  ++L  F     I     ++    G P G A VA+E +        +L
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 92  NGAQILGRTIRV 103
           N   I  R +++
Sbjct: 78  NDRPIGSRKVKL 89

>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 = 69.9 bits (172), Expect = 7e-15
 Identities = 16/92 (17%), Positives = 37/92 (40%), Gaps = 6/92 (6%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--- 89
                +++G +  + +  +L    ++     D+ +V  + TG  R F +V +E   +   
Sbjct: 11  TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEK 69

Query: 90  --NLNGAQILGRTIRVDHVAKYKKKEEEDEET 119
              L G ++ G  I+++       K+     T
Sbjct: 70  ALELTGLKVFGNEIKLEKPKGRDSKKVRAART 101

>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 = 69.6 bits (171), Expect = 1e-14
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 11/77 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +    + F++TE +L  VF    EI           GK +G A++ ++ + +        
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEK 156

Query: 92  NGAQILGRTIRVDHVAK 108
            GA+I GR++ + +  +
Sbjct: 157 QGAEIDGRSVSLYYTGE 173

>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 = 68.3 bits (167), Expect = 8e-15
 Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 13/97 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIV-DVNLVRDKG-TGKPRGFAFVAYEDQRN------ 89
           +++GGIP      ++L   A+  E V DV +        K RGFAFV YE  R       
Sbjct: 11  LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 70

Query: 90  --NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
                  Q+ G  I VD     + + + DE+  + + 
Sbjct: 71  KLMPGRIQLWGHQIAVDWA---EPEIDVDEDVMETVS 104

>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 = 67.7 bits (166), Expect = 9e-15
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +PF ++  ++L  F     I     ++    G P G A VA+E +        +L
Sbjct: 18  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77

Query: 92  NGAQILGRTIRVD 104
           N   I  R +++ 
Sbjct: 78  NDRPIGSRKVKLV 90

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 67.1 bits (165), Expect = 9e-15
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ +  T+  L   F Q GE+ +  ++RD  T + RGF FV + DQ         +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 93  GAQILGRTIRVDH 105
             ++  +TI    
Sbjct: 63  RHELDSKTIDPKV 75

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 69.2 bits (169), Expect = 1e-14
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQR------N 89
           VYVG   +  T+  L+ V    G  ++V++    ++  G+ +G+A V    +        
Sbjct: 58  VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117

Query: 90  NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQR 122
            L G  + G  + V    +    + E +  ++ 
Sbjct: 118 LLPGKVLNGEKVDVRPATRQNLSQFEAQARKRE 150

>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 = 67.3 bits (165), Expect = 1e-14
 Identities = 21/85 (24%), Positives = 41/85 (48%), Gaps = 12/85 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIV-DVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           +++G +   + E  +   FA  GE V  V ++R++ TG P G+ FV + D        + 
Sbjct: 12  LWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHK 71

Query: 91  LNGAQILG----RTIRVDHVAKYKK 111
           +NG  + G    +  ++++ A Y  
Sbjct: 72  INGKPLPGATPAKRFKLNY-ATYSG 95

>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 = 67.7 bits (166), Expect = 1e-14
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  + F +++ D+  +FA+ G +    +  D+ +G+  G A V +E +          
Sbjct: 32  LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 90

Query: 92  NGAQILGRTIRVDHV 106
           NG  + GR + +  V
Sbjct: 91  NGVPLDGRPMNIQLV 105

>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 = 67.6 bits (165), Expect = 1e-14
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 13/85 (15%)

Query: 38  VYVGGIPFDLTEGDLLA---VFAQCGEIVDVNLVRDKGTGK---PRGFAFVAYEDQR--- 88
           V+V G+   L + ++L     F + G+I  V +           P   A+V Y       
Sbjct: 18  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 77

Query: 89  ---NNLNGAQILGRTIRVDH-VAKY 109
                +N   + GRT++      KY
Sbjct: 78  RAIQCVNNVVVDGRTLKASLGTTKY 102

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 8/74 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNL 91
           ++V  IPF   + DL  +F Q G+I+DV ++ ++     +GF FV +E+       R  L
Sbjct: 32  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89

Query: 92  NGAQILGRTIRVDH 105
           +G  + GR I V++
Sbjct: 90  HGTVVEGRKIEVNN 103

>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 = 66.5 bits (163), Expect = 3e-14
 Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 9/82 (10%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKP---RGFAFVAYEDQR- 88
             S+ +++  + F  TE  L  VF++ G I    + + K         GF FV Y+    
Sbjct: 3   SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62

Query: 89  -----NNLNGAQILGRTIRVDH 105
                  L G  + G  + V  
Sbjct: 63  AQKALKQLQGHTVDGHKLEVRI 84

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 65.9 bits (161), Expect = 4e-14
 Identities = 18/94 (19%), Positives = 30/94 (31%), Gaps = 17/94 (18%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
               + +  IP  L    L ++  Q G +     V             V Y  +      
Sbjct: 14  RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET---AVVNVTYSSKDQARQA 70

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQ 121
            + LNG Q+   T++V ++         DE   Q
Sbjct: 71  LDKLNGFQLENFTLKVAYI--------PDEMAAQ 96

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 65.3 bits (160), Expect = 5e-14
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 13/83 (15%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +Y+G +   +T  DL  +F      +              G+AFV Y DQ         L
Sbjct: 11  LYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIETL 64

Query: 92  NG-AQILGRTIRVDHVAKYKKKE 113
           +G  ++ G+ + VD+    K + 
Sbjct: 65  SGKVELHGKIMEVDYSVSKKLRS 87

>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 = 68.6 bits (167), Expect = 6e-14
 Identities = 18/99 (18%), Positives = 40/99 (40%), Gaps = 8/99 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQR------N 89
           +Y+G + +  T+ DL       G  +I+++    ++  G+ +GFA V    +       +
Sbjct: 71  LYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMD 130

Query: 90  NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
            L   ++ G+   V  V K    + E +  +     +  
Sbjct: 131 LLPKRELHGQNPVVTPVNKQFLSQFEMQSRKTTQSGQMS 169

>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 = 65.7 bits (161), Expect = 7e-14
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 7/76 (9%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           D   +Y+  +P  + E +L  +    G+++   ++RD  +G  RG  F   E        
Sbjct: 24  DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAV 82

Query: 89  -NNLNGAQILGRTIRV 103
             + NG  I       
Sbjct: 83  IGHFNGKFIKTPPGVS 98

>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 = 64.9 bits (159), Expect = 8e-14
 Identities = 21/87 (24%), Positives = 39/87 (44%), Gaps = 7/87 (8%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDV-NLVRDKGTGKPRGFAFVAYEDQR---- 88
            S+ +++G +  ++ E  L   F+  G I+    ++RD  TG  +G+AF+ +        
Sbjct: 4   GSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63

Query: 89  --NNLNGAQILGRTIRVDHVAKYKKKE 113
               +NG  +  R I V +  K   K 
Sbjct: 64  AIEAMNGQYLCNRPITVSYAFKKDSKG 90

>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 = 65.4 bits (160), Expect = 8e-14
 Identities = 27/92 (29%), Positives = 43/92 (46%), Gaps = 7/92 (7%)

Query: 21  GISDDASWHAKYKDSAY--VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRG 78
           G S  +  H   KD+ +  ++VGG+P+  T+  L   F   G+I +  ++ D+ TGK RG
Sbjct: 1   GSSGSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 60

Query: 79  FAFVAYEDQRN-----NLNGAQILGRTIRVDH 105
           + FV   D+             I GR   V+ 
Sbjct: 61  YGFVTMADRAAAERACKDPNPIIDGRKANVNL 92

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 65.0 bits (159), Expect = 1e-13
 Identities = 26/96 (27%), Positives = 41/96 (42%), Gaps = 12/96 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           VYVG +     +G+L   F+  G +  V + R+     P GFAFV +ED R        L
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGL 57

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREER 127
           +G  I G  +RV+  +    +    +    R +   
Sbjct: 58  DGKVICGSRVRVEL-STGMPRRSRFDRPPARRKLLE 92

>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 = 65.1 bits (159), Expect = 2e-13
 Identities = 16/90 (17%), Positives = 37/90 (41%), Gaps = 10/90 (11%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  + F +++ D+  +FA+ G +    +  D+ +G+  G A V +E +          
Sbjct: 38  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQY 96

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQ 121
            G  + GR + +  V     + + +     
Sbjct: 97  KGVPLDGRPMDIQLV---ASQIDLEHHHHH 123

>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 = 64.6 bits (158), Expect = 2e-13
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 5/73 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGG+ +  T+  L + F+Q GE+VD  +++DK T + RGF FV ++D           
Sbjct: 19  LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78

Query: 93  GAQILGRTIRVDH 105
              + GR I    
Sbjct: 79  PHTLDGRNIDPKP 91

>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 = 67.8 bits (166), Expect = 2e-13
 Identities = 18/94 (19%), Positives = 34/94 (36%), Gaps = 8/94 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +   ++   L   F+Q G +    +V D   G+  G  FV +  +          
Sbjct: 99  LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERC 157

Query: 92  NGAQIL-GRTIRVDHVAKYKKKEEEDEETRQRMR 124
                L   T R   V   ++ ++ED    + M+
Sbjct: 158 GDGAFLLTTTPRPVIVEPMEQFDDEDGLPEKLMQ 191

>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 = 63.6 bits (155), Expect = 5e-12
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 12/79 (15%)

Query: 31  KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN- 89
            Y     ++VG +P D+TE D   +F + GE  +V + RD      RGF F+  E +   
Sbjct: 18  TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLA 71

Query: 90  -----NLNGAQILGRTIRV 103
                 L+G  +  R +R+
Sbjct: 72  EIAKAELDGTILKSRPLRI 90

>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 = 63.7 bits (156), Expect = 2e-13
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGG+ +D ++ DL   F + GE+VD  +  D  TG+ RGF F+ ++D  +     +  
Sbjct: 14  MFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQK 73

Query: 93  GAQILGRTIRVD 104
             ++ GR I   
Sbjct: 74  EHRLDGRVIDPK 85

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 9/85 (10%)

Query: 21 GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
          G S  +      + ++ + V G+P+  TE DL   F+  GE++ V + +D  TG  +GF 
Sbjct: 1  GSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60

Query: 81 FVAYED---------QRNNLNGAQI 96
          FV + +         QR+ ++G   
Sbjct: 61 FVRFTEYETQVKVMSQRHMIDGRWC 85

>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 = 64.2 bits (157), Expect = 2e-13
 Identities = 22/104 (21%), Positives = 45/104 (43%), Gaps = 14/104 (13%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +   ++      ++VG +    +E D+L +F   G I +  ++R    G  +G A
Sbjct: 1   GSSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCA 59

Query: 81  FVAYEDQR------NNLNGAQIL---GRTIRVDHVAKYKKKEEE 115
           FV +          + L+G+Q +     ++ V    K+   ++E
Sbjct: 60  FVKFSSHTEAQAAIHALHGSQTMPGASSSLVV----KFADTDKE 99

>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 = 64.3 bits (157), Expect = 2e-13
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 10/97 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V+V  + + +    L  VF+  G +V  +++ DK  GK RG   V +E         +  
Sbjct: 18  VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMF 76

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
           NG  +  R + V      ++   + +       ++ G
Sbjct: 77  NGQLLFDRPMHVKMD---ERALPKGDFFPPERPQQSG 110

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 18/97 (18%), Positives = 42/97 (43%), Gaps = 17/97 (17%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V  +   +TE  L   F+Q G++  V         K + +AF+ ++++         +
Sbjct: 14  LFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAMEEM 65

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
           NG  + G  I +      K  +++ +E + + +   G
Sbjct: 66  NGKDLEGENIEIVFA---KPPDQKRKERKAQRQAASG 99

>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 = 63.8 bits (156), Expect = 3e-13
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 11/83 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV  +   + +  L   F+  G I    ++ +   G+ +GF FV +            +
Sbjct: 18  LYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEM 75

Query: 92  NGAQILGRTIRVDHVAKYKKKEE 114
           NG  +  + +    VA  ++KEE
Sbjct: 76  NGRIVATKPLY---VALAQRKEE 95

>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 = 63.4 bits (155), Expect = 4e-13
 Identities = 25/100 (25%), Positives = 42/100 (42%), Gaps = 11/100 (11%)

Query: 11  QHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRD 70
            H +S       S   S   K      +++GG+ +  T+  L   F Q GE+ +  ++RD
Sbjct: 7   HHHHSSGLVPRGSHMGSSGCK------MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRD 60

Query: 71  KGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH 105
             T + RGF FV + DQ         +  ++  +TI    
Sbjct: 61  PLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV 100

>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 = 61.9 bits (151), Expect = 9e-13
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 13/73 (17%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-------N 90
           +YVGG+   +TE DL   F Q GEI  + +V+ +        AF+ +  ++        +
Sbjct: 15  LYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ------QCAFIQFATRQAAEVAAEKS 68

Query: 91  LNGAQILGRTIRV 103
            N   + GR + V
Sbjct: 69  FNKLIVNGRRLNV 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 = 62.0 bits (151), Expect = 1e-12
 Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 9/74 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVG +P D+   D+  VF + G I D++L   +G      FAFV +ED R         
Sbjct: 25  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG---GPPFAFVEFEDPRDAEDAVYGR 81

Query: 92  NGAQILGRTIRVDH 105
           +G    G  +RV+ 
Sbjct: 82  DGYDYDGYRLRVEF 95

>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 = 61.1 bits (149), Expect = 2e-12
 Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++G +P + TE ++ ++F Q G++++ +++        + + FV  ED+        NL
Sbjct: 11  LFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNL 62

Query: 92  NGAQILGRTIRVDH 105
           +  ++ G  I V+ 
Sbjct: 63  HHYKLHGVNINVEA 76

>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 = 61.9 bits (151), Expect = 2e-12
 Identities = 19/73 (26%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ F+ TE  L   + Q G++ D  ++RD  + + RGF FV +             
Sbjct: 30  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89

Query: 93  GAQILGRTIRVDH 105
              I GR +    
Sbjct: 90  PHSIDGRVVEPKR 102

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 61.7 bits (150), Expect = 2e-12
 Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 15/90 (16%)

Query: 35  SAYVYVGGIP------FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR 88
            + + V  +P       +  +  +  +F++ G+I +     +   GK +G+ F+ Y    
Sbjct: 15  DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPA 72

Query: 89  N------NLNGAQILGR-TIRVDHVAKYKK 111
           +      N +G ++  + T RV+    + K
Sbjct: 73  HAVDAVKNADGYKLDKQHTFRVNLFTDFDK 102

>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 = 62.6 bits (152), Expect = 2e-12
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 12/81 (14%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           VYVG +  +  + +L   F   G +  V + R+     P GFAFV +ED R        L
Sbjct: 76  VYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVREL 130

Query: 92  NGAQILGRTIRVDHVAKYKKK 112
           +G  + G  +RV+  +  +K+
Sbjct: 131 DGRTLCGCRVRVEL-SNGEKR 150

>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 = 60.7 bits (148), Expect = 3e-12
 Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG +    T  +L ++F + G +++ ++V        + +AFV  E +         L
Sbjct: 12  IFVGNVSAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQL 63

Query: 92  NGAQILGRTIRVDH 105
           NG ++ G+ I V+ 
Sbjct: 64  NGKEVKGKRINVEL 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 = 63.2 bits (153), Expect = 4e-12
 Identities = 10/84 (11%), Positives = 26/84 (30%), Gaps = 6/84 (7%)

Query: 32  YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR--- 88
              S  ++    P ++TE +   +  + G     ++    G  +      + ++ +    
Sbjct: 120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDAL 179

Query: 89  ---NNLNGAQILGRTIRVDHVAKY 109
                LN  Q+        +  K 
Sbjct: 180 ETLGFLNHYQMKNPNGPYPYTLKL 203

>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 = 50.9 bits (121), Expect = 8e-08
 Identities = 19/101 (18%), Positives = 32/101 (31%), Gaps = 13/101 (12%)

Query: 34  DSAYVYVGGI-PFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--- 89
           DS  + V G+    +    +  VF   G +  V  ++ K      G A V   D      
Sbjct: 3   DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDR 57

Query: 90  ---NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREER 127
              +LN   + G+ + V  V+K            +      
Sbjct: 58  AITHLNNNFMFGQKMNV-CVSKQPAIMPGQSYGLEDGSCSY 97

>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 = 60.3 bits (147), Expect = 4e-12
 Identities = 18/94 (19%), Positives = 43/94 (45%), Gaps = 17/94 (18%)

Query: 38  VYVGGIPFDLTEGDL----LAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           +Y+  +   + + +L     A+F++ G+I+D+ + R   + K RG AFV +++       
Sbjct: 11  IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 67

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQ 121
             ++ G     + +R+     Y K + +     +
Sbjct: 68  LRSMQGFPFYDKPMRIQ----YAKTDSDIIAKMK 97

>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 = 60.0 bits (146), Expect = 6e-12
 Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           +YV G   D+T   L   F+  G I+D+++   +        AFV YE   +       L
Sbjct: 18  LYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPR------NCAFVTYEKMESADQAVAEL 69

Query: 92  NGAQILGRTIRVDH 105
           NG Q+    ++V+ 
Sbjct: 70  NGTQVESVQLKVNI 83

>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 = 59.4 bits (144), Expect = 7e-12
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 10/76 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL-----VRDKGTGKPRGFAFVAYEDQRN--- 89
           +YVG IPF +TE  ++  F     +  +       V      + + FAF+ +        
Sbjct: 9   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 68

Query: 90  --NLNGAQILGRTIRV 103
               +G    G+++++
Sbjct: 69  AMAFDGIIFQGQSLKI 84

>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 = 59.8 bits (145), Expect = 9e-12
 Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 15/99 (15%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +  H K   S  V+V G+   + E DL+    + G I  V ++  K        A
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK------RQA 54

Query: 81  FVAYED--------QRNNLNGAQILGRTIRVDHVAKYKK 111
            V +E+                 I G+    ++ +  K+
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNY-STSKR 92

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 59.4 bits (144), Expect = 1e-11
 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 7/90 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           VY+ G P D T  D+       G+++++ + R       +G  FV ++   +        
Sbjct: 14  VYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP 72

Query: 93  GAQILGRTIRVDHVAKY-KKKEEEDEETRQ 121
           G +     + +     Y  KK EE ++ + 
Sbjct: 73  GQKYKETDLLILFKDDYFAKKNEERKQNKV 102

>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 = 59.1 bits (143), Expect = 2e-11
 Identities = 13/99 (13%), Positives = 40/99 (40%), Gaps = 15/99 (15%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +        S  +++  +P ++TE +++A+    G++ ++ +++ K        A
Sbjct: 1   GSSGSSGDKMDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGK------NQA 54

Query: 81  FVAYED--------QRNNLNGAQILGRTIRVDHVAKYKK 111
           F+               +     +  + I + + + +K+
Sbjct: 55  FLELATEEAAITMVNYYSAVTPHLRNQPIYIQY-SNHKE 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 = 59.4 bits (144), Expect = 2e-11
 Identities = 20/113 (17%), Positives = 41/113 (36%), Gaps = 8/113 (7%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +            ++  IPF +T+ D+L          +   V     G+  G A
Sbjct: 1   GSSGSSGEGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQA 60

Query: 81  FVAYEDQRN-----NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
            V ++++ +      L+  ++ GR   V  V     ++  + E     + + G
Sbjct: 61  LVQFKNEDDARKSERLHRKKLNGREAFVHVVT---LEDMREIEKNPPAQGKSG 110

>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 = 58.0 bits (141), Expect = 2e-11
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 14/75 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VGG+  + +   L   F + G I  ++ V+         FA++ YE           +
Sbjct: 20  LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKM 73

Query: 92  NGAQILG--RTIRVD 104
            G  + G  R +RVD
Sbjct: 74  RGFPLGGPDRRLRVD 88

>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 = 61.8 bits (149), Expect = 3e-11
 Identities = 25/195 (12%), Positives = 54/195 (27%), Gaps = 14/195 (7%)

Query: 38  VYVGGIPFDLTEGDLL----AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------ 87
           +Y+  +   + + +L     A+F+Q G+I+D+ + R   + K RG AFV +++       
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNA 68

Query: 88  RNNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFS 147
             ++ G     + +R+ + AK         +     R+ +   R  +  E          
Sbjct: 69  LRSMQGFPFYDKPMRIQY-AKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQG 127

Query: 148 HNEQRAANTGGGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEK 207
                      GP                           G                   
Sbjct: 128 GGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPP 187

Query: 208 RSIRHDHREKPREDH 222
           + +        +   
Sbjct: 188 QQLMPGQMPPAQPLS 202

>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 = 46.0 bits (108), Expect = 5e-06
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 16/81 (19%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ------RNNLN 92
           ++  +P +  E  L  +F Q     +V LV  +        AFV ++++      R+ L 
Sbjct: 211 FLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQ 265

Query: 93  GAQIL-GRTIRVDHVAKYKKK 112
           G +I     +++     + KK
Sbjct: 266 GFKITQNNAMKI----SFAKK 282

>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 = 58.6 bits (142), Expect = 3e-11
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           D  YV V G+PF   E D+   F     +  V+L++D   G+  G   V +   ++    
Sbjct: 15  DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEA 72

Query: 90  -NLNGAQILGRTIRVD 104
              N   ++ R + V 
Sbjct: 73  LKRNRMLMIQRYVEVS 88

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 59.9 bits (145), Expect = 4e-11
 Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 7/77 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  + F +++ D+  +FA+ G +    +  D+ +G+  G A V +E +          
Sbjct: 91  LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQY 149

Query: 92  NGAQILGRTIRVDHVAK 108
            G  + GR + +  VA 
Sbjct: 150 KGVPLDGRPMDIQLVAS 166

>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 = 57.7 bits (140), Expect = 4e-11
 Identities = 18/82 (21%), Positives = 30/82 (36%), Gaps = 13/82 (15%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV  +    +E  +   F          +       K R +AFV + ++         L
Sbjct: 18  LYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKAL 71

Query: 92  NGAQILGRTIRVDHVAKYKKKE 113
           NG  + G  I V  +AK   K+
Sbjct: 72  NGKVLDGSPIEVT-LAKPVDKD 92

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 57.6 bits (139), Expect = 5e-11
 Identities = 14/96 (14%), Positives = 42/96 (43%), Gaps = 15/96 (15%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----- 89
           S  +++  +P D+TEG+++++    G++ ++ +++ K        AF+    +       
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMV 69

Query: 90  ---NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQR 122
                    + G+ I +   + +K+ + +    + R
Sbjct: 70  NYYTSVTPVLRGQPIYIQF-SNHKELKTDSSPNQAR 104

>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 = 56.9 bits (138), Expect = 6e-11
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++VG I    T  +L A F + G +++ ++V        + +AFV  E           L
Sbjct: 13  LHVGNISPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGL 64

Query: 92  NGAQILGRTIRVDH 105
           +  +  G+ + V  
Sbjct: 65  DNTEFQGKRMHVQL 78

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 56.9 bits (138), Expect = 6e-11
 Identities = 21/96 (21%), Positives = 34/96 (35%), Gaps = 17/96 (17%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           V+V G P  +    L   F   G +  V + +DKG      FA V   D        + +
Sbjct: 11  VFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGV-----FAIVEMGDVGAREAVLSQS 65

Query: 93  GAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
              + G  +RV       +  E+ E      +  +G
Sbjct: 66  QHSLGGHRLRV-------RPREQKEFQSPASKSPKG 94

>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 = 57.9 bits (140), Expect = 7e-11
 Identities = 20/102 (19%), Positives = 44/102 (43%), Gaps = 6/102 (5%)

Query: 29  HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR 88
            + ++    VY+ G+PF+     ++  F +   + D   +     GK  G  FV + ++ 
Sbjct: 19  RSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEA 78

Query: 89  N-----NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMRE 125
           +       +   +  R I+V  + K K   E+ +  R+R++ 
Sbjct: 79  DYKAALCRHKQYMGNRFIQVHPITK-KGMLEKIDMIRKRLQS 119

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 57.1 bits (138), Expect = 7e-11
 Identities = 18/78 (23%), Positives = 28/78 (35%), Gaps = 14/78 (17%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED-------- 86
           S  V++ G+   + E DL+    + G I  V ++  K        A V +ED        
Sbjct: 21  SPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKK------RQALVEFEDVLGACNAV 74

Query: 87  QRNNLNGAQILGRTIRVD 104
                N   I G    V+
Sbjct: 75  NYAADNQIYIAGHPAFVN 92

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 55.9 bits (135), Expect = 1e-10
 Identities = 15/80 (18%), Positives = 33/80 (41%), Gaps = 15/80 (18%)

Query: 37  YVYVGGIP------FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR-- 88
            + V  +P       +  +  +  +F++ G+I +     +   GK +G+ F+ Y      
Sbjct: 3   VIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHA 60

Query: 89  ----NNLNGAQILGR-TIRV 103
                N +G ++  + T RV
Sbjct: 61  VDAVKNADGYKLDKQHTFRV 80

>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 = 56.7 bits (137), Expect = 1e-10
 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 5/88 (5%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +       +  +V + G+PF  ++ +++  F+    + +   +     G+  G A
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 81  FVAYEDQRN-----NLNGAQILGRTIRV 103
           FV +  Q         +  +I  R I +
Sbjct: 61  FVQFASQEIAEKALKKHKERIGHRYIEI 88

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 56.5 bits (137), Expect = 1e-10
 Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 14/74 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V   P D+ E +L  +F   G + +V +          GFAFV +E+          +
Sbjct: 34  LFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEEV 85

Query: 92  NGAQILGRTIRVDH 105
           +G     + + V +
Sbjct: 86  HGKSFANQPLEVVY 99

>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 = 56.1 bits (136), Expect = 1e-10
 Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 9/71 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED----QRNNLNG 93
           V+VG    D+T  +L   F Q GE+VDV + +       R FAFV + D    Q      
Sbjct: 14  VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF-----RAFAFVTFADDKVAQSLCGED 68

Query: 94  AQILGRTIRVD 104
             I G ++ + 
Sbjct: 69  LIIKGISVHIS 79

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 55.7 bits (135), Expect = 1e-10
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 9/71 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED----QRNNLNG 93
           V+VG    D+TE +L   F+Q G+++DV + +       R FAFV + D    Q      
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLCGED 62

Query: 94  AQILGRTIRVD 104
             I G ++ + 
Sbjct: 63  LIIKGISVHIS 73

>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 = 60.2 bits (145), Expect = 2e-10
 Identities = 45/254 (17%), Positives = 78/254 (30%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
           ++V  + +D TE  L   F   G I  +++V  K +GKPRG+AF+ YE +R+  +  +  
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164

Query: 98  GRTIRVDHVAKYKKKEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTG 157
                         +     +  +  R   G+    + G              +     G
Sbjct: 165 DGKKIDGRRVLVDVERGRTVKGWRPRRLGGGLGGTRRGGADVNIRHSGRDDTSRYDERPG 224

Query: 158 GGPQDRSSRWGHEKFEGFSWGKNDSSSRATGSGRVALEGNPNQSDRREEKRSIRHDHREK 217
             P     R    + E     +     R     R       ++S  +EE+R  R   ++K
Sbjct: 225 PSPLPHRDRDRDRERERRERSRERDKERERRRSRSRDRRRRSRSRDKEERRRSRERSKDK 284

Query: 218 PREDHGRREDKRSRRHSDNNEFEARSREDHYRRDEKRPKRHESESYLREDQDRRGGDKSS 277
            R+   R    R R   +    E          +         +     +    G D   
Sbjct: 285 DRDRKRRSSRSRERARRERERKEELRGGGGDMAEPSEAGDAPPDDGPPGELGPDGPDGPE 344

Query: 278 TGRGDSSSHRHRER 291
               D    R R  
Sbjct: 345 EKGRDRDRERRRSH 358

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 56.0 bits (135), Expect = 2e-10
 Identities = 22/73 (30%), Positives = 30/73 (41%), Gaps = 11/73 (15%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           VYVG +P D    DL     + G  V + L        PR  AF+ Y D        + L
Sbjct: 22  VYVGNLPRDARVSDLKRALRELG-SVPLRLTWQ----GPRRRAFLHYPDSAAAQQAVSCL 76

Query: 92  NGAQILGRTIRVD 104
            G ++   T+RV 
Sbjct: 77  QGLRLGTDTLRVA 89

>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 = 56.1 bits (135), Expect = 3e-10
 Identities = 14/96 (14%), Positives = 41/96 (42%), Gaps = 15/96 (15%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED-------- 86
           S  +++  +P D+TEG+++++    G++ ++ +++ K        AF+            
Sbjct: 31  SRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGK------NQAFIEMNTEEAANTMV 84

Query: 87  QRNNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQR 122
                    + G+ I +   + +K+ + +    + R
Sbjct: 85  NYYTSVTPVLRGQPIYIQF-SNHKELKTDSSPNQAR 119

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 56.1 bits (135), Expect = 3e-10
 Identities = 12/99 (12%), Positives = 36/99 (36%), Gaps = 14/99 (14%)

Query: 38  VYVGGIPFDLTEGDL----LAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           V +  I  ++ +  L     A+ +  G+I+D+ +     +    G A++ +  Q      
Sbjct: 32  VLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAF 88

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREE 126
                G    G  + +   ++  + +  ++ + +     
Sbjct: 89  VEAFQGYPFQGNPLVITF-SETPQSQVAEDGSLEHHHHH 126

>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 = 54.6 bits (132), Expect = 4e-10
 Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 7/71 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           V + G PF++TE +++   A     V + +VR+   G   G+ FV + ++         N
Sbjct: 13  VKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQALKCN 70

Query: 93  GAQILGRTIRV 103
              + GR I V
Sbjct: 71  REYMGGRYIEV 81

>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 = 55.3 bits (133), Expect = 6e-10
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 23  SDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV 82
               S  A   +  +V + G+PF  T+ +++  F+    + +   +     GK  G AFV
Sbjct: 30  MGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFV 89

Query: 83  AYEDQRN-----NLNGAQILGRTIRV 103
            +  Q         +  +I  R I V
Sbjct: 90  QFASQELAEKALGKHKERIGHRYIEV 115

>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 = 54.3 bits (131), Expect = 7e-10
 Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 15/75 (20%)

Query: 38  VYVGGIPFDL-TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           V++G +   L  + D+  +F++ G +   ++         +G+AFV Y ++R        
Sbjct: 30  VFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLG 81

Query: 91  LNGAQILGRTIRVDH 105
            NG  + G+T+ ++ 
Sbjct: 82  ENGRVLAGQTLDINM 96

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 54.3 bits (131), Expect = 8e-10
 Identities = 16/88 (18%), Positives = 34/88 (38%), Gaps = 7/88 (7%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +    +      V++ G+P+  TE D+   F+     + V++      G+  G A
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEA 58

Query: 81  FVAYEDQRN-----NLNGAQILGRTIRV 103
            V +    +       + A +  R + +
Sbjct: 59  DVEFATHEDAVAAMAKDKANMQHRYVEL 86

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 54.2 bits (130), Expect = 9e-10
 Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 2/58 (3%)

Query: 33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK--GTGKPRGFAFVAYEDQR 88
            S  V+VGG+P D+ E ++ A F + G +V     + +      P+G+AF+ ++++ 
Sbjct: 6  SGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEES 63

>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 = 54.8 bits (132), Expect = 1e-09
 Identities = 19/111 (17%), Positives = 40/111 (36%), Gaps = 10/111 (9%)

Query: 23  SDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFV 82
           S D+ +  +      V++ G+P+  TE D+   F+     V V++      G+  G A V
Sbjct: 34  SGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGP-DGRVTGEADV 91

Query: 83  AYEDQRN-----NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
            +          + + A +  R I +            +     ++ +  G
Sbjct: 92  EFATHEEAVAAMSKDRANMQHRYIELF---LNSTTGASNGAYSSQVMQGMG 139

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 53.4 bits (129), Expect = 1e-09
 Identities = 12/90 (13%), Positives = 38/90 (42%), Gaps = 16/90 (17%)

Query: 38  VYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           +++G +P  ++++ DL  +F+  G I+ +N+           F F+ +++ +        
Sbjct: 13  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEC 64

Query: 91  LNGAQILGRTIRVDHVAKYKKKEEEDEETR 120
            +     G+ + ++  +    + + D    
Sbjct: 65  ESQEMNFGKKLILEV-SSSNARPQFDHGDH 93

>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 = 55.7 bits (134), Expect = 1e-09
 Identities = 20/108 (18%), Positives = 44/108 (40%), Gaps = 13/108 (12%)

Query: 35  SAYVYVGGI-PFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           ++ + V  + P  +T   L  +F   G++  V ++ +K     +  A V   D       
Sbjct: 3   NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLA 57

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERGVCRAFQR 135
            ++LNG ++ G+ IR+   +K++  +   E    +   +        R
Sbjct: 58  MSHLNGHKLHGKPIRITL-SKHQNVQLPREGQEDQGLTKDYGNSPLHR 104

>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 = 55.3 bits (133), Expect = 2e-09
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 11/86 (12%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
            ++   +  SA +++  IP  ++E DL  +F+  G +V       K     R  A +   
Sbjct: 111 KNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD----RKMALIQMG 166

Query: 86  DQ------RNNLNGAQIL-GRTIRVD 104
                     +L+   +     +RV 
Sbjct: 167 SVEEAVQALIDLHNHDLGENHHLRVS 192

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 53.7 bits (129), Expect = 2e-09
 Identities = 24/124 (19%), Positives = 47/124 (37%), Gaps = 15/124 (12%)

Query: 14  NSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD----VNLVR 69
           +S  +  G S++ +     ++   V + G+PF  T  +++A F Q   I      +  V 
Sbjct: 2   SSGSSGGGTSNEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVT 61

Query: 70  DKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
               G+P G AFV +  +         +   +  R I +     ++    E ++   R  
Sbjct: 62  YP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIEL-----FRSTAAEVQQVLNRFS 115

Query: 125 EERG 128
              G
Sbjct: 116 SASG 119

>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 = 52.2 bits (125), Expect = 5e-09
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 12/99 (12%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVR--DKGTGKPRGFAFVAYEDQR-- 88
            D   +   G+P+  T  D+L  F+ C      N +       GK RG A +  E ++  
Sbjct: 9   DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDV 68

Query: 89  ---NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
                 +   +  R + V     Y+   E+ +   + ++
Sbjct: 69  QKALEKHRMYMGQRYVEV-----YEINNEDVDALMKSLQ 102

>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 = 51.2 bits (123), Expect = 7e-09
 Identities = 11/82 (13%), Positives = 36/82 (43%), Gaps = 16/82 (19%)

Query: 38  VYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           +++G +P  ++++ DL  +F+  G I+ +N+           F F+ +++ +        
Sbjct: 25  LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEX 76

Query: 91  LNGAQILGRTIRVDHVAKYKKK 112
            +     G+ + ++  +    +
Sbjct: 77  ESQEMNFGKKLILEV-SSSNAR 97

>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 = 53.8 bits (129), Expect = 9e-09
 Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 11/98 (11%)

Query: 14  NSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT 73
           NS           ++   +  SA +++  IP  ++E DL  +F+  G +V       K  
Sbjct: 130 NSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD- 188

Query: 74  GKPRGFAFVAYEDQ------RNNLNGAQIL-GRTIRVD 104
              R  A +             +L+   +     +RV 
Sbjct: 189 ---RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVS 223

>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 = 53.1 bits (127), Expect = 1e-08
 Identities = 19/96 (19%), Positives = 41/96 (42%), Gaps = 15/96 (15%)

Query: 38  VYVGGI-PFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           + V  + P  +T   L  +F   G++  V ++ +K     +  A V   D        ++
Sbjct: 37  LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSH 91

Query: 91  LNGAQILGRTIRV---DHVAKYKKKEEEDEETRQRM 123
           LNG ++ G+ IR+    H      +E ++++   + 
Sbjct: 92  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKD 127

>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 = 23/92 (25%), Positives = 40/92 (43%), Gaps = 10/92 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQC-GEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           ++VG +  D+ +G L   F +         +V D+ TG  +G+ FV + D+         
Sbjct: 12  LFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTE 70

Query: 91  LNGAQILG-RTIRVDHVAKYKKKEEEDEETRQ 121
             GA  LG + +R+  VA  K    +  E+  
Sbjct: 71  CQGAVGLGSKPVRLS-VAIPKASRVKPVESGP 101

>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 = 50.7 bits (121), Expect = 2e-08
 Identities = 17/97 (17%), Positives = 34/97 (35%), Gaps = 18/97 (18%)

Query: 8  KRIQHINSKEADLGISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNL 67
             +H   +   +     A+       S  V  GG+   ++   LL V  +CG +  + +
Sbjct: 6  SGAKHTLLRHEGIETVSYAT------QSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLM 59

Query: 68 VRDKGTGKPRGFAFVAYEDQ------RNNLNGAQILG 98
            +K       ++F  Y            LNG +++ 
Sbjct: 60 PPNK------PYSFARYRTTEESKRAYVTLNGKEVVD 90

>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 = 49.7 bits (119), Expect = 3e-08
 Identities = 8/72 (11%), Positives = 21/72 (29%), Gaps = 13/72 (18%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL 91
           + V  +P D    ++  +            ++     + +  AFV   +           
Sbjct: 8   ILVKNLPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMF 60

Query: 92  NGAQILGRTIRV 103
           +     G+ + V
Sbjct: 61  HQYSFRGKDLIV 72

>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 = 50.6 bits (121), Expect = 4e-08
 Identities = 17/96 (17%), Positives = 42/96 (43%), Gaps = 12/96 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL-----VRDKGTGKPRGFAFVAYEDQR---- 88
           +YV  +   + E DL  +F +  +           +R    G+ +G AF+   +++    
Sbjct: 48  IYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAK 107

Query: 89  --NNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQR 122
                NG  + G+ + V   A+  + +++ +E +++
Sbjct: 108 ALKEANGYVLFGKPMVV-QFARSARPKQDPKEGKRK 142

>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 = 49.0 bits (117), Expect = 7e-08
 Identities = 10/109 (9%), Positives = 35/109 (32%), Gaps = 14/109 (12%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
            S  +  +    +    +P      ++   F++ G +  V L            A V + 
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGG------ITAIVEFL 54

Query: 86  DQR------NNLNGAQILGRTIRVD--HVAKYKKKEEEDEETRQRMREE 126
           +         +L  ++     + ++   +  +    ++ +   ++  E+
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAEK 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 = 48.4 bits (115), Expect = 1e-07
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 9/74 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQC---GEIVDVNLVRDKGTGKPRGFAFVAYEDQR-----N 89
           V + G+P+  +  D+    + C     +  V+ +  +  G+  G AFV  E +       
Sbjct: 20  VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTR-EGRQSGEAFVELESEDDVKLAL 78

Query: 90  NLNGAQILGRTIRV 103
             +   +  R I V
Sbjct: 79  KKDRESMGHRYIEV 92

>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 = 47.5 bits (112), Expect = 9e-07
 Identities = 16/93 (17%), Positives = 34/93 (36%), Gaps = 6/93 (6%)

Query: 28  WHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
            +     +  VY+ G P D T  D+       G+++++ + R       +G  FV ++  
Sbjct: 102 EYKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSI 160

Query: 88  RN-----NLNGAQILGRTIRVDHVAKYKKKEEE 115
            +        G +     + +     Y  K+ E
Sbjct: 161 ESAKKFVETPGQKYKETDLLILFKDDYFAKKNE 193

>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 = 44.6 bits (105), Expect = 4e-06
 Identities = 14/81 (17%), Positives = 26/81 (32%), Gaps = 7/81 (8%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVR--DKGTGKPRGFAFVAYEDQ 87
            +  +   V + G+P+  +  D+    + C        V       G+  G AFV    +
Sbjct: 39  PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSE 98

Query: 88  R-----NNLNGAQILGRTIRV 103
                    +   +  R I V
Sbjct: 99  DDVKMALKKDRESMGHRYIEV 119

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 43.2 bits (102), Expect = 6e-06
 Identities = 14/97 (14%), Positives = 27/97 (27%), Gaps = 13/97 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V V G+P   +  DL     + G++   ++ RD       G   V +  +         L
Sbjct: 18  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 70

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREERG 128
           +  +         ++             R R      
Sbjct: 71  DNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSSGPSS 107

>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 = 41.5 bits (97), Expect = 4e-05
 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 15/83 (18%)

Query: 38  VYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED--------QR 88
           +++  +P    ++  +L +    G+I +  L+R K        AF+  E           
Sbjct: 28  IHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMK------SQAFIEMETREDAMAMVDH 81

Query: 89  NNLNGAQILGRTIRVDHVAKYKK 111
                    GR ++VD   KYKK
Sbjct: 82  CLKKALWFQGRCVKVDLSEKYKK 104

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens} Length = 72

 Score = 40.2 bits (94), Expect = 4e-05
 Identities = 11/34 (32%), Positives = 16/34 (47%)

Query: 116 DEETRQRMREERGVCRAFQRGECTRGDGCKFSHN 149
                    E+  VC+ + RG C +GD C+F H 
Sbjct: 5   HHHHSHMSGEKTVVCKHWLRGLCKKGDQCEFLHE 38

>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 Length = 102

 Score = 40.6 bits (95), Expect = 6e-05
 Identities = 16/105 (15%), Positives = 31/105 (29%), Gaps = 15/105 (14%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDL-TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGF 79
           G S  +    + +    V++            LL +    G I +  ++           
Sbjct: 1   GSSGSSGQKGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI------NE 54

Query: 80  AFVAYED--------QRNNLNGAQILGRTIRVDHVAKYKKKEEED 116
           AF+                   A + G+ +RV    KYK+ +   
Sbjct: 55  AFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKRIKSGP 99

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 40.6 bits (95), Expect = 7e-05
 Identities = 10/72 (13%), Positives = 20/72 (27%), Gaps = 9/72 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + +  +P   +  DL  +  +              T    G   + +  +         L
Sbjct: 31  ITMKNLPEGCSWQDLKDLARENSLETT---FSSVNTRDFDGTGALEFPSEEILVEALERL 87

Query: 92  NGAQILGRTIRV 103
           N  +  G  I V
Sbjct: 88  NNIEFRGSVITV 99

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens} Length = 89

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 1/32 (3%)

Query: 129 VCRAFQRGECTRGDG-CKFSHNEQRAANTGGG 159
           VCR FQRG C+R D  CKF+H  +      G 
Sbjct: 19  VCRQFQRGTCSRSDEECKFAHPPKSCQVENGR 50

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 38.7 bits (90), Expect = 1e-04
 Identities = 10/20 (50%), Positives = 14/20 (70%)

Query: 129 VCRAFQRGECTRGDGCKFSH 148
           VC+ + RG C +GD C+F H
Sbjct: 12  VCKHWLRGLCKKGDQCEFLH 31

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens} Length = 83

 Score = 38.2 bits (88), Expect = 3e-04
 Identities = 14/21 (66%), Positives = 16/21 (76%), Gaps = 1/21 (4%)

Query: 129 VCRAFQRGECTRGDG-CKFSH 148
           VCR FQRG C+R D  CKF+H
Sbjct: 11  VCREFQRGTCSRPDTECKFAH 31

>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 = 39.0 bits (91), Expect = 3e-04
 Identities = 15/93 (16%), Positives = 28/93 (30%), Gaps = 13/93 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V V G+P   +  DL     + G++   ++ RD       G   V +  +         L
Sbjct: 19  VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKL 71

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
           +  +         ++             R R R
Sbjct: 72  DNTKFRSHEGETAYIRVKVDGPRSPSYGRSRSR 104

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A Length = 70

 Score = 36.6 bits (84), Expect = 7e-04
 Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)

Query: 129 VCRAFQRGECTRGDG-CKFSHNEQ 151
           VCR +QRG C RG+  C+F+H   
Sbjct: 8   VCREYQRGNCNRGENDCRFAHPAD 31

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	291
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.89
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.84
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.82
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.8
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.79
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.79
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.79
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.78
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.78
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.78
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.78
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.78
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.78
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.78
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.78
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.78
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.77
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.77
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.77
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.77
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.77
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.77
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.77
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.77
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.77
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.77
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.77
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.77
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.77
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.77
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.76
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.76
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.76
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.76
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.76
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.76
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.76
2div_A	99	TRNA selenocysteine associated protein; structural	99.76
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.76
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.76
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.76
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.75
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.75
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.75
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.75
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.75
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.75
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.75
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.75
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.75
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.75
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.75
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.74
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.74
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.74
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.74
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.74
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.74
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.73
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.73
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.73
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.73
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.73
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.73
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.73
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.73
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.73
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.72
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.72
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.72
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.72
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.72
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.72
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.72
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.72
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.72
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.72
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.72
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.72
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.71
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.71
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.71
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.71
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.71
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.71
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.71
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.7
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.7
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.7
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.7
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.7
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.7
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.7
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.69
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.69
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.69
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.69
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.69
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.68
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.68
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.68
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.68
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.68
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.68
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.68
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.68
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.67
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.67
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.67
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.67
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.67
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.67
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.67
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.48
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.66
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.66
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.66
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.66
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.66
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.66
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.66
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.66
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.66
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.65
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.65
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.65
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.65
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.64
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.64
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.64
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.64
1x5p_A	97	Negative elongation factor E; structure genomics,	99.64
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.64
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.63
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.63
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.63
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.63
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.62
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.62
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.62
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.61
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.61
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.6
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.6
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.6
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.6
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.59
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.58
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.58
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.57
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.57
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.56
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.56
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.55
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.55
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.55
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.55
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.53
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.53
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.52
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.52
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.51
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.51
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.49
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.49
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.49
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.49
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.48
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.48
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.45
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.44
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.43
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.41
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.41
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.4
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.4
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.36
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.35
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.32
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.28
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.21
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.08
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.06
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.02
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.76
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.49
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.07
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	97.84
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.25
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	96.91
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	96.87
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.74
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.62
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.21
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.48
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.08
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	93.09
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	88.3
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	85.17
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	82.59

>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=99.89  E-value=8e-23  Score=193.84  Aligned_cols=79  Identities=33%  Similarity=0.563  Sum_probs=73.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.||+++|..+|++||.|+.|.|+.++.||+++|||||+|.+.++      +|||+.|+|+.|.|.+
T Consensus        99 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~  178 (437)
T 3pgw_S           99 GDAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDV  178 (437)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999887      7899999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus       179 a~~~~  183 (437)
T 3pgw_S          179 ERGRT  183 (437)
T ss_pred             eCCCC
Confidence            97554

>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=8e-21  Score=144.10  Aligned_cols=77  Identities=30%  Similarity=0.585  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ....++|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++      .|||..|+|++|.|.+
T Consensus        16 ~~~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           16 YFQGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999999999999999999999887      7999999999999999


Q ss_pred             cCC
Q 022814          106 VAK  108 (291)
Q Consensus       106 a~~  108 (291)
                      |.|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            865

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.82  E-value=7.4e-20  Score=141.45  Aligned_cols=79  Identities=22%  Similarity=0.227  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .+|.++|||+|||+.+++++|+++|++||.|..|.|+.|+.||+++|||||+|.+.++      .|||..|+|+.|.|.+
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            3678999999999999999999999999999999999999999999999999999887      7999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +....
T Consensus        83 a~~~~   87 (110)
T 3s8s_A           83 DIKGQ   87 (110)
T ss_dssp             CSTTH
T ss_pred             CCCCc
Confidence            86443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.80  E-value=4.3e-20  Score=137.83  Aligned_cols=78  Identities=28%  Similarity=0.468  Sum_probs=70.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh------hc-CCceeCCeEEEEecc
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL-NGAQILGRTIRVDHV  106 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l-ng~~i~gr~i~V~~a  106 (291)
                      +++|||+|||+.+|+++|+++|++|| +|.+|.|+.++.||.++|||||+|.+.++      .| ++..|+|++|.|.+|
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            47899999999999999999999999 89999999999999999999999999887      34 457899999999999


Q ss_pred             CCcccc
Q 022814          107 AKYKKK  112 (291)
Q Consensus       107 ~~~~~~  112 (291)
                      .+..+.
T Consensus        81 ~~~~~~   86 (91)
T 2lxi_A           81 DPKPKI   86 (91)
T ss_dssp             CSCCCC
T ss_pred             CCCCCC
Confidence            876543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.79  E-value=9.8e-20  Score=137.08  Aligned_cols=77  Identities=23%  Similarity=0.386  Sum_probs=70.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCC--eeEEEEeecCCCCCcceEEEEEEcChhh------hcCCc----eeCCe
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGE--IVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGA----QILGR   99 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~--I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~----~i~gr   99 (291)
                      ....+||||+|||+.+|+++|.++|++||.  |..|.|++|+.||.++|||||+|.+.++      .|||.    .|+|+
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            456789999999999999999999999995  6799999999999999999999999887      67775    59999


Q ss_pred             EEEEeccCC
Q 022814          100 TIRVDHVAK  108 (291)
Q Consensus       100 ~i~V~~a~~  108 (291)
                      +|.|.+|.+
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999864

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=6.4e-19  Score=131.74  Aligned_cols=80  Identities=36%  Similarity=0.554  Sum_probs=74.1

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      ....++.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.
T Consensus         9 ~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   88 (95)
T 2cqc_A            9 RANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR   88 (95)
T ss_dssp             CCSCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3456778999999999999999999999999999999999999999999999999999887      6999999999999


Q ss_pred             EeccCC
Q 022814          103 VDHVAK  108 (291)
Q Consensus       103 V~~a~~  108 (291)
                      |.++..
T Consensus        89 v~~a~~   94 (95)
T 2cqc_A           89 VSGPSS   94 (95)
T ss_dssp             EECCSC
T ss_pred             EEecCC
Confidence            999863

>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=5.2e-19  Score=134.89  Aligned_cols=83  Identities=28%  Similarity=0.549  Sum_probs=76.3

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      .....+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   88 (105)
T 1x5u_A            9 ISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   88 (105)
T ss_dssp             CCCCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3455778999999999999999999999999999999999999899999999999999887      6999999999999


Q ss_pred             EeccCCccc
Q 022814          103 VDHVAKYKK  111 (291)
Q Consensus       103 V~~a~~~~~  111 (291)
                      |.++.+...
T Consensus        89 v~~a~~~~~   97 (105)
T 1x5u_A           89 VNKASAHNK   97 (105)
T ss_dssp             EEETTTTSC
T ss_pred             EEECCCCCc
Confidence            999976553

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.78  E-value=1.1e-18  Score=135.43  Aligned_cols=84  Identities=29%  Similarity=0.533  Sum_probs=76.7

Q ss_pred             cccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           28 WHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        28 ~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      ......+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   87 (115)
T 2dgo_A            8 QKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI   87 (115)
T ss_dssp             SCCCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            33455788999999999999999999999999999999999998899999999999999887      689999999999


Q ss_pred             EEeccCCccc
Q 022814          102 RVDHVAKYKK  111 (291)
Q Consensus       102 ~V~~a~~~~~  111 (291)
                      .|.++.+...
T Consensus        88 ~V~~a~~~~~   97 (115)
T 2dgo_A           88 RTNWATRKPP   97 (115)
T ss_dssp             EEEESSCCCC
T ss_pred             EEEEccCCCC
Confidence            9999976654

>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=8.1e-19  Score=135.06  Aligned_cols=84  Identities=24%  Similarity=0.404  Sum_probs=76.6

Q ss_pred             cccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcC------Cce
Q 022814           28 WHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN------GAQ   95 (291)
Q Consensus        28 ~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~ln------g~~   95 (291)
                      ......+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++      .||      +..
T Consensus         8 ~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~   87 (111)
T 1x4h_A            8 LPSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   87 (111)
T ss_dssp             CCCCCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCcCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcE
Confidence            33456778999999999999999999999999999999999999999999999999999887      688      999


Q ss_pred             eCCeEEEEeccCCccc
Q 022814           96 ILGRTIRVDHVAKYKK  111 (291)
Q Consensus        96 i~gr~i~V~~a~~~~~  111 (291)
                      |+|+.|.|.++.+...
T Consensus        88 ~~g~~l~v~~a~~~~~  103 (111)
T 1x4h_A           88 LDGRQLKVDLAVTRDE  103 (111)
T ss_dssp             SSSCEEEEECCCCCCC
T ss_pred             EcCEEEEEEECCCCcc
Confidence            9999999999976543

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.78  E-value=1e-18  Score=128.67  Aligned_cols=77  Identities=30%  Similarity=0.620  Sum_probs=71.1

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      ....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.||.++|||||+|.+.++     .+++..|+|+.|.|.
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~   85 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPK   85 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEE
Confidence            345678999999999999999999999999999999999999999999999999999887     678899999999998


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      +|
T Consensus        86 ~A   87 (87)
T 3s7r_A           86 KA   87 (87)
T ss_dssp             EC
T ss_pred             eC
Confidence            75

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=7.7e-19  Score=133.52  Aligned_cols=81  Identities=26%  Similarity=0.451  Sum_probs=75.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|.
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            45678999999999999999999999999999999999999899999999999999887      699999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9976654

>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=99.78  E-value=7.4e-19  Score=129.24  Aligned_cols=77  Identities=30%  Similarity=0.587  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.+
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            3567899999999999999999999999999999999998899999999999999887      6899999999999999


Q ss_pred             cCC
Q 022814          106 VAK  108 (291)
Q Consensus       106 a~~  108 (291)
                      +.+
T Consensus        83 a~~   85 (87)
T 3bs9_A           83 ATR   85 (87)
T ss_dssp             EC-
T ss_pred             cCC
Confidence            865

>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=1e-18  Score=127.37  Aligned_cols=76  Identities=24%  Similarity=0.541  Sum_probs=71.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      ..+|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.++.+
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            3589999999999999999999999999999999998899999999999999887      6999999999999999976


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        81 ~~   82 (83)
T 3md1_A           81 LE   82 (83)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.78  E-value=1.1e-18  Score=130.94  Aligned_cols=80  Identities=30%  Similarity=0.607  Sum_probs=74.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      |+++|||+|||+.+++++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.++.
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            57899999999999999999999999999999999999899999999999999887      789999999999999998


Q ss_pred             Cccccc
Q 022814          108 KYKKKE  113 (291)
Q Consensus       108 ~~~~~~  113 (291)
                      +.....
T Consensus        81 ~~~~~~   86 (96)
T 2x1f_A           81 NSDISG   86 (96)
T ss_dssp             CSSGGG
T ss_pred             CCCCCC
Confidence            766543

>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=99.78  E-value=1e-18  Score=135.59  Aligned_cols=82  Identities=24%  Similarity=0.446  Sum_probs=75.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...++.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        20 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           20 KEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CCCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345677999999999999999999999999999999999999999999999999999887      78999999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus       100 ~~a~~~~~  107 (115)
T 2cpz_A          100 QLKRSKND  107 (115)
T ss_dssp             ECCCCSCC
T ss_pred             EEcCCCCc
Confidence            99976543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.78  E-value=1.6e-18  Score=131.79  Aligned_cols=81  Identities=35%  Similarity=0.604  Sum_probs=74.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      ....+.++|||+|||+.+++++|+++|++|| |..|.|+.++.||.++|||||+|.+.++     .||+..|+|+.|.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   88 (103)
T 2dng_A           10 LPTEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVD   88 (103)
T ss_dssp             CCSSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEE
Confidence            3456789999999999999999999999997 9999999999999999999999999887     789999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        89 ~a~~~~~   95 (103)
T 2dng_A           89 IAEGRKQ   95 (103)
T ss_dssp             ECCCCCC
T ss_pred             EecCCCC
Confidence            9976543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=131.78  Aligned_cols=82  Identities=29%  Similarity=0.609  Sum_probs=75.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++     .||+..|+|+.|.|.+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEE
Confidence            34678999999999999999999999999999999999999999999999999999887     7899999999999999


Q ss_pred             cCCcccc
Q 022814          106 VAKYKKK  112 (291)
Q Consensus       106 a~~~~~~  112 (291)
                      +.+....
T Consensus        86 a~~~~~~   92 (99)
T 2dgs_A           86 AEPRDSK   92 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCCccc
Confidence            9866543

>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=99.77  E-value=9.4e-19  Score=128.13  Aligned_cols=75  Identities=37%  Similarity=0.634  Sum_probs=71.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4678999999999999999999999999999999999998899999999999999887      7899999999999998


Q ss_pred             c
Q 022814          106 V  106 (291)
Q Consensus       106 a  106 (291)
                      +
T Consensus        84 a   84 (85)
T 3mdf_A           84 A   84 (85)
T ss_dssp             C
T ss_pred             c
Confidence            7

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=7.1e-19  Score=133.40  Aligned_cols=82  Identities=35%  Similarity=0.585  Sum_probs=75.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus         8 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   87 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            35678999999999999999999999999999999999999899999999999999887      689999999999999


Q ss_pred             ccCCcccc
Q 022814          105 HVAKYKKK  112 (291)
Q Consensus       105 ~a~~~~~~  112 (291)
                      ++.+....
T Consensus        88 ~a~~~~~~   95 (102)
T 2cqb_A           88 LAKPMRIK   95 (102)
T ss_dssp             ECCCCCCC
T ss_pred             eCCCCCCC
Confidence            99876543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=133.46  Aligned_cols=84  Identities=25%  Similarity=0.512  Sum_probs=76.4

Q ss_pred             cccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeec-CCCCCcceEEEEEEcChhh------hc-CCceeCCe
Q 022814           28 WHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRD-KGTGKPRGFAFVAYEDQRN------NL-NGAQILGR   99 (291)
Q Consensus        28 ~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d-~~tg~s~G~aFV~F~~~~~------~l-ng~~i~gr   99 (291)
                      ......+.++|||+|||+.+|+++|+.+|++||.|..|.|+.+ ..++.++|||||+|.+.++      .| |+..|.|+
T Consensus         8 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~   87 (107)
T 2cph_A            8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   87 (107)
T ss_dssp             SSCCSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             ccccCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCC
Confidence            3445678899999999999999999999999999999999999 7899999999999999887      67 99999999


Q ss_pred             EEEEeccCCccc
Q 022814          100 TIRVDHVAKYKK  111 (291)
Q Consensus       100 ~i~V~~a~~~~~  111 (291)
                      .|.|.++.+...
T Consensus        88 ~l~v~~a~~~~~   99 (107)
T 2cph_A           88 RLVLEWADSEVT   99 (107)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEeCCCCCC
Confidence            999999976543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=1.1e-18  Score=130.59  Aligned_cols=79  Identities=34%  Similarity=0.689  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .+++++|||+|||+.+++++|+++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|.+
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            3578999999999999999999999999999999999999899999999999999887      6999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus        82 a~~~~   86 (95)
T 2dnz_A           82 VTERL   86 (95)
T ss_dssp             SSCCC
T ss_pred             ccccc
Confidence            97654

>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=1.1e-18  Score=131.86  Aligned_cols=79  Identities=29%  Similarity=0.475  Sum_probs=73.4

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCcceEEEEEEcChhh------hcCCc
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD--------VNLVRDKGTGKPRGFAFVAYEDQRN------NLNGA   94 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~--------i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~   94 (291)
                      ....++.++|||+|||+.+++++|+++|++||.|..        |.|+.++.+|.++|||||+|.+.++      .|||.
T Consensus         7 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~   86 (99)
T 2la6_A            7 HHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGK   86 (99)
T ss_dssp             CCSCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCC
Confidence            345678899999999999999999999999999999        9999999899999999999999887      68999


Q ss_pred             eeCCeEEEEeccC
Q 022814           95 QILGRTIRVDHVA  107 (291)
Q Consensus        95 ~i~gr~i~V~~a~  107 (291)
                      .|+|+.|.|.+|.
T Consensus        87 ~~~g~~l~V~~A~   99 (99)
T 2la6_A           87 EFSGNPIKVSFAT   99 (99)
T ss_dssp             BSSSSBCEEEECC
T ss_pred             EeCCcEEEEEecC
Confidence            9999999999873

>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=1.5e-18  Score=129.48  Aligned_cols=77  Identities=34%  Similarity=0.675  Sum_probs=72.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...++.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   90 (94)
T 2e5h_A           11 GLAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKA   90 (94)
T ss_dssp             SCCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            345778999999999999999999999999999999999999899999999999999887      79999999999999


Q ss_pred             ecc
Q 022814          104 DHV  106 (291)
Q Consensus       104 ~~a  106 (291)
                      .+|
T Consensus        91 ~~a   93 (94)
T 2e5h_A           91 SIA   93 (94)
T ss_dssp             EEC
T ss_pred             Eec
Confidence            987

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=1.4e-18  Score=131.05  Aligned_cols=80  Identities=26%  Similarity=0.448  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            4578999999999999999999999999999999999999899999999999999887      7899999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        85 a~~~~~   90 (99)
T 1whw_A           85 STIKKE   90 (99)
T ss_dssp             CCCCST
T ss_pred             cCCCcc
Confidence            976654

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=8.8e-19  Score=131.34  Aligned_cols=79  Identities=25%  Similarity=0.500  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDV-NLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i-~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++++|||+|||+.+++++|..+|++||.|..| .|+.++.+|.++|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            578999999999999999999999999999999 999998899999999999999887      6999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        83 a~~~~~   88 (96)
T 1x5t_A           83 AFKKDS   88 (96)
T ss_dssp             SCCCCC
T ss_pred             ecccCC
Confidence            976553

>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=99.77  E-value=1e-18  Score=134.51  Aligned_cols=86  Identities=29%  Similarity=0.597  Sum_probs=77.5

Q ss_pred             CCcccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC
Q 022814           24 DDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        24 ~~~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~   97 (291)
                      ...+.+...++.++|||+|||+.+++++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+
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            334445556788999999999999999999999999999999999999899999999999999887      68999999


Q ss_pred             CeEEEEeccCCc
Q 022814           98 GRTIRVDHVAKY  109 (291)
Q Consensus        98 gr~i~V~~a~~~  109 (291)
                      |+.|.|.++.+.
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            999999998754

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=8.4e-19  Score=133.32  Aligned_cols=82  Identities=29%  Similarity=0.537  Sum_probs=75.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.|+.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2dnm_A            8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRV   87 (103)
T ss_dssp             SCCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEE
T ss_pred             CCCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            345678999999999999999999999999999999999999999999999999999887      69999999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2dnm_A           88 QVARYGRR   95 (103)
T ss_dssp             EECSSCCS
T ss_pred             EECCcCCC
Confidence            99976543

>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=1.8e-18  Score=131.80  Aligned_cols=82  Identities=23%  Similarity=0.429  Sum_probs=74.6

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC---eE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG---RT  100 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g---r~  100 (291)
                      ...++.++|||+|||+.+++++|.++|++||.|..|.|+.++ +|.++|||||+|.+.++      .||+..|.+   +.
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            345678999999999999999999999999999999999998 89999999999999887      689999998   99


Q ss_pred             EEEeccCCcccc
Q 022814          101 IRVDHVAKYKKK  112 (291)
Q Consensus       101 i~V~~a~~~~~~  112 (291)
                      |.|.++.+....
T Consensus        89 l~V~~a~~~~~~  100 (105)
T 2dnh_A           89 LVVKFADTDKES  100 (105)
T ss_dssp             CEEEESCSSCCC
T ss_pred             EEEEECccCccc
Confidence            999999876543

>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=2.6e-18  Score=129.87  Aligned_cols=80  Identities=26%  Similarity=0.558  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   91 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVA   91 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            45678999999999999999999999999999999999998 99999999999999887      789999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        92 ~a~~~~~   98 (100)
T 2do4_A           92 ISNSGPS   98 (100)
T ss_dssp             ECCCCSC
T ss_pred             ECCCCCC
Confidence            9976543

>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=99.77  E-value=1.8e-18  Score=131.82  Aligned_cols=80  Identities=25%  Similarity=0.482  Sum_probs=73.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC-CCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT-GKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~t-g~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|+++|++|| |..|.|+.++.| |.++|||||+|.+.++     .||+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~   89 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVD   89 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEE
Confidence            346779999999999999999999999999 999999999988 9999999999999887     789999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        90 ~a~~~~~   96 (104)
T 1wi8_A           90 VADQAQD   96 (104)
T ss_dssp             ECCCCCC
T ss_pred             EccCCCC
Confidence            9976543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=133.34  Aligned_cols=80  Identities=31%  Similarity=0.545  Sum_probs=73.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+++++|.++|++||.|..|.|+.++.||.++|||||+|.+.++      .|||..|+|+.|.|
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            345677899999999999999999999999999999999999999999999999999887      68999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus        98 ~~a~~~  103 (106)
T 1p27_B           98 DWCFVR  103 (106)
T ss_dssp             EESEES
T ss_pred             EeecCC
Confidence            998654

>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=1.3e-18  Score=133.78  Aligned_cols=81  Identities=32%  Similarity=0.545  Sum_probs=74.7

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            345678899999999999999999999999999999999999999999999999999887      69999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus       101 ~~a~~~~  107 (110)
T 1oo0_B          101 DWCFVKG  107 (110)
T ss_dssp             EESEESS
T ss_pred             EEcccCC
Confidence            9987544

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.76  E-value=1.6e-19  Score=155.04  Aligned_cols=132  Identities=22%  Similarity=0.355  Sum_probs=96.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..|.+||||+|||+.+|+++|.++|++||+|.+|.|+.++.||.++|||||+|.+.++      .||+..+.|+.|.|.+
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            4578899999999999999999999999999999999999999999999999999887      7899999999999998


Q ss_pred             cCCccccchhHHHH-H----HhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          106 VAKYKKKEEEDEET-R----QRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       106 a~~~~~~~~~~~~~-~----~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      +............. .    ...-....+...|.  .+|.+..|.+..+..+           .+|||||.|....
T Consensus        92 ~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~--~~G~i~~~~i~~d~~~-----------~~g~~fV~f~~~~  154 (213)
T 4f02_A           92 SQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFS--AFGNILSCKVVCDENG-----------SKGYGFVHFETQE  154 (213)
T ss_dssp             CCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHG--GGSCEEEEEEEEETTE-----------EEEEEEEEESSHH
T ss_pred             ccccccccccccccceECCcccccHHHHHHHHHh--hcCCeEEEEeeccCCC-----------CceEEEEEeCCHH
Confidence            86543221100000 0    00001223333333  3567888888877432           3578899987644

>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=8.6e-19  Score=138.13  Aligned_cols=85  Identities=29%  Similarity=0.490  Sum_probs=76.5

Q ss_pred             cccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe
Q 022814           26 ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR   99 (291)
Q Consensus        26 ~~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr   99 (291)
                      .+......+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.++.++|||||+|.+.++      .|||..|+|+
T Consensus        13 ~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           13 EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             -CCBCCCSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            3334556778999999999999999999999999999999999999999999999999999887      6899999999


Q ss_pred             EEEEeccCCcc
Q 022814          100 TIRVDHVAKYK  110 (291)
Q Consensus       100 ~i~V~~a~~~~  110 (291)
                      .|.|.++.+..
T Consensus        93 ~l~v~~a~~~~  103 (126)
T 3ex7_B           93 PISVDWCFVRG  103 (126)
T ss_dssp             BCEEEESEESS
T ss_pred             EEEEEEecCCC
Confidence            99999986544

>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=3e-19  Score=132.70  Aligned_cols=77  Identities=21%  Similarity=0.443  Sum_probs=66.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G--~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .+|||+|||+.+|+++|+++|++||  .|..|.|+.++.||.++|||||+|.+.++      .|||..|+|+.|.|.++.
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  99999999999999999999999999887      799999999999999997


Q ss_pred             Ccccc
Q 022814          108 KYKKK  112 (291)
Q Consensus       108 ~~~~~  112 (291)
                      +....
T Consensus        82 ~~~~~   86 (90)
T 3p5t_L           82 KLEHH   86 (90)
T ss_dssp             -----
T ss_pred             CCccc
Confidence            66543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.76  E-value=2e-18  Score=132.95  Aligned_cols=83  Identities=24%  Similarity=0.407  Sum_probs=70.4

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      .....+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.||.++|||||+|.+.++     .+.+..|+|+.|.|
T Consensus        19 ~~~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V   98 (109)
T 2rs2_A           19 SHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDP   98 (109)
T ss_dssp             -------CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEE
T ss_pred             cccCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEE
Confidence            3445678999999999999999999999999999999999999999999999999999887     44569999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus        99 ~~a~~~~~  106 (109)
T 2rs2_A           99 KVAFPRRA  106 (109)
T ss_dssp             EECCCCCC
T ss_pred             EEccCCCC
Confidence            99976543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=1.8e-18  Score=130.18  Aligned_cols=79  Identities=25%  Similarity=0.455  Sum_probs=72.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC---CCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKG---TGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~---tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ++.++|||+|||+.+++++|.++|++||.|..|.|+.++.   |+.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            5789999999999999999999999999999999999876   66999999999999887      69999999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus        83 ~~a~~~~~   90 (98)
T 2cpf_A           83 RISERATK   90 (98)
T ss_dssp             ECSSCSSC
T ss_pred             EEccCCCC
Confidence            99976553

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.1e-18  Score=132.28  Aligned_cols=80  Identities=39%  Similarity=0.717  Sum_probs=74.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..++.++|||+|||+.+++++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus         8 ~~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   87 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   87 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            45678999999999999999999999999999999999999899999999999999887      789999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus        88 ~a~~~~   93 (102)
T 1x5s_A           88 QAGKSS   93 (102)
T ss_dssp             EEECCC
T ss_pred             ECCCCC
Confidence            987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.8e-18  Score=132.62  Aligned_cols=82  Identities=33%  Similarity=0.528  Sum_probs=75.3

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEEcChhh------hcCCce
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV--------DVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQ   95 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~--------~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~   95 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.|.        .|.|+.++.+|.++|||||+|.+.++      .||+..
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~   89 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKD   89 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCE
T ss_pred             ccCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCc
Confidence            4457889999999999999999999999999999        69999998899999999999999887      689999


Q ss_pred             eCCeEEEEeccCCccc
Q 022814           96 ILGRTIRVDHVAKYKK  111 (291)
Q Consensus        96 i~gr~i~V~~a~~~~~  111 (291)
                      |.|+.|.|.++.+...
T Consensus        90 ~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           90 FQGSKLKVSLARKKPP  105 (113)
T ss_dssp             ETTEECEEECSSCCCC
T ss_pred             cCCCEEEEEECCCCCC
Confidence            9999999999976543

>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=2.2e-18  Score=133.95  Aligned_cols=76  Identities=22%  Similarity=0.468  Sum_probs=68.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ...+|||+|||+.+|+++|+++|++||.|.+|.|+.+.  +.++|||||+|.+.++      +|||..|+|+.|.|.++.
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            35789999999999999999999999999999999986  5589999999999887      789999999999999987


Q ss_pred             Cccc
Q 022814          108 KYKK  111 (291)
Q Consensus       108 ~~~~  111 (291)
                      +...
T Consensus        82 ~~~~   85 (115)
T 4f25_A           82 SRKE   85 (115)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            6543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.1e-18  Score=130.05  Aligned_cols=79  Identities=27%  Similarity=0.480  Sum_probs=73.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCee-EEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE----
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV-DVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT----  100 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~-~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~----  100 (291)
                      ..++++|||+|||+.+++++|+++|++||.|. .|.|+.++.+|.++|||||+|.+.++      .|||..|.|+.    
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            46789999999999999999999999999999 99999999999999999999999887      69999999999    


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++.+..
T Consensus        86 l~v~~a~~~~   95 (99)
T 2div_A           86 FKLNYATYSG   95 (99)
T ss_dssp             CCEEETTCCS
T ss_pred             EEEeecCCCC
Confidence            9999987553

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=2.9e-18  Score=130.80  Aligned_cols=81  Identities=28%  Similarity=0.493  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ...+.++|||+|||+.+++++|+++|++||+|..|.|+.++.++.++|||||+|.+.++     .++++.|+|+.|.|.+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            45678999999999999999999999999999999999999899999999999999887     4499999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        92 a~~~~~   97 (105)
T 2dh8_A           92 CTPRGM   97 (105)
T ss_dssp             SCCSSC
T ss_pred             ccCCCC
Confidence            976654

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=1.2e-18  Score=133.12  Aligned_cols=76  Identities=17%  Similarity=0.298  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ..+.++|||+|||+.+|+++|.++|++||+|..|.|+.++. |.++|||||+|.+.++     .|++..|+|+.|.|.++
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            45678999999999999999999999999999999999986 9999999999999887     78999999999999987


Q ss_pred             CC
Q 022814          107 AK  108 (291)
Q Consensus       107 ~~  108 (291)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            53

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.76  E-value=3.3e-19  Score=135.27  Aligned_cols=77  Identities=22%  Similarity=0.474  Sum_probs=71.7

Q ss_pred             CCCCEEEEcCCCC------CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC-e
Q 022814           33 KDSAYVYVGGIPF------DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG-R   99 (291)
Q Consensus        33 ~~~~~lfVgnL~~------~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g-r   99 (291)
                      ...++|||+|||+      .+++++|.++|++||.|..|.|+.++.||+++|||||+|.+.++      .|||..|+| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      99999999999999999999999999999999999999999877      799999999 9


Q ss_pred             EEEEeccCCc
Q 022814          100 TIRVDHVAKY  109 (291)
Q Consensus       100 ~i~V~~a~~~  109 (291)
                      .|.|.++.+.
T Consensus        84 ~l~V~~a~~~   93 (100)
T 3ns6_A           84 RLFLYTMKDV   93 (100)
T ss_dssp             BCEEEESHHH
T ss_pred             EEEEEECchh
Confidence            9999998643

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.76  E-value=2.7e-18  Score=133.74  Aligned_cols=76  Identities=21%  Similarity=0.465  Sum_probs=71.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..++.++|||+|||+.+++++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34667999999999999999999999999999999999999899999999999999887      699999999999998


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      ++
T Consensus       116 ~a  117 (118)
T 2khc_A          116 LK  117 (118)
T ss_dssp             EC
T ss_pred             ec
Confidence            86

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=6.1e-18  Score=131.37  Aligned_cols=80  Identities=30%  Similarity=0.510  Sum_probs=73.2

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.|+.++|||||+|.+.++      .|++ .|+|+.|.|
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            445678999999999999999999999999999999999999999999999999999887      6777 899999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        91 ~~a~~~~   97 (116)
T 2cqd_A           91 NLAYLGA   97 (116)
T ss_dssp             EESTTTC
T ss_pred             EEcccCC
Confidence            9996543

>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=99.75  E-value=9e-19  Score=147.27  Aligned_cols=135  Identities=19%  Similarity=0.359  Sum_probs=99.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++     .+++..|+|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            34567899999999999999999999999999999999999999999999999999887     6688999999999999


Q ss_pred             cCCccccchhHHHHHH---------hhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          106 VAKYKKKEEEDEETRQ---------RMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       106 a~~~~~~~~~~~~~~~---------~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      +.+.............         ..-....+...|.  .+|.+..+.+..+..++.         ..||+||.|....
T Consensus        89 ~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~--~~G~i~~v~i~~~~~~g~---------~~g~afV~F~~~~  157 (196)
T 1l3k_A           89 AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE--QYGKIEVIEIMTDRGSGK---------KRGFAFVTFDDHD  157 (196)
T ss_dssp             CCC-----------CCSEEEEECCTTTCCHHHHHHHHT--TTSCEEEEEEEECTTTCC---------EEEEEEEEESSHH
T ss_pred             ccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHh--cCCCeEEEEEeecCCCCC---------ccceEEEEECCHH
Confidence            8765332111100000         0002233344443  467788888888876655         4578899887643

>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=99.75  E-value=3.7e-18  Score=130.52  Aligned_cols=76  Identities=22%  Similarity=0.467  Sum_probs=71.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  103 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQ  103 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45678999999999999999999999999999999999999 99999999999999887      699999999999999


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      ++.
T Consensus       104 ~a~  106 (107)
T 3ulh_A          104 LVT  106 (107)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=2.8e-18  Score=130.38  Aligned_cols=80  Identities=18%  Similarity=0.405  Sum_probs=73.5

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|.++|++||.|..|.|+.+  +|.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   87 (103)
T 2d9p_A           10 ITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV   87 (103)
T ss_dssp             CCCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEE
Confidence            34567899999999999999999999999999999999998  89999999999999887      69999999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2d9p_A           88 ALAQRKEE   95 (103)
T ss_dssp             EECSSCCC
T ss_pred             EEeccccc
Confidence            99976654

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.75  E-value=1.9e-18  Score=131.89  Aligned_cols=82  Identities=28%  Similarity=0.549  Sum_probs=74.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee---CCeE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI---LGRT  100 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i---~gr~  100 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++      .||+..|   .++.
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~   87 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRP   87 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSC
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCce
Confidence            345678999999999999999999999999999999999999999999999999999887      6999888   8999


Q ss_pred             EEEeccCCccc
Q 022814          101 IRVDHVAKYKK  111 (291)
Q Consensus       101 i~V~~a~~~~~  111 (291)
                      |.|.++.+...
T Consensus        88 l~v~~a~~~~~   98 (106)
T 2dgp_A           88 IQVKPADSESR   98 (106)
T ss_dssp             CEEEECCCCSC
T ss_pred             EEEEECCcccc
Confidence            99999976543

>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=99.75  E-value=8.2e-18  Score=127.81  Aligned_cols=82  Identities=26%  Similarity=0.398  Sum_probs=73.6

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh----hcCCceeCCeEEEEec
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~----~lng~~i~gr~i~V~~  105 (291)
                      ....+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++    ..++..|+|+.|.|.+
T Consensus        10 ~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           10 RAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEEC
T ss_pred             CccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEe
Confidence            345678999999999999999999999999999999999999899999999999999887    2357889999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        90 a~~~~~   95 (103)
T 2cqg_A           90 PNSKQS   95 (103)
T ss_dssp             CCTTCC
T ss_pred             cCCCCc
Confidence            976543

>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=99.75  E-value=2.4e-18  Score=133.54  Aligned_cols=79  Identities=22%  Similarity=0.309  Sum_probs=72.5

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCe-eEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEI-VDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I-~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.| ..|.|+.++ +|.++|||||+|.+.++     .+|+..|+|+.|.|
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            345678999999999999999999999999999 899999999 99999999999999887     56999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus        89 ~~a~~~   94 (114)
T 2cpy_A           89 HVVTLE   94 (114)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            998643

>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=99.75  E-value=5.2e-18  Score=138.68  Aligned_cols=81  Identities=32%  Similarity=0.533  Sum_probs=75.0

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|.++|++||+|..|.|+.++.|+.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        34 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           34 KLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            344678999999999999999999999999999999999999999999999999999887      69999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus       114 ~~a~~~~  120 (156)
T 1h2v_Z          114 DWDAGFK  120 (156)
T ss_dssp             EEESCCC
T ss_pred             EECCCCC
Confidence            9997654

>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=99.75  E-value=6.6e-18  Score=124.63  Aligned_cols=76  Identities=32%  Similarity=0.625  Sum_probs=71.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++     .||+..|+|+.|.|.++.+
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            35799999999999999999999999999999999999899999999999999887     7999999999999999865


Q ss_pred             c
Q 022814          109 Y  109 (291)
Q Consensus       109 ~  109 (291)
                      .
T Consensus        85 ~   85 (89)
T 3ucg_A           85 N   85 (89)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=2.8e-18  Score=126.29  Aligned_cols=78  Identities=21%  Similarity=0.443  Sum_probs=71.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC-cceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGK-PRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~-s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+++|||+|||+.+|+++|.++|++||.|..|.|+.+..++. ++|||||+|.+.++      .|||..|+|+.|.|.+
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            4578999999999999999999999999999999999987766 99999999999887      6999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus        82 a~~~~   86 (88)
T 4a8x_A           82 VLAPW   86 (88)
T ss_dssp             ECCCC
T ss_pred             CCCCC
Confidence            87653

>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=99.75  E-value=9.3e-18  Score=127.50  Aligned_cols=80  Identities=24%  Similarity=0.490  Sum_probs=71.8

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+++++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++      .||+..|.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~--~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   87 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEH--TSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKV   87 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCC--CSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecC--CCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEE
Confidence            445678999999999999999999999999999999999986  3379999999999887      69999999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus        88 ~~a~~~~~   95 (103)
T 2cqi_A           88 NWATTPSS   95 (103)
T ss_dssp             EECCCTTC
T ss_pred             EECCCCcc
Confidence            99976543

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.75  E-value=3.8e-18  Score=139.89  Aligned_cols=76  Identities=24%  Similarity=0.480  Sum_probs=70.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G--~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..++|||+|||+.+|+++|.++|++||  .|..|.|+.|+.||.++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  99999999999999999999999999887      7899999999999999


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      +.+.
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9754

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=2.6e-18  Score=133.50  Aligned_cols=78  Identities=24%  Similarity=0.507  Sum_probs=72.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      .+.++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++     .+++..|+|+.|.|.++.
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            446899999999999999999999999999999999999899999999999999887     458999999999999997


Q ss_pred             Ccc
Q 022814          108 KYK  110 (291)
Q Consensus       108 ~~~  110 (291)
                      +..
T Consensus       105 ~~~  107 (116)
T 1x4b_A          105 ARE  107 (116)
T ss_dssp             SCC
T ss_pred             CCc
Confidence            654

>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=99.75  E-value=2.7e-18  Score=129.25  Aligned_cols=79  Identities=22%  Similarity=0.315  Sum_probs=72.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..+..++|||+|||+.+++++|+++|++||.|..|.|+.+..+|.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus        11 ~~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   90 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLV   90 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999887      789999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++...
T Consensus        91 ~a~~~   95 (98)
T 2cqp_A           91 LGSGP   95 (98)
T ss_dssp             ESSCS
T ss_pred             EcCCC
Confidence            98643

>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=6e-18  Score=126.50  Aligned_cols=76  Identities=30%  Similarity=0.601  Sum_probs=70.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+++++|+++|++||+|..|.|+.++ +|.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDR-EGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVS   90 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEE
Confidence            45677999999999999999999999999999999999998 49999999999999887      699999999999999


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      ++.
T Consensus        91 ~a~   93 (95)
T 2ywk_A           91 GPS   93 (95)
T ss_dssp             CCC
T ss_pred             EcC
Confidence            885

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-17  Score=126.61  Aligned_cols=82  Identities=28%  Similarity=0.553  Sum_probs=73.1

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      .....+.++|||+|||+.+|+++|+++|++||.|..|.|+.+..  .++|||||+|.+.++      .||+..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   86 (103)
T 2cq3_A            9 SESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIE   86 (103)
T ss_dssp             SCCSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            34567789999999999999999999999999999999999863  489999999999887      6899999999999


Q ss_pred             EeccCCcccc
Q 022814          103 VDHVAKYKKK  112 (291)
Q Consensus       103 V~~a~~~~~~  112 (291)
                      |.++.+....
T Consensus        87 v~~a~~~~~~   96 (103)
T 2cq3_A           87 VNNATARVMT   96 (103)
T ss_dssp             EEECCSSCCC
T ss_pred             EEEcccCCCC
Confidence            9999876543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=129.30  Aligned_cols=80  Identities=24%  Similarity=0.424  Sum_probs=73.1

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+++++|+++|++||.|..|.|+.++ +|.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   88 (114)
T 2do0_A           10 QAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHV   88 (114)
T ss_dssp             CCCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEE
Confidence            345678999999999999999999999999999999999998 79999999999999887      69999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++....
T Consensus        89 ~~a~~~~   95 (114)
T 2do0_A           89 KMDERAL   95 (114)
T ss_dssp             EECSCCC
T ss_pred             EEcccCC
Confidence            9986543

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.74  E-value=5.1e-18  Score=132.19  Aligned_cols=78  Identities=33%  Similarity=0.666  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~   82 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQ   82 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3567899999999999999999999999999999999998 99999999999999887      6999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus        83 a~~~~   87 (116)
T 2fy1_A           83 AKKPS   87 (116)
T ss_dssp             CCCSS
T ss_pred             CCCCC
Confidence            97554

>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=99.74  E-value=5.2e-18  Score=140.10  Aligned_cols=82  Identities=32%  Similarity=0.536  Sum_probs=74.1

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.||.++|||||+|.+.++      .|||..|+|+.|.|
T Consensus        67 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  146 (165)
T 1rk8_A           67 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  146 (165)
T ss_dssp             CCCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345667899999999999999999999999999999999999999999999999999887      69999999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus       147 ~~a~~~~~  154 (165)
T 1rk8_A          147 DWCFVKGP  154 (165)
T ss_dssp             EESEECC-
T ss_pred             EEecCCCC
Confidence            99976543

>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=3.6e-18  Score=135.60  Aligned_cols=81  Identities=37%  Similarity=0.565  Sum_probs=74.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...++.++|||+|||+.+++++|+++|++||+|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|
T Consensus        41 ~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V  120 (129)
T 2kxn_B           41 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV  120 (129)
T ss_dssp             SCCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345678999999999999999999999999999999999999999999999999999887      69999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus       121 ~~a~~~~  127 (129)
T 2kxn_B          121 DFSITKR  127 (129)
T ss_dssp             SCCSSSS
T ss_pred             EEecCCC
Confidence            9987643

>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=99.74  E-value=2.1e-18  Score=129.00  Aligned_cols=77  Identities=22%  Similarity=0.368  Sum_probs=69.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+|+++|+++|++||.|..|.|+.+..+|.++|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             ---CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            4567999999999999999999999999999999999998899999999999999887      6899999999999998


Q ss_pred             cCC
Q 022814          106 VAK  108 (291)
Q Consensus       106 a~~  108 (291)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            753

>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=2.2e-18  Score=123.33  Aligned_cols=70  Identities=29%  Similarity=0.519  Sum_probs=66.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      +|||+|||+.+++++|..+|++||+|..|.|+.++.+|.++|||||+|.+.++     .||+..|+|++|.|.+|
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            59999999999999999999999999999999999899999999999999887     78999999999999875

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=4.3e-18  Score=129.50  Aligned_cols=78  Identities=22%  Similarity=0.395  Sum_probs=72.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhc-CCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCce-eCCeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQ-CGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQ-ILGRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~-~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~-i~gr~i~V  103 (291)
                      ..+.++|||+|||+.+|+++|.++|++ ||.|..|.|+.+. +|.++|||||+|.+.++      .||+.. |+|+.|.|
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            467899999999999999999999999 9999999999999 99999999999999887      699999 99999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        85 ~~a~~~~   91 (104)
T 2dhg_A           85 SVAIPKA   91 (104)
T ss_dssp             CBCCCCC
T ss_pred             EEccCCC
Confidence            9987554

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.74  E-value=9.6e-18  Score=134.31  Aligned_cols=80  Identities=29%  Similarity=0.449  Sum_probs=74.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+++++|.++|+.||.|..|.|+.++.||.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            44667899999999999999999999999999999999999899999999999999887      699999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus       118 ~a~~~~  123 (139)
T 1u6f_A          118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            997554

>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=99.73  E-value=8.2e-18  Score=124.87  Aligned_cols=76  Identities=29%  Similarity=0.508  Sum_probs=62.7

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--hcCCcee--CCeEEEEec
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--NLNGAQI--LGRTIRVDH  105 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--~lng~~i--~gr~i~V~~  105 (291)
                      ...++.++|||+|||+.+|+++|+++|++||.|..|.|+.+     ++|||||+|.+.++  +|++..+  .|+.|.|.+
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~   80 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISN   80 (89)
T ss_dssp             -----CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEE
Confidence            44678899999999999999999999999999999999875     69999999999988  7888665  599999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus        81 a~~k~   85 (89)
T 3d2w_A           81 AEPKH   85 (89)
T ss_dssp             CC---
T ss_pred             cCCCC
Confidence            87654

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.73  E-value=1.5e-18  Score=137.96  Aligned_cols=80  Identities=24%  Similarity=0.329  Sum_probs=73.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE--EEEeecCCCCCcceEEEEEEcChhh-----hcCCc----eeCCe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD--VNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGA----QILGR   99 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~--i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~----~i~gr   99 (291)
                      ...+.++|||+|||+.+|+++|+++|++||.|..  |.|+.|+.||.++|||||+|.+.++     .|||.    .|+|+
T Consensus        19 ~~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHHHHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCHHHHHHHHHhcCCCCCccCCCE
Confidence            3467889999999999999999999999999977  9999999999999999999999832     89999    99999


Q ss_pred             EEEEeccCCcc
Q 022814          100 TIRVDHVAKYK  110 (291)
Q Consensus       100 ~i~V~~a~~~~  110 (291)
                      .|.|.++.+..
T Consensus        99 ~l~V~~a~~~~  109 (131)
T 2m2b_A           99 TINVEFAKGSK  109 (131)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEECCCCC
Confidence            99999997653

>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=99.73  E-value=5e-18  Score=129.29  Aligned_cols=79  Identities=18%  Similarity=0.254  Sum_probs=70.7

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      ....+.++|||+|||+.+|+++|+++|++|| |+.|.|+.++ +|+++|||||+|.+.++     +||+..|+++.|.|.
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (102)
T 1wez_A           10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEE
Confidence            3456778999999999999999999999999 4599999998 99999999999999887     789999999999998


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      .+.+..
T Consensus        88 ~~~~~~   93 (102)
T 1wez_A           88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            876443

>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=99.73  E-value=9.6e-18  Score=127.97  Aligned_cols=79  Identities=20%  Similarity=0.358  Sum_probs=70.8

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~-i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.|.. |.|+.+ .+|+++|||||+|.+.++     .+|+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v   88 (104)
T 1wg5_A           10 PDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEI   88 (104)
T ss_dssp             SSCSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEE
Confidence            34467899999999999999999999999999987 889888 699999999999999887     55999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      ..+...
T Consensus        89 ~~~~~~   94 (104)
T 1wg5_A           89 FKSSRA   94 (104)
T ss_dssp             EEECTT
T ss_pred             EECCHH
Confidence            887643

>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=99.73  E-value=7.6e-18  Score=130.05  Aligned_cols=81  Identities=21%  Similarity=0.354  Sum_probs=72.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHH---HHHhcCCCeeEEEEeecCCCC---CcceEEEEEEcChhh------hcCCceeC
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLL---AVFAQCGEIVDVNLVRDKGTG---KPRGFAFVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~---~~F~~~G~I~~i~i~~d~~tg---~s~G~aFV~F~~~~~------~lng~~i~   97 (291)
                      ....+.++|||+|||+.+++++|.   ++|++||+|..|.|+.+..++   .++|||||+|.+.++      .|||..|+
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            445678899999999999999999   999999999999999988654   566999999999887      78999999


Q ss_pred             CeEEEEeccCCcc
Q 022814           98 GRTIRVDHVAKYK  110 (291)
Q Consensus        98 gr~i~V~~a~~~~  110 (291)
                      |+.|.|.++.+..
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            9999999997654

>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=99.73  E-value=1.2e-17  Score=125.54  Aligned_cols=77  Identities=23%  Similarity=0.271  Sum_probs=70.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLL----AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~----~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      ..+.++|||+|||+.+++++|+    ++|++||+|..|.|+.++.+   +|||||+|.+.++      .|||..|+|+.|
T Consensus         6 ~~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l   82 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKI   82 (96)
T ss_dssp             CSSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            4678899999999999999999    99999999999999999855   8999999999887      699999999999


Q ss_pred             EEeccCCccc
Q 022814          102 RVDHVAKYKK  111 (291)
Q Consensus       102 ~V~~a~~~~~  111 (291)
                      .|.++.+...
T Consensus        83 ~V~~a~~~~~   92 (96)
T 2dgx_A           83 LVSLATGASG   92 (96)
T ss_dssp             EEEECCCSSC
T ss_pred             EEEEcCCCCC
Confidence            9999976543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=8.4e-18  Score=128.42  Aligned_cols=76  Identities=16%  Similarity=0.333  Sum_probs=67.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcC--CceeCCeEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN--GAQILGRTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~ln--g~~i~gr~i~  102 (291)
                      ..++.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++      .|+  +..|.|++|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~   85 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY   85 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            4678899999999999999999999999999999999975      7999999999886      454  5899999999


Q ss_pred             EeccCCcccc
Q 022814          103 VDHVAKYKKK  112 (291)
Q Consensus       103 V~~a~~~~~~  112 (291)
                      |.++.+....
T Consensus        86 V~~A~~~~~~   95 (105)
T 1sjq_A           86 IQFSNHKELK   95 (105)
T ss_dssp             BCCCSSSSCC
T ss_pred             EEEcCCCCCC
Confidence            9999766544

>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=99.73  E-value=1.1e-17  Score=129.50  Aligned_cols=76  Identities=24%  Similarity=0.477  Sum_probs=71.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      +.++|||+|||+.+++++|+++|++||.|..|.|+.++.||.++|||||+|.+.++     .||+..|+|+.|.|.++.+
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            45799999999999999999999999999999999999999999999999999887     7899999999999999864


Q ss_pred             c
Q 022814          109 Y  109 (291)
Q Consensus       109 ~  109 (291)
                      .
T Consensus       104 ~  104 (114)
T 2cq4_A          104 E  104 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.73  E-value=1e-17  Score=128.48  Aligned_cols=80  Identities=31%  Similarity=0.481  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEe-ecCCCCCcceEEEEEEcChhh------hcC--CceeCCeEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGE-IVDVNLV-RDKGTGKPRGFAFVAYEDQRN------NLN--GAQILGRTI  101 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~-I~~i~i~-~d~~tg~s~G~aFV~F~~~~~------~ln--g~~i~gr~i  101 (291)
                      ..+.++|||+|||+.+|+++|.++|++||. |..|.|+ .+..+|.++|||||+|.+.++      .|+  +..|+|+.|
T Consensus         5 s~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CCCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             ccCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            467899999999999999999999999998 9999998 888899999999999999887      675  589999999


Q ss_pred             EEeccCCccc
Q 022814          102 RVDHVAKYKK  111 (291)
Q Consensus       102 ~V~~a~~~~~  111 (291)
                      .|.++.+...
T Consensus        85 ~V~~a~~~~~   94 (109)
T 2dis_A           85 AVDWAEPEID   94 (109)
T ss_dssp             EEEESCSSCS
T ss_pred             EEEEcCCCCC
Confidence            9999976553

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.72  E-value=2.1e-17  Score=132.11  Aligned_cols=77  Identities=36%  Similarity=0.620  Sum_probs=71.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...++.++|||+|||+.+|+++|+++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|
T Consensus        58 ~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           58 GSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             SSCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345678999999999999999999999999999999999999899999999999999887      68999999999999


Q ss_pred             ecc
Q 022814          104 DHV  106 (291)
Q Consensus       104 ~~a  106 (291)
                      .+|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            875

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=99.72  E-value=1.4e-17  Score=136.21  Aligned_cols=80  Identities=30%  Similarity=0.518  Sum_probs=74.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|++|.|.+
T Consensus        67 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~  146 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  146 (158)
T ss_dssp             CCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            4567899999999999999999999999999999999999899999999999999887      6899999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus       147 a~~~~~  152 (158)
T 2kn4_A          147 ARYGRP  152 (158)
T ss_dssp             ECCSSC
T ss_pred             CCCCCC
Confidence            986543

>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=2.8e-18  Score=129.98  Aligned_cols=79  Identities=27%  Similarity=0.481  Sum_probs=69.3

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK-GTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~-~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      ......++|||+|||+.+++++|+.+|++|| |..|.|+.+. .+|+++|||||+|.+.++     .|||..|+|+.|.|
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V   92 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRV   92 (100)
T ss_dssp             ------CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCC
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEE
Confidence            3456789999999999999999999999999 9999999998 699999999999999887     88999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus        93 ~~a~~~   98 (100)
T 2j76_E           93 DVADQA   98 (100)
T ss_dssp             EECCCS
T ss_pred             EeccCC
Confidence            998754

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=1.8e-18  Score=126.82  Aligned_cols=76  Identities=22%  Similarity=0.410  Sum_probs=70.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+++++|+.+|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|.|+.|+|.+
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            3578999999999999999999999999999999999999899999999999999887      6999999999998876


Q ss_pred             cC
Q 022814          106 VA  107 (291)
Q Consensus       106 a~  107 (291)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.72  E-value=1.3e-17  Score=123.94  Aligned_cols=78  Identities=26%  Similarity=0.484  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+++++|+.+|++||.|..|.|+.+  +|.++|||||+|.+.++      .||+..|+|+.|.|.+
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            467899999999999999999999999999999999985  79999999999999887      6999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        83 a~~~~~   88 (92)
T 2dgv_A           83 DRNASG   88 (92)
T ss_dssp             CSCCSS
T ss_pred             cCCCCC
Confidence            976543

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.72  E-value=1.6e-17  Score=127.00  Aligned_cols=77  Identities=19%  Similarity=0.371  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCCC------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe
Q 022814           32 YKDSAYVYVGGIPFDL------TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR   99 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~------te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr   99 (291)
                      ....++|||+|||+.+      |+++|..+|++||.|..|.|+  ..+|.++|||||+|.+.++      .|||..|+|+
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            3457899999999999      789999999999999999998  3589999999999999886      6999999998


Q ss_pred             -EEEEeccCCcc
Q 022814          100 -TIRVDHVAKYK  110 (291)
Q Consensus       100 -~i~V~~a~~~~  110 (291)
                       +|.|.++....
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

>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=99.72  E-value=1.6e-17  Score=128.54  Aligned_cols=79  Identities=20%  Similarity=0.479  Sum_probs=71.8

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee-------
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI-------   96 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i-------   96 (291)
                      ....+.++|||+|||+.+|+++|+.+|++||.|..|.|+.++ +|.++|||||+|.+.++      .|||..|       
T Consensus        20 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~   98 (114)
T 1x5o_A           20 QQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVS   98 (114)
T ss_dssp             CCCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcccc
Confidence            345678999999999999999999999999999999999998 99999999999999887      6999999       


Q ss_pred             -CCeEEEEeccCCc
Q 022814           97 -LGRTIRVDHVAKY  109 (291)
Q Consensus        97 -~gr~i~V~~a~~~  109 (291)
                       .+++|.|.++.+.
T Consensus        99 ~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           99 APTEPLLCKFSGPS  112 (114)
T ss_dssp             CCSSCBEEEECCCS
T ss_pred             CCCCceeEEccCCC
Confidence             5788999988743

>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=6.4e-18  Score=128.44  Aligned_cols=80  Identities=44%  Similarity=0.815  Sum_probs=73.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   85 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeC
Confidence            356899999999999999999999999999999999999899999999999999887      69999999999999999


Q ss_pred             CCcccc
Q 022814          107 AKYKKK  112 (291)
Q Consensus       107 ~~~~~~  112 (291)
                      .+....
T Consensus        86 ~~~~~~   91 (104)
T 1p1t_A           86 ASEKNK   91 (104)
T ss_dssp             TCTTHH
T ss_pred             CCccch
Confidence            765543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=2.9e-17  Score=121.88  Aligned_cols=77  Identities=25%  Similarity=0.417  Sum_probs=71.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ..+.++|||+|||+.+|+++|+++|++| .|..|.|+.+ .+|.++|||||+|.+.++     .||+..|+|+.|.|.++
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEEC
Confidence            4568999999999999999999999999 9999999999 699999999999999887     78999999999999998


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      .+..
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            7654

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.72  E-value=8.9e-18  Score=132.04  Aligned_cols=81  Identities=22%  Similarity=0.413  Sum_probs=74.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++      .|||..|+|+.|.|.
T Consensus        31 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  109 (124)
T 2kt5_A           31 GVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQ  109 (124)
T ss_dssp             CCSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            34567899999999999999999999999999999999998 99999999999999887      699999999999999


Q ss_pred             ccCCcccc
Q 022814          105 HVAKYKKK  112 (291)
Q Consensus       105 ~a~~~~~~  112 (291)
                      +|.+....
T Consensus       110 ~a~~~~~~  117 (124)
T 2kt5_A          110 LVASQIDL  117 (124)
T ss_dssp             EECCTTCC
T ss_pred             EeCCCCCC
Confidence            99765443

>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=99.72  E-value=3.1e-18  Score=139.93  Aligned_cols=131  Identities=23%  Similarity=0.362  Sum_probs=95.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|.|++|.|.++.
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            36899999999999999999999999999999999999999999999999999887      589999999999999987


Q ss_pred             CccccchhHHHH---HHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          108 KYKKKEEEDEET---RQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       108 ~~~~~~~~~~~~---~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      +.........-.   ....-....+...|.  .+|.+..+.+..+..++.         ..||+++.|...
T Consensus        81 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~--~~G~i~~~~i~~~~~~g~---------~~g~afV~f~~~  140 (167)
T 1fxl_A           81 PSSASIRDANLYVSGLPKTMTQKELEQLFS--QYGRIITSRILVDQVTGV---------SRGVGFIRFDKR  140 (167)
T ss_dssp             CCCGGGTTCEEEEESCCTTCCHHHHHHHHG--GGSCEEEEEEEECTTTCC---------EEEEEEEEESSH
T ss_pred             CCcccCCCCcEEECCCCCcCCHHHHHHHHH--hcCCEeEEEEEecCCCCC---------ccceEEEEeCCH
Confidence            654321100000   000001122233333  245677777777765554         457778888653

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.72  E-value=1.2e-17  Score=142.53  Aligned_cols=133  Identities=23%  Similarity=0.383  Sum_probs=98.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus        25 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~  104 (216)
T 2qfj_A           25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGR  104 (216)
T ss_dssp             HHHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEEC
T ss_pred             cCcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEec
Confidence            3457899999999999999999999999999999999999899999999999999887      5899999999999998


Q ss_pred             cCCccccchhHHHHHHhhh--------------hhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCC
Q 022814          106 VAKYKKKEEEDEETRQRMR--------------EERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEK  171 (291)
Q Consensus       106 a~~~~~~~~~~~~~~~~~~--------------~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~  171 (291)
                      +..................              ....+...|.  .+|.+..+.+..+..++.         ..||+||.
T Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~--~~G~v~~v~i~~~~~~g~---------~~g~afV~  173 (216)
T 2qfj_A          105 PSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFE--AFGKIKSATLARDPTTGK---------HKGYGFIE  173 (216)
T ss_dssp             CSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHT--TSSCEEEEEEEECTTTCC---------EEEEEEEE
T ss_pred             CCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHh--ccCCeeEEEEEecCCCCC---------cCceEEEE
Confidence            8765543322211111111              1233333333  467788888888876655         45677888


Q ss_pred             ccCC
Q 022814          172 FEGF  175 (291)
Q Consensus       172 ~~~~  175 (291)
                      |...
T Consensus       174 F~~~  177 (216)
T 2qfj_A          174 YEKA  177 (216)
T ss_dssp             ESSH
T ss_pred             ecCH
Confidence            8653

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.71  E-value=2.2e-17  Score=129.61  Aligned_cols=77  Identities=31%  Similarity=0.613  Sum_probs=72.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~  108 (291)
                      +.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++     .|||..|+|+.|.|.++.+
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            46899999999999999999999999999999999998899999999999999887     7899999999999999865


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus       115 ~~  116 (124)
T 2jwn_A          115 NM  116 (124)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.71  E-value=3.4e-17  Score=124.48  Aligned_cols=76  Identities=12%  Similarity=0.209  Sum_probs=66.6

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------h--cCCceeCCeEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------N--LNGAQILGRTI  101 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~--lng~~i~gr~i  101 (291)
                      ...++.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++      .  +++..|.|++|
T Consensus        10 ~~~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l   83 (101)
T 2cq1_A           10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPI   83 (101)
T ss_dssp             CCSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEEC
T ss_pred             ccCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEE
Confidence            34568899999999999999999999999999999998865      7999999999886      3  35788999999


Q ss_pred             EEeccCCccc
Q 022814          102 RVDHVAKYKK  111 (291)
Q Consensus       102 ~V~~a~~~~~  111 (291)
                      .|.++.+...
T Consensus        84 ~V~~a~~~~~   93 (101)
T 2cq1_A           84 YIQYSNHKEL   93 (101)
T ss_dssp             EEEECSCSSC
T ss_pred             EEEEcCcccC
Confidence            9999976543

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=99.71  E-value=2.6e-18  Score=140.81  Aligned_cols=131  Identities=18%  Similarity=0.267  Sum_probs=97.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|+|..|.|++|.|.++.
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            57899999999999999999999999999999999999899999999999999887      689999999999999987


Q ss_pred             CccccchhHHH---HHHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          108 KYKKKEEEDEE---TRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       108 ~~~~~~~~~~~---~~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      +.........-   .....-....+...|.  .+|.+..+.+..+..++.         ..||+++.|...
T Consensus        82 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~--~~G~i~~~~i~~~~~~~~---------~~g~afV~f~~~  141 (168)
T 1b7f_A           82 PGGESIKDTNLYVTNLPRTITDDQLDTIFG--KYGSIVQKNILRDKLTGR---------PRGVAFVRYNKR  141 (168)
T ss_dssp             CCSSTTTTCEEEEESCCTTCCHHHHHHHHT--SSSCEEEEEEEECTTTCC---------EEEEEEEEESSH
T ss_pred             CCcccCCCCCEEEeCCCCCCCHHHHHHhhh--cCCcEEEEEEEEcCCCCC---------cceEEEEEECCH
Confidence            65432110000   0000001222333333  356677778877765555         456788888653

>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=99.71  E-value=5.1e-18  Score=121.30  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=66.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      +|||+|||+.+++++|..+|++||+|..|.|+.++.+|.++|||||+|.+.++     .+++..|+|+.|.|.+|
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            59999999999999999999999999999999999899999999999999887     67889999999999865

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.71  E-value=2e-17  Score=131.01  Aligned_cols=78  Identities=17%  Similarity=0.301  Sum_probs=69.0

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLL----AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR   99 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~----~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr   99 (291)
                      ...++.++|||+|||+.+++++|+    ++|++||.|..|.|+.   ++.++|||||+|.+.++      .|||..|.|+
T Consensus        24 ~~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr  100 (127)
T 2a3j_A           24 PHTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGN  100 (127)
T ss_dssp             CCCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTS
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCC
Confidence            445678999999999999999876    6999999999988753   68899999999999876      8999999999


Q ss_pred             EEEEeccCCcc
Q 022814          100 TIRVDHVAKYK  110 (291)
Q Consensus       100 ~i~V~~a~~~~  110 (291)
                      +|.|.++....
T Consensus       101 ~l~V~~a~~~~  111 (127)
T 2a3j_A          101 PLVITFSETPQ  111 (127)
T ss_dssp             CCEEEECCCCC
T ss_pred             EEEEEEccCcc
Confidence            99999997654

>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=99.71  E-value=1.6e-17  Score=144.47  Aligned_cols=76  Identities=22%  Similarity=0.451  Sum_probs=70.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCG--EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G--~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..++|||+|||+.||+++|+++|++||  .|+.|.|+.++.||+++|||||+|.+.++      .||++.|+|+.|.|.+
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  99999999999999999999999999877      6999999999999999


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      +.+.
T Consensus       147 a~~~  150 (229)
T 3q2s_C          147 VNKQ  150 (229)
T ss_dssp             CCHH
T ss_pred             CCCC
Confidence            8644

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=7.2e-18  Score=121.02  Aligned_cols=70  Identities=29%  Similarity=0.524  Sum_probs=66.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ++|||+|||+.+++++|+.+|++||+|..|.|+.++.+|.++|||||+|.+.++      .|+ ..|+|+.|.|.+|
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999999999999999899999999999999887      667 9999999999886

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=6.6e-17  Score=124.10  Aligned_cols=78  Identities=29%  Similarity=0.496  Sum_probs=69.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.|..|.|+.+   +.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   93 (109)
T 1x4a_A           17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV   93 (109)
T ss_dssp             CCCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34567899999999999999999999999999999999654   5689999999999887      78999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        94 ~~a~~~~  100 (109)
T 1x4a_A           94 EFPRSGR  100 (109)
T ss_dssp             ECCCCCC
T ss_pred             EEcccCC
Confidence            9997654

>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=3.5e-18  Score=126.61  Aligned_cols=77  Identities=32%  Similarity=0.643  Sum_probs=68.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCCcc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAKYK  110 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~~~  110 (291)
                      ++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++     .|||..|+|+.|.|.+|.+..
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTHHHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            689999999999999999999999999999999999999999999999999877     799999999999999997654


Q ss_pred             cc
Q 022814          111 KK  112 (291)
Q Consensus       111 ~~  112 (291)
                      ..
T Consensus        82 ~~   83 (90)
T 2ki2_A           82 SL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            43

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=4.4e-17  Score=123.27  Aligned_cols=76  Identities=24%  Similarity=0.422  Sum_probs=68.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|+++|++||.|   .|+.+ .++.++|||||+|.+.++      .||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   86 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE   86 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            45678999999999999999999999999987   56666 589999999999999887      699999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus        87 ~a~~~~   92 (101)
T 2fc9_A           87 LQGPRG   92 (101)
T ss_dssp             ECSSCC
T ss_pred             EcCCCC
Confidence            997654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.70  E-value=2.6e-17  Score=128.53  Aligned_cols=75  Identities=20%  Similarity=0.347  Sum_probs=69.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGE---IVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~---I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      ..+.++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |+++|||||+|.+.++     .||+..|+|+.|.|
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V   92 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEV   92 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEE
Confidence            456789999999999999999999999999   89999999985 9999999999999887     78999999999999


Q ss_pred             eccC
Q 022814          104 DHVA  107 (291)
Q Consensus       104 ~~a~  107 (291)
                      .++.
T Consensus        93 ~~a~   96 (118)
T 2db1_A           93 FKSH   96 (118)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            9885

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=1.3e-17  Score=126.95  Aligned_cols=75  Identities=19%  Similarity=0.257  Sum_probs=65.4

Q ss_pred             cCCCCCCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCC--ceeCCeE
Q 022814           30 AKYKDSAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNG--AQILGRT  100 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng--~~i~gr~  100 (291)
                      ....|+++|||+|||+ .+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++      .||+  ..|.|++
T Consensus        10 ~~~~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~   83 (102)
T 1x4d_A           10 GRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKP   83 (102)
T ss_dssp             CCCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcE
Confidence            3456889999999999 9999999999999999999999875      5899999999877      4554  5699999


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++....
T Consensus        84 l~V~~a~~~~   93 (102)
T 1x4d_A           84 VRVHLSQKYK   93 (102)
T ss_dssp             CEEEEECCCT
T ss_pred             EEEEECCCCC
Confidence            9999997543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=3.2e-17  Score=126.12  Aligned_cols=78  Identities=29%  Similarity=0.602  Sum_probs=70.8

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++      .|||..|+|+.|.|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            345678999999999999999999999999999999999985  4599999999999887      69999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            998754

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.70  E-value=3.3e-17  Score=123.94  Aligned_cols=74  Identities=23%  Similarity=0.249  Sum_probs=64.8

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCc--eeCCeEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGA--QILGRTI  101 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~--~i~gr~i  101 (291)
                      ...+|+.+|||+|||+.+|+++|.++|++||.|..|.|+.      ++|||||+|.+.++      .|++.  .|.|++|
T Consensus        16 ~~~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i   89 (100)
T 3r27_A           16 HKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPA   89 (100)
T ss_dssp             -CCCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEE
T ss_pred             ccCCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEE
Confidence            3457899999999999999999999999999999999985      37899999999887      56665  4889999


Q ss_pred             EEeccCCc
Q 022814          102 RVDHVAKY  109 (291)
Q Consensus       102 ~V~~a~~~  109 (291)
                      .|.++.+.
T Consensus        90 ~V~~S~~k   97 (100)
T 3r27_A           90 FVNYSTSQ   97 (100)
T ss_dssp             EEEECSCS
T ss_pred             EEEecccc
Confidence            99999754

>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=99.70  E-value=7.4e-18  Score=132.61  Aligned_cols=78  Identities=21%  Similarity=0.362  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.++.+..+|.++|||||+|.+.++     .||+..|+|+.|.|.++
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            4567899999999999999999999999999987777777799999999999999887     79999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      .+.
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            643

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.70  E-value=1.2e-17  Score=133.67  Aligned_cols=80  Identities=30%  Similarity=0.518  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~  123 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM  123 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4557899999999999999999999999999999999999899999999999999887      6899999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus       124 a~~~~~  129 (135)
T 2lea_A          124 ARYGRP  129 (135)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            976554

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.70  E-value=3.9e-17  Score=127.93  Aligned_cols=76  Identities=16%  Similarity=0.194  Sum_probs=68.4

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcC------hh---h-------hcCCce
Q 022814           36 AYVYVGGI----PFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QR---N-------NLNGAQ   95 (291)
Q Consensus        36 ~~lfVgnL----~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~------~~---~-------~lng~~   95 (291)
                      ++|||+||    |+.|++.+|+++|++||+|.+|.++.|+.||.++|||||+|.+      ..   +       .|||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            78999999    9999999999999999999999999999999999999999995      21   1       479999


Q ss_pred             eCCeEEEEeccCCccc
Q 022814           96 ILGRTIRVDHVAKYKK  111 (291)
Q Consensus        96 i~gr~i~V~~a~~~~~  111 (291)
                      |+|+.|.|.+......
T Consensus        83 I~Gr~irV~ln~~g~~   98 (136)
T 2j8a_A           83 IMGFKFEVILNKHSIL   98 (136)
T ss_dssp             ETTEEEEEEECCTTHH
T ss_pred             ecCcEEEEEECcccHH
Confidence            9999999998766544

>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=4e-17  Score=124.74  Aligned_cols=75  Identities=21%  Similarity=0.222  Sum_probs=65.3

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcC--CceeCCeEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN--GAQILGRTI  101 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~ln--g~~i~gr~i  101 (291)
                      ...+|.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++      .|+  +..|+|++|
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            44678899999999999999999999999999999998864      7999999999886      454  456999999


Q ss_pred             EEeccCCcc
Q 022814          102 RVDHVAKYK  110 (291)
Q Consensus       102 ~V~~a~~~~  110 (291)
                      .|.++....
T Consensus        84 ~V~~a~~~~   92 (104)
T 1wex_A           84 FFNYSTSKR   92 (104)
T ss_dssp             EEEECSSSS
T ss_pred             EEEEccCcc
Confidence            999997654

>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=99.69  E-value=1.2e-16  Score=122.70  Aligned_cols=72  Identities=21%  Similarity=0.317  Sum_probs=66.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC-----eE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG-----RT  100 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g-----r~  100 (291)
                      ....++|||+|||+.+|+++|+++|++||+|..|.|+.+       |||||+|.+.++      .||+..|+|     +.
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            456789999999999999999999999999999999876       899999999876      699999999     99


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++.+..
T Consensus        85 i~V~~a~~~~   94 (108)
T 1x4c_A           85 IRVKVDGPRS   94 (108)
T ss_dssp             EEEEESSCCS
T ss_pred             EEEEeCCCCC
Confidence            9999997644

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.69  E-value=3.1e-17  Score=124.32  Aligned_cols=77  Identities=22%  Similarity=0.540  Sum_probs=70.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh---hc-CCceeCCeEEEEeccCC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NL-NGAQILGRTIRVDHVAK  108 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~l-ng~~i~gr~i~V~~a~~  108 (291)
                      .+.++|||+|||+.+++++|..+|++||.|..|.|+.+. +|.++|||||+|.+.++   ++ ++..|+|+.|.|.++.+
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            7 IMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCc
Confidence            456899999999999999999999999999999999998 99999999999999887   22 78899999999998875


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        86 ~~   87 (102)
T 2xs2_A           86 KQ   87 (102)
T ss_dssp             CC
T ss_pred             Cc
Confidence            44

>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=99.69  E-value=2.7e-17  Score=131.70  Aligned_cols=78  Identities=18%  Similarity=0.319  Sum_probs=71.3

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGE---IVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTI  101 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~---I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i  101 (291)
                      ....+.++|||+|||+.+|+++|+++|++||.   |..|.|+.++. |+++|||||+|.+.++     .||+..|+|+.|
T Consensus        39 ~~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i  117 (136)
T 2hgl_A           39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYI  117 (136)
T ss_dssp             SSCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEE
Confidence            34566789999999999999999999999999   89999999986 9999999999999887     789999999999


Q ss_pred             EEeccCC
Q 022814          102 RVDHVAK  108 (291)
Q Consensus       102 ~V~~a~~  108 (291)
                      .|.++.+
T Consensus       118 ~V~~a~~  124 (136)
T 2hgl_A          118 EVFKSHR  124 (136)
T ss_dssp             EEEECCH
T ss_pred             EEEECCh
Confidence            9998853

>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=99.69  E-value=3.1e-17  Score=134.33  Aligned_cols=131  Identities=18%  Similarity=0.363  Sum_probs=94.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh----hcCCceeCCeEEEEeccCCc
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~----~lng~~i~gr~i~V~~a~~~  109 (291)
                      ++++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++    ..++..|+|+.|.|.++.+.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~   81 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPR   81 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCH
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccch
Confidence            57899999999999999999999999999999999999899999999999999887    23467899999999887653


Q ss_pred             cccchhHHHH---HHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          110 KKKEEEDEET---RQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       110 ~~~~~~~~~~---~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      ........-.   ....-....+...|.  .+|.+..+.+..+..++.         ..||+|+.|...
T Consensus        82 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~--~~G~i~~~~i~~~~~~g~---------~~g~afV~f~~~  139 (167)
T 2cjk_A           82 DEQDKTGKIFVGGIGPDVRPKEFEEFFS--QWGTIIDAQLMLDKDTGQ---------SRGFGFVTYDSA  139 (167)
T ss_dssp             HHHHHCEEEEEEEECTTCCHHHHHHHHH--TTSCCSEEECCCSSSSST---------TSEEEEEEESSH
T ss_pred             hhccCCCeEEECCCCCCCCHHHHHHHHH--hCccEEEEEEEEcCCCCc---------cceEEEEEECCH
Confidence            2110000000   000001223333343  366788888888776665         567888888653

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=2e-17  Score=120.29  Aligned_cols=67  Identities=22%  Similarity=0.429  Sum_probs=61.4

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe-EE
Q 022814           35 SAYVYVGGIPFDL------TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR-TI  101 (291)
Q Consensus        35 ~~~lfVgnL~~~~------te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr-~i  101 (291)
                      +++|||+|||+.+      |+++|..+|++||+|..|.|+  ..+|.++|||||+|.+.++      .|||..|+|+ +|
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      789999999999999999988  3589999999999999887      6999999999 88


Q ss_pred             EE
Q 022814          102 RV  103 (291)
Q Consensus       102 ~V  103 (291)
                      .|
T Consensus        79 ~V   80 (81)
T 2krb_A           79 RV   80 (81)
T ss_dssp             CC
T ss_pred             Ee
Confidence            76

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.8e-17  Score=127.70  Aligned_cols=76  Identities=16%  Similarity=0.330  Sum_probs=66.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcC--CceeCCeEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLN--GAQILGRTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~ln--g~~i~gr~i~  102 (291)
                      ..+++++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++      .|+  +..|.|++|.
T Consensus        27 ~~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~  100 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIY  100 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEE
Confidence            3567899999999999999999999999999999999976      7999999999887      455  4689999999


Q ss_pred             EeccCCcccc
Q 022814          103 VDHVAKYKKK  112 (291)
Q Consensus       103 V~~a~~~~~~  112 (291)
                      |.++.+...+
T Consensus       101 V~~a~~k~~~  110 (119)
T 2ad9_A          101 IQFSNHKELK  110 (119)
T ss_dssp             EEECSSSSCC
T ss_pred             EEEccCCCCC
Confidence            9999766543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.69  E-value=6.5e-17  Score=118.74  Aligned_cols=68  Identities=18%  Similarity=0.303  Sum_probs=63.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .+.-|||+||++.+|+++|+++|.+||+|.+|.|+.      ++|||||+|.+.++      .||+..|+|++|.|++|.
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            467799999999999999999999999999999975      58999999999876      899999999999999984

>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=1.3e-17  Score=129.05  Aligned_cols=81  Identities=22%  Similarity=0.363  Sum_probs=68.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..++.++|||+|||+.+|+++|.++|++||.|..|.+..+..+|.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           21 PGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             CCSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            34578999999999999999999999999999544333333389999999999999887      689999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus       101 ~a~~~~~  107 (115)
T 2cpx_A          101 FGKNKKQ  107 (115)
T ss_dssp             ECCCCSC
T ss_pred             EccCCCC
Confidence            9976654

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=8.5e-17  Score=121.32  Aligned_cols=78  Identities=23%  Similarity=0.514  Sum_probs=69.4

Q ss_pred             ccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE
Q 022814           27 SWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT  100 (291)
Q Consensus        27 ~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~  100 (291)
                      +.....++.++|||+|||+.+|+++|+.+|++||.|..|.|+.+      +|||||+|.+.++      .||+..|+|+.
T Consensus         7 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~   80 (99)
T 2cpj_A            7 GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQ   80 (99)
T ss_dssp             CCSCCCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBC
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCce
Confidence            33445678899999999999999999999999999999999854      7899999999887      78999999999


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++.+..
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpj_A           81 LRVRFACHSA   90 (99)
T ss_dssp             CEEEESSCCS
T ss_pred             EEEEEcCCCC
Confidence            9999997654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.1e-16  Score=121.22  Aligned_cols=78  Identities=26%  Similarity=0.464  Sum_probs=70.2

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|+++|+.|+   .|.|+.++.++.++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            4467889999999999999999999999873   67888888899999999999999887      68999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        87 ~~a~~~~   93 (102)
T 2fc8_A           87 DWAKPKG   93 (102)
T ss_dssp             EECCCCC
T ss_pred             EEecCCC
Confidence            9997654

>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=6.7e-18  Score=127.82  Aligned_cols=78  Identities=19%  Similarity=0.353  Sum_probs=70.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ..+.++|||+|||+.+|+++|+.+|++||.|.. .++.+..+|.++|||||+|.+.++     .||+..|.|+.|.|.++
T Consensus        14 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            346789999999999999999999999999988 677777789999999999999887     79999999999999999


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      .+..
T Consensus        93 ~~~~   96 (101)
T 1fj7_A           93 KGRD   96 (101)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            7654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=5.8e-17  Score=124.90  Aligned_cols=72  Identities=26%  Similarity=0.489  Sum_probs=66.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      +..+|||+|||+.+|+++|+++|++| .|..|.|+.++ +|+++|||||+|.+.++     .||+..|+|+.|.|..+.
T Consensus        15 ~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDH-VGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCT-TCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECC-CCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            35799999999999999999999999 89999999998 49999999999999887     789999999999998775

>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=99.68  E-value=3.8e-17  Score=122.58  Aligned_cols=78  Identities=21%  Similarity=0.454  Sum_probs=69.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLL----AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT  100 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~----~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~  100 (291)
                      ..+++++|||+|||+.+++++|.    .+|++||.|..|.|+.   +|.++|||||+|.+.++      .|||..|+|+.
T Consensus         4 ~~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   80 (97)
T ss_dssp             --CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcE
Confidence            35688999999999999999999    9999999999999874   67889999999999887      68999999999


Q ss_pred             EEEeccCCccc
Q 022814          101 IRVDHVAKYKK  111 (291)
Q Consensus       101 i~V~~a~~~~~  111 (291)
                      |.|.++.+...
T Consensus        81 l~v~~a~~~~~   91 (97)
T 1nu4_A           81 MRIQYAKTDSD   91 (97)
T ss_dssp             CEEEECSSCCT
T ss_pred             EEEEEccCCCc
Confidence            99999987653

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.6e-16  Score=116.25  Aligned_cols=71  Identities=30%  Similarity=0.447  Sum_probs=64.8

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hc-CCceeCCeEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL-NGAQILGRTIR  102 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l-ng~~i~gr~i~  102 (291)
                      ...++.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++      .| ++..|+|++|.
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~   80 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLN   80 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECC
T ss_pred             CCCCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEE
Confidence            34567899999999999999999999999999999999874      7999999999887      57 99999999999


Q ss_pred             Eecc
Q 022814          103 VDHV  106 (291)
Q Consensus       103 V~~a  106 (291)
                      |.++
T Consensus        81 v~~a   84 (85)
T 2ytc_A           81 VKWG   84 (85)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9987

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.68  E-value=1.1e-17  Score=136.36  Aligned_cols=128  Identities=22%  Similarity=0.345  Sum_probs=94.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.++ ++.++|||||+|.+.++      .|||..|.|+.|.|.++.+.
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            589999999999999999999999999999999997 68899999999999887      78999999999999998665


Q ss_pred             cccchhHHHH-----HHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          110 KKKEEEDEET-----RQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       110 ~~~~~~~~~~-----~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      ..........     ....-....+...|  ..+|.+..+.+..+..++.         ..||+++.|...
T Consensus        80 ~~~~~~~~~~l~v~nl~~~~t~~~l~~~f--~~~G~i~~~~i~~~~~~~~---------~~g~afV~f~~~  139 (166)
T 3md3_A           80 QQSSSDDTFNLFVGDLNVNVDDETLRNAF--KDFPSYLSGHVMWDMQTGS---------SRGYGFVSFTSQ  139 (166)
T ss_dssp             CCCCCTTCEEEEEESCCTTCCHHHHHHHH--TTSTTEEEEEEEECTTTCC---------EEEEEEEEESCH
T ss_pred             CCCCCCCCceEEECCCCCCCCHHHHHHHH--hccCCeeEEEEEecCCCCC---------cceEEEEEeCCH
Confidence            4321110000     00000122333333  3467778888888776655         557788888653

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.67  E-value=9.2e-17  Score=124.16  Aligned_cols=75  Identities=13%  Similarity=0.096  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ..+...+|||+|||+.+|+++|+++|++|| +|..|.|+.    ..++|||||+|.+.++      .|||..|+|+.|.|
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 LPAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV   99 (111)
T ss_dssp             -CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            455678999999999999999999999999 899998864    3589999999999887      79999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++...
T Consensus       100 ~~a~~~  105 (111)
T 2jvr_A          100 ERDDNP  105 (111)
T ss_dssp             EESCC-
T ss_pred             EECCCC
Confidence            998643

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=1.7e-16  Score=119.21  Aligned_cols=75  Identities=24%  Similarity=0.430  Sum_probs=67.7

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC--CeEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL--GRTI  101 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~--gr~i  101 (291)
                      ...++.++|||+|||+.+|+++|+++|++||.|..|.|+.+      +|||||+|.+.++      .||+..|.  |+.|
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            34577899999999999999999999999999999999854      7899999999887      69999999  9999


Q ss_pred             EEeccCCcc
Q 022814          102 RVDHVAKYK  110 (291)
Q Consensus       102 ~V~~a~~~~  110 (291)
                      .|.++.+..
T Consensus        86 ~V~~a~~~~   94 (97)
T 1why_A           86 RVDFAKSGP   94 (97)
T ss_dssp             EEEECCCCC
T ss_pred             EEEECCCCC
Confidence            999997654

>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=99.67  E-value=1.2e-16  Score=123.71  Aligned_cols=78  Identities=22%  Similarity=0.418  Sum_probs=70.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .+++++|||+|||+.+|+++|..+|++||.|..|.|+.+   +.++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   81 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLY   81 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            456889999999999999999999999999999999875   5669999999999887      6999999999999999


Q ss_pred             cCCcccc
Q 022814          106 VAKYKKK  112 (291)
Q Consensus       106 a~~~~~~  112 (291)
                      +.+....
T Consensus        82 a~~~~~~   88 (115)
T 3lqv_A           82 YNANRAF   88 (115)
T ss_dssp             CCHHHHT
T ss_pred             ecCChhh
Confidence            9865443

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.67  E-value=9.7e-17  Score=134.17  Aligned_cols=79  Identities=23%  Similarity=0.437  Sum_probs=72.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+++++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~  163 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  163 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3457899999999999999999999999999999999999 99999999999999887      6999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.....
T Consensus       164 a~~~~~  169 (177)
T 2f3j_A          164 VASQID  169 (177)
T ss_dssp             ESSGGG
T ss_pred             ecCCCC
Confidence            976543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=1.3e-16  Score=119.88  Aligned_cols=75  Identities=29%  Similarity=0.407  Sum_probs=66.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..+..++|||+|||+.+|+++|+.+|++||.|. |.|+.    +.++|||||+|.+.++      .|||..|+|+.|.|.
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   89 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVA   89 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            445688999999999999999999999999997 66664    4689999999999886      789999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus        90 ~a~~~~   95 (97)
T 2e5j_A           90 LARQQR   95 (97)
T ss_dssp             ECCCCC
T ss_pred             EcCCCC
Confidence            997654

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2e-16  Score=117.16  Aligned_cols=72  Identities=24%  Similarity=0.531  Sum_probs=66.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+        +|||||+|.+.++      .||+..|+|+.|.|.+
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            4678999999999999999999999999999999997        6899999999887      7999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        77 a~~~~~   82 (90)
T 2dnq_A           77 SKNKSK   82 (90)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            976553

>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=99.67  E-value=2.8e-17  Score=125.98  Aligned_cols=77  Identities=21%  Similarity=0.399  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGE---IVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~---I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~  102 (291)
                      .....++|||+|||+.+|+++|+++|+.||.   |..|.|+.++. |.++|||||+|.+.++     .||+..|+|+.|.
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~   85 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVE   85 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEE
Confidence            3457889999999999999999999999998   89999999986 9999999999999887     7899999999999


Q ss_pred             EeccCC
Q 022814          103 VDHVAK  108 (291)
Q Consensus       103 V~~a~~  108 (291)
                      |.++.+
T Consensus        86 V~~a~~   91 (107)
T 2lmi_A           86 VYEINN   91 (107)
T ss_dssp             CEECCH
T ss_pred             EEECCH
Confidence            998864

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.48  E-value=5.2e-18  Score=131.83  Aligned_cols=79  Identities=28%  Similarity=0.458  Sum_probs=72.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCcceEEEEEEcChhh------hcCCceeC
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVD--------VNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~--------i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~   97 (291)
                      ..+.++|||+|||+.+++++|+.+|++||.|..        |.|+.++.+|.++|||||+|.+.++      .||+..|+
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            467899999999999999999999999999998        9999998899999999999999887      68999999


Q ss_pred             CeEEEEeccCCcc
Q 022814           98 GRTIRVDHVAKYK  110 (291)
Q Consensus        98 gr~i~V~~a~~~~  110 (291)
                      |+.|.|.++.+..
T Consensus        84 g~~l~V~~a~~~~   96 (116)
T 2lcw_A           84 GNPIKVSFATRRA   96 (116)
Confidence            9999999986543

>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=99.66  E-value=2.7e-17  Score=132.15  Aligned_cols=79  Identities=20%  Similarity=0.280  Sum_probs=68.6

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      ......++|||+|||+.+|+++|+++|++|| |+.|.|+.++. |+++|||||+|.+.++     +||+..|+++.|.|.
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            3445678999999999999999999999999 77999999984 9999999999999887     789999999999998


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      .+.+..
T Consensus       119 ~a~~~~  124 (139)
T 2hgn_A          119 LNSTTG  124 (139)
T ss_dssp             ECCCSC
T ss_pred             ECCCCC
Confidence            886543

>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=99.66  E-value=8.8e-17  Score=126.97  Aligned_cols=75  Identities=29%  Similarity=0.438  Sum_probs=67.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCee--EEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV--DVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~--~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      ...+.++|||+|||+.+|+++|+++|++| .|+  .|.|+.++. |.++|||||+|.+.++     .+++..|+|+.|.|
T Consensus        38 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V  115 (126)
T 2hgm_A           38 DSANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEV  115 (126)
T ss_dssp             CSSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEE
Confidence            34567899999999999999999999999 677  999999985 9999999999999887     56889999999999


Q ss_pred             eccC
Q 022814          104 DHVA  107 (291)
Q Consensus       104 ~~a~  107 (291)
                      ..+.
T Consensus       116 ~~a~  119 (126)
T 2hgm_A          116 FKSS  119 (126)
T ss_dssp             EEEC
T ss_pred             EECC
Confidence            8775

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.66  E-value=2.3e-16  Score=121.25  Aligned_cols=73  Identities=23%  Similarity=0.475  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|..+|++||.|..|.|+        +|||||+|.+.++      .|||..|+|+.|.|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            45678999999999999999999999999999999998        7899999999887      689999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        99 ~a~~~~~  105 (108)
T 2jvo_A           99 YSKLPAK  105 (108)
T ss_dssp             SCSCCC-
T ss_pred             EecCCCC
Confidence            9976543

>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=3.3e-16  Score=117.94  Aligned_cols=74  Identities=15%  Similarity=0.468  Sum_probs=64.8

Q ss_pred             cccCCCCCCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE
Q 022814           28 WHAKYKDSAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT  100 (291)
Q Consensus        28 ~~~~~~~~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~  100 (291)
                      .....++.++|||+|||+ .+++++|..+|++||.|..|.|.        +|||||+|.+.++      .|||..|+|+.
T Consensus        15 ~~~~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           15 VPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             ----CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             ccCCCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            334567899999999998 99999999999999999999983        7899999999887      69999999999


Q ss_pred             EEEeccCCc
Q 022814          101 IRVDHVAKY  109 (291)
Q Consensus       101 i~V~~a~~~  109 (291)
                      |.|.++.+.
T Consensus        87 l~V~~a~~~   95 (97)
T 2xnq_A           87 LILEVSSSN   95 (97)
T ss_dssp             CEEEECCCC
T ss_pred             EEEEecCCC
Confidence            999998654

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=5.8e-16  Score=116.71  Aligned_cols=74  Identities=22%  Similarity=0.388  Sum_probs=66.1

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcC--CCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQC--GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT  100 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~--G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~  100 (291)
                      .....+.++|||+|||+.+|+++|+.+|++|  |.|..|.++        +|||||+|.+.++      .||+..|+|+.
T Consensus         9 ~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   80 (99)
T 2cpd_A            9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSP   80 (99)
T ss_dssp             CSCSSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEE
T ss_pred             ccccCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcE
Confidence            3445678999999999999999999999999  999999875        5799999999887      69999999999


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++.+..
T Consensus        81 l~v~~a~~~~   90 (99)
T 2cpd_A           81 IEVTLAKPVD   90 (99)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEECCCCC
Confidence            9999997654

>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=99.66  E-value=2.7e-16  Score=120.71  Aligned_cols=75  Identities=23%  Similarity=0.498  Sum_probs=68.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..++.++|||+|||+.+++++|+.+|++||.|..|.|+.+      +|||||+|.+.++      .|||..|+|+.|.|.
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            4567899999999999999999999999999999999876      7899999999887      789999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        95 ~a~~~~~  101 (109)
T 1x4g_A           95 WGKESPD  101 (109)
T ss_dssp             CCCCCCS
T ss_pred             ecCCCCC
Confidence            9976543

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=6.7e-17  Score=127.19  Aligned_cols=75  Identities=24%  Similarity=0.349  Sum_probs=67.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCe----eEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEI----VDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIR  102 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I----~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~  102 (291)
                      ..+..+|||+|||+.+|+++|+++|++||.|    ..|.|+.+. +|+++|||||+|.+.++     .+|+..|+++.|.
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 KENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIE   98 (123)
T ss_dssp             CCSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEE
Confidence            3567899999999999999999999999975    689999985 99999999999999887     5699999999999


Q ss_pred             EeccC
Q 022814          103 VDHVA  107 (291)
Q Consensus       103 V~~a~  107 (291)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98775

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.66  E-value=3.1e-17  Score=132.12  Aligned_cols=81  Identities=20%  Similarity=0.381  Sum_probs=68.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEE--Eeec---CCCCCcceEEEEEEcChhh------hcCCceeCCeE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVN--LVRD---KGTGKPRGFAFVAYEDQRN------NLNGAQILGRT  100 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~--i~~d---~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~  100 (291)
                      ..+.++|||+|||+.+|+++|..+|++||.|..|.  ++.+   ..+|.++|||||+|.+.++      .|||..|+|+.
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            56789999999999999999999999999998751  1111   2479999999999999887      69999999999


Q ss_pred             EEEeccCCcccc
Q 022814          101 IRVDHVAKYKKK  112 (291)
Q Consensus       101 i~V~~a~~~~~~  112 (291)
                      |.|.++.+...+
T Consensus       122 l~V~~a~~~~~~  133 (143)
T 3egn_A          122 MVVQFARSARPK  133 (143)
T ss_dssp             CEEEECCCSCC-
T ss_pred             EEEEECCCCCCc
Confidence            999999776544

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=2e-16  Score=119.69  Aligned_cols=71  Identities=27%  Similarity=0.483  Sum_probs=64.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .+..++|||+|||+.+++++|+.+|++||.|..|.|+      .++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   97 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGW   97 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCB
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEe
Confidence            4557899999999999999999999999999999998      358999999999886      7899999999999999


Q ss_pred             cCC
Q 022814          106 VAK  108 (291)
Q Consensus       106 a~~  108 (291)
                      +.+
T Consensus        98 a~~  100 (101)
T 2la4_A           98 GKE  100 (101)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            864

>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=2e-16  Score=116.64  Aligned_cols=73  Identities=30%  Similarity=0.531  Sum_probs=64.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--hcCCcee--CCeEEEEeccCC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--NLNGAQI--LGRTIRVDHVAK  108 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--~lng~~i--~gr~i~V~~a~~  108 (291)
                      .++++|||+|||+.+|+++|+.+|++||.|..|.|+.+     ++|||||+|.+.++  +|++..+  .++.|.|.++.+
T Consensus         3 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCC
Confidence            46799999999999999999999999999999999865     68999999999988  6777544  899999999876


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        78 ~~   79 (88)
T 1wf0_A           78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=1.3e-16  Score=119.48  Aligned_cols=75  Identities=25%  Similarity=0.464  Sum_probs=66.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+++++|+.+|++||.|..|     ..++.++|||||+|.+.++      .|||..|+|+.|.|.
T Consensus        12 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   86 (96)
T 1fjc_A           12 KVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY   86 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            34578999999999999999999999999988766     3478999999999999887      699999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus        87 ~a~~~~   92 (96)
T 1fjc_A           87 YTGEKG   92 (96)
T ss_dssp             ECSSSC
T ss_pred             EcCCCC
Confidence            997654

>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=99.65  E-value=4.2e-16  Score=119.79  Aligned_cols=72  Identities=22%  Similarity=0.533  Sum_probs=64.8

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           31 KYKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...+.++|||+|||+. +|+++|+.+|++||.|..|.|        ++|||||+|.+.++      .||+..|+|+.|.|
T Consensus        23 ~~~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   94 (110)
T 1wf1_A           23 PKSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI   94 (110)
T ss_dssp             CTTCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCE
T ss_pred             CCCCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            3456689999999999 999999999999999999998        48999999999887      78999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        95 ~~a~~~~  101 (110)
T 1wf1_A           95 NMAGEPK  101 (110)
T ss_dssp             EESCCCC
T ss_pred             EECCCCC
Confidence            9997543

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.65  E-value=1.6e-16  Score=122.84  Aligned_cols=75  Identities=23%  Similarity=0.398  Sum_probs=65.1

Q ss_pred             cCCCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hc--CCceeCCeE
Q 022814           30 AKYKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL--NGAQILGRT  100 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l--ng~~i~gr~  100 (291)
                      ...+++++|||+|||+. +|+++|+++|++||.|..|.|+.      ++|||||+|.+.++      .|  ++..|.|++
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 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRC   93 (112)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             ccCCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEE
Confidence            34678899999999998 99999999999999999999974      37999999999876      44  456799999


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++....
T Consensus        94 l~V~~a~~~~  103 (112)
T 1x4f_A           94 VKVDLSEKYK  103 (112)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEECcccc
Confidence            9999997554

>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=99.65  E-value=4.7e-16  Score=118.15  Aligned_cols=72  Identities=19%  Similarity=0.417  Sum_probs=65.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+        +|||||+|.+.++      .||+..|+|+.|.|.+
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   79 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVF   79 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEE
Confidence            4567999999999999999999999999999999987        4599999999887      6899999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        80 a~~~~~   85 (103)
T 2dgu_A           80 AKPPDQ   85 (103)
T ss_dssp             CCCCCC
T ss_pred             cCCCcc
Confidence            976553

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.4e-16  Score=114.53  Aligned_cols=73  Identities=25%  Similarity=0.436  Sum_probs=65.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|+.+|++||.|..|.|+.        +||||+|.+.++      .||+..|.|+.|.|.
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   77 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQ   77 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEE
Confidence            456789999999999999999999999999999999984        399999999877      789999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        78 ~a~~~~~   84 (92)
T 2dgt_A           78 LSTSRLR   84 (92)
T ss_dssp             ESSCCCS
T ss_pred             EccCCCC
Confidence            9976543

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=5.8e-16  Score=114.62  Aligned_cols=73  Identities=26%  Similarity=0.537  Sum_probs=65.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|+.+|++||.|..|.|+.        +||||+|.+.++      .|||..|+|+.|.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   76 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVE   76 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEE
Confidence            356789999999999999999999999999999999984        499999999887      699999999999999


Q ss_pred             ccCCccc
Q 022814          105 HVAKYKK  111 (291)
Q Consensus       105 ~a~~~~~  111 (291)
                      ++.+...
T Consensus        77 ~a~~~~~   83 (90)
T 2dnp_A           77 LSTKGQK   83 (90)
T ss_dssp             ESCCCCC
T ss_pred             ECCCCCC
Confidence            9976643

>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=99.64  E-value=3.3e-16  Score=127.08  Aligned_cols=75  Identities=31%  Similarity=0.512  Sum_probs=68.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|..+|++||.|..|.|+.+     ++|||||+|.+.++      .|||..|+|++|.|
T Consensus        68 ~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  142 (150)
T 2i2y_A           68 DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRV  142 (150)
T ss_dssp             SSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEE
T ss_pred             cCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            34567899999999999999999999999999999999887     58999999999887      69999999999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus       143 ~~a~~~  148 (150)
T 2i2y_A          143 ELSNGE  148 (150)
T ss_dssp             EECCCC
T ss_pred             EEcCCC
Confidence            998764

>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=99.64  E-value=5.4e-17  Score=133.61  Aligned_cols=130  Identities=21%  Similarity=0.394  Sum_probs=91.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC--CcceEEEEEEcChhh------hcCCceeC---CeEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTG--KPRGFAFVAYEDQRN------NLNGAQIL---GRTIR  102 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg--~s~G~aFV~F~~~~~------~lng~~i~---gr~i~  102 (291)
                      +.++|||+|||+.+|+++|.++|++||+|..|.|+.++.++  .++|||||+|.+.++      .|++..+.   ++.|.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            57899999999999999999999999999999999999777  899999999999887      68998776   67888


Q ss_pred             EeccCCccccchhHHHHHH----hhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          103 VDHVAKYKKKEEEDEETRQ----RMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       103 V~~a~~~~~~~~~~~~~~~----~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      |.++.+.............    ..-....+...|.  .+|.+..+.+..+.. +.         ..||+|+.|...
T Consensus        82 ~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~--~~G~i~~v~~~~~~~-g~---------~~g~afV~f~~~  146 (175)
T 3nmr_A           82 MKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFS--SFGQIEECRILRGPD-GL---------SRGCAFVTFTTR  146 (175)
T ss_dssp             EEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHG--GGSCEEEEEEEECTT-SC---------EEEEEEEEESSH
T ss_pred             EccccccccccCCCCeEEEcCCCCcCCHHHHHHHHH--hCCCEEEEEEEECCC-CC---------EEEEEEEEECCH
Confidence            8877654332110000000    0001122233332  355677777777642 33         457888888654

>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=2e-15  Score=113.41  Aligned_cols=75  Identities=31%  Similarity=0.484  Sum_probs=66.2

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      .....+.++|||+||  .+|+++|+.+|++||.|..|.|.      .++|||||+|.+.++      .||+..|+|+.|.
T Consensus         9 ~~~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   80 (97)
T 1x5p_A            9 RRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLK   80 (97)
T ss_dssp             CCCCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEE
T ss_pred             cCCCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            345567899999996  89999999999999999999984      568999999999887      7899999999999


Q ss_pred             EeccCCccc
Q 022814          103 VDHVAKYKK  111 (291)
Q Consensus       103 V~~a~~~~~  111 (291)
                      |.++.+...
T Consensus        81 v~~a~~~~~   89 (97)
T 1x5p_A           81 VNIARKQPM   89 (97)
T ss_dssp             EECCSSCCC
T ss_pred             EEECCCCCC
Confidence            999976543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=3.2e-16  Score=117.33  Aligned_cols=76  Identities=22%  Similarity=0.258  Sum_probs=67.2

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDV-NLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i-~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      +.....++|||+|||+.+|+++|+.+|++||.|..| .|+.++.+|.    |||+|.+.++      .|||..|+|+.|.
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 PKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLK   85 (96)
T ss_dssp             CCCCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCE
T ss_pred             CCCCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            334567899999999999999999999999999999 5888875543    9999999887      6999999999999


Q ss_pred             EeccCCc
Q 022814          103 VDHVAKY  109 (291)
Q Consensus       103 V~~a~~~  109 (291)
                      |.++.+.
T Consensus        86 V~~a~~~   92 (96)
T 2e44_A           86 VAYIPDE   92 (96)
T ss_dssp             EEECCCC
T ss_pred             EEEcCcc
Confidence            9999765

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.63  E-value=9.7e-16  Score=124.80  Aligned_cols=77  Identities=23%  Similarity=0.529  Sum_probs=72.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|++|.|.
T Consensus        83 ~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~  162 (166)
T 3md3_A           83 SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN  162 (166)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Confidence            34567899999999999999999999999999999999998899999999999999887      699999999999999


Q ss_pred             ccC
Q 022814          105 HVA  107 (291)
Q Consensus       105 ~a~  107 (291)
                      +|.
T Consensus       163 ~a~  165 (166)
T 3md3_A          163 WAA  165 (166)
T ss_dssp             ESC
T ss_pred             ecC
Confidence            985

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.63  E-value=1.8e-16  Score=119.86  Aligned_cols=70  Identities=36%  Similarity=0.629  Sum_probs=65.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ++|||+|||+.+|+++|+++|++||+|..|.|+.+     ++|||||+|.+.++      .||+..|+|+.|.|.++.+.
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            58999999999999999999999999999999987     78999999999887      68999999999999999765


Q ss_pred             c
Q 022814          110 K  110 (291)
Q Consensus       110 ~  110 (291)
                      .
T Consensus        76 ~   76 (101)
T 2hvz_A           76 P   76 (101)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1.1e-15  Score=114.23  Aligned_cols=74  Identities=26%  Similarity=0.370  Sum_probs=65.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ....++|||+|||+.+|+++|+.+|++||.|..|  +.+..+|.   ||||+|.+.++     .||+..|+|+.|.|.++
T Consensus         5 ~~~~~~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            5 SSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPR   79 (94)
T ss_dssp             CTTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCS
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEEC
Confidence            3456899999999999999999999999999987  66666666   99999999887     89999999999999988


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      .+..
T Consensus        80 ~~~~   83 (94)
T 2e5g_A           80 EQKE   83 (94)
T ss_dssp             CCSC
T ss_pred             CcCC
Confidence            6543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.63  E-value=3.1e-16  Score=117.68  Aligned_cols=72  Identities=15%  Similarity=0.511  Sum_probs=64.0

Q ss_pred             CCCCCCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           31 KYKDSAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ..++.++|||+|||+ .+|+++|..+|++||.|..|.|+        +|||||+|.+.++      .|||..|.|+.|.|
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   77 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLIL   77 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCE
T ss_pred             cCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEE
Confidence            357899999999999 99999999999999999999984        7899999999887      69999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        78 ~~a~~~~   84 (96)
T 2kvi_A           78 EVSSSNA   84 (96)
T ss_dssp             EEEECCC
T ss_pred             EEcCcCC
Confidence            9986554

>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=99.62  E-value=1.6e-15  Score=127.17  Aligned_cols=80  Identities=30%  Similarity=0.504  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++     .+++..|+|+.|.|.++.
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            456899999999999999999999999999999999999899999999999999887     568999999999999997


Q ss_pred             Ccccc
Q 022814          108 KYKKK  112 (291)
Q Consensus       108 ~~~~~  112 (291)
                      +....
T Consensus       182 ~k~~~  186 (196)
T 1l3k_A          182 SKQEM  186 (196)
T ss_dssp             -----
T ss_pred             ChhHh
Confidence            66543

>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=99.62  E-value=3.9e-16  Score=120.47  Aligned_cols=71  Identities=11%  Similarity=0.154  Sum_probs=64.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...++|||+|||+.+|+++|+.+|++||.|..|.|+.      ++|||||+|.+.++      .|||..|+|++|.|.++
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   81 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            3568999999999999999999999999999999874      57899999999887      79999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus        82 ~~~   84 (111)
T 1whx_A           82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            653

>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=99.62  E-value=1.7e-15  Score=124.48  Aligned_cols=75  Identities=28%  Similarity=0.561  Sum_probs=70.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      +|||..|+|+.|.|.+|
T Consensus        92 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             TTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            447899999999999999999999999999999999998899999999999999887      79999999999999987


Q ss_pred             C
Q 022814          107 A  107 (291)
Q Consensus       107 ~  107 (291)
                      .
T Consensus       172 s  172 (172)
T 2g4b_A          172 S  172 (172)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.61  E-value=3e-15  Score=125.81  Aligned_cols=79  Identities=28%  Similarity=0.527  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.++
T Consensus       112 ~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  191 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA  191 (198)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            567999999999999999999999999999999999998899999999999999887      69999999999999999


Q ss_pred             CCccc
Q 022814          107 AKYKK  111 (291)
Q Consensus       107 ~~~~~  111 (291)
                      .+..+
T Consensus       192 ~~~~~  196 (198)
T 2yh0_A          192 SVGAK  196 (198)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77653

>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=99.61  E-value=5.3e-16  Score=115.49  Aligned_cols=73  Identities=27%  Similarity=0.450  Sum_probs=63.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEeecCCCCCcceEEEEEEcChhh------hcCC-ceeCCeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGE-IVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNG-AQILGRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~-I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng-~~i~gr~i~V  103 (291)
                      ..+.++|||+|||+.+|+++|+.+|++||. |..+.|.       ++|||||+|.+.++      .||| ..|+|+.|.|
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v   77 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEV   77 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEE
Confidence            457889999999999999999999999999 6666553       47999999999886      7999 9999999999


Q ss_pred             eccCCccc
Q 022814          104 DHVAKYKK  111 (291)
Q Consensus       104 ~~a~~~~~  111 (291)
                      .++.+...
T Consensus        78 ~~a~~~~~   85 (93)
T 2cqh_A           78 DYSVSKKL   85 (93)
T ss_dssp             EECCCCCC
T ss_pred             EEccCccc
Confidence            99976543

>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=99.60  E-value=1.1e-15  Score=118.41  Aligned_cols=74  Identities=22%  Similarity=0.439  Sum_probs=64.7

Q ss_pred             CCCCCCEEEE--cCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee-----C
Q 022814           31 KYKDSAYVYV--GGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI-----L   97 (291)
Q Consensus        31 ~~~~~~~lfV--gnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i-----~   97 (291)
                      ...|..+|||  |||++.+|+++|+++|++||+|..|.|+.+      +|||||+|.+.++      +|||..|     .
T Consensus        21 ~~~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~   94 (114)
T 2cq2_A           21 VSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQ   94 (114)
T ss_dssp             CSSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSC
T ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEccccCC
Confidence            3467889999  779999999999999999999999988642      7999999999876      8999998     6


Q ss_pred             CeEEEEeccCCcc
Q 022814           98 GRTIRVDHVAKYK  110 (291)
Q Consensus        98 gr~i~V~~a~~~~  110 (291)
                      +.+|.|.++....
T Consensus        95 g~~l~v~~a~~~p  107 (114)
T 2cq2_A           95 KITLYLNFVEKVQ  107 (114)
T ss_dssp             EEECEEEEESCCC
T ss_pred             CcEEEEEecccCc
Confidence            8999999987543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.60  E-value=2.2e-15  Score=128.33  Aligned_cols=79  Identities=29%  Similarity=0.538  Sum_probs=73.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+.++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|+.|.|.++
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            466899999999999999999999999999999999999899999999999999887      69999999999999999


Q ss_pred             CCccc
Q 022814          107 AKYKK  111 (291)
Q Consensus       107 ~~~~~  111 (291)
                      .+...
T Consensus       203 ~~~~~  207 (216)
T 2qfj_A          203 VTPPM  207 (216)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            76643

>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=99.60  E-value=8.2e-16  Score=136.98  Aligned_cols=133  Identities=17%  Similarity=0.268  Sum_probs=99.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++      .|+|..|+|+.|.|.+
T Consensus        92 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~  171 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHW  171 (284)
T ss_dssp             CCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            4577899999999999999999999999999999999999999999999999999887      7899999999999999


Q ss_pred             cCCccccchhHHHHHH------hh-hhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          106 VAKYKKKEEEDEETRQ------RM-REERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       106 a~~~~~~~~~~~~~~~------~~-~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      +.+............-      .. .....+...|.  .+|.+..+.+..+. ++.         ..||+||.|....
T Consensus       172 a~~~~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~--~~G~i~~v~i~~~~-~g~---------~~g~afV~f~~~~  237 (284)
T 3smz_A          172 TDAGQLTPALLHSRCLCVDRLPPGFNDVDALCRALS--AVHSPTFCQLACGQ-DGQ---------LKGFAVLEYETAE  237 (284)
T ss_dssp             CCGGGCCTTTTSCSEEEEECCCTTCCCHHHHHHHTC--SSSCCSEEEEEECS-SCC---------EEEEEEEECSSHH
T ss_pred             CCCCCCCcccCCccEEEEecCCcccCCHHHHHHHhh--CCCCeEEEEEEECC-CCC---------cccEEEEEeCCHH
Confidence            9765533211000000      00 01223334443  36778888888765 333         4578899987643

>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=99.60  E-value=8e-16  Score=125.84  Aligned_cols=77  Identities=30%  Similarity=0.545  Sum_probs=71.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      .+..+|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++     .|++..|+|++|.|.++.
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            356799999999999999999999999999999999998899999999999999887     789999999999999987


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      +.
T Consensus       165 pk  166 (167)
T 2cjk_A          165 PR  166 (167)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.5e-15  Score=116.37  Aligned_cols=76  Identities=24%  Similarity=0.466  Sum_probs=63.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCcceEEEEEEcChhh---hcCC-ceeCCeEEEEe
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGT---GKPRGFAFVAYEDQRN---NLNG-AQILGRTIRVD  104 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~t---g~s~G~aFV~F~~~~~---~lng-~~i~gr~i~V~  104 (291)
                      ..+.++|||+|||+.+|+++|+++|++||.|. +.++.+..+   |.++|||||+|.+.++   +|.. ..|+|+.|.|.
T Consensus         5 ~~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~   83 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCV   83 (114)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEE
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEec
Confidence            35678999999999999999999999999999 888888877   7999999999999887   2221 35788888887


Q ss_pred             ccCC
Q 022814          105 HVAK  108 (291)
Q Consensus       105 ~a~~  108 (291)
                      .+..
T Consensus        84 ~~~~   87 (114)
T 2dnl_A           84 SSPT   87 (114)
T ss_dssp             CCSS
T ss_pred             cCCC
Confidence            6543

>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=99.59  E-value=2.1e-15  Score=111.27  Aligned_cols=70  Identities=13%  Similarity=0.173  Sum_probs=63.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...++|||+|||+.+++++|+++|++| .|..|.|.      .++|||||+|.+.++      .|||..|+|+.|.|.++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   75 (88)
T 1wg1_A            3 SGSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQ   75 (88)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEc
Confidence            357899999999999999999999999 99999885      578999999999887      69999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus        76 ~~~   78 (88)
T 1wg1_A           76 PTD   78 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.58  E-value=1.1e-15  Score=118.74  Aligned_cols=64  Identities=19%  Similarity=0.329  Sum_probs=56.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...++|||+|||+.+|+++|+++|++||+|..|.|+.+       |||||+|.+.++      +||+..|+|+.|.|
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~   83 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   83 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeee
Confidence            35689999999999999999999999999999999876       899999999887      69999999998433

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.58  E-value=6.1e-16  Score=136.73  Aligned_cols=126  Identities=22%  Similarity=0.395  Sum_probs=91.0

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|..+|++||.|..|.|+.+      +|||||+|.+.++      .|||..|.|+.|.|
T Consensus        17 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v   90 (261)
T 3sde_A           17 KTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLRI   90 (261)
T ss_dssp             CSSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeEe
Confidence            34566789999999999999999999999999999999654      7999999999887      69999999999999


Q ss_pred             eccCCccccchhHHHHHHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCCC
Q 022814          104 DHVAKYKKKEEEDEETRQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGFS  176 (291)
Q Consensus       104 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~~  176 (291)
                      .++.+....--.....   ......+...|.  .+|.+..+.+..+. ++.         ..|||||.|....
T Consensus        91 ~~a~~~~~l~v~nl~~---~~t~~~l~~~F~--~~G~i~~v~i~~~~-~g~---------~~g~afV~f~~~~  148 (261)
T 3sde_A           91 RFATHGAALTVKNLSP---VVSNELLEQAFS--QFGPVEKAVVVVDD-RGR---------ATGKGFVEFAAKP  148 (261)
T ss_dssp             EECCCSSEEEEESCCT---TCCHHHHHHHHG--GGSCEEEEEEEEET-TSC---------EEEEEEEEESSHH
T ss_pred             eecccCCcccccCCCC---CCCHHHHHHHHH--hcCCeEEEEeeeCC-CCC---------cCcEEEEEeCCHH
Confidence            9987643211000000   001122333333  35667888888873 444         4578888886644

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.57  E-value=4e-15  Score=127.49  Aligned_cols=74  Identities=20%  Similarity=0.446  Sum_probs=68.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ...+|||+|||+.+|+++|.++|++||.|..|.|+.+.  +.++|||||+|.+.++      +|||..|+|++|.|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            46799999999999999999999999999999999985  5589999999999887      799999999999999987


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      +.
T Consensus       180 ~~  181 (213)
T 4f02_A          180 SR  181 (213)
T ss_dssp             CH
T ss_pred             CC
Confidence            54

>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=99.57  E-value=7.8e-15  Score=124.23  Aligned_cols=75  Identities=19%  Similarity=0.344  Sum_probs=67.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCCc
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~~  109 (291)
                      .++|||+|||+.+|+++|+++|++||+|..|.|+.+. +|.++|||||+|.+.++     .+.+..|+|+.|.|.++...
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            4799999999999999999999999999999999987 69999999999999887     45567999999999987654


Q ss_pred             c
Q 022814          110 K  110 (291)
Q Consensus       110 ~  110 (291)
                      .
T Consensus       188 ~  188 (193)
T 2voo_A          188 F  188 (193)
T ss_dssp             -
T ss_pred             H
Confidence            3

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.57  E-value=4.4e-15  Score=110.08  Aligned_cols=69  Identities=20%  Similarity=0.409  Sum_probs=60.8

Q ss_pred             CCCCCE-EEEcCCCCCCCHHH----HHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe
Q 022814           32 YKDSAY-VYVGGIPFDLTEGD----LLAVFAQC-GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR   99 (291)
Q Consensus        32 ~~~~~~-lfVgnL~~~~te~~----L~~~F~~~-G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr   99 (291)
                      .+|+.| |||+|||+.+++++    |..+|++| |+|.+|       ||   |||||+|.+.++      .|||..|.|+
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            456777 99999999999988    55899999 599988       44   999999999987      8999999999


Q ss_pred             EEEEeccCCcc
Q 022814          100 TIRVDHVAKYK  110 (291)
Q Consensus       100 ~i~V~~a~~~~  110 (291)
                      +|.|.+|....
T Consensus        75 ~i~v~~A~~~s   85 (96)
T 2diu_A           75 RIIVSFTPKNR   85 (96)
T ss_dssp             CCEEESSCCSC
T ss_pred             eEEEEecCCCc
Confidence            99999997654

>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=99.56  E-value=9.5e-15  Score=119.38  Aligned_cols=75  Identities=35%  Similarity=0.599  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~V  103 (291)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++      .|||..|.|  ++|.|
T Consensus        86 ~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V  165 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV  165 (168)
T ss_dssp             TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEE
T ss_pred             cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEE
Confidence            4567899999999999999999999999999999999999899999999999999887      699999988  99999


Q ss_pred             ecc
Q 022814          104 DHV  106 (291)
Q Consensus       104 ~~a  106 (291)
                      .+|
T Consensus       166 ~~A  168 (168)
T 1b7f_A          166 RLA  168 (168)
T ss_dssp             EEC
T ss_pred             EeC
Confidence            875

>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=99.56  E-value=8e-15  Score=125.26  Aligned_cols=71  Identities=24%  Similarity=0.383  Sum_probs=65.5

Q ss_pred             CCCCEEEEcCCC-CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           33 KDSAYVYVGGIP-FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        33 ~~~~~lfVgnL~-~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      +++++|||+||| +.+|+++|.++|++||.|..|.|+.+.     +|||||+|.+.++      .|||..|.|++|.|.+
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            468899999999 799999999999999999999998763     7999999999887      7999999999999999


Q ss_pred             cCC
Q 022814          106 VAK  108 (291)
Q Consensus       106 a~~  108 (291)
                      +..
T Consensus        77 s~~   79 (205)
T 3tyt_A           77 SKQ   79 (205)
T ss_dssp             CSC
T ss_pred             ccC
Confidence            864

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=99.56  E-value=3.3e-16  Score=129.39  Aligned_cols=80  Identities=19%  Similarity=0.350  Sum_probs=69.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ...+.++|||+|||+.+|+++|+++|++||.|.. .++.+..+|.++|||||+|.+.++     +|||..|.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~   87 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEK   87 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEEC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEec
Confidence            4567899999999999999999999999998866 345555689999999999999987     8999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      +.+...
T Consensus        88 ~~~~~~   93 (175)
T 1fje_B           88 PKGRDS   93 (175)
T ss_dssp             CCCSSC
T ss_pred             CCCccc
Confidence            976543

>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=99.55  E-value=1.1e-14  Score=106.75  Aligned_cols=67  Identities=25%  Similarity=0.636  Sum_probs=61.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCcee
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQC----G-------EIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQI   96 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~----G-------~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i   96 (291)
                      .+.++|||+|||+.+++++|+++|++|    |       .|..|.|+.+      +|||||+|.+.++     .|||..|
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAMAFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHHhcCCCEE
Confidence            457899999999999999999999999    8       9999998865      7999999999887     8999999


Q ss_pred             CCeEEEEec
Q 022814           97 LGRTIRVDH  105 (291)
Q Consensus        97 ~gr~i~V~~  105 (291)
                      +|+.|.|..
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999964

>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=99.55  E-value=6.3e-15  Score=121.13  Aligned_cols=74  Identities=24%  Similarity=0.452  Sum_probs=67.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC---CeEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL---GRTIR  102 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~---gr~i~  102 (291)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.|+.+. +|.++|||||+|.+.++      +|||..|.   +++|.
T Consensus        92 ~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~  170 (175)
T 3nmr_A           92 AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMV  170 (175)
T ss_dssp             CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCE
T ss_pred             cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeE
Confidence            3467899999999999999999999999999999999997 69999999999999887      88998776   49999


Q ss_pred             Eecc
Q 022814          103 VDHV  106 (291)
Q Consensus       103 V~~a  106 (291)
                      |.+|
T Consensus       171 V~~a  174 (175)
T 3nmr_A          171 VKFA  174 (175)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9987

>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=99.55  E-value=1e-14  Score=119.69  Aligned_cols=71  Identities=20%  Similarity=0.321  Sum_probs=63.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEEEecc
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIRVDHV  106 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~V~~a  106 (291)
                      ..+|||+||++.+|+++|..+|++||.|..|.|+..    .++|||||+|.+.++      .|||..|.+  +.|.|.++
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            457899999999999999999999999999998643    357999999999876      899999965  99999999


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      .+.
T Consensus       122 k~~  124 (164)
T 1sjr_A          122 KLT  124 (164)
T ss_dssp             SSS
T ss_pred             cCC
Confidence            765

>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=1.5e-14  Score=114.41  Aligned_cols=72  Identities=21%  Similarity=0.376  Sum_probs=63.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceE-EEEEEcChhh------hcCCceeCC--eEEEEe
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGF-AFVAYEDQRN------NLNGAQILG--RTIRVD  104 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~-aFV~F~~~~~------~lng~~i~g--r~i~V~  104 (291)
                      +-..|||+||++.+|+++|..+|++||.|..|.|+...     +|| |||+|.+.++      +|||..|.|  +.|+|+
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 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  101 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEE
Confidence            44567899999999999999999999999999887643     688 9999999876      899999998  999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus       102 ~ak~~~  107 (130)
T 3zzy_A          102 FSKLTS  107 (130)
T ss_dssp             ECSCSS
T ss_pred             ecCCCc
Confidence            997543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=2.8e-14  Score=112.15  Aligned_cols=72  Identities=19%  Similarity=0.353  Sum_probs=61.6

Q ss_pred             CCCCE--EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceE-EEEEEcChhh------hcCCceeCC--eEE
Q 022814           33 KDSAY--VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGF-AFVAYEDQRN------NLNGAQILG--RTI  101 (291)
Q Consensus        33 ~~~~~--lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~-aFV~F~~~~~------~lng~~i~g--r~i  101 (291)
                      +|+++  |||+||++.+|+++|..+|++||.|..|.|+. +     .|| |||+|.+.++      +|||..|.|  +.|
T Consensus        21 ~ps~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l   94 (124)
T 2e5i_A           21 GGNKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTL   94 (124)
T ss_dssp             CCCSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEE
T ss_pred             CCCcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEE
Confidence            45554  57999999999999999999999999999865 2     286 9999999875      899999988  699


Q ss_pred             EEeccCCcc
Q 022814          102 RVDHVAKYK  110 (291)
Q Consensus       102 ~V~~a~~~~  110 (291)
                      .|.+|.+..
T Consensus        95 ~V~~Ak~~~  103 (124)
T 2e5i_A           95 KIEYARPTR  103 (124)
T ss_dssp             EEECCSCSC
T ss_pred             EEEEecCCc
Confidence            999997553

>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=99.53  E-value=1.9e-14  Score=117.19  Aligned_cols=74  Identities=32%  Similarity=0.595  Sum_probs=68.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE--EEEe
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT--IRVD  104 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~--i~V~  104 (291)
                      .+..+|||+|||+.+++++|..+|++||.|..|.|+.+..+|.++|||||+|.+.++      .|||..|+|+.  |.|.
T Consensus        86 ~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~  165 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK  165 (167)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEE
Confidence            457899999999999999999999999999999999999899999999999999887      69999999965  8887


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      ||
T Consensus       166 ~A  167 (167)
T 1fxl_A          166 FA  167 (167)
T ss_dssp             EC
T ss_pred             eC
Confidence            65

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.52  E-value=5.1e-14  Score=107.61  Aligned_cols=76  Identities=14%  Similarity=0.153  Sum_probs=67.0

Q ss_pred             CCCCCEEEEcCCCC-----CCCHHHHHHHHhcCCCeeEEEEeecCCC-CCcceEEEEEEcChhh------hcCCceeCCe
Q 022814           32 YKDSAYVYVGGIPF-----DLTEGDLLAVFAQCGEIVDVNLVRDKGT-GKPRGFAFVAYEDQRN------NLNGAQILGR   99 (291)
Q Consensus        32 ~~~~~~lfVgnL~~-----~~te~~L~~~F~~~G~I~~i~i~~d~~t-g~s~G~aFV~F~~~~~------~lng~~i~gr   99 (291)
                      ..++.+|+|.||..     ..++++|+++|++||.|..|.|+.++.+ +.++|||||+|.+.++      +|||..|+|+
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            46789999999963     2478999999999999999999998654 6899999999999886      8999999999


Q ss_pred             EEEEeccC
Q 022814          100 TIRVDHVA  107 (291)
Q Consensus       100 ~i~V~~a~  107 (291)
                      .|.|.++.
T Consensus        85 ~i~v~~a~   92 (105)
T 2pe8_A           85 VVKACFYN   92 (105)
T ss_dssp             ECEEEECC
T ss_pred             EEEEEEcC
Confidence            99999985

>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=99.52  E-value=3e-14  Score=126.66  Aligned_cols=77  Identities=22%  Similarity=0.463  Sum_probs=69.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLL----AVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRT  100 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~----~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~  100 (291)
                      ...++++|||+|||+.+|+++|+    ++|++||.|..|.|+.   +|.++|||||+|.+.++      .|||..|.|+.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKP   81 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcE
Confidence            45779999999999999999966    8999999999999886   78899999999999887      88999999999


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.++....
T Consensus        82 l~v~~a~~~~   91 (282)
T 3pgw_A           82 MRIQYAKTDS   91 (282)
T ss_pred             EEEEEeccCc
Confidence            9999986544

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=99.51  E-value=1.9e-14  Score=118.10  Aligned_cols=127  Identities=15%  Similarity=0.337  Sum_probs=89.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCcee
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQC----G-------EIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQI   96 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~----G-------~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i   96 (291)
                      .+.++|||+|||+.+|+++|.++|++|    |       .|..+.+.      .++|||||+|.+.++     .||+..|
T Consensus         2 r~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~~~~~~~~   75 (172)
T 2g4b_A            2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAMAFDGIIF   75 (172)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHGGGTTCEE
T ss_pred             CcccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHHHhCCcEe
Confidence            357899999999999999999999999    6       67777665      348999999999887     8899999


Q ss_pred             CCeEEEEeccCCccccchhHHHH---HHhhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCcc
Q 022814           97 LGRTIRVDHVAKYKKKEEEDEET---RQRMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFE  173 (291)
Q Consensus        97 ~gr~i~V~~a~~~~~~~~~~~~~---~~~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~  173 (291)
                      .|+.|.|.++...........-.   ....-....+...|.  .+|.+..+.+..+..++.         ..||+++.|.
T Consensus        76 ~g~~i~v~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~--~~G~v~~v~i~~~~~~g~---------~~g~afV~f~  144 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLT--SFGPLKAFNLVKDSATGL---------SKGYAFCEYV  144 (172)
T ss_dssp             TTEECEEECCSSCCCCTTTTCEEEECCCTTCCHHHHHHHHH--TTSCEEEEEEEECTTTCS---------EEEEEEEEES
T ss_pred             cCceeeecCCcccCCCCCCCEEEEEcCCCcCCHHHHHHHHH--hcCCceEEEEEecCCCCC---------cceEEEEEeC
Confidence            99999999886553321100000   000001222333333  356678888888776655         4578888886


Q ss_pred             CCC
Q 022814          174 GFS  176 (291)
Q Consensus       174 ~~~  176 (291)
                      ...
T Consensus       145 ~~~  147 (172)
T 2g4b_A          145 DIN  147 (172)
T ss_dssp             STT
T ss_pred             CHH
Confidence            543

>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=99.51  E-value=6.9e-15  Score=131.48  Aligned_cols=132  Identities=14%  Similarity=0.210  Sum_probs=87.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..+.++|||+|||+.+++++|.++|++|| .|..|.|+.+.. |.++|||||+|.+.++      .|||..|.|+.|.|.
T Consensus       114 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  192 (292)
T 2ghp_A          114 HLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTK  192 (292)
T ss_dssp             ECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            45789999999999999999999999999 999999999874 8899999999999887      599999999999999


Q ss_pred             ccCCccccchhHHHHHH----------hh-hhhhccccccccCCCCCCCceeEeecCC-CCCCCCCCCCCCCCCCCCCCc
Q 022814          105 HVAKYKKKEEEDEETRQ----------RM-REERGVCRAFQRGECTRGDGCKFSHNEQ-RAANTGGGPQDRSSRWGHEKF  172 (291)
Q Consensus       105 ~a~~~~~~~~~~~~~~~----------~~-~~~~~~~~~f~~~~~g~~~~~~~~~d~~-~~~~~g~g~~~~~~g~g~~~~  172 (291)
                      ++.+.............          .. -....+...|.  .+|.+..+.+..+.. ++.         ..||+||.|
T Consensus       193 ~a~~~~~~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~--~~G~v~~v~i~~~~~~tg~---------~~g~afV~F  261 (292)
T 2ghp_A          193 VSNPLEKSKRTDSATLEGREIMIRNLSTELLDENLLRESFE--GFGSIEKINIPAGQKEHSF---------NNCCAFMVF  261 (292)
T ss_dssp             ECCCC---------CCTTTEEEEEEECTTTCCHHHHHHHHG--GGSCEEEEECCSCCC---C---------CCEEEEEEE
T ss_pred             ECCCCcccccccccCCCCceEEEECCCcccCCHHHHHHHHh--ccCCeeEEEEEecCCcCCC---------CceEEEEEe
Confidence            98765433211000000          00 11122333333  256677777766554 233         567889988


Q ss_pred             cCC
Q 022814          173 EGF  175 (291)
Q Consensus       173 ~~~  175 (291)
                      ...
T Consensus       262 ~~~  264 (292)
T 2ghp_A          262 ENK  264 (292)
T ss_dssp             SSH
T ss_pred             CCH
Confidence            653

>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=99.49  E-value=7.3e-14  Score=124.29  Aligned_cols=82  Identities=20%  Similarity=0.266  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEcCCCCCC-CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           31 KYKDSAYVYVGGIPFDL-TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~-te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ...+.++|||+|||+.+ |+++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++      .|||..|+|++|.|
T Consensus       180 ~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v  258 (284)
T 3smz_A          180 ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRV  258 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEE
Confidence            34578899999999994 999999999999999999999987 89999999999999887      79999999999999


Q ss_pred             eccCCccccc
Q 022814          104 DHVAKYKKKE  113 (291)
Q Consensus       104 ~~a~~~~~~~  113 (291)
                      .++.+.....
T Consensus       259 ~~a~~~~~~~  268 (284)
T 3smz_A          259 SFCAPGPPGR  268 (284)
T ss_dssp             EECCSSSCHH
T ss_pred             EEecCCCccc
Confidence            9998776543

>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=99.49  E-value=6.4e-14  Score=125.17  Aligned_cols=78  Identities=19%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCC-CCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           32 YKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKG-TGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~-tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      ..+.++|||+|||+. +|+++|.++|++||.|..|.|+.+.. ||.++|||||+|.+.++     .|||..|+|+.|.|.
T Consensus       207 ~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~~l~g~~~~g~~i~V~  286 (292)
T 2ghp_A          207 TLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVS  286 (292)
T ss_dssp             CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEEE
Confidence            456789999999999 99999999999999999999999876 69999999999999887     799999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++.+.
T Consensus       287 ~a~~k  291 (292)
T 2ghp_A          287 LADKK  291 (292)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            99754

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.49  E-value=5.3e-14  Score=121.78  Aligned_cols=75  Identities=21%  Similarity=0.362  Sum_probs=68.5

Q ss_pred             cCCCCCCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           30 AKYKDSAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      ...+++++|||+|||+ .+++++|.++|++||.|..|.|+.++     +|||||+|.+.++      .|||..|.|+.|.
T Consensus        29 ~~~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~  103 (229)
T 2adc_A           29 LAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIR  103 (229)
T ss_dssp             GGCCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCE
T ss_pred             CCCCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEE
Confidence            3457789999999999 99999999999999999999999876     8899999999887      6999999999999


Q ss_pred             EeccCCc
Q 022814          103 VDHVAKY  109 (291)
Q Consensus       103 V~~a~~~  109 (291)
                      |.++...
T Consensus       104 v~~a~~~  110 (229)
T 2adc_A          104 ITLSKHQ  110 (229)
T ss_dssp             EECCSCC
T ss_pred             EEEecCc
Confidence            9998754

>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=99.49  E-value=4.2e-14  Score=116.64  Aligned_cols=73  Identities=25%  Similarity=0.467  Sum_probs=65.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+.++|||+|||+.+|+++|.++|++||.|..|     ..+|.++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus        96 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~  170 (175)
T 1fje_B           96 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYY  170 (175)
T ss_dssp             TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEE
T ss_pred             cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEe
Confidence            3457899999999999999999999999988766     4589999999999999887      6999999999999999


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      +.+.
T Consensus       171 a~~k  174 (175)
T 1fje_B          171 TGEK  174 (175)
T ss_dssp             CSSC
T ss_pred             cCCC
Confidence            8754

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.48  E-value=3.3e-14  Score=123.87  Aligned_cols=74  Identities=26%  Similarity=0.416  Sum_probs=64.5

Q ss_pred             CCCCCEEEEcCCCCCC---------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee
Q 022814           32 YKDSAYVYVGGIPFDL---------TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI   96 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~---------te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i   96 (291)
                      ..+.++||||||++.+         ++++|..+|++||+|..|.|+.+      +|||||+|.+.++      +|+|..|
T Consensus       131 ~~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          131 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            4578999999999998         79999999999999999999853      7999999999876      8999999


Q ss_pred             ------------CCeEEEEeccCCccc
Q 022814           97 ------------LGRTIRVDHVAKYKK  111 (291)
Q Consensus        97 ------------~gr~i~V~~a~~~~~  111 (291)
                                  .|+.|.|.+|.....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC----
T ss_pred             eccccccccccCCCCEEEEEEccCCCC
Confidence                        899999999976543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.48  E-value=1.5e-14  Score=121.51  Aligned_cols=70  Identities=24%  Similarity=0.611  Sum_probs=60.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQC----G-------EIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQIL   97 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~----G-------~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~   97 (291)
                      ..++|||+|||+.+|+++|.++|++|    |       .|..+.+      +.++|||||+|.+.++     .|||..|.
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al~l~g~~~~   76 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAMAFDGIIFQ   76 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHGGGTTEEET
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHHHhcCCEEc
Confidence            47899999999999999999999999    4       5555554      4568999999999887     78999999


Q ss_pred             CeEEEEeccCCc
Q 022814           98 GRTIRVDHVAKY  109 (291)
Q Consensus        98 gr~i~V~~a~~~  109 (291)
                      |+.|.|.++...
T Consensus        77 g~~i~v~~~~~~   88 (198)
T 2yh0_A           77 GQSLKIRRPHDY   88 (198)
T ss_dssp             TEEEEEECCCCC
T ss_pred             CceEEEeCCCCC
Confidence            999999998654

>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=3.7e-13  Score=103.70  Aligned_cols=78  Identities=22%  Similarity=0.339  Sum_probs=65.1

Q ss_pred             ccCCCCCCEEEEcCCCCCCC-----------HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hc
Q 022814           29 HAKYKDSAYVYVGGIPFDLT-----------EGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL   91 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~t-----------e~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l   91 (291)
                      .....++++|+|.||.....           +++|+++|++||.|..|.| .+.   .++|||||+|.+.++      .|
T Consensus         9 ~~~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~l   84 (112)
T 2dit_A            9 PSRMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTL   84 (112)
T ss_dssp             CCCCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHS
T ss_pred             CCCCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHc
Confidence            34567899999999954432           5899999999999999955 443   389999999999886      89


Q ss_pred             CCceeCCeEEEEeccCCcc
Q 022814           92 NGAQILGRTIRVDHVAKYK  110 (291)
Q Consensus        92 ng~~i~gr~i~V~~a~~~~  110 (291)
                      ||..|+|++|.|.++.+..
T Consensus        85 ng~~~~gr~l~v~~a~~~~  103 (112)
T 2dit_A           85 DGRWFGGRQITAQAWDGTT  103 (112)
T ss_dssp             TTCEETTEECEEEECCSCC
T ss_pred             CCCEECCcEEEEEEeCCCC
Confidence            9999999999999987643

>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=99.44  E-value=3.3e-13  Score=119.89  Aligned_cols=72  Identities=19%  Similarity=0.382  Sum_probs=65.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~V  103 (291)
                      ..++.++|||+|||+.+|+++|.++|++||.|..|.|+.+.     +|||||+|.+.++      .|||..|+ |+.|.|
T Consensus       203 ~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  277 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKI  277 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEE
Confidence            34567899999999999999999999999999999999664     6899999999887      79999999 999999


Q ss_pred             eccC
Q 022814          104 DHVA  107 (291)
Q Consensus       104 ~~a~  107 (291)
                      .|+.
T Consensus       278 ~~ak  281 (282)
T 3pgw_A          278 SFAK  281 (282)
T ss_pred             EEec
Confidence            9974

>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=99.43  E-value=1.4e-13  Score=117.61  Aligned_cols=73  Identities=14%  Similarity=0.229  Sum_probs=64.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCe--eEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe----
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEI--VDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR----   99 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I--~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr----   99 (291)
                      .+|.++|||+|||+.+|+++|+++|++||.|  ..|.|+.+.  +.++|||||+|.+.++      .|||..|.|.    
T Consensus       120 ~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~  197 (205)
T 3tyt_A          120 QHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPY  197 (205)
T ss_dssp             CCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSS
T ss_pred             CCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCc
Confidence            3678899999999999999999999999999  899998875  6677999999999876      8999999886    


Q ss_pred             EEEEecc
Q 022814          100 TIRVDHV  106 (291)
Q Consensus       100 ~i~V~~a  106 (291)
                      ++.|+++
T Consensus       198 p~~vk~~  204 (205)
T 3tyt_A          198 PYTLKLC  204 (205)
T ss_dssp             CEECEEE
T ss_pred             ceEEEec
Confidence            6777654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.41  E-value=1.7e-13  Score=115.41  Aligned_cols=71  Identities=23%  Similarity=0.410  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           34 DSAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        34 ~~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+++|||+|||+ .+++++|.++|++||.|..|.|+.++     +|||||+|.+.++      .|||..|.|+.|.|.++
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     7899999999887      69999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus        77 ~~~   79 (198)
T 1qm9_A           77 KHQ   79 (198)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            754

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.41  E-value=2.9e-13  Score=113.94  Aligned_cols=73  Identities=19%  Similarity=0.352  Sum_probs=66.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~V  103 (291)
                      .++.++|||+|||+.+++++|.++|++|| .|..|.|+.+.     +|||||+|.+.++      .|||..|+ |+.|.|
T Consensus       117 ~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v  191 (198)
T 1qm9_A          117 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  191 (198)
T ss_dssp             CCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEE
Confidence            46789999999999999999999999999 99999997643     7999999999887      69999999 999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus       192 ~~a~~~  197 (198)
T 1qm9_A          192 SFSKST  197 (198)
T ss_dssp             EEECCC
T ss_pred             Eeeccc
Confidence            998653

>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=99.40  E-value=7.8e-13  Score=114.37  Aligned_cols=73  Identities=19%  Similarity=0.346  Sum_probs=66.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCG-EIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G-~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~V  103 (291)
                      .++.++|||+|||+.+++++|.++|++|| .|..|.|+..     .+|||||+|.+.++      .|||..|+ |+.|.|
T Consensus       148 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v  222 (229)
T 2adc_A          148 FPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRV  222 (229)
T ss_dssp             CCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEE
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEE
Confidence            46789999999999999999999999999 9999999653     37899999999887      69999999 999999


Q ss_pred             eccCCc
Q 022814          104 DHVAKY  109 (291)
Q Consensus       104 ~~a~~~  109 (291)
                      .++.+.
T Consensus       223 ~~a~~~  228 (229)
T 2adc_A          223 SFSKST  228 (229)
T ss_dssp             EECSSC
T ss_pred             EEecCC
Confidence            998753

>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=99.40  E-value=6.2e-13  Score=117.32  Aligned_cols=78  Identities=22%  Similarity=0.353  Sum_probs=69.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hc-CCceeC---CeEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL-NGAQIL---GRTI  101 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l-ng~~i~---gr~i  101 (291)
                      ..+..+|||+|||+.+|+++|.++|++||.|..|.|+.+. +|.++|||||+|.+.++      .| ++..+.   +++|
T Consensus        93 a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i  171 (261)
T 3sde_A           93 ATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDD-RGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPV  171 (261)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET-TSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBC
T ss_pred             cccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCC-CCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceE
Confidence            3567899999999999999999999999999999999995 99999999999999887      66 555655   9999


Q ss_pred             EEeccCCcc
Q 022814          102 RVDHVAKYK  110 (291)
Q Consensus       102 ~V~~a~~~~  110 (291)
                      .|.++.+..
T Consensus       172 ~v~~~~~~~  180 (261)
T 3sde_A          172 IVEPMEQFD  180 (261)
T ss_dssp             EEEECCCEE
T ss_pred             EEeeccccC
Confidence            999987543

>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=99.36  E-value=2.4e-13  Score=103.62  Aligned_cols=68  Identities=15%  Similarity=0.336  Sum_probs=59.0

Q ss_pred             EEEcCCCCCCCHHHHHHHH------------hcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCe
Q 022814           38 VYVGGIPFDLTEGDLLAVF------------AQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGR   99 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F------------~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr   99 (291)
                      .++.+||+.+++++|.++|            ++||+|..|.|+.+. ++.++|||||+|.+.++      +|||..|+|+
T Consensus        18 ~~~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr   96 (104)
T 1jmt_A           18 QSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQ   96 (104)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTE
T ss_pred             cccCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCE
Confidence            3477888888888888777            999999999999887 58999999999999886      7999999999


Q ss_pred             EEEEecc
Q 022814          100 TIRVDHV  106 (291)
Q Consensus       100 ~i~V~~a  106 (291)
                      +|.|.++
T Consensus        97 ~i~v~~s  103 (104)
T 1jmt_A           97 PIHAELS  103 (104)
T ss_dssp             ECCEEEC
T ss_pred             EEEEEEc
Confidence            9999886

>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=99.35  E-value=1.7e-12  Score=99.02  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=64.5

Q ss_pred             CCCCEEEEcCC--CCCC--------CHHHHHHHHhcCCCeeEEEEeecCCC--CCcceEEEEEEcChhh------hcCCc
Q 022814           33 KDSAYVYVGGI--PFDL--------TEGDLLAVFAQCGEIVDVNLVRDKGT--GKPRGFAFVAYEDQRN------NLNGA   94 (291)
Q Consensus        33 ~~~~~lfVgnL--~~~~--------te~~L~~~F~~~G~I~~i~i~~d~~t--g~s~G~aFV~F~~~~~------~lng~   94 (291)
                      .|+.+|+|.||  |..+        .+++|+++|++||+|.+|.|+.+..+  +.++|||||+|.+.++      +|||.
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            47889999998  3233        24799999999999999999998754  4789999999999886      89999


Q ss_pred             eeCCeEEEEeccC
Q 022814           95 QILGRTIRVDHVA  107 (291)
Q Consensus        95 ~i~gr~i~V~~a~  107 (291)
                      .|+|+.|.|.++.
T Consensus        83 ~f~GR~i~v~~~~   95 (105)
T 3v4m_A           83 KFANRVVVTKYCD   95 (105)
T ss_dssp             EETTEECEEEEEC
T ss_pred             EeCCCEEEEEEeC
Confidence            9999999999875

>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=99.32  E-value=2.3e-12  Score=100.43  Aligned_cols=75  Identities=19%  Similarity=0.247  Sum_probs=64.9

Q ss_pred             CCCCEEEEcCCCC--C---CCHHHHHHHHhcCCCeeEEEEeecCC----CCCcceEEEEEEcChhh------hcCCceeC
Q 022814           33 KDSAYVYVGGIPF--D---LTEGDLLAVFAQCGEIVDVNLVRDKG----TGKPRGFAFVAYEDQRN------NLNGAQIL   97 (291)
Q Consensus        33 ~~~~~lfVgnL~~--~---~te~~L~~~F~~~G~I~~i~i~~d~~----tg~s~G~aFV~F~~~~~------~lng~~i~   97 (291)
                      +|+++|+|.||-.  .   -.+++|++.|++||+|..|.|+.+..    ++.++|||||+|.+.++      +|||..|+
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~   97 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA   97 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEEC
Confidence            3789999999942  1   23689999999999999999998864    46788999999999886      89999999


Q ss_pred             CeEEEEeccC
Q 022814           98 GRTIRVDHVA  107 (291)
Q Consensus        98 gr~i~V~~a~  107 (291)
                      |+.|.|.++.
T Consensus        98 GR~i~v~~~~  107 (118)
T 3ue2_A           98 GRKVVAEVYD  107 (118)
T ss_dssp             TEECEEEEEC
T ss_pred             CcEEEEEEcC
Confidence            9999999875

>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=99.28  E-value=5.2e-12  Score=115.54  Aligned_cols=73  Identities=21%  Similarity=0.444  Sum_probs=61.3

Q ss_pred             cCCCCCCEEEEcC--CCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC---C
Q 022814           30 AKYKDSAYVYVGG--IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL---G   98 (291)
Q Consensus        30 ~~~~~~~~lfVgn--L~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~---g   98 (291)
                      ....|+.+|||||  |++.+|+++|+++|++||+|..|.|+.      ++|||||+|.+.++      +|||..|.   |
T Consensus        13 ~~~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g   86 (345)
T 3tht_A           13 TVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLG   86 (345)
T ss_dssp             CCSSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTS
T ss_pred             ecCCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccC
Confidence            3467899999999  578999999999999999999987754      47999999999876      89999883   4


Q ss_pred             e--EEEEeccCC
Q 022814           99 R--TIRVDHVAK  108 (291)
Q Consensus        99 r--~i~V~~a~~  108 (291)
                      +  .|.|.++..
T Consensus        87 ~~~~ly~~~~~~   98 (345)
T 3tht_A           87 QKITLYLNFVEK   98 (345)
T ss_dssp             CEEECEEEECSS
T ss_pred             CceEEEEEEeec
Confidence            4  678887753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.21  E-value=2.9e-11  Score=91.38  Aligned_cols=62  Identities=16%  Similarity=0.335  Sum_probs=51.9

Q ss_pred             CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh---hc-CCceeCCeEEEEeccCCccc
Q 022814           45 FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NL-NGAQILGRTIRVDHVAKYKK  111 (291)
Q Consensus        45 ~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~l-ng~~i~gr~i~V~~a~~~~~  111 (291)
                      ..+++++|+++|++||+|..|.|+     +.++|||||+|.+.++   ++ .+..+.+++|.|.++.+...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a~~~~~   92 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEGQPQ   92 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECSSCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEccCCCC
Confidence            568999999999999999999998     4679999999999887   22 24456799999999876543

>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=99.08  E-value=3.2e-10  Score=87.62  Aligned_cols=72  Identities=14%  Similarity=0.233  Sum_probs=59.8

Q ss_pred             CCCCCEEEEcCCCCCCC----------HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCce
Q 022814           32 YKDSAYVYVGGIPFDLT----------EGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQ   95 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~t----------e~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~   95 (291)
                      ..|+.+|.|.||-....          +++|++.|++||.|..|.|+.+.    ++|||||+|.+.++      +|||..
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            35677888888843221          35889999999999999997663    58999999999876      899999


Q ss_pred             eCCeEEEEeccC
Q 022814           96 ILGRTIRVDHVA  107 (291)
Q Consensus        96 i~gr~i~V~~a~  107 (291)
                      |+|+.|.|.++.
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            999999999985

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.06  E-value=2.8e-10  Score=88.58  Aligned_cols=71  Identities=17%  Similarity=0.263  Sum_probs=61.5

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcC-hhh------hc--CCceeCCeE
Q 022814           31 KYKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED-QRN------NL--NGAQILGRT  100 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~-~~~------~l--ng~~i~gr~  100 (291)
                      ..++.+.|||+||++. ++.++|+++|++||+|.+|.|+.+..      .|||.|.+ ..+      +|  ++..|++..
T Consensus        14 ~~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~   87 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKE   87 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSS
T ss_pred             cccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcE
Confidence            4688999999999999 99999999999999999999998864      59999999 433      66  478899988


Q ss_pred             EEEeccC
Q 022814          101 IRVDHVA  107 (291)
Q Consensus       101 i~V~~a~  107 (291)
                      +.|....
T Consensus        88 ~~~evL~   94 (121)
T 1owx_A           88 VTWEVLE   94 (121)
T ss_dssp             EEEEECC
T ss_pred             EEEEECC
Confidence            8887654

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.02  E-value=1.2e-09  Score=80.12  Aligned_cols=71  Identities=27%  Similarity=0.418  Sum_probs=60.1

Q ss_pred             CCCCCEEEEcCCC----CCCCH----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCC
Q 022814           32 YKDSAYVYVGGIP----FDLTE----GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILG   98 (291)
Q Consensus        32 ~~~~~~lfVgnL~----~~~te----~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~g   98 (291)
                      .||..||+|.-++    .++-.    .+|...|++||+|..++|+.+.        +||+|.+.++     .|||+.|+|
T Consensus         4 GPpd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~mnG~~v~G   75 (91)
T 2dnr_A            4 GSSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLSLNGKELLN   75 (91)
T ss_dssp             CCSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGGGTTCEETT
T ss_pred             CCCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHhcCCeEeCC
Confidence            4788899997776    23434    6788999999999999999874        8999999877     899999999


Q ss_pred             eEEEEeccCCcc
Q 022814           99 RTIRVDHVAKYK  110 (291)
Q Consensus        99 r~i~V~~a~~~~  110 (291)
                      +.|+|+++.+..
T Consensus        76 r~LkV~lkt~dW   87 (91)
T 2dnr_A           76 RTITIALKSPSG   87 (91)
T ss_dssp             EEEEEEECCCSS
T ss_pred             eEEEEEeCCCCc
Confidence            999999987654

>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=98.76  E-value=9.4e-09  Score=75.76  Aligned_cols=70  Identities=19%  Similarity=0.291  Sum_probs=58.9

Q ss_pred             cCCCCCCEEEEcCCCCC-----CCH----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCce
Q 022814           30 AKYKDSAYVYVGGIPFD-----LTE----GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQ   95 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~-----~te----~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~   95 (291)
                      ..-||..||+|.-++..     +-.    .+|...|++||+|..++|+.+.        +||+|.+.++     .|||+.
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            45688999999888743     323    5688999999999999999885        9999998877     899999


Q ss_pred             eCCeEEEEeccC
Q 022814           96 ILGRTIRVDHVA  107 (291)
Q Consensus        96 i~gr~i~V~~a~  107 (291)
                      |+|+.|+|.+-.
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            999999998654

>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=98.49  E-value=1.8e-07  Score=80.05  Aligned_cols=62  Identities=21%  Similarity=0.279  Sum_probs=54.2

Q ss_pred             CCCHHHHHHHHhcCCCeeEEEEeecC----CCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           46 DLTEGDLLAVFAQCGEIVDVNLVRDK----GTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        46 ~~te~~L~~~F~~~G~I~~i~i~~d~----~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .-.+++|.+.|++||.|..|.|+.+.    .++.++||+||+|.+.++      .|||..++|+.|.|.++.
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            34568999999999999999998554    355899999999999876      899999999999999875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.07  E-value=1.1e-05  Score=60.71  Aligned_cols=67  Identities=19%  Similarity=0.265  Sum_probs=61.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcC-----CCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQC-----GEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~-----G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      ..++|-|-|||-.+++..|..+++++     |.|+.|.|+.|.      |-|+|+|.+...      +|+|.+|+|+.|.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            46788888999999999999999999     999999999884      689999999876      8999999999999


Q ss_pred             Eecc
Q 022814          103 VDHV  106 (291)
Q Consensus       103 V~~a  106 (291)
                      |.-.
T Consensus        94 ~gTv   97 (117)
T 2l9w_A           94 SGTI   97 (117)
T ss_dssp             EECH
T ss_pred             ecCH
Confidence            9755

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=97.84  E-value=9.4e-06  Score=76.59  Aligned_cols=42  Identities=31%  Similarity=0.379  Sum_probs=25.0

Q ss_pred             CCCCCCCHHHHHHHHhcCCCeeEEEEee----cC-CCCCcceEE--EEEEcChh
Q 022814           42 GIPFDLTEGDLLAVFAQCGEIVDVNLVR----DK-GTGKPRGFA--FVAYEDQR   88 (291)
Q Consensus        42 nL~~~~te~~L~~~F~~~G~I~~i~i~~----d~-~tg~s~G~a--FV~F~~~~   88 (291)
                      .||++     |..+|.++|+|..|..+.    +. .+....|++  |++|....
T Consensus         4 ~lPp~-----L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~   52 (437)
T 3pgw_S            4 FLPPN-----LLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPR   52 (437)
T ss_pred             cCCcc-----HHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcc
Confidence            45654     778999999998874332    22 122333444  77776543

>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=97.25  E-value=0.00096  Score=49.79  Aligned_cols=71  Identities=8%  Similarity=0.149  Sum_probs=57.6

Q ss_pred             CCCCEEEEcCCCCCC-C----HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           33 KDSAYVYVGGIPFDL-T----EGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~-t----e~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      .-+++|+|+||+..+ +    .+.++.+|..|+++....+....      .=..|.|.++++      .|++..+.|..|
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            346889999998854 3    25778999999998877666543      356899999887      899999999999


Q ss_pred             EEeccCCc
Q 022814          102 RVDHVAKY  109 (291)
Q Consensus       102 ~V~~a~~~  109 (291)
                      +|-++++.
T Consensus        77 r~YFgq~~   84 (104)
T 1wey_A           77 KLYFAQTL   84 (104)
T ss_dssp             EEECCCCS
T ss_pred             EEEecCCC
Confidence            99999854

>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=96.91  E-value=0.0036  Score=45.73  Aligned_cols=63  Identities=16%  Similarity=0.220  Sum_probs=50.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--cceEEEEEEcChhh------hcCCceeCC
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGK--PRGFAFVAYEDQRN------NLNGAQILG   98 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~--s~G~aFV~F~~~~~------~lng~~i~g   98 (291)
                      ++|.|.+||+.+||+++.+.++....+.....+..+.+.+  ...-|||.|.+.++      .++|+.+-+
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D   72 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEc
Confidence            5799999999999999999999998887776665544433  34679999999887      788877643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=96.87  E-value=0.0043  Score=46.12  Aligned_cols=65  Identities=12%  Similarity=0.221  Sum_probs=52.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhc-----CCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQ-----CGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~-----~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      -..+|.|-|||+.+.++.|+.+|+.     -|+|..|....        +-|+|+|.+...     +...+.|.+.+|.|
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV   78 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQADHELHGAQLSL   78 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcCCcceecCeEEEE
Confidence            4678999999999999999999986     26888886643        579999999887     33468888888888


Q ss_pred             ecc
Q 022814          104 DHV  106 (291)
Q Consensus       104 ~~a  106 (291)
                      ...
T Consensus        79 ~P~   81 (104)
T 2dhx_A           79 RPA   81 (104)
T ss_dssp             EEC
T ss_pred             EcC
Confidence            643

>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=96.74  E-value=0.002  Score=47.57  Aligned_cols=46  Identities=22%  Similarity=0.417  Sum_probs=40.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      .+.|+| .+|+.+...+|..+|++|| -..|.++-|.       -|||.|.+++.
T Consensus         6 ~HV~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~   51 (101)
T 3ctr_A            6 DHVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQ   51 (101)
T ss_dssp             EEEEEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECH
T ss_pred             CeEEEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHH
Confidence            467778 9999999999999999999 5568888886       89999999877

>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=96.62  E-value=0.004  Score=45.79  Aligned_cols=49  Identities=22%  Similarity=0.415  Sum_probs=42.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      +.-.+.|+| .+|+.+...||..+|+.||. ..|.++-|.       -|||.|.+++.
T Consensus        13 p~r~HVf~l-~FP~ewKt~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~   61 (100)
T 1whv_A           13 PKRDHVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQ   61 (100)
T ss_dssp             CCCCSEEEE-ECCTTCCHHHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHH
T ss_pred             CCCCeEEEE-eCChhhhhHHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHH
Confidence            445678888 99999999999999999995 457888876       89999999887

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.21  E-value=0.00026  Score=56.70  Aligned_cols=24  Identities=13%  Similarity=0.105  Sum_probs=19.9

Q ss_pred             EEEEeecCCCCCcceEEEEEEcChhh
Q 022814           64 DVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        64 ~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      .+.|+.+.  ..++|||||+|.+.++
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~   25 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAAT   25 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHH
T ss_pred             cEEEEecC--ccccchhHHHHHHHHh
Confidence            46777775  4699999999999887

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.48  E-value=0.0085  Score=56.50  Aligned_cols=49  Identities=18%  Similarity=0.268  Sum_probs=37.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      .++|||. .|..+++.+|.++|++||+|..+.+-.+.     .-||.|||.+.++
T Consensus        53 ~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~  101 (464)
T 3pq1_A           53 QRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKES  101 (464)
T ss_dssp             HTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---C
T ss_pred             cceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHH
Confidence            4789996 89999999999999999999999877654     3799999999887

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.08  E-value=0.019  Score=42.28  Aligned_cols=65  Identities=14%  Similarity=0.144  Sum_probs=44.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--cceEEEEEEcChhh------hcCCceeCC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGK--PRGFAFVAYEDQRN------NLNGAQILG   98 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~--s~G~aFV~F~~~~~------~lng~~i~g   98 (291)
                      -+-+|.|..||+.+||+++.+.++..=++.....+....+.+  ...-|||.|.+.++      .++|..+-+
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D   80 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLD   80 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEEC
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEe
Confidence            456799999999999999888777654443333332222222  23568999999988      778877643

>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=93.09  E-value=0.32  Score=37.05  Aligned_cols=67  Identities=22%  Similarity=0.308  Sum_probs=51.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCC-eEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILG-RTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~g-r~i~V~~a  106 (291)
                      ...+.|.|-+.|+.. ...|...|++||+|+.....      ....+-.|.|.+..+     ..||..|++ -.|-|...
T Consensus        22 ~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           22 LDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            346678888998875 67788899999999988762      124699999999877     779999985 66666553

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=88.30  E-value=0.6  Score=36.08  Aligned_cols=72  Identities=19%  Similarity=0.333  Sum_probs=48.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecC--------CCC-----CcceEEEEEEcChhh-----hcCCce
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVD-VNLVRDK--------GTG-----KPRGFAFVAYEDQRN-----NLNGAQ   95 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~-i~i~~d~--------~tg-----~s~G~aFV~F~~~~~-----~lng~~   95 (291)
                      ...|.|=+.|+.. ...|...|++||.|.. +.+....        .+.     ....+-.|+|.+..+     ..||..
T Consensus         7 e~~VtVFGFp~~~-~~~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETM-ANQVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGG-HHHHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHH-HHHHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            4456677887655 5678888999999976 2222100        001     124577999999887     779999


Q ss_pred             eCCeEEEEeccC
Q 022814           96 ILGRTIRVDHVA  107 (291)
Q Consensus        96 i~gr~i~V~~a~  107 (291)
                      |+|..|-|....
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999888776653

>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=85.17  E-value=1.2  Score=42.27  Aligned_cols=47  Identities=21%  Similarity=0.432  Sum_probs=39.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      -+..|+|+ +|..|...+|..+|+.||. ..|.++.+.       .|||.|.+.+.
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~  485 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQ  485 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHH
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHH
Confidence            35688887 9999999999999999995 467777665       79999999887

>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=82.59  E-value=0.94  Score=35.16  Aligned_cols=34  Identities=18%  Similarity=0.155  Sum_probs=29.8

Q ss_pred             CCcceEEEEEEcChhh------hc-CCceeCCeEEEEeccCC
Q 022814           74 GKPRGFAFVAYEDQRN------NL-NGAQILGRTIRVDHVAK  108 (291)
Q Consensus        74 g~s~G~aFV~F~~~~~------~l-ng~~i~gr~i~V~~a~~  108 (291)
                      ...+|+++|+|.+.++      +| ||..|+| .|.|+++..
T Consensus        10 ~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~   50 (150)
T 2i2y_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATK   50 (150)
T ss_dssp             SSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTT
T ss_pred             ccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccC
Confidence            4679999999999887      56 9999999 999998865

---

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	291
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	1e-14
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-13
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	4e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	2e-12
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	1e-11
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-11
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	2e-11
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-11
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	7e-11
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	9e-11
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-10
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	1e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-10
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-10
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:) 5e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	9e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-09
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	2e-09
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-09
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	4e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	4e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	7e-09
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	9e-09
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-08
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	2e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	3e-08
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-08
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	4e-08
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	4e-08
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	4e-08
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	5e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	5e-08
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-08
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	8e-08
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	8e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-07
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-07
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	4e-07
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	4e-07
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	5e-07
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-07
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-07
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	6e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	8e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	9e-07
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	2e-06
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-06
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-06
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	9e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-05
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-05
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	6e-05
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-04
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	1e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-04
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-04
d1wi6a1	75	d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding	5e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	6e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	8e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.001
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	0.002
d1ufwa_	95	d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens)	0.004

>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 = 65.3 bits (159), Expect = 1e-14
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 36  AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------N 89
           A +YVG +  D+TE  L   F+  G I+ + + RD  T +  G+A+V ++         +
Sbjct: 1   ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD 60

Query: 90  NLNGAQILGRTIRVD 104
            +N   I G+ +R+ 
Sbjct: 61  TMNFDVIKGKPVRIM 75

>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 = 63.0 bits (153), Expect = 1e-13
 Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 9/93 (9%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRD-KGTGKPRGFAFVAYEDQ- 87
            K + ++ + V  IPF   + ++  +F+  GE+  V L +   GTG  RGF FV +  + 
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQ 62

Query: 88  ------RNNLNGAQILGRTIRVDHVAKYKKKEE 114
                     +   + GR + ++  A  +   +
Sbjct: 63  DAKKAFNALCHSTHLYGRRLVLEW-ADSEVTVQ 94

>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 = 61.1 bits (148), Expect = 4e-13
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ +  T+  L   F Q GE+ +  ++RD  T + RGF FV + DQ         +
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 93  GAQILGRTIRVD 104
             ++  +TI   
Sbjct: 63  RHELDSKTIDPK 74

>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 = 60.4 bits (146), Expect = 2e-12
 Identities = 21/102 (20%), Positives = 49/102 (48%), Gaps = 13/102 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +Y+  +P+ +T  ++  +F + G I  +       T + RG A+V YED        ++L
Sbjct: 10  LYIRNLPYKITAEEMYDIFGKYGPIRQIR---VGNTPETRGTAYVVYEDIFDAKNACDHL 66

Query: 92  NGAQILGRTIRVDHVAKYKKKEEEDEETRQ----RMREERGV 129
           +G  +  R + V +    +  ++ D + ++     ++E+ G+
Sbjct: 67  SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGI 108

>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 = 58.0 bits (140), Expect = 1e-11
 Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR---- 88
           K S  +YVG + F  TE  +  +F++ G+I  + +  DK      GF FV Y  +     
Sbjct: 5   KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAEN 64

Query: 89  --NNLNGAQILGRTIRVDHVAKYKK 111
               +NG ++  R IR D  A +K+
Sbjct: 65  AMRYINGTRLDDRIIRTDWDAGFKE 89

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 57.7 bits (139), Expect = 1e-11
 Identities = 26/79 (32%), Positives = 39/79 (49%), Gaps = 8/79 (10%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
               +YV  +P  +T+  L  +F + G IV  N++RDK TG+PRG AFV Y  +      
Sbjct: 5   KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEA 64

Query: 89  -NNLNGAQILG--RTIRVD 104
            + LN     G  + + V 
Sbjct: 65  ISALNNVIPEGGSQPLSVR 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 57.4 bits (138), Expect = 2e-11
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +PF ++  ++L  F     I     ++    G P G A VA+E +        +L
Sbjct: 12  IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 71

Query: 92  NGAQILGRTIRV 103
           N   I  R +++
Sbjct: 72  NDRPIGSRKVKL 83

>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 = 56.9 bits (137), Expect = 2e-11
 Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +P D+T+ +L A+F   G I    ++RD  TG   G+AFV +  +         L
Sbjct: 5   LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 64

Query: 92  NGAQILGRTIRVDH 105
           NG  +  + ++V +
Sbjct: 65  NGITVRNKRLKVSY 78

>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 = 56.6 bits (136), Expect = 5e-11
 Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED-----Q 87
           +D+  V+   +   +   DL   F+  G++ DV ++ D+ + + +G A+V + +      
Sbjct: 16  RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 75

Query: 88  RNNLNGAQILGRTIRVDHVAKYKKK 112
              L G ++LG  I V      K +
Sbjct: 76  AIGLTGQRLLGVPIIVQASQAEKNR 100

>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 = 55.8 bits (134), Expect = 6e-11
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++GG+P  L +  +  +    G +   NLV+D  TG  +G+AF  Y D          L
Sbjct: 4   LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63

Query: 92  NGAQILGRTIRVDHVAKYKKK 112
           NG Q+  + + V   A    K
Sbjct: 64  NGMQLGDKKLLVQR-ASVGAK 83

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 7e-11
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 5/73 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ F+ T+  L + F Q G + D  ++RD  T + RGF FV Y          N  
Sbjct: 9   LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR 68

Query: 93  GAQILGRTIRVDH 105
             ++ GR +    
Sbjct: 69  PHKVDGRVVEPKR 81

>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 = 55.0 bits (132), Expect = 7e-11
 Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ +D T+ DL   F++ GE+VD  L  D  TG+ RGF FV +++  +     +  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 93  GAQILGRTIRV 103
             ++ G+ I  
Sbjct: 62  EHKLNGKVIDP 72

>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 = 54.9 bits (132), Expect = 9e-11
 Identities = 17/75 (22%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  + F +++ D+  +FA+ G +    +  D+ +G+  G A V +E +          
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 61

Query: 92  NGAQILGRTIRVDHV 106
           NG  + GR + +  V
Sbjct: 62  NGVPLDGRPMNIQLV 76

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (132), Expect = 1e-10
 Identities = 16/83 (19%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNL-----VRDKGTGKPRGFAFVAYEDQRN--- 89
           +YVG IPF +TE  ++  F     +  +       V      + + FAF+ +        
Sbjct: 4   LYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQ 63

Query: 90  --NLNGAQILGRTIRVDHVAKYK 110
               +G    G+++++     Y+
Sbjct: 64  AMAFDGIIFQGQSLKIRRPHDYQ 86

>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 = 54.7 bits (131), Expect = 1e-10
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV G+P  +T+ +L  +F+Q G I+   ++ D+ TG  RG  F+ ++ +         L
Sbjct: 9   LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 68

Query: 92  NGAQILGRT--IRVD 104
           NG +  G T  I V 
Sbjct: 69  NGQKPSGATEPITVK 83

>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 = 54.2 bits (130), Expect = 1e-10
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGG+  D  E  +   F   GE+  + L  D  T K RGF F+ ++++          
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 93  GAQILGRTIRV 103
              +      +
Sbjct: 62  YHNVGLSKCEI 72

>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 = 53.9 bits (129), Expect = 2e-10
 Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 10/83 (12%)

Query: 39  YVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK---GTGKPRGFAFVAYEDQR------N 89
           ++  + F  TE  L  VF++ G I    + + K   G     GF FV Y+          
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 90  NLNGAQILGRTIRVDHVAKYKKK 112
            L G  + G  + V  +++   K
Sbjct: 62  QLQGHTVDGHKLEVR-ISERATK 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 = 54.3 bits (130), Expect = 2e-10
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 6/82 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YVGG+  ++ +  L A F   G+I D+ +  D  T K RGFAFV +E         +N+
Sbjct: 8   LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67

Query: 92  NGAQILGRTIRVDHVAKYKKKE 113
           N +++ GRTIRV+     + KE
Sbjct: 68  NESELFGRTIRVNLAKPMRIKE 89

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 4e-10
 Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 13/95 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVD--VNLVRDKGTGKPRGFAFVAYEDQRN------ 89
           +++GGIP      ++L   A+  E V   +         K RGFAFV YE  R       
Sbjct: 4   LFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARR 63

Query: 90  --NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQR 122
                  Q+ G  I VD     + + + DE+  + 
Sbjct: 64  KLMPGRIQLWGHQIAVDWA---EPEIDVDEDVMET 95

>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 = 53.9 bits (129), Expect = 5e-10
 Identities = 11/73 (15%), Positives = 26/73 (35%), Gaps = 7/73 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           V +     +  E     +  + GE+ ++N+  +       G  +V +  +        +L
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDL 88

Query: 92  NGAQILGRTIRVD 104
           N     G+ I  +
Sbjct: 89  NNRWFNGQPIHAE 101

>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 = 52.7 bits (126), Expect = 9e-10
 Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 7/81 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           VYVGG+   ++E  L  +F Q G +V+ ++ +D+ TG+ +G+ FV +  +         +
Sbjct: 12  VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 71

Query: 92  NGAQILGRTIRVDHVAKYKKK 112
           +  ++ G+ IRV+  A    K
Sbjct: 72  DMIKLYGKPIRVNK-ASAHNK 91

>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 = 51.7 bits (123), Expect = 1e-09
 Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGG+  + T  D+   F Q G++ D  L+ DK T + RGF FV +E +        ++
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 93  GAQILGRTIRVDH 105
             +I  + +    
Sbjct: 62  FHEINNKMVECKK 74

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++GG+ F+ TE  L   + Q G++ D  ++RD  + + RGF FV +             
Sbjct: 23  LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 82

Query: 93  GAQILGRTIRVDHVAKYKKKEE 114
              I GR +          +EE
Sbjct: 83  PHSIDGRVVEPKRA---VAREE 101

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.6 bits (123), Expect = 2e-09
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 6/74 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  +P ++T+ +  ++F   GEI    LVRDK TG+  G+ FV Y D +      N L
Sbjct: 5   LIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL 64

Query: 92  NGAQILGRTIRVDH 105
           NG ++  +TI+V +
Sbjct: 65  NGLRLQTKTIKVSY 78

>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 = 51.2 bits (122), Expect = 2e-09
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           +  + V G+    TE DL  VF++ G I DV++V D+ + + RGFAFV +E+        
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 89  NNLNGAQILGRTIRV 103
              NG ++ GR IRV
Sbjct: 69  ERANGMELDGRRIRV 83

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 23/88 (26%), Positives = 40/88 (45%), Gaps = 7/88 (7%)

Query: 33  KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNL- 91
           + ++ + V G+P+  TE DL   F+  GE++ V + +D  TG  +GF FV + +    + 
Sbjct: 6   QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVK 65

Query: 92  ---NGAQILGRTIRVDHVAKYKKKEEED 116
                  I GR            K+ +D
Sbjct: 66  VMSQRHMIDGRWCDCK---LPNSKQSQD 90

>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 = 50.7 bits (121), Expect = 4e-09
 Identities = 17/71 (23%), Positives = 32/71 (45%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNG 93
            +  VY GGI   LT+  +   F+  G+I+++ +  +KG    R     +      ++NG
Sbjct: 17  KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNG 76

Query: 94  AQILGRTIRVD 104
             I G  ++  
Sbjct: 77  TTIEGHVVKCY 87

>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 = 49.7 bits (118), Expect = 7e-09
 Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 7/82 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLV-RDKGTGKPRGFAFVAYEDQR------NN 90
           +++G +  ++ E  L   F+  G I+    + RD  TG  +G+AF+ +            
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 91  LNGAQILGRTIRVDHVAKYKKK 112
           +NG  +  R I V +  K   K
Sbjct: 61  MNGQYLCNRPITVSYAFKKDSK 82

>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 = 49.3 bits (117), Expect = 9e-09
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D  +        
Sbjct: 5   IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK 64

Query: 93  GAQILGRTIRVD 104
              + G    V 
Sbjct: 65  YHTVNGHNCEVR 76

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 49.3 bits (117), Expect = 1e-08
 Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 7/79 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           ++V  I  +  E ++   F   GEI +++L  D+ TG  +G+A V YE  +        L
Sbjct: 10  LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 69

Query: 92  NGAQILGRTIRVDHVAKYK 110
           NGA+I+G+TI+VD     K
Sbjct: 70  NGAEIMGQTIQVDW-CFVK 87

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 31  KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR-- 88
           +  D+A + V  +  D  E DL  +F   G I  + L +DK TG+ +GFAF+++  +   
Sbjct: 4   RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDA 63

Query: 89  ----NNLNGAQILGRTIRVD 104
                 ++G       + V+
Sbjct: 64  ARAIAGVSGFGYDHLILNVE 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 = 48.3 bits (114), Expect = 2e-08
 Identities = 11/73 (15%), Positives = 25/73 (34%), Gaps = 6/73 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +++   P   T+ ++  +      +     +        R FA++    +         L
Sbjct: 4   LWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL 63

Query: 92  NGAQILGRTIRVD 104
           NG +I G T+   
Sbjct: 64  NGLKIEGYTLVTK 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 = 48.3 bits (114), Expect = 2e-08
 Identities = 12/72 (16%), Positives = 20/72 (27%), Gaps = 3/72 (4%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE---DQRNNLNGA 94
           V V  +P    +  +   F  CG I+ V++               A              
Sbjct: 3   VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHK 62

Query: 95  QILGRTIRVDHV 106
            +    I V H+
Sbjct: 63  VVGQNEIIVSHL 74

>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 = 48.3 bits (115), Expect = 3e-08
 Identities = 22/100 (22%), Positives = 46/100 (46%), Gaps = 15/100 (15%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLT-EGDLLAVFAQCGEIVDVNLVRDKGTGKPRGF 79
           G S  +        ++ V++G +   +  + D+ A+F++ G+IV  ++         +GF
Sbjct: 1   GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGF 52

Query: 80  AFVAYEDQR------NNLNGAQILGRTIRVDHVAKYKKKE 113
           AFV Y ++R         +G  I G+ + ++  A+ K   
Sbjct: 53  AFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEPKVNR 92

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.9 bits (113), Expect = 3e-08
 Identities = 15/78 (19%), Positives = 29/78 (37%), Gaps = 12/78 (15%)

Query: 38  VYVGGIPFDLTEGDLLAVF---AQCGEIVDVNLVRDKGTGKPRGFAFVAY---------E 85
           V+V G+   L + ++L       + G+I  V +         +G +  AY          
Sbjct: 11  VFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDAL 70

Query: 86  DQRNNLNGAQILGRTIRV 103
                +N   + GRT++ 
Sbjct: 71  RAIQCVNNVVVDGRTLKA 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 = 47.7 bits (113), Expect = 4e-08
 Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 5/81 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA-FVAYEDQRN---NLNG 93
           +YVG +  D+TE  +L +F+Q G      ++ +  +  P  F  F  + D       +NG
Sbjct: 11  LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 70

Query: 94  AQILGRTIRVDHVAKYKKKEE 114
            +ILG+ ++V+  A     ++
Sbjct: 71  RKILGKEVKVNW-ATTPSSQK 90

>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 = 48.2 bits (114), Expect = 4e-08
 Identities = 27/91 (29%), Positives = 43/91 (47%), Gaps = 8/91 (8%)

Query: 29  HAKYKDSAY--VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED 86
           H   KD+ +  ++VGG+P+  T+  L   F   G+I +  ++ D+ TGK RG+ FV   D
Sbjct: 2   HGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMAD 61

Query: 87  QRN-----NLNGAQILGRTIRVDHVAKYKKK 112
           +             I GR   V+ +A    K
Sbjct: 62  RAAAERACKDPNPIIDGRKANVN-LAYLGAK 91

>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 = 47.7 bits (113), Expect = 4e-08
 Identities = 18/82 (21%), Positives = 29/82 (35%), Gaps = 13/82 (15%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +YV  +    +E  +   F                  K R +AFV + ++         L
Sbjct: 11  LYVRNLMLSTSEEMIEKEFNNIKPGAVER------VKKIRDYAFVHFSNREDAVEAMKAL 64

Query: 92  NGAQILGRTIRVDHVAKYKKKE 113
           NG  + G  I V  +AK   K+
Sbjct: 65  NGKVLDGSPIEVT-LAKPVDKD 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 47.7 bits (113), Expect = 5e-08
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 11/88 (12%)

Query: 24  DDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVA 83
           +D     K + +  +    + F++TE +L  VF    EI  V+       GK +G A++ 
Sbjct: 5   EDPCTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ-----DGKSKGIAYIE 59

Query: 84  YEDQR------NNLNGAQILGRTIRVDH 105
           ++ +           GA+I GR++ + +
Sbjct: 60  FKSEADAEKNLEEKQGAEIDGRSVSLYY 87

>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 = 47.3 bits (112), Expect = 5e-08
 Identities = 19/75 (25%), Positives = 38/75 (50%)

Query: 31  KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNN 90
            +   + ++VG +P D+TE ++  +F + G+  +V + +DKG G  R       E  +  
Sbjct: 4   TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVE 63

Query: 91  LNGAQILGRTIRVDH 105
           L+   + G+ +RV  
Sbjct: 64  LDNMPLRGKQLRVRF 78

>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 = 46.9 bits (111), Expect = 7e-08
 Identities = 13/73 (17%), Positives = 24/73 (32%), Gaps = 12/73 (16%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---- 89
           D  +V V G P       +L  FAQ G I+   +           +  + Y+ +      
Sbjct: 3   DDTWVTVFGFPQASAS-YILLQFAQYGNILKHVMSNTG------NWMHIRYQSKLQARKA 55

Query: 90  -NLNGAQILGRTI 101
            + +G       +
Sbjct: 56  LSKDGRIFGESIM 68

>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 = 15/89 (16%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ-- 87
            +      +++  +   +    L   F+  G I+   +V D+   K  GF     ++   
Sbjct: 3   LRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAE 62

Query: 88  --RNNLNGAQILGRTIRVDHVAKYKKKEE 114
                +NG  +  R + V    ++K ++E
Sbjct: 63  RAIEKMNGMLLNDRKVFVG---RFKSRKE 88

>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 = 49.2 bits (116), Expect = 8e-08
 Identities = 27/92 (29%), Positives = 41/92 (44%), Gaps = 8/92 (8%)

Query: 28  WHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
               +     ++VGGI  D  E  L   F Q G+I  + ++ D+G+GK RGFAFV ++D 
Sbjct: 90  RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH 149

Query: 88  RN-----NLNGAQILGRTIRVDHVAKYKKKEE 114
            +           + G    V    K   K+E
Sbjct: 150 DSVDKIVIQKYHTVNGHNCEVR---KALSKQE 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 = 46.9 bits (110), Expect = 4e-07
 Identities = 18/50 (36%), Positives = 29/50 (58%)

Query: 38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ 87
          +++GG+ F+ T+  L + F Q G + D  ++RD  T + RGF FV Y   
Sbjct: 9  LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 58

>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 = 46.6 bits (110), Expect = 8e-08
 Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 14/82 (17%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +Y+G +   +T  DL  +F      +              G+AFV Y DQ         L
Sbjct: 4   LYIGNLSPAVTADDLRQLFGDRKLPLAGQ------VLLKSGYAFVDYPDQNWAIRAIETL 57

Query: 92  NGA-QILGRTIRVDHVAKYKKK 112
           +G  ++ G+ + VD+ +  KK 
Sbjct: 58  SGKVELHGKIMEVDY-SVSKKL 78

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 10/83 (12%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED----QRN 89
            S+ V+VG    D+TE +L   F+Q G+++DV           R FAFV + D    Q  
Sbjct: 4   GSSGVFVGRCTGDMTEDELREFFSQYGDVMDV-----FIPKPFRAFAFVTFADDQIAQSL 58

Query: 90  NLNGAQILGRTIRVDHVAKYKKK 112
                 I G ++ + + A+ K  
Sbjct: 59  CGEDLIIKGISVHISN-AEPKHN 80

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 7/88 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
            S  ++V  + +  +E DL  +F+  G + +++   D  T KP+GFAFV +         
Sbjct: 7   GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKKEEE 115
              ++G    GR + V   +  KK+  +
Sbjct: 67  YAEVDGQVFQGRMLHVLP-STIKKEASQ 93

>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 = 45.4 bits (107), Expect = 2e-07
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGAQIL 97
           +YV G   D+T   L   F+  G I+D+++   +           + +     LNG Q+ 
Sbjct: 8   LYVYG--EDMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 65

Query: 98  GRTIRVD 104
              ++V+
Sbjct: 66  SVQLKVN 72

>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 = 45.5 bits (107), Expect = 3e-07
 Identities = 30/78 (38%), Positives = 45/78 (57%), Gaps = 6/78 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           D   ++VGG+ FD  E  L  VF++ G+I +V +V+D+ T + RGF FV +E+       
Sbjct: 4   DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 63

Query: 89  -NNLNGAQILGRTIRVDH 105
              +NG  + GR IRVD 
Sbjct: 64  MMAMNGKSVDGRQIRVDQ 81

>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 = 45.5 bits (107), Expect = 4e-07
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 5/81 (6%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
            ++G +P+D+TE  +   F                  + +GF +  +ED  +     +LN
Sbjct: 18  AFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLN 77

Query: 93  GAQILGRTIRVDHVAKYKKKE 113
              +  + IRVD   + + K+
Sbjct: 78  EESLGNKRIRVDVADQAQDKD 98

>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 = 38/91 (41%), Positives = 53/91 (58%), Gaps = 6/91 (6%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR- 88
           A  +    V+VG IP++ TE  L  +F++ G +V   LV D+ TGKP+G+ F  Y+DQ  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET 62

Query: 89  -----NNLNGAQILGRTIRVDHVAKYKKKEE 114
                 NLNG +  GR +RVD+ A  K KEE
Sbjct: 63  ALSAMRNLNGREFSGRALRVDNAASEKNKEE 93

>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 = 45.1 bits (106), Expect = 5e-07
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ----RNNLNG 93
           ++V  IPF   + DL  +F Q G+I+DV ++ ++   K  GF            R  L+G
Sbjct: 14  LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHG 73

Query: 94  AQILGRTIRVDH 105
             + GR I V++
Sbjct: 74  TVVEGRKIEVNN 85

>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 = 45.1 bits (106), Expect = 6e-07
 Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
           + A +++  +P +  + DLL +F   G +V   +  DK T   + F FV+Y++       
Sbjct: 17  EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 76

Query: 89  -NNLNGAQILGRTIRVD 104
             ++NG QI  + ++V 
Sbjct: 77  IQSMNGFQIGMKRLKVQ 93

>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 = 44.7 bits (105), Expect = 6e-07
 Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 4/78 (5%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NLNGA 94
           +YVG +P D+   D+  VF + G I D++L   +G        F    D  +     +G 
Sbjct: 17  IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 76

Query: 95  QILGRTIRVDHVAKYKKK 112
              G  +RV+   +  + 
Sbjct: 77  DYDGYRLRVEF-PRSGRG 93

>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 = 44.8 bits (105), Expect = 6e-07
 Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 14/85 (16%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLV--------RDKGTGKPRGFAFVAYE 85
           D++ +YV G+   +T  DL   F QCG +               DK TGKP+G A V+YE
Sbjct: 7   DNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYE 66

Query: 86  DQR------NNLNGAQILGRTIRVD 104
           D           +G    G  ++V 
Sbjct: 67  DPPTAKAAVEWFDGKDFQGSKLKVS 91

>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 = 44.6 bits (105), Expect = 8e-07
 Identities = 16/93 (17%), Positives = 35/93 (37%), Gaps = 13/93 (13%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  + + +T   L  +F++ G ++ +           +  A + Y D         +L
Sbjct: 10  IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSL 65

Query: 92  NGAQIL--GRTIRVDHVAKYKKKEEEDEETRQR 122
           +G  I     T+R+D  +K      +    + R
Sbjct: 66  DGQNIYNACCTLRIDF-SKLTSLNVKYNNDKSR 97

>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 = 44.4 bits (104), Expect = 8e-07
 Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 5/89 (5%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +       +  +V + G+PF  ++ +++  F+    + +   +     G+  G A
Sbjct: 1   GSSGSSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEA 60

Query: 81  FVAYEDQRN-----NLNGAQILGRTIRVD 104
           FV +  Q         +  +I  R I + 
Sbjct: 61  FVQFASQEIAEKALKKHKERIGHRYIEIF 89

>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 = 44.5 bits (104), Expect = 9e-07
 Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 5/92 (5%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
            ++  IPF +T+ D+L          +   V     G+  G A V ++++ +      L+
Sbjct: 11  AHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLH 70

Query: 93  GAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
             ++ GR   V  V     +E E     Q   
Sbjct: 71  RKKLNGREAFVHVVTLEDMREIEKNPPAQGKS 102

>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 = 42.8 bits (100), Expect = 2e-06
 Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +Y+ G+    T+ DL+ +    G+IV    + DK T K +G+ FV ++           L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 92  NGAQILGRTIR 102
             + +  +  +
Sbjct: 61  KASGVQAQMAK 71

>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 = 43.6 bits (102), Expect = 2e-06
 Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 7/81 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           +Y+  +   +TE DL+++FA+  E     +     TG+ RG AF+ + ++       + +
Sbjct: 21  LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 80

Query: 92  NGAQILGRTIRVDHVAKYKKK 112
           NG ++ G+ + ++   K KK+
Sbjct: 81  NGYKLYGKILVIEF-GKNKKQ 100

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.6 bits (102), Expect = 2e-06
 Identities = 20/100 (20%), Positives = 37/100 (37%), Gaps = 15/100 (15%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +  H K   S  V+V G+   + E DL+    + G I  V ++        +  A
Sbjct: 1   GSSGSSGSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMP------FKRQA 54

Query: 81  FVAYEDQRN--------NLNGAQILGRTIRVDHVAKYKKK 112
            V +E+  +              I G+    ++ +  K+ 
Sbjct: 55  LVEFENIDSAKECVTFAADVPVYIAGQQAFFNY-STSKRI 93

>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 = 42.9 bits (100), Expect = 3e-06
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 13/95 (13%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED--- 86
           +   +   V++  + FD  E  L  V  Q G++  V +V    T   +G AF  +     
Sbjct: 3   SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA 62

Query: 87  ---------QRNNLNGAQILGRTIRVDHVAKYKKK 112
                          G ++ GR ++VD  A  + +
Sbjct: 63  AQKCLAAASLEAEGGGLKLDGRQLKVDL-AVTRDE 96

>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 = 41.2 bits (96), Expect = 9e-06
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 38  VYVGGIPFDLTEGDL-LAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NN 90
           +Y+  +   + + +L  ++ A       +  +    + K RG AFV +++         +
Sbjct: 6   IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65

Query: 91  LNGAQILGRTIRVDHVAKYKKK 112
           + G     + +R+ + AK    
Sbjct: 66  MQGFPFYDKPMRIQY-AKTDSD 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 = 40.5 bits (94), Expect = 2e-05
 Identities = 11/74 (14%), Positives = 25/74 (33%), Gaps = 7/74 (9%)

Query: 38  VYVGGIPFDLTEGDLLAVF--AQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----N 90
           + +  +  +L + +LL                   K        AF+ +E++ +      
Sbjct: 7   IMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ 66

Query: 91  LNGAQILGRTIRVD 104
           +N + +  R I V 
Sbjct: 67  MNRSLLGNREISVS 80

>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 = 40.5 bits (94), Expect = 2e-05
 Identities = 13/87 (14%), Positives = 28/87 (32%), Gaps = 3/87 (3%)

Query: 21  GISDDASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA 80
           G S  +    +      V++ G+P+  TE D+   F+    +     +   G        
Sbjct: 1   GSSGSSGSSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADV 60

Query: 81  FVAYEDQRNN---LNGAQILGRTIRVD 104
             A  +        + A +  R + + 
Sbjct: 61  EFATHEDAVAAMAKDKANMQHRYVELF 87

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 17/80 (21%), Positives = 33/80 (41%), Gaps = 3/80 (3%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRNNLNGA 94
           +  ++VGG+  + +   L   F + G I  ++ V+       +  +  A +     + G 
Sbjct: 17  TTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGF 76

Query: 95  QILG--RTIRVDHVAKYKKK 112
            + G  R +RVD  AK    
Sbjct: 77  PLGGPDRRLRVDF-AKSGPS 95

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 4e-05
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 13/85 (15%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           S  V  GG+   ++   LL V  +CG +  +           + ++F  Y          
Sbjct: 20  SLVVANGGLGNGVSRNQLLPVLEKCGLVDALL------MPPNKPYSFARYRTTEESKRAY 73

Query: 89  NNLNGAQIL-GRTIRVDHVAKYKKK 112
             LNG +++     ++     + +K
Sbjct: 74  VTLNGKEVVDDLGQKITLYLNFVEK 98

>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 = 39.4 bits (91), Expect = 6e-05
 Identities = 16/91 (17%), Positives = 30/91 (32%), Gaps = 1/91 (1%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFA-FVAYEDQRNNLNGAQI 96
            + G +       DL  +F+  GEI  ++ VR    G             +  + N   +
Sbjct: 14  KFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKEALGKAKDANNGNL 73

Query: 97  LGRTIRVDHVAKYKKKEEEDEETRQRMREER 127
             R   V       + E+E  +     ++E 
Sbjct: 74  QLRNKEVTWEVLEGEVEKEALKKIIEDQQES 104

>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 = 39.5 bits (91), Expect = 1e-04
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 7/81 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNL 91
           + V  IP  + E  L  +F + G I  V +V D+ T + RG+ FV ++           L
Sbjct: 45  LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104

Query: 92  NGAQILGRTIRVDHVAKYKKK 112
           NG  IL + ++V   A    +
Sbjct: 105 NGFNILNKRLKVAL-AASGHQ 124

>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 = 38.4 bits (88), Expect = 1e-04
 Identities = 14/72 (19%), Positives = 34/72 (47%), Gaps = 6/72 (8%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           +++G +  + +  +L    ++     D+ +V  + TG  R F +V +E   +      L 
Sbjct: 16  LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKALELT 74

Query: 93  GAQILGRTIRVD 104
           G ++ G  I+++
Sbjct: 75  GLKVFGNEIKLE 86

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 19/100 (19%), Positives = 42/100 (42%), Gaps = 6/100 (6%)

Query: 30  AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN 89
           + ++    VY+ G+PF+     ++  F +   + D   +     GK  G  FV + ++ +
Sbjct: 13  SPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD 72

Query: 90  -----NLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMR 124
                  +   +  R I+V      K   E+ +  R+R++
Sbjct: 73  YKAALCRHKQYMGNRFIQVH-PITKKGMLEKIDMIRKRLQ 111

>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 = 38.0 bits (88), Expect = 1e-04
 Identities = 17/75 (22%), Positives = 26/75 (34%), Gaps = 13/75 (17%)

Query: 45  FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------NNLNGAQILG 98
            +    DL    ++ G+I  + L        P G A V++ D          L+G    G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDRH----PDGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 99  RTIRV---DHVAKYK 110
           R I     D    Y+
Sbjct: 85  RQITAQAWDGTTDYQ 99

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.8 bits (87), Expect = 2e-04
 Identities = 14/92 (15%), Positives = 25/92 (27%), Gaps = 15/92 (16%)

Query: 29  HAKYKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED- 86
             + +    V++            LL +    G I +               AF+     
Sbjct: 2   KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHL------ILNKINEAFIEMATT 55

Query: 87  -------QRNNLNGAQILGRTIRVDHVAKYKK 111
                         A + G+ +RV    KYK+
Sbjct: 56  EDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR 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 = 37.4 bits (86), Expect = 2e-04
 Identities = 9/85 (10%), Positives = 23/85 (27%), Gaps = 14/85 (16%)

Query: 34  DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR----- 88
            S+ + V  +P D    ++  +             +     + +  AFV   +       
Sbjct: 4   GSSGILVKNLPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNA 56

Query: 89  -NNLNGAQILGRTIRVDHVAKYKKK 112
               +     G+ + V  +      
Sbjct: 57  IQMFHQYSFRGKDLIVQ-LQPTDAL 80

>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 = 36.1 bits (82), Expect = 5e-04
 Identities = 12/73 (16%), Positives = 28/73 (38%), Gaps = 13/73 (17%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYED------QRNNL 91
           + + G+P D+T  ++  + +           +     K +G AFV   +        N  
Sbjct: 1   ILIRGLPGDVTNQEVHDLLSDYEL-------KYCFVDKYKGTAFVTLLNGEQAEAAINTF 53

Query: 92  NGAQILGRTIRVD 104
           + +++  R + V 
Sbjct: 54  HQSRLRERELSVQ 66

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (84), Expect = 6e-04
 Identities = 10/80 (12%), Positives = 24/80 (30%), Gaps = 10/80 (12%)

Query: 44  PFDLTEGDLLAVFAQCGEIVDVNLVRDK--GTGKPRGFAFVAYEDQR------NNLNGAQ 95
            ++    D+    ++ G +  + + R          G  FV +            L G +
Sbjct: 23  EYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK 82

Query: 96  ILGRTIRVD--HVAKYKKKE 113
              R +         Y +++
Sbjct: 83  FANRVVVTKYCDPDSYHRRD 102

>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 = 35.5 bits (81), Expect = 8e-04
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 11/77 (14%)

Query: 35  SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQR------ 88
           SA +++  IP  ++E DL  +F+  G +V           K R  A +            
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQAL 65

Query: 89  NNLNGAQIL-GRTIRVD 104
            +L+   +     +RV 
Sbjct: 66  IDLHNHDLGENHHLRVS 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 = 35.1 bits (80), Expect = 0.001
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 6/77 (7%)

Query: 38  VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLN 92
           VY+ G P D T  D+       G+++++  +R       +G  FV ++   +        
Sbjct: 9   VYIKGFPTDATLDDIKEWLEDKGQVLNIQ-MRRTLHKAFKGSIFVVFDSIESAKKFVETP 67

Query: 93  GAQILGRTIRVDHVAKY 109
           G +     + +     Y
Sbjct: 68  GQKYKETDLLILFKDDY 84

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 111

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.3 bits (80), Expect = 0.002
 Identities = 9/102 (8%), Positives = 28/102 (27%)

Query: 26  ASWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYE 85
            S  +  +    +    +P      ++   F++ G +  V L     T        +   
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 86  DQRNNLNGAQILGRTIRVDHVAKYKKKEEEDEETRQRMREER 127
               +L  ++     + ++            ++  Q  +   
Sbjct: 61  KAFRHLAYSKFHHVPLYLEWAPIGVFGAAPQKKDSQHEQPAE 102

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {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: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.0 bits (78), Expect = 0.004
 Identities = 10/58 (17%), Positives = 25/58 (43%), Gaps = 13/58 (22%)

Query: 51  DLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV 103
           +L+      G IV V + + +          V + D  +     +++G ++ GR +++
Sbjct: 40  ELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLDVDGMKVKGRAVKI 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	291
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.83
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.83
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.82
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.82
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.82
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.82
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.82
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.81
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.81
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.81
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.8
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.8
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.8
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.79
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.78
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.78
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.78
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.78
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.77
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.77
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.76
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.76
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.76
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.75
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.75
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.75
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.74
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.73
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.72
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.72
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.71
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.71
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.71
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.7
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.7
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.7
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.7
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.68
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.68
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.67
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.67
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.65
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.65
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.64
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.63
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.61
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.59
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.59
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.58
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.51
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.47
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	99.43
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.39
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.24
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.22
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.13
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.33
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	96.97
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.4
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	93.04

>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=1e-20  Score=140.08  Aligned_cols=79  Identities=33%  Similarity=0.557  Sum_probs=73.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+++||||+|||+.+|+++|.++|++||+|.+|.|+.++.+|.++|||||+|.+.++      .|||..|+|++|.|.|
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            4578999999999999999999999999999999999999999999999999999887      7999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus        84 a~~~~   88 (93)
T d1h2vz_          84 DAGFK   88 (93)
T ss_dssp             ESCCC
T ss_pred             cCCCC
Confidence            86543

>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=6.8e-21  Score=137.65  Aligned_cols=74  Identities=28%  Similarity=0.515  Sum_probs=70.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      +++|||+|||+.+|+++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      .|||..|+|++|.|.+|.|
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            5789999999999999999999999999999999999999999999999999987      7999999999999999875

>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=99.83  E-value=1.2e-20  Score=142.05  Aligned_cols=80  Identities=25%  Similarity=0.457  Sum_probs=74.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..++.++|||+|||+.+++++|.++|++||.|..|.|+.++.+|.++|||||+|.+.++      +|||..|+|+.|.|.
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            44678899999999999999999999999999999999999999999999999999887      799999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++.+..
T Consensus        94 ~a~~k~   99 (102)
T d2cpza1          94 LKRSKN   99 (102)
T ss_dssp             CCCCSC
T ss_pred             EeCCCC
Confidence            997654

>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=5.9e-21  Score=140.24  Aligned_cols=78  Identities=36%  Similarity=0.626  Sum_probs=73.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...++|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++      .|||..|+|++|.|.+|
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            346799999999999999999999999999999999999999999999999999986      78999999999999999


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      .+..
T Consensus        83 ~p~~   86 (89)
T d2cqba1          83 KPMR   86 (89)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.82  E-value=1.3e-20  Score=138.04  Aligned_cols=78  Identities=33%  Similarity=0.580  Sum_probs=72.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+..+|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.+.++      .|||..|+|+.|.|.
T Consensus         3 ~s~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~   82 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVD   82 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999887      799999999999999


Q ss_pred             ccCC
Q 022814          105 HVAK  108 (291)
Q Consensus       105 ~a~~  108 (291)
                      ||.+
T Consensus        83 ~a~~   86 (88)
T d1rk8a_          83 WCFV   86 (88)
T ss_dssp             ESEE
T ss_pred             EecC
Confidence            9864

>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=1.6e-20  Score=135.13  Aligned_cols=71  Identities=28%  Similarity=0.511  Sum_probs=68.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +|||+|||+.+|+++|.++|++||+|..|.|+.++.||.++|||||+|.++++      .|||..|+|++|+|.+|.
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            69999999999999999999999999999999999999999999999999887      799999999999999985

>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=2.1e-20  Score=134.94  Aligned_cols=74  Identities=34%  Similarity=0.590  Sum_probs=70.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      .++|||+|||+.+++++|.++|++||+|..|.|+.+..+|.++|||||+|.+.++      .|||..|+|++|.|.+|.|
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            3579999999999999999999999999999999999899999999999999987      7999999999999999875

>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=99.82  E-value=3.7e-21  Score=137.51  Aligned_cols=71  Identities=28%  Similarity=0.512  Sum_probs=67.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      |+|||+|||+.+|+++|.++|++||.|..|.|+.|+.||+++|||||+|.+.++     +||++.|+|+.|.|..|
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            689999999999999999999999999999999999999999999999999887     78999999999999876

>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=99.82  E-value=1.7e-20  Score=137.99  Aligned_cols=79  Identities=27%  Similarity=0.459  Sum_probs=73.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...+.++|||+|||+.+++++|.++|++||+|..|.|+.++.||.++|||||+|.+.++      .|||..|+|+.|.|.
T Consensus         4 ~~~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~   83 (90)
T d2cq0a1           4 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   83 (90)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999999999999999999999886      799999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      +|.+.
T Consensus        84 ~akp~   88 (90)
T d2cq0a1          84 WAKPS   88 (90)
T ss_dssp             ESSCC
T ss_pred             eeeCC
Confidence            99764

>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=1.7e-20  Score=138.91  Aligned_cols=79  Identities=28%  Similarity=0.563  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus         6 ~~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   85 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK   85 (93)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            3456899999999999999999999999999999999999999999999999999887      7999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      |.+..
T Consensus        86 A~~~~   90 (93)
T d1x5ua1          86 ASAHN   90 (93)
T ss_dssp             TTTTS
T ss_pred             cCCCC
Confidence            97654

>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=99.82  E-value=2.5e-20  Score=135.36  Aligned_cols=74  Identities=28%  Similarity=0.573  Sum_probs=69.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      ...+|||+|||+.+|+++|.++|++||+|..|.|+.|+.||.++|||||+|.+.++     .++++.|+|+.|.|..|.
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            34689999999999999999999999999999999999999999999999999887     789999999999998774

>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=99.82  E-value=2e-20  Score=135.56  Aligned_cols=72  Identities=39%  Similarity=0.605  Sum_probs=68.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ++++++|||+|||+.||+++|+++|++||.|.+|.|+.++.||.++|||||+|.+.++      +|||..|+|+.|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            3567899999999999999999999999999999999999999999999999999887      79999999999987

>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=1.2e-20  Score=142.43  Aligned_cols=76  Identities=25%  Similarity=0.511  Sum_probs=71.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCCc
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~~  109 (291)
                      .++|||+|||+.+|+++|+++|++||+|..|.|+.++.|+.++|||||+|.+.++     +|+++.|+|+.|.|.+|.+.
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            4799999999999999999999999999999999999999999999999999887     88999999999999998765


Q ss_pred             c
Q 022814          110 K  110 (291)
Q Consensus       110 ~  110 (291)
                      .
T Consensus       100 e  100 (103)
T d1x4ba1         100 E  100 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.81  E-value=4.5e-20  Score=135.73  Aligned_cols=79  Identities=27%  Similarity=0.438  Sum_probs=71.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh---hc-CCceeCCeEEEEeccC
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN---NL-NGAQILGRTIRVDHVA  107 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~---~l-ng~~i~gr~i~V~~a~  107 (291)
                      ....++|||+|||+.+|+++|+++|++||.|..|.|+.|+.||.++|||||+|.+.++   +| +...|+|+.|.|.++.
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCC
Confidence            3467889999999999999999999999999999999999999999999999999987   22 4568999999999997


Q ss_pred             Ccc
Q 022814          108 KYK  110 (291)
Q Consensus       108 ~~~  110 (291)
                      +..
T Consensus        85 ~k~   87 (90)
T d2cqga1          85 SKQ   87 (90)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            654

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=1.6e-20  Score=136.79  Aligned_cols=75  Identities=28%  Similarity=0.531  Sum_probs=71.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ++|||+|||+.+|+++|.++|++||+|..|.|+.|+.||.++|||||+|.++++      .|||..|+|++|.|.+|.+.
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            479999999999999999999999999999999999999999999999999987      79999999999999999765


Q ss_pred             c
Q 022814          110 K  110 (291)
Q Consensus       110 ~  110 (291)
                      .
T Consensus        82 ~   82 (85)
T d2u2fa_          82 A   82 (85)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.81  E-value=3e-20  Score=139.07  Aligned_cols=78  Identities=27%  Similarity=0.462  Sum_probs=73.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .++++|||+|||+.+|+++|+++|++||.|..|.|+.++.||.++|||||+|.+.++      .||+..|+|++|+|.++
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            457789999999999999999999999999999999999999999999999999886      79999999999999998


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      .+..
T Consensus        86 ~~~~   89 (99)
T d1whwa_          86 TIKK   89 (99)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7654

>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=3.9e-20  Score=146.89  Aligned_cols=79  Identities=29%  Similarity=0.450  Sum_probs=73.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ....++|||+|||+.+|+++|.++|++||.|.+|.|+.++.||.++|||||+|.+.++      .|||+.|+|+.|.|.+
T Consensus        39 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3456799999999999999999999999999999999999999999999999999887      7999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      +.+..
T Consensus       119 a~~~~  123 (139)
T d1u6fa1         119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            87554

>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=99.80  E-value=7.2e-20  Score=131.20  Aligned_cols=72  Identities=33%  Similarity=0.578  Sum_probs=68.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      .++|||+|||+++|+++|+++|++||.|..+.++.++.++.++|||||+|.++++     +|||+.|+|+.|.|..|
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            3689999999999999999999999999999999999999999999999999887     89999999999999876

>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=99.80  E-value=2.7e-20  Score=132.28  Aligned_cols=70  Identities=23%  Similarity=0.432  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      +|||||||+.+|+++|+++|++||+|..|.|+.++.||+++|||||+|.+.++     .++++.|+|+.|.|..|
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            59999999999999999999999999999999999999999999999999887     56778999999999765

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=4.1e-20  Score=138.88  Aligned_cols=74  Identities=24%  Similarity=0.504  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      +.+||||+|||+.+|+++|+++|+.||+|..|.|+.+..||+++|||||+|.+.++     +|||..|+|+.|.|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            45799999999999999999999999999999999999999999999999999887     899999999999999874

>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=133.34  Aligned_cols=73  Identities=32%  Similarity=0.606  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEEEec
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIRVDH  105 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~V~~  105 (291)
                      ..++|||+|||+.+|+++|+++|++||+|.+|.|+.++.+|.++|||||+|.+.++      .|||..|.|  ++|.|.|
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            35789999999999999999999999999999999999999999999999999887      799999997  5699987


Q ss_pred             c
Q 022814          106 V  106 (291)
Q Consensus       106 a  106 (291)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.80  E-value=4.9e-20  Score=130.93  Aligned_cols=70  Identities=31%  Similarity=0.636  Sum_probs=66.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      +|||+|||+.+|+++|.++|++||+|..|.|+.++.||+++|||||+|.++++     .+++..|+|+.|.|..|
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            49999999999999999999999999999999999999999999999999987     78999999999999654

>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=99.79  E-value=2e-19  Score=135.60  Aligned_cols=79  Identities=30%  Similarity=0.517  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ..+..++|||+|||+.+|+++|.++|++||+|.+|.|+.++.||.++|||||+|.+.++      .+|+ .|+|+.|.|.
T Consensus         6 ~d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~   84 (103)
T d2cqda1           6 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   84 (103)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEE
Confidence            34556789999999999999999999999999999999999999999999999999887      5554 7999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++....
T Consensus        85 ~a~~~~   90 (103)
T d2cqda1          85 LAYLGA   90 (103)
T ss_dssp             ESTTTC
T ss_pred             EcCCCC
Confidence            886543

>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=9.4e-20  Score=135.10  Aligned_cols=79  Identities=25%  Similarity=0.542  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCcceEEEEEEcChhh------hc-CCceeCCeEEEE
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK-GTGKPRGFAFVAYEDQRN------NL-NGAQILGRTIRV  103 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~-~tg~s~G~aFV~F~~~~~------~l-ng~~i~gr~i~V  103 (291)
                      ..+.++|||+|||+.+++++|.++|++||.|..|.|+.+. .+|.++|||||+|.+.++      .| |+..|+|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            4567899999999999999999999999999999999885 489999999999999887      56 899999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .+|.+..
T Consensus        85 ~~A~~~~   91 (94)
T d2cpha1          85 EWADSEV   91 (94)
T ss_dssp             EECCCCC
T ss_pred             EEcCCCC
Confidence            9997654

>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=7.8e-20  Score=131.69  Aligned_cols=74  Identities=15%  Similarity=0.247  Sum_probs=63.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      .+||||+|||+++|+++|.++|++||.|..+.++.+..+|.++|||||+|.+.++      .|||..|+|++|.|.++.|
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            3799999999999999999999999999999888888899999999999999887      7999999999999999976

>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=1.4e-19  Score=131.66  Aligned_cols=74  Identities=35%  Similarity=0.616  Sum_probs=69.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEEEe
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIRVD  104 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~V~  104 (291)
                      ...++|||+|||+.+++++|.++|++||+|..|.|+.++.+|.++|||||+|.+.++      .|||..+.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            356789999999999999999999999999999999999999999999999999887      799999976  889998


Q ss_pred             cc
Q 022814          105 HV  106 (291)
Q Consensus       105 ~a  106 (291)
                      +|
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            86

>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=99.79  E-value=2.9e-19  Score=131.35  Aligned_cols=77  Identities=25%  Similarity=0.518  Sum_probs=69.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..+++||||+|||+.+|+++|.++|++||+|..|.|+.+..++  +|||||+|.+.++      .|||..|.|+.|+|.+
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~   82 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNW   82 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4567899999999999999999999999999999999987554  7999999999887      7999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      |.+..
T Consensus        83 a~~~~   87 (90)
T d2cqia1          83 ATTPS   87 (90)
T ss_dssp             CCCTT
T ss_pred             cCCCC
Confidence            97654

>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=1.8e-19  Score=130.87  Aligned_cols=73  Identities=25%  Similarity=0.503  Sum_probs=66.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC---CcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTG---KPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg---~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      |||+|||+.||+++|..+|++||+|.+|.|+.++.++   .++|||||+|.+.++      .|||..|+|+.|.|.++..
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            8999999999999999999999999999999987665   479999999999887      7999999999999999865


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.78  E-value=1e-19  Score=133.75  Aligned_cols=78  Identities=40%  Similarity=0.751  Sum_probs=72.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      .+..+|||+|||+.+|+++|.++|++||.|..|.++.+..+|.++|||||+|.+.++      .|||..|+|+.|.|.++
T Consensus         3 ~~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a   82 (90)
T d1x5sa1           3 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   82 (90)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            457789999999999999999999999999999999999899999999999999887      78999999999999998


Q ss_pred             CCcc
Q 022814          107 AKYK  110 (291)
Q Consensus       107 ~~~~  110 (291)
                      .+..
T Consensus        83 ~~~~   86 (90)
T d1x5sa1          83 GKSS   86 (90)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            7554

>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=99.78  E-value=2.2e-19  Score=128.42  Aligned_cols=70  Identities=24%  Similarity=0.507  Sum_probs=66.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +|||+|||+.+++++|.++|++||+|..|.|+.++ +|+++|||||+|.+.++      .|||..|+|++|.|.++.
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            59999999999999999999999999999999987 89999999999999887      799999999999999875

>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=99.78  E-value=1.5e-19  Score=130.73  Aligned_cols=73  Identities=26%  Similarity=0.542  Sum_probs=67.9

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCcc
Q 022814           38 VYVGGIPFDLTEGDLLAVFAQCGEIVDV-NLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKYK  110 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F~~~G~I~~i-~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~~  110 (291)
                      |||+|||+++|+++|.++|++||.|..+ .|+.++.||+++|||||+|.+.++      .|||..|+|++|.|.+|.+..
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            8999999999999999999999999765 789999999999999999999987      799999999999999997654

>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=99.78  E-value=9.2e-20  Score=137.59  Aligned_cols=76  Identities=45%  Similarity=0.826  Sum_probs=71.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~  108 (291)
                      .++|||+|||+.+|+++|+++|++||+|..|.|+.++.||.++|||||+|.+.++      .|||..|.|+.|.|.++.+
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            4689999999999999999999999999999999999999999999999999887      7899999999999999876


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        88 ~~   89 (104)
T d1p1ta_          88 EK   89 (104)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=6.5e-19  Score=132.79  Aligned_cols=79  Identities=25%  Similarity=0.489  Sum_probs=69.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDK-GTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~-~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ..|+++|||+|||+.||+++|+++|++|| |+.|.|+.+. .+|.++|||||+|.+.++     +||++.|+|+.|.|.+
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            34679999999999999999999999999 7788777664 578999999999999887     8999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      |.+...
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876543

>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=6.8e-19  Score=129.03  Aligned_cols=75  Identities=21%  Similarity=0.454  Sum_probs=68.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ...+|||+|||+.+|+++|+++|++||.|..|.|+.+.  +.++|||||+|.+.++      .|||..|+|+.|.|.++.
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35689999999999999999999999999999999986  4578999999999987      789999999999999997


Q ss_pred             Ccc
Q 022814          108 KYK  110 (291)
Q Consensus       108 ~~~  110 (291)
                      +..
T Consensus        85 ~~~   87 (89)
T d1cvja2          85 SRK   87 (89)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            543

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=2.5e-19  Score=126.92  Aligned_cols=70  Identities=29%  Similarity=0.519  Sum_probs=66.9

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           37 YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        37 ~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      .|||+|||+++|+++|.++|++||.|..|.++.++.++.++|||||+|.+.++     +|||+.|+|++|.|..|
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            49999999999999999999999999999999999999999999999999887     89999999999999865

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=9.7e-19  Score=130.23  Aligned_cols=79  Identities=25%  Similarity=0.423  Sum_probs=71.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hc------CCceeCCe
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL------NGAQILGR   99 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l------ng~~i~gr   99 (291)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|.++.+..++.++|||||+|.+.++      .|      +|..|.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            4567899999999999999999999999999999999999999999999999999987      33      47889999


Q ss_pred             EEEEeccCCcc
Q 022814          100 TIRVDHVAKYK  110 (291)
Q Consensus       100 ~i~V~~a~~~~  110 (291)
                      .|.|.++.+..
T Consensus        85 ~l~v~~a~~k~   95 (98)
T d1x4ha1          85 QLKVDLAVTRD   95 (98)
T ss_dssp             EEEEECCCCCC
T ss_pred             EEEEEECCCCC
Confidence            99999997643

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.76  E-value=5.3e-19  Score=128.82  Aligned_cols=76  Identities=21%  Similarity=0.309  Sum_probs=65.5

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHHhcCCCeeEEEEeec-CCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           34 DSAYVYVGGIPFDLT-EGDLLAVFAQCGEIVDVNLVRD-KGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        34 ~~~~lfVgnL~~~~t-e~~L~~~F~~~G~I~~i~i~~d-~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      ..++|||+|||+.+| ++.|.++|++||.|..|.|+.+ ..+|+++|||||+|.+.++     +||++.|+|+.|.|.++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            467999999999876 5669999999999999998764 5689999999999999887     89999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      .+.
T Consensus        83 ~~k   85 (86)
T d2ghpa3          83 DKK   85 (86)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.76  E-value=1.9e-18  Score=127.71  Aligned_cols=78  Identities=29%  Similarity=0.588  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      .....++|||+|||+.+++++|.++|++||+|..|.|+.+.  +.++|||||+|.+.++      .||+..|+|+.|.|.
T Consensus         7 ~~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   84 (93)
T d2cq3a1           7 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVN   84 (93)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999999999999999999999999999999986  4479999999999887      789999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      +|.+..
T Consensus        85 ~A~~r~   90 (93)
T d2cq3a1          85 NATARV   90 (93)
T ss_dssp             ECCSSC
T ss_pred             ecCcCC
Confidence            997653

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=6.2e-19  Score=132.33  Aligned_cols=78  Identities=21%  Similarity=0.449  Sum_probs=71.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...++++|||+|||+++++++|.++|++||.|..|.++.+. ++.++|||||+|.+.++      .|||..|.|+++.|.
T Consensus        14 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~   92 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSA   92 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCC
T ss_pred             ccCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccC
Confidence            34567899999999999999999999999999999998885 89999999999999887      799999999999998


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++.|.
T Consensus        93 ~~~Pl   97 (101)
T d1x5oa1          93 PTEPL   97 (101)
T ss_dssp             CSSCB
T ss_pred             CCCCc
Confidence            77654

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.75  E-value=1.8e-18  Score=132.44  Aligned_cols=74  Identities=24%  Similarity=0.472  Sum_probs=67.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ..+++|||+|||+.+|+++|.++|++||.|..|.|+.   ++.++|||||+|.+.++      .|||..|+|+.|.|.++
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~---~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a   81 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN---TPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYY   81 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEC---STTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccc---cCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4567999999999999999999999999999999975   46779999999999887      89999999999999998


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      .+.
T Consensus        82 ~~~   84 (114)
T d2f9da1          82 NAN   84 (114)
T ss_dssp             CHH
T ss_pred             CCC
Confidence            653

>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=99.75  E-value=1.8e-18  Score=129.56  Aligned_cols=80  Identities=34%  Similarity=0.544  Sum_probs=71.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEEcChhh------hcCCcee
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIV--------DVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI   96 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~--------~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i   96 (291)
                      ...+.++|||+|||+.+|+++|.++|++||.|.        .+.++.+..+|.++|||||+|.+.++      .|||+.|
T Consensus         4 ~~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~   83 (101)
T d2cpea1           4 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   83 (101)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEE
Confidence            346788999999999999999999999999873        56778888899999999999999887      7999999


Q ss_pred             CCeEEEEeccCCcc
Q 022814           97 LGRTIRVDHVAKYK  110 (291)
Q Consensus        97 ~gr~i~V~~a~~~~  110 (291)
                      +|+.|.|.++.+..
T Consensus        84 ~gr~i~V~~a~~~~   97 (101)
T d2cpea1          84 QGSKLKVSLARKKP   97 (101)
T ss_dssp             TTEECEEECSSCCC
T ss_pred             CCEEEEEEEcCCCC
Confidence            99999999997643

>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=99.74  E-value=3.9e-18  Score=123.85  Aligned_cols=72  Identities=18%  Similarity=0.335  Sum_probs=67.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      .++|||+|||+.+|+++|.++|+.||+|..|.|+.+. +|.++|||||+|.++++     ++++..|.|+.|.|.+..
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            5789999999999999999999999999999998876 89999999999999987     889999999999998753

>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=3.9e-19  Score=133.49  Aligned_cols=80  Identities=23%  Similarity=0.370  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ..|+++|||+|||+.+++++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++      .|||..|.|++|.|.+
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            4578999999999999999999999999999999999888899999999999999987      7999999999999999


Q ss_pred             cCCccc
Q 022814          106 VAKYKK  111 (291)
Q Consensus       106 a~~~~~  111 (291)
                      |.+...
T Consensus        95 ak~k~~  100 (102)
T d2cpxa1          95 GKNKKQ  100 (102)
T ss_dssp             CCCCSC
T ss_pred             CCCccc
Confidence            986543

>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=99.73  E-value=3.9e-19  Score=130.91  Aligned_cols=76  Identities=18%  Similarity=0.382  Sum_probs=68.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      .....+|||+|||+.+|+++|+++|++||.|..|.|+.+ .+|+++|||||+|.+.++     +|||..|+|++|.|.+|
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            345669999999999999999999999999999988755 489999999999999887     79999999999999998


Q ss_pred             CC
Q 022814          107 AK  108 (291)
Q Consensus       107 ~~  108 (291)
                      .+
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.72  E-value=1.3e-17  Score=123.60  Aligned_cols=76  Identities=30%  Similarity=0.496  Sum_probs=67.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ...++++|||+|||+.+|+++|+++|++||.|..|.++.+   +.++|||||+|.+.++      .||++.|.|++|.|.
T Consensus        10 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~   86 (95)
T d1x4aa1          10 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVE   86 (95)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3467789999999999999999999999999999987654   5678999999999887      799999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++.+.
T Consensus        87 ~a~~~   91 (95)
T d1x4aa1          87 FPRSG   91 (95)
T ss_dssp             CCCCC
T ss_pred             eccCC
Confidence            98653

>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=99.72  E-value=5.9e-18  Score=122.27  Aligned_cols=72  Identities=19%  Similarity=0.365  Sum_probs=65.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeC-CeEEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQIL-GRTIRV  103 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~-gr~i~V  103 (291)
                      ..||+++|||+|||+.+|+++|..+|++||.|..|.|+.+.     +|||||+|.+.++      .|+|..|. |++|+|
T Consensus         4 ~~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v   78 (83)
T d2b0ga1           4 EQPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKI   78 (83)
T ss_dssp             CCSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEE
Confidence            45788999999999999999999999999999999998653     7899999999887      79998885 689999


Q ss_pred             eccC
Q 022814          104 DHVA  107 (291)
Q Consensus       104 ~~a~  107 (291)
                      .||.
T Consensus        79 ~~ak   82 (83)
T d2b0ga1          79 TFAK   82 (83)
T ss_dssp             EECC
T ss_pred             EEec
Confidence            9984

>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=99.72  E-value=9.2e-18  Score=126.46  Aligned_cols=82  Identities=17%  Similarity=0.287  Sum_probs=72.8

Q ss_pred             ccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEE
Q 022814           29 HAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRV  103 (291)
Q Consensus        29 ~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V  103 (291)
                      .+...+..+|||+|||+.+|+++|+++|.+||.|..+.++.+..++.++|||||+|.++++     .||+..|+|+.|.|
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            3445567789999999999999999999999999887777777799999999999999988     88999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        89 ~~~~~~~   95 (104)
T d1wg5a_          89 FKSSRAE   95 (104)
T ss_dssp             EEECTTT
T ss_pred             EECCHHH
Confidence            9887654

>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=99.72  E-value=9e-18  Score=124.72  Aligned_cols=72  Identities=24%  Similarity=0.519  Sum_probs=66.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      .++.++|||+|||+.+++++|+++|++||.|..|.|+.+      +|||||+|.+.++      .|||..|+|+.|+|.|
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            456789999999999999999999999999999999976      7899999999987      7999999999999999


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      +.+.
T Consensus        89 ak~~   92 (96)
T d1x4ga1          89 GKES   92 (96)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>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=99.71  E-value=1.2e-17  Score=118.29  Aligned_cols=69  Identities=20%  Similarity=0.342  Sum_probs=63.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      +||||+|||+.+++++|+++|++||.|..|.|+.++.  ...+||||+|.+.++     .||+..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            5899999999999999999999999999999999873  446899999999887     89999999999999765

>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=99.71  E-value=6.2e-18  Score=123.54  Aligned_cols=73  Identities=29%  Similarity=0.451  Sum_probs=64.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh----hcCCceeCCeEEEEeccCC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN----NLNGAQILGRTIRVDHVAK  108 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~----~lng~~i~gr~i~V~~a~~  108 (291)
                      ..+++|||+|||+.+|+++|+++|++||.|..|.++.     .++|||||+|.+.++    .++++.|+|+.|.|.++.+
T Consensus         3 ~~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEP   77 (88)
T ss_dssp             SCCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCC
Confidence            4678999999999999999999999999999998754     458999999999887    4578899999999999976


Q ss_pred             cc
Q 022814          109 YK  110 (291)
Q Consensus       109 ~~  110 (291)
                      ..
T Consensus        78 k~   79 (88)
T d1wf0a_          78 KH   79 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.71  E-value=1.4e-17  Score=121.58  Aligned_cols=75  Identities=21%  Similarity=0.307  Sum_probs=65.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee-CCeEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI-LGRTIR  102 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i-~gr~i~  102 (291)
                      ...||+++|||+|||+.+|+++|.++|++||.|..+.++.    ++++|||||+|.+.++      .|+|..| +|++|.
T Consensus         5 ~~~pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~   80 (88)
T d2adca2           5 NIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLR   80 (88)
T ss_dssp             TCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCE
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEE
Confidence            3468899999999999999999999999999998887654    4468899999999887      7999988 589999


Q ss_pred             EeccCC
Q 022814          103 VDHVAK  108 (291)
Q Consensus       103 V~~a~~  108 (291)
                      |.|+.+
T Consensus        81 v~~sk~   86 (88)
T d2adca2          81 VSFSKS   86 (88)
T ss_dssp             EEECSS
T ss_pred             EEeCCC
Confidence            999864

>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=99.70  E-value=1.3e-17  Score=125.18  Aligned_cols=79  Identities=18%  Similarity=0.254  Sum_probs=69.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEe
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVD  104 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~  104 (291)
                      .......+|||.|||+.+|+++|+++|..|| |..|.|+.+. +|.++|||||+|.+.++     +||+..|+|+.|.|.
T Consensus        10 ~~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~   87 (102)
T d1weza_          10 FQSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELF   87 (102)
T ss_dssp             CCCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEE
T ss_pred             CcCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEE
Confidence            4456778999999999999999999999998 4578888876 79999999999999887     889999999999999


Q ss_pred             ccCCcc
Q 022814          105 HVAKYK  110 (291)
Q Consensus       105 ~a~~~~  110 (291)
                      ++....
T Consensus        88 ~s~~~~   93 (102)
T d1weza_          88 LNSTAG   93 (102)
T ss_dssp             EECCCC
T ss_pred             EcCCCC
Confidence            887554

>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=99.70  E-value=1.2e-17  Score=123.99  Aligned_cols=76  Identities=25%  Similarity=0.457  Sum_probs=67.1

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           30 AKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      ....+.++|||+|||+.+|+++|.++|++||.|..|.+     ++.++|||||+|.+.++      .|||..|+|++|.|
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            34566889999999999999999999999998866542     68899999999999887      79999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .++.+..
T Consensus        86 ~~a~~k~   92 (96)
T d1fjca_          86 YYTGEKG   92 (96)
T ss_dssp             EECSSSC
T ss_pred             EEeCCCC
Confidence            9998654

>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=8.1e-18  Score=123.20  Aligned_cols=70  Identities=21%  Similarity=0.384  Sum_probs=63.5

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHHhcCCCeeEEEEeecCCCCCc---ceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           34 DSAYVYVGGIPFDLTEGDL---LAVFAQCGEIVDVNLVRDKGTGKP---RGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L---~~~F~~~G~I~~i~i~~d~~tg~s---~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      ..++|||+|||+.+++++|   .++|++||+|..|.|+.++.++.+   .|||||+|.+.++      .|||..|+|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            4578999999999999999   678999999999999999877654   4999999999887      799999999999


Q ss_pred             EE
Q 022814          102 RV  103 (291)
Q Consensus       102 ~V  103 (291)
                      +|
T Consensus        87 kv   88 (89)
T d2cpia1          87 KA   88 (89)
T ss_dssp             EE
T ss_pred             EE
Confidence            97

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1.8e-17  Score=123.04  Aligned_cols=78  Identities=32%  Similarity=0.495  Sum_probs=67.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEeecC-CCCCcceEEEEEEcChhh------hcC--CceeCCeEEEEe
Q 022814           35 SAYVYVGGIPFDLTEGDLLAVFAQCGE-IVDVNLVRDK-GTGKPRGFAFVAYEDQRN------NLN--GAQILGRTIRVD  104 (291)
Q Consensus        35 ~~~lfVgnL~~~~te~~L~~~F~~~G~-I~~i~i~~d~-~tg~s~G~aFV~F~~~~~------~ln--g~~i~gr~i~V~  104 (291)
                      +|+|||+|||+.+|+++|.++|++||+ |..|.|+.+. .+|.++|||||+|.++++      .|+  +..++|++|.|.
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            468999999999999999999999996 8999999885 468999999999999987      454  567789999999


Q ss_pred             ccCCcccc
Q 022814          105 HVAKYKKK  112 (291)
Q Consensus       105 ~a~~~~~~  112 (291)
                      ||.+....
T Consensus        81 ~A~p~~~~   88 (96)
T d2disa1          81 WAEPEIDV   88 (96)
T ss_dssp             ESCSSCST
T ss_pred             EcCCCCCC
Confidence            99765543

>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=1.6e-17  Score=120.80  Aligned_cols=73  Identities=25%  Similarity=0.565  Sum_probs=66.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEec
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDH  105 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~  105 (291)
                      ....++|||+|||+.+++++|..+|++||+|..|.|+.+      +|||||+|.+.++      .|||..|+|+.|.|.+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~   78 (86)
T d2cpja1           5 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   78 (86)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            345678999999999999999999999999999999865      6899999999887      7999999999999999


Q ss_pred             cCCcc
Q 022814          106 VAKYK  110 (291)
Q Consensus       106 a~~~~  110 (291)
                      |.+..
T Consensus        79 A~~~~   83 (86)
T d2cpja1          79 ACHSA   83 (86)
T ss_dssp             SSCCS
T ss_pred             CCCcC
Confidence            97654

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=2.1e-17  Score=123.20  Aligned_cols=72  Identities=28%  Similarity=0.567  Sum_probs=63.4

Q ss_pred             cCCCCCCEEEEcCCC-CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           30 AKYKDSAYVYVGGIP-FDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~-~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      ......++|||+||| ..+++++|+++|++||.|..|.|        ++|||||+|.+.++      .|||+.|+|+.|.
T Consensus        10 ~~~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~   81 (98)
T d1wf2a_          10 DPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLD   81 (98)
T ss_dssp             CCSSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            344567789999997 46888999999999999999998        37999999999987      7999999999999


Q ss_pred             EeccCCc
Q 022814          103 VDHVAKY  109 (291)
Q Consensus       103 V~~a~~~  109 (291)
                      |.++.+.
T Consensus        82 V~~a~~~   88 (98)
T d1wf2a_          82 INLAAEP   88 (98)
T ss_dssp             EEETTSC
T ss_pred             EEECCCC
Confidence            9999654

>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=99.68  E-value=1.7e-17  Score=120.56  Aligned_cols=74  Identities=23%  Similarity=0.364  Sum_probs=64.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      +..++|||+|||+.+++++|+++|+.||.|..+.++.+..+|.++|||||+|.++++      .||+..|+|++|.|.++
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            456789999999999999999999999999764444444589999999999999887      79999999999999764

>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=99.68  E-value=1.3e-17  Score=119.71  Aligned_cols=71  Identities=27%  Similarity=0.453  Sum_probs=62.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCc-eeCCeEEEEeccCC
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGA-QILGRTIRVDHVAK  108 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~-~i~gr~i~V~~a~~  108 (291)
                      ++|||+|||+.+|+++|+++|++||.|..+.++.      ++|||||+|.+.++      .|||. .|+|++|.|.++.+
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            5799999999999999999999999988776665      37899999999887      79985 69999999999987


Q ss_pred             cccc
Q 022814          109 YKKK  112 (291)
Q Consensus       109 ~~~~  112 (291)
                      ..++
T Consensus        76 k~~r   79 (80)
T d2cqha1          76 KKLR   79 (80)
T ss_dssp             CCCC
T ss_pred             cCcC
Confidence            6543

>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=3.1e-17  Score=124.32  Aligned_cols=70  Identities=23%  Similarity=0.415  Sum_probs=63.8

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           35 SAYVYVGGIPF-DLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        35 ~~~lfVgnL~~-~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +++|||+|||+ .+|+++|.++|++||+|..|.|+.++     +|||||+|.+.++      .|||..|+|+.|.|.++.
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            57999999976 59999999999999999999999875     7999999999887      899999999999999985


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.68  E-value=1.8e-17  Score=121.81  Aligned_cols=74  Identities=20%  Similarity=0.455  Sum_probs=65.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEE
Q 022814           34 DSAYVYVGGIPFDLTEGDLLA----VFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRV  103 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~----~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V  103 (291)
                      |++||||+|||+.+++++|++    +|++||+|..|.+..   +++++|||||+|.+.++      +|||..|+|+.|.|
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            679999999999999998864    689999999998764   57789999999999887      79999999999999


Q ss_pred             eccCCcc
Q 022814          104 DHVAKYK  110 (291)
Q Consensus       104 ~~a~~~~  110 (291)
                      .+|.+..
T Consensus        79 ~~ak~~~   85 (91)
T d1nu4a_          79 QYAKTDS   85 (91)
T ss_dssp             EECSSCC
T ss_pred             EEeCCCc
Confidence            9997543

>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=1.2e-16  Score=115.90  Aligned_cols=72  Identities=22%  Similarity=0.309  Sum_probs=64.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      ..++|||+|||+.+|+++|..+|++||.|..+.+.      .++|||||+|.+.++      .|||..|+|+.|.|.++.
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 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            45799999999999999999999999999887764      357899999999987      799999999999999998


Q ss_pred             Cccc
Q 022814          108 KYKK  111 (291)
Q Consensus       108 ~~~~  111 (291)
                      |..+
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6543

>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=99.67  E-value=9e-17  Score=117.20  Aligned_cols=74  Identities=12%  Similarity=0.237  Sum_probs=65.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--------hcCCceeCCeEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--------NLNGAQILGRTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--------~lng~~i~gr~i~  102 (291)
                      ..+|+++|||+|||+.+++++|.++|++||.|..|.++.+      +|||||+|.+.++        ++++..|.|++|.
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~   77 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIY   77 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEE
Confidence            3578999999999999999999999999999999998865      5799999999887        3578899999999


Q ss_pred             EeccCCcc
Q 022814          103 VDHVAKYK  110 (291)
Q Consensus       103 V~~a~~~~  110 (291)
                      |.|+....
T Consensus        78 v~~sk~~~   85 (88)
T d2cq1a1          78 IQYSNHKE   85 (88)
T ss_dssp             EEECSCSS
T ss_pred             EEECCCCC
Confidence            99996543

>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=99.67  E-value=8.6e-18  Score=118.01  Aligned_cols=65  Identities=25%  Similarity=0.507  Sum_probs=61.4

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEE
Q 022814           38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIR  102 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~  102 (291)
                      |||+|||+.||+++|.++|++||.|..+.++.++.++.++|||||+|.+.++      .|||..|.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            8999999999999999999999999999999999999999999999999887      7999999998763

>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=99.67  E-value=4.5e-17  Score=122.33  Aligned_cols=76  Identities=21%  Similarity=0.291  Sum_probs=67.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEecc
Q 022814           32 YKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a  106 (291)
                      .....+|||+|||+.+|+++|.++|+.||.|..+.++....+|.++|||||+|.+.++     .||+..|+|+.|.|.++
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            3456789999999999999999999999999876555555699999999999999987     88999999999999887


Q ss_pred             C
Q 022814          107 A  107 (291)
Q Consensus       107 ~  107 (291)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=2.8e-17  Score=124.90  Aligned_cols=71  Identities=11%  Similarity=0.154  Sum_probs=63.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...++|||+|||+.+++++|.++|++||+|..|.|..      ++|||||+|.+.++      .|||..|.|++|.|.++
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a   81 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWA   81 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEEC
Confidence            3457999999999999999999999999999998853      47999999999987      79999999999999988


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      ...
T Consensus        82 ~~~   84 (111)
T d1whxa_          82 PIG   84 (111)
T ss_dssp             ETT
T ss_pred             CCC
Confidence            543

>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=99.66  E-value=1.6e-17  Score=121.03  Aligned_cols=67  Identities=18%  Similarity=0.279  Sum_probs=61.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      ++|||+|||+.||+++|+++|++||+|..|.|+.+       |||||+|.+.++      .|||..|.|+.|.|.++...
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            47999999999999999999999999999998754       799999999887      79999999999999887543

>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=1.3e-16  Score=118.45  Aligned_cols=74  Identities=26%  Similarity=0.463  Sum_probs=66.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCC--eEEE
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILG--RTIR  102 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~g--r~i~  102 (291)
                      +.+|+++|||+|||+.+++++|+++|++||+|..|.|+.+      ++||||+|.+.++      .||+..|.|  ++|.
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            4578899999999999999999999999999999999765      6899999999887      899999986  5899


Q ss_pred             EeccCCcc
Q 022814          103 VDHVAKYK  110 (291)
Q Consensus       103 V~~a~~~~  110 (291)
                      |.|+.+.+
T Consensus        87 v~~ak~~~   94 (97)
T d1whya_          87 VDFAKSGP   94 (97)
T ss_dssp             EEECCCCC
T ss_pred             EEeCCCCC
Confidence            99987543

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=1e-16  Score=114.52  Aligned_cols=69  Identities=30%  Similarity=0.485  Sum_probs=62.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ...+||||+|||  +|+++|.++|++||.|..|.|..+      +|||||+|.+.++      +|||..|+|+.|+|.++
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   74 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   74 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            457899999996  899999999999999999998754      6899999999887      89999999999999999


Q ss_pred             CCc
Q 022814          107 AKY  109 (291)
Q Consensus       107 ~~~  109 (291)
                      .+.
T Consensus        75 ~~~   77 (79)
T d2bz2a1          75 RKQ   77 (79)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            654

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.64  E-value=4.6e-17  Score=124.21  Aligned_cols=77  Identities=21%  Similarity=0.377  Sum_probs=68.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccC
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~  107 (291)
                      .+..+|||+|||+.+|+++|.++|+.||.|..+.++.+..+|.++|||||+|.+.++     .||+..|+|+.|.|..+.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            456799999999999999999999999999876666666699999999999999887     899999999999998775


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      +.
T Consensus        96 ~~   97 (112)
T d1wela1          96 KK   97 (112)
T ss_dssp             HH
T ss_pred             hH
Confidence            43

>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=4.2e-16  Score=117.21  Aligned_cols=77  Identities=22%  Similarity=0.210  Sum_probs=66.6

Q ss_pred             ccccCCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hc--CCceeCC
Q 022814           27 SWHAKYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NL--NGAQILG   98 (291)
Q Consensus        27 ~~~~~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~l--ng~~i~g   98 (291)
                      ......+|+.+|||+|||+.+|+++|..+|++||.|..|.|+.+      +|||||+|.+.++      .|  ++..|+|
T Consensus         7 g~~~~~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g   80 (104)
T d1wexa_           7 GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAG   80 (104)
T ss_dssp             CSCCCCCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSS
T ss_pred             CCCCcCCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEee
Confidence            33456688999999999999999999999999999999998754      6899999999887      22  6788999


Q ss_pred             eEEEEeccCCc
Q 022814           99 RTIRVDHVAKY  109 (291)
Q Consensus        99 r~i~V~~a~~~  109 (291)
                      ++|.|.++...
T Consensus        81 ~~l~v~~s~~~   91 (104)
T d1wexa_          81 QQAFFNYSTSK   91 (104)
T ss_dssp             SBCEEEECSSS
T ss_pred             EEEEEEEcCCC
Confidence            99999998653

>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=99.63  E-value=2.2e-16  Score=117.54  Aligned_cols=72  Identities=17%  Similarity=0.311  Sum_probs=64.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEe
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVD  104 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~  104 (291)
                      ......+|||+|||+.+++++|+++|++||+|+.|.|..       +|||||+|.+.++      .|||..|.|+.|.|.
T Consensus        11 ~~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~   83 (98)
T d1wg4a_          11 TRRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETS   83 (98)
T ss_dssp             CCSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEE
Confidence            344577899999999999999999999999999999864       4899999999987      799999999999999


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++...
T Consensus        84 ~~~~~   88 (98)
T d1wg4a_          84 YIRVY   88 (98)
T ss_dssp             EEEEE
T ss_pred             EEecC
Confidence            87543

>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=99.61  E-value=1.8e-16  Score=130.44  Aligned_cols=129  Identities=19%  Similarity=0.379  Sum_probs=94.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEeccCCcc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDHVAKYK  110 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~a~~~~  110 (291)
                      ++|||+|||+.+|+++|.++|++||.|..|.|+.+..+|.++|||||+|.+.++     .+++..|..+.+.+....+..
T Consensus         7 r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~   86 (183)
T d1u1qa_           7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSRE   86 (183)
T ss_dssp             HEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcc
Confidence            699999999999999999999999999999999999999999999999999987     677888999998887665443


Q ss_pred             ccchhHHHHHH---------hhhhhhccccccccCCCCCCCceeEeecCCCCCCCCCCCCCCCCCCCCCCccCC
Q 022814          111 KKEEEDEETRQ---------RMREERGVCRAFQRGECTRGDGCKFSHNEQRAANTGGGPQDRSSRWGHEKFEGF  175 (291)
Q Consensus       111 ~~~~~~~~~~~---------~~~~~~~~~~~f~~~~~g~~~~~~~~~d~~~~~~~g~g~~~~~~g~g~~~~~~~  175 (291)
                      ...........         ..-....+...|.  .+|.+..+.+..+..++.         ..||+|+.|...
T Consensus        87 ~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~--~~G~v~~~~i~~~~~~~~---------~~g~~fV~f~~~  149 (183)
T d1u1qa_          87 DSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFE--QYGKIEVIEIMTDRGSGK---------KRGFAFVTFDDH  149 (183)
T ss_dssp             GGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHG--GGSCEEEEEEEECTTTCC---------EEEEEEEEESCH
T ss_pred             cccccccccccceeEEccCCCcCCHHHHhhhhc--cCCceeeeeeecccccCc---------cceeEEEEECCH
Confidence            22211100000         0001222333332  366677888888877665         457889988764

>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=99.61  E-value=5.1e-16  Score=113.17  Aligned_cols=69  Identities=13%  Similarity=0.177  Sum_probs=59.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      .+.+|||+|||+.+++++|+++|++|| |..+.+      +.++|||||+|.+.++      .||++.|+|+.|.|.++.
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            467899999999999999999999999 333433      3458999999999987      899999999999999986


Q ss_pred             Cc
Q 022814          108 KY  109 (291)
Q Consensus       108 ~~  109 (291)
                      ..
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>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=99.61  E-value=1.6e-15  Score=124.67  Aligned_cols=79  Identities=30%  Similarity=0.494  Sum_probs=73.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           31 KYKDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ......+|||+|||+.+|+++|.++|+.||.|..|.|+.+..+|.++|||||+|.+.++     .+++..|+|+.|.|.+
T Consensus        93 ~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~~~~~~~~G~~i~V~~  172 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK  172 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHTSSCEEETTEEEEEEE
T ss_pred             cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHHhCCCeECCEEEEEEe
Confidence            34567899999999999999999999999999999999999899999999999999987     7889999999999998


Q ss_pred             cCCc
Q 022814          106 VAKY  109 (291)
Q Consensus       106 a~~~  109 (291)
                      |.+.
T Consensus       173 A~~k  176 (183)
T d1u1qa_         173 ALSK  176 (183)
T ss_dssp             CCCH
T ss_pred             cCCc
Confidence            8754

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=4.7e-16  Score=115.88  Aligned_cols=75  Identities=23%  Similarity=0.374  Sum_probs=65.5

Q ss_pred             cCCCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--------hcCCceeCCeE
Q 022814           30 AKYKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--------NLNGAQILGRT  100 (291)
Q Consensus        30 ~~~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--------~lng~~i~gr~  100 (291)
                      +...++++|||+|||.. +|+++|.++|++||.|..|.|+.+      +|||||+|.+.++        .+++..|+|+.
T Consensus        13 ~~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~   86 (99)
T d1x4fa1          13 QKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRC   86 (99)
T ss_dssp             CSSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSC
T ss_pred             cCCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEE
Confidence            34567789999999985 899999999999999999999865      6899999999887        47899999999


Q ss_pred             EEEeccCCcc
Q 022814          101 IRVDHVAKYK  110 (291)
Q Consensus       101 i~V~~a~~~~  110 (291)
                      |.|.+|....
T Consensus        87 l~V~~s~~~~   96 (99)
T d1x4fa1          87 VKVDLSEKYK   96 (99)
T ss_dssp             CEEEEECSCS
T ss_pred             EEEEEcCCcc
Confidence            9999986543

>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=99.59  E-value=5.2e-17  Score=118.95  Aligned_cols=72  Identities=19%  Similarity=0.445  Sum_probs=63.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEe-----ecCCCCCcceEEEEEEcChhh-----hcCCceeCCeEEEEec
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLV-----RDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRTIRVDH  105 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~-----~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~i~V~~  105 (291)
                      ++|||+|||+.+|+++|.++|++||.|..+.++     .+..++.++|||||+|.+.++     +|||+.|.|+.|+|..
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            579999999999999999999999988776653     455678999999999999887     8999999999999976


Q ss_pred             cC
Q 022814          106 VA  107 (291)
Q Consensus       106 a~  107 (291)
                      +.
T Consensus        82 ~k   83 (90)
T d1u2fa_          82 PH   83 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>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=99.59  E-value=6.2e-16  Score=117.03  Aligned_cols=73  Identities=19%  Similarity=0.293  Sum_probs=64.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee--CCeEEEEe
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI--LGRTIRVD  104 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i--~gr~i~V~  104 (291)
                      .+..+|||+|||+.+|+++|.++|++||.|..|.|+.++    ++|||||+|.+.++      .|||..|  .+..|.|.
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            466789999999999999999999999999999998764    58999999999887      7999988  47888998


Q ss_pred             ccCCc
Q 022814          105 HVAKY  109 (291)
Q Consensus       105 ~a~~~  109 (291)
                      ++.+.
T Consensus        81 ~s~~~   85 (108)
T d2adba1          81 FSKLT   85 (108)
T ss_dssp             ECSSC
T ss_pred             ecCCc
Confidence            88654

>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=99.58  E-value=1.3e-15  Score=111.23  Aligned_cols=73  Identities=19%  Similarity=0.248  Sum_probs=64.5

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh--------hcCCceeCCeEEE
Q 022814           32 YKDSAYVYVGGIPFD-LTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN--------NLNGAQILGRTIR  102 (291)
Q Consensus        32 ~~~~~~lfVgnL~~~-~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~--------~lng~~i~gr~i~  102 (291)
                      ..++.+|||+|||.. +|+++|.++|++||.|..|.|+.+      ++||||+|++.++        .+++..|.|++|.
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            467899999999986 889999999999999999999876      4699999999887        3578999999999


Q ss_pred             EeccCCcc
Q 022814          103 VDHVAKYK  110 (291)
Q Consensus       103 V~~a~~~~  110 (291)
                      |.+|....
T Consensus        79 V~~s~~~~   86 (89)
T d1x4da1          79 VHLSQKYK   86 (89)
T ss_dssp             EEEECCCT
T ss_pred             EEECCCcc
Confidence            99997543

>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=99.58  E-value=2.8e-15  Score=105.83  Aligned_cols=65  Identities=17%  Similarity=0.313  Sum_probs=57.6

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccCCc
Q 022814           38 VYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVAKY  109 (291)
Q Consensus        38 lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~~~  109 (291)
                      |||+|||+.+++++|+++|++|| |..+.+      +.++|||||+|.+.++      .|||..|.|++|.|.++...
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            89999999999999999999999 555544      4568999999999887      89999999999999998654

>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=6.9e-15  Score=110.41  Aligned_cols=72  Identities=10%  Similarity=0.164  Sum_probs=62.8

Q ss_pred             CCCCEEEEcCCCCCC-CH----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEE
Q 022814           33 KDSAYVYVGGIPFDL-TE----GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTI  101 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~-te----~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i  101 (291)
                      +..++|||+||+..+ ++    ++|+.+|++||.|..|.++.      +++||||+|.+.++      +|||..|+|++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            467899999999975 33    57999999999999999874      47899999999887      899999999999


Q ss_pred             EEeccCCcc
Q 022814          102 RVDHVAKYK  110 (291)
Q Consensus       102 ~V~~a~~~~  110 (291)
                      +|.|+.+..
T Consensus        77 ~v~~a~~~~   85 (104)
T d1weya_          77 KLYFAQTLH   85 (104)
T ss_dssp             EEECCCCSS
T ss_pred             EEeecccCC
Confidence            999997554

>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=99.47  E-value=4e-14  Score=107.74  Aligned_cols=71  Identities=18%  Similarity=0.276  Sum_probs=59.2

Q ss_pred             CCCCC-EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcCh-hh------hcCCceeCCeEEEE
Q 022814           32 YKDSA-YVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQ-RN------NLNGAQILGRTIRV  103 (291)
Q Consensus        32 ~~~~~-~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~-~~------~lng~~i~gr~i~V  103 (291)
                      .+..+ .+||||||+.||+++|+++|++||+|.+|.|+.+      +|||||.|.+. ++      +||+..|.++.+.|
T Consensus         7 ~~~g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v   80 (113)
T d1owxa_           7 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEV   80 (113)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSE
T ss_pred             CCCCCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEE
Confidence            34444 4599999999999999999999999999999864      68999999885 32      88998888877777


Q ss_pred             eccCC
Q 022814          104 DHVAK  108 (291)
Q Consensus       104 ~~a~~  108 (291)
                      .++..
T Consensus        81 ~~~~~   85 (113)
T d1owxa_          81 TWEVL   85 (113)
T ss_dssp             EEEEC
T ss_pred             EEeec
Confidence            76643

>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=99.43  E-value=6.6e-15  Score=110.52  Aligned_cols=70  Identities=16%  Similarity=0.222  Sum_probs=64.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEecc
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHV  106 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a  106 (291)
                      ..|+|.+|+..++|++|.++|++||+|..|.|+.+. +|+++|||||+|.+.++      .|||..|+|++|.|.++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~-~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCC-CCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            358888999999999999999999999999998775 89999999999999887      89999999999999886

>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=99.39  E-value=1.9e-13  Score=101.85  Aligned_cols=67  Identities=16%  Similarity=0.370  Sum_probs=55.9

Q ss_pred             CCCCCEEEEcC--CCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCcee-CCeEEE
Q 022814           32 YKDSAYVYVGG--IPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQI-LGRTIR  102 (291)
Q Consensus        32 ~~~~~~lfVgn--L~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i-~gr~i~  102 (291)
                      ..|..+|||+|  ||+.+|+++|+.+|++||.|..|.++.+      +|||||+|.+.++      +|||..| ++..+.
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~~~~~~~   88 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCCCCCCcE
Confidence            45778999955  9999999999999999999999988765      5799999999887      8999877 344444


Q ss_pred             Ee
Q 022814          103 VD  104 (291)
Q Consensus       103 V~  104 (291)
                      |.
T Consensus        89 i~   90 (101)
T d2cq2a1          89 IT   90 (101)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=99.24  E-value=4.9e-12  Score=90.09  Aligned_cols=67  Identities=22%  Similarity=0.287  Sum_probs=55.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCceeCCeE-EEEeccC
Q 022814           34 DSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQILGRT-IRVDHVA  107 (291)
Q Consensus        34 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i~gr~-i~V~~a~  107 (291)
                      +.+.|||++||+.++++.| .+|++||+|.+|.+..      ++|||||+|.+.++     .|||..|+|+. |-|....
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~------~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEecC------CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            3567999999999986655 5799999999998753      47999999999987     78999999975 5676654

>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=99.22  E-value=1.3e-11  Score=91.27  Aligned_cols=76  Identities=24%  Similarity=0.402  Sum_probs=63.1

Q ss_pred             CCCCCCEEEEcCC--CCCC---------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCC
Q 022814           31 KYKDSAYVYVGGI--PFDL---------TEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNG   93 (291)
Q Consensus        31 ~~~~~~~lfVgnL--~~~~---------te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng   93 (291)
                      ....+.+|+|.||  |..+         .+++|.+.|++||.|..|.++.+    .++|||||+|.+.++      .|||
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            3456889999999  5432         23688999999999999988754    467999999999987      8999


Q ss_pred             ceeCCeEEEEeccCCcc
Q 022814           94 AQILGRTIRVDHVAKYK  110 (291)
Q Consensus        94 ~~i~gr~i~V~~a~~~~  110 (291)
                      ..|+|++|.|.+..+..
T Consensus        80 ~~~~gr~i~v~~~~g~~   96 (99)
T d2dita1          80 RWFGGRQITAQAWDGTT   96 (99)
T ss_dssp             CEETTEECEEEECCSCC
T ss_pred             cEECCEEEEEEEeCCcC
Confidence            99999999999986543

>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=99.13  E-value=1.5e-11  Score=91.72  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=63.3

Q ss_pred             CCCCEEEEcCC--CCCC--------CHHHHHHHHhcCCCeeEEEEeecCCC--CCcceEEEEEEcChhh------hcCCc
Q 022814           33 KDSAYVYVGGI--PFDL--------TEGDLLAVFAQCGEIVDVNLVRDKGT--GKPRGFAFVAYEDQRN------NLNGA   94 (291)
Q Consensus        33 ~~~~~lfVgnL--~~~~--------te~~L~~~F~~~G~I~~i~i~~d~~t--g~s~G~aFV~F~~~~~------~lng~   94 (291)
                      +|+.+|+|.||  |..+        ..++|++.|++||.|..|.|+++..+  ....|++||+|.+.++      .|||.
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            57899999999  4433        23578999999999999999887644  3457999999999887      89999


Q ss_pred             eeCCeEEEEeccC
Q 022814           95 QILGRTIRVDHVA  107 (291)
Q Consensus        95 ~i~gr~i~V~~a~  107 (291)
                      .++|+.|.|.++.
T Consensus        82 ~f~gR~v~v~f~~   94 (104)
T d1o0pa_          82 KFANRVVVTKYCD   94 (104)
T ss_dssp             CSSSSCCEEEEEC
T ss_pred             EECCeEEEEEEcC
Confidence            9999999999975

>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=97.33  E-value=0.00022  Score=49.82  Aligned_cols=69  Identities=22%  Similarity=0.349  Sum_probs=55.4

Q ss_pred             CCCCCCEEEEcCCCCCCCH---------HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh-----hcCCcee
Q 022814           31 KYKDSAYVYVGGIPFDLTE---------GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN-----NLNGAQI   96 (291)
Q Consensus        31 ~~~~~~~lfVgnL~~~~te---------~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~-----~lng~~i   96 (291)
                      +-||.-||.|.=+.+...+         .+|...|..||+|.-|+++.+        -..|+|.+-.+     .|+|.+|
T Consensus        11 qGPpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l~g~~v   82 (95)
T d1ufwa_          11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDVDGMKV   82 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHGGGSEE
T ss_pred             cCCCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhccCCeEE
Confidence            4678888988655544333         367788999999999999977        58999999776     8999999


Q ss_pred             CCeEEEEeccC
Q 022814           97 LGRTIRVDHVA  107 (291)
Q Consensus        97 ~gr~i~V~~a~  107 (291)
                      +|+.|+|....
T Consensus        83 ~G~~l~It~~~   93 (95)
T d1ufwa_          83 KGRAVKISGPS   93 (95)
T ss_dssp             TTEEEEEECCC
T ss_pred             cceEEEEecCC
Confidence            99999997543

>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=96.97  E-value=0.0011  Score=46.60  Aligned_cols=63  Identities=16%  Similarity=0.220  Sum_probs=51.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--cceEEEEEEcChhh------hcCCceeCC
Q 022814           36 AYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGK--PRGFAFVAYEDQRN------NLNGAQILG   98 (291)
Q Consensus        36 ~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~--s~G~aFV~F~~~~~------~lng~~i~g   98 (291)
                      ++|.|..||+.+||+++.+.++..|++.....+..+.+-+  ...-|||.|.+.++      .++|+.+.+
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D   72 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLD   72 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEEC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEc
Confidence            5799999999999999999999999998887766554433  34578999999988      778877643

>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=94.40  E-value=0.054  Score=37.94  Aligned_cols=49  Identities=22%  Similarity=0.364  Sum_probs=38.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh
Q 022814           33 KDSAYVYVGGIPFDLTEGDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN   89 (291)
Q Consensus        33 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~   89 (291)
                      +.-.-||.-.+|..+...+|..+|++||.|. |..|-+.       -|||...+.+.
T Consensus        13 p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-------Sa~V~L~~~e~   61 (100)
T d1whva_          13 PKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-------SAFVSLSQPEQ   61 (100)
T ss_dssp             CCCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-------EEEEECSCHHH
T ss_pred             CCcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-------eEEEEecCHHH
Confidence            4444567779999999999999999999875 4455554       79999887776

>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=93.04  E-value=0.21  Score=32.64  Aligned_cols=55  Identities=24%  Similarity=0.236  Sum_probs=44.0

Q ss_pred             HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEEcChhh------hcCCceeCCeEEEEeccC
Q 022814           50 GDLLAVFAQCGEIVDVNLVRDKGTGKPRGFAFVAYEDQRN------NLNGAQILGRTIRVDHVA  107 (291)
Q Consensus        50 ~~L~~~F~~~G~I~~i~i~~d~~tg~s~G~aFV~F~~~~~------~lng~~i~gr~i~V~~a~  107 (291)
                      +.|..+|.++|.|.++.|.... .|  .-.|-|...+..+      .|+-..|+.+.|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            4566889999999999886543 23  3378898888776      899999999999998875