Citrus Sinensis ID: 030822

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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-
Protein Sequence
MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFSHTT
Secondary Structure (PSIPRED)
ccccccccccccEEEEEEccHHHHHHHHHcccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHHccccEEEEEccccEEEEEEccHHHHHHHHHHcccccccccEEEEEccc
Secondary Structure Prediction (SSPRO)
ccccccccccccEEEEEEccHHHHHHHHHcccEEccEEEEEEEEccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccEEEEccccccccHHHHHHHHHHcccEEEEEEcccccEEEccHHHHHHHHHcHcHcHHEccccccccccc
Coil and Loop (DISEMBL)
mpkdqgskahrgigfitfasadsVENLMVDThelggstvvvdratpkeddfrpvgrmshggygaYNAYISAATRYAalgaptlydhpgsfygrgessqrigkkifvgrlpqeatAEDLRRYFSRFGrildvyvpkrfwfchlcgrscsrscfskVSRNLwtagcnrfshtt
Flexible Loop (DISEMBL)
mpkdqgskahrgiGFITFASADSVENLMVDTHELGgstvvvdratpkeddfrpvgrmshGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIfvgrlpqeataeDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRscfskvsrnlwtagcnrfshtt
Low Complexity Region (SEG)
MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFSHTT
Disordered region (IsUnstruct)
***********GIGFITFASADSVENLMVDTHELGGSTVVVDRA******FRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNR*****
Disordered Region (DISOPRED)
******SKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDR**********************************************************KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRF**T*
Disordered Region (DISEMBL)
*********HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFSHTT
Disordered Region (DISPRO)
********AHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED*********HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNR*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFSHTT
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	171	2.2.26 [Sep-21-2011]
Q28F51	409	TAR DNA-binding protein 4	yes	no	0.210	0.088	0.472	1e-05
O94432	474	Uncharacterized RNA-bindi	yes	no	0.561	0.202	0.230	4e-05
Q921F2	414	TAR DNA-binding protein 4	yes	no	0.204	0.084	0.444	5e-05
Q13148	414	TAR DNA-binding protein 4	yes	no	0.204	0.084	0.444	5e-05
Q5R5W2	414	TAR DNA-binding protein 4	yes	no	0.204	0.084	0.444	5e-05
Q5ZLN5	414	TAR DNA-binding protein 4	yes	no	0.204	0.084	0.416	7e-05
Q4R979	364	RNA-binding protein 4 OS=	N/A	no	0.309	0.145	0.315	0.0001
Q9BWF3	364	RNA-binding protein 4 OS=	no	no	0.309	0.145	0.315	0.0001
Q9BQ04	359	RNA-binding protein 4B OS	no	no	0.309	0.147	0.315	0.0001
Q9BDY9	359	RNA-binding protein 4 OS=	no	no	0.309	0.147	0.315	0.0001

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

 Score = 48.9 bits (115), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 31/36 (86%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +K+FVGR  ++ +AE+LR++FS++G ++DV++PK F
Sbjct: 191 RKVFVGRCTEDMSAEELRQFFSQYGEVVDVFIPKPF 226

Probably involved in transcriptional repression.
Xenopus tropicalis (taxid: 8364)

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

 Score = 47.8 bits (112), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 35/152 (23%), Positives = 53/152 (34%), Gaps = 56/152 (36%)

Query: 11  RGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYIS 70
           RG GF+TF +   V  +M   H L G  +   RA P+E+                     
Sbjct: 204 RGFGFLTFKNPKCVNEVMSKEHHLDGKIIDPKRAIPREE--------------------- 242

Query: 71  AATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD 130
                                      Q    K+FVG +P + T E+ R +F++FGR+LD
Sbjct: 243 ---------------------------QEKTAKMFVGGVPGDCTEEEFRNFFNQFGRVLD 275

Query: 131 VYV--------PKRFWFCHLCGRSCSRSCFSK 154
             +        P+ F F      S   +  S+
Sbjct: 276 ATLMMDKDTGRPRGFGFVTYENESAVEATMSQ 307

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

>sp|Q921F2|TADBP_MOUSE TAR DNA-binding protein 43 OS=Mus musculus GN=Tardbp PE=1 SV=1

 Score = 47.4 bits (111), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 30/36 (83%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +K+FVGR  ++ TAE+L+++F ++G ++DV++PK F
Sbjct: 191 RKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 226

DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division.

Mus musculus (taxid: 10090)

>sp|Q13148|TADBP_HUMAN TAR DNA-binding protein 43 OS=Homo sapiens GN=TARDBP PE=1 SV=1

 Score = 47.4 bits (111), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 29/36 (80%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +K+FVGR  ++ T ++LR +FS++G ++DV++PK F
Sbjct: 191 RKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPF 226

DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat. Stabilizes the low molecular weight neurofilament (NFL) mRNA through a direct interaction with the 3' UTR.

Homo sapiens (taxid: 9606)

>sp|Q5R5W2|TADBP_PONAB TAR DNA-binding protein 43 OS=Pongo abelii GN=TARDBP PE=2 SV=1

 Score = 47.4 bits (111), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 29/36 (80%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +K+FVGR  ++ T ++LR +FS++G ++DV++PK F
Sbjct: 191 RKVFVGRCTEDMTEDELREFFSQYGDVMDVFIPKPF 226

DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division.

Pongo abelii (taxid: 9601)

>sp|Q5ZLN5|TADBP_CHICK TAR DNA-binding protein 43 OS=Gallus gallus GN=TARDBP PE=2 SV=1

 Score = 47.0 bits (110), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 15/36 (41%), Positives = 31/36 (86%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +K+FVGR  ++ TA++L+++F+++G ++DV++PK F
Sbjct: 191 RKVFVGRCTEDMTADELQQFFAQYGEVVDVFIPKPF 226

Probably involved in transcriptional repression.

Gallus gallus (taxid: 9031)

>sp|Q4R979|RBM4_MACFA RNA-binding protein 4 OS=Macaca fascicularis GN=RBM4 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 4/57 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNL 159
           K+F+G LP+EAT +++R  F ++G++L+  + K + F H+  ++ +        RNL
Sbjct: 3   KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAI----RNL 55

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Macaca fascicularis (taxid: 9541)

>sp|Q9BWF3|RBM4_HUMAN RNA-binding protein 4 OS=Homo sapiens GN=RBM4 PE=1 SV=1

 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 4/57 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNL 159
           K+F+G LP+EAT +++R  F ++G++L+  + K + F H+  ++ +        RNL
Sbjct: 3   KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAI----RNL 55

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Homo sapiens (taxid: 9606)

>sp|Q9BQ04|RBM4B_HUMAN RNA-binding protein 4B OS=Homo sapiens GN=RBM4B PE=1 SV=1

 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 4/57 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNL 159
           K+F+G LP+EAT +++R  F ++G++L+  + K + F H+  ++ +        RNL
Sbjct: 3   KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAI----RNL 55

Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA.

Homo sapiens (taxid: 9606)

>sp|Q9BDY9|RBM4_RABIT RNA-binding protein 4 OS=Oryctolagus cuniculus GN=RBM4 PE=2 SV=1

 Score = 45.8 bits (107), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 4/57 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNL 159
           K+F+G LP+EAT +++R  F ++G++L+  + K + F H+  ++ +        RNL
Sbjct: 3   KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAI----RNL 55

RNA-binding factor involved in multiple aspects of cellular processes like alternative splicing of pre-mRNA and translation regulation. Modulates alternative 5'-splice site and exon selection. Acts as a muscle cell differentiation-promoting factor. Activates exon skipping of the PTB pre-mRNA during muscle cell differentiation. Antagonizes the activity of the splicing factor PTBP1 to modulate muscle cell-specific exon selection of alpha tropomyosin. Binds to intronic pyrimidine-rich sequence of the TPM1 and MAPT pre-mRNAs. Required for the translational activation of PER1 mRNA in response to circadian clock. Binds directly to the 3'-UTR of the PER1 mRNA. Exerts a suppressive activity on Cap-dependent translation via binding to CU-rich responsive elements within the 3'UTR of mRNAs, a process increased under stress conditions or during myocytes differentiation. Recruits EIF4A1 to stimulate IRES-dependent translation initiation in respons to cellular stress. Associates to internal ribosome entry segment (IRES) in target mRNA species under stress conditions. Plays a role for miRNA-guided RNA cleavage and translation suppression by promoting association of EIF2C2-containing miRNPs with their cognate target mRNAs. Associates with miRNAs during muscle cell differentiation. Binds preferentially to 5'-CGCGCG[GCA]-3' motif in vitro.

Oryctolagus cuniculus (taxid: 9986)

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	171
224094314	367	predicted protein [Populus trichocarpa]	0.532	0.247	0.874	9e-63
255565200	359	RNA-binding protein, putative [Ricinus c	0.526	0.250	0.866	1e-62
359480888	359	PREDICTED: uncharacterized RNA-binding p	0.538	0.256	0.844	1e-61
224084344	367	predicted protein [Populus trichocarpa]	0.532	0.247	0.837	1e-60
356496896	362	PREDICTED: DAZ-associated protein 1-like	0.789	0.372	0.8	1e-58
356541820	365	PREDICTED: DAZ-associated protein 1-like	0.783	0.367	0.783	9e-57
217074298	397	unknown [Medicago truncatula] gi|3885030	0.789	0.340	0.794	6e-56
357482897	403	RNA-binding protein [Medicago truncatula	0.789	0.334	0.767	5e-54
449460598	377	PREDICTED: RNA-binding protein Musashi h	0.789	0.358	0.773	5e-54
358349448	371	RNA-binding protein [Medicago truncatula	0.789	0.363	0.744	2e-52

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

 Score =  244 bits (623), Expect = 9e-63,   Method: Compositional matrix adjust.
 Identities = 118/135 (87%), Positives = 126/135 (93%)

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

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

Query: 121 YFSRFGRILDVYVPK 135
           YF RFG ILDVYVPK
Sbjct: 242 YFGRFGHILDVYVPK 256

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  244 bits (622), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 117/135 (86%), Positives = 124/135 (91%)

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

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

Query: 121 YFSRFGRILDVYVPK 135
           YF RFG ILDVYVPK
Sbjct: 243 YFGRFGHILDVYVPK 257

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  240 bits (612), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 114/135 (84%), Positives = 126/135 (93%)

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

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

Query: 121 YFSRFGRILDVYVPK 135
           YF RFGRILDVYVPK
Sbjct: 243 YFGRFGRILDVYVPK 257

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  237 bits (604), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 113/135 (83%), Positives = 124/135 (91%)

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

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

Query: 121 YFSRFGRILDVYVPK 135
           YF RFG I+DVYVPK
Sbjct: 242 YFGRFGHIIDVYVPK 256

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  230 bits (587), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 112/140 (80%), Positives = 123/140 (87%), Gaps = 5/140 (3%)

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

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

Query: 116 EDLRRYFSRFGRILDVYVPK 135
           +DLR+YF RFGRILDVYVP+
Sbjct: 243 DDLRQYFGRFGRILDVYVPR 262

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  224 bits (571), Expect = 9e-57,   Method: Compositional matrix adjust.
 Identities = 112/143 (78%), Positives = 123/143 (86%), Gaps = 9/143 (6%)

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

Query: 60  -------GGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQE 112
                  GGYGAYNAYISAATRYAALGAPTLYDHPG  YGRG+ ++R  KKIFVGRLP E
Sbjct: 183 PPPPPQGGGYGAYNAYISAATRYAALGAPTLYDHPGPIYGRGD-ARRTSKKIFVGRLPPE 241

Query: 113 ATAEDLRRYFSRFGRILDVYVPK 135
           AT++DLR+YF RFGRILDVYVP+
Sbjct: 242 ATSDDLRQYFGRFGRILDVYVPR 264

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  221 bits (564), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 108/136 (79%), Positives = 117/136 (86%), Gaps = 1/136 (0%)

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

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

Query: 120 RYFSRFGRILDVYVPK 135
           +YF RFGRI DV +P+
Sbjct: 243 QYFGRFGRIEDVCIPR 258

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  215 bits (548), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 109/142 (76%), Positives = 118/142 (83%), Gaps = 7/142 (4%)

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

Query: 59  H-GGYGAYNAYISAATRYAALGAPTLYDHPGSFY----GRGESSQRIGKKIFVGRLPQEA 113
             GGYGAYNAYIS ATRYAALGAPTLYDHPG  Y    GRGE  +RI KKIFVGRLP EA
Sbjct: 183 QGGGYGAYNAYISTATRYAALGAPTLYDHPGPIYGSKHGRGEPRRRISKKIFVGRLPPEA 242

Query: 114 TAEDLRRYFSRFGRILDVYVPK 135
            +EDLR+YF RFGRI DVY+P+
Sbjct: 243 NSEDLRQYFGRFGRIEDVYIPR 264

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  215 bits (547), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 113/146 (77%), Positives = 123/146 (84%), Gaps = 11/146 (7%)

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

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

Query: 110 PQEATAEDLRRYFSRFGRILDVYVPK 135
           PQEA+A+DLR+YF RFGRILDVYVPK
Sbjct: 242 PQEASADDLRQYFGRFGRILDVYVPK 267

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 102/137 (74%), Positives = 114/137 (83%), Gaps = 2/137 (1%)

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

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

Query: 119 RRYFSRFGRILDVYVPK 135
           R YF RFG ILDVY+P+
Sbjct: 243 RLYFGRFGHILDVYIPR 259

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	171
TAIR|locus:2115169	379	AT4G36960 [Arabidopsis thalian	0.578	0.261	0.686	2.8e-34
UNIPROTKB|F8VYN5	113	HNRNPA1 "Heterogeneous nuclear	0.298	0.451	0.365	2e-10
TAIR|locus:2173967	460	AT5G55550 [Arabidopsis thalian	0.187	0.069	0.562	8.3e-08
FB|FBgn0036496	318	CG7804 [Drosophila melanogaste	0.421	0.226	0.376	8.7e-08
TAIR|locus:2133862	455	AT4G26650 [Arabidopsis thalian	0.421	0.158	0.413	0.00059
GENEDB_PFALCIPARUM|PF11_0083	588	PF11_0083 "nucleic acid bindin	0.239	0.069	0.439	1.2e-06
UNIPROTKB|Q8IIT2	588	PF11_0083 "Nucleic acid bindin	0.239	0.069	0.439	1.2e-06
TAIR|locus:504955752	358	AT3G13224 [Arabidopsis thalian	0.263	0.125	0.4	1.4e-06
TAIR|locus:2077392	495	AT3G07810 [Arabidopsis thalian	0.263	0.090	0.478	0.00011
ASPGD|ASPL0000063757	559	AN10941 [Emericella nidulans (	0.163	0.050	0.535	2.2e-06

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

 Score = 372 (136.0 bits), Expect = 2.8e-34, P = 2.8e-34
 Identities = 79/115 (68%), Positives = 87/115 (75%)

Query:     1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRP----VGR 56
             MPKD  SK HRGIGFITF+SADSVE+LM DTH+LGG+TV VDRATPKEDD  P    V R
Sbjct:   122 MPKDYNSKQHRGIGFITFSSADSVEDLMEDTHDLGGTTVAVDRATPKEDDHPPRPPPVAR 181

Query:    57 MSH------------GGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQR 99
             MS             GGYGAY+AYISAATRYAALGAPTLYD+P +FYGRGE + R
Sbjct:   182 MSRPPVAIAGGFGAPGGYGAYDAYISAATRYAALGAPTLYDNPATFYGRGEPTTR 236

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|F8VYN5 HNRNPA1 "Heterogeneous nuclear ribonucleoprotein A1" [Homo sapiens (taxid:9606)]

 Score = 91 (37.1 bits), Expect = 2.0e-10, Sum P(2) = 2.0e-10
 Identities = 19/52 (36%), Positives = 29/52 (55%)

Query:     3 KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRP 53
             +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP
Sbjct:     2 RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP 53

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 92 (37.4 bits), Expect = 8.3e-08, Sum P(2) = 8.3e-08
 Identities = 18/32 (56%), Positives = 21/32 (65%)

Query:   102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
             KKIFVG LP   T E+ + YF +FG I DV V
Sbjct:   110 KKIFVGGLPSSITEEEFKNYFDQFGTIADVVV 141

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

FB|FBgn0036496 CG7804 [Drosophila melanogaster (taxid:7227)]

 Score = 128 (50.1 bits), Expect = 8.7e-08, P = 8.7e-08
 Identities = 29/77 (37%), Positives = 46/77 (59%)

Query:    62 YGAYNAYISAAT-RYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
             +G+Y+  +   + R++  G       P S   RG  +Q  GK +FVGR  ++  A+DLR 
Sbjct:   155 FGSYDVQMHVLSKRHSIDGRWCEVKVPAS---RGMGNQEPGK-VFVGRCTEDIEADDLRE 210

Query:   121 YFSRFGRILDVYVPKRF 137
             YFS+FG ++DV++PK F
Sbjct:   211 YFSKFGEVIDVFIPKPF 227

GO:0003729 "mRNA binding" evidence=ISS

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 108 (43.1 bits), Expect = 0.00059, P = 0.00059
 Identities = 31/75 (41%), Positives = 38/75 (50%)

Query:     4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKEDDFRPVGRMSHGGY 62
             D  ++  RG GFITF S +SV+ ++  T HEL G  V V RA PKE       R    GY
Sbjct:   156 DHNTQRPRGFGFITFDSEESVDMVLHKTFHELNGKMVEVKRAVPKELSSTTPNRSPLIGY 215

Query:    63 GAYNAYISAATRYAA 77
             G  N Y     R +A
Sbjct:   216 G--NNYGVVPNRSSA 228

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

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

GENEDB_PFALCIPARUM|PF11_0083 PF11_0083 "nucleic acid binding factor, putative" [Plasmodium falciparum (taxid:5833)]

 Score = 100 (40.3 bits), Expect = 1.2e-06, Sum P(2) = 1.2e-06
 Identities = 18/41 (43%), Positives = 26/41 (63%)

Query:    94 GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
             G+   + G K+FV +L    T E LR YF +FG I+D+Y+P
Sbjct:   494 GDEWNKRGYKLFVTKLNSATTIEKLRNYFEKFGEIIDIYMP 534

GO:0006139 "nucleobase-containing compound metabolic process" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q8IIT2 PF11_0083 "Nucleic acid binding protein, putative" [Plasmodium falciparum 3D7 (taxid:36329)]

 Score = 100 (40.3 bits), Expect = 1.2e-06, Sum P(2) = 1.2e-06
 Identities = 18/41 (43%), Positives = 26/41 (63%)

Query:    94 GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
             G+   + G K+FV +L    T E LR YF +FG I+D+Y+P
Sbjct:   494 GDEWNKRGYKLFVTKLNSATTIEKLRNYFEKFGEIIDIYMP 534

GO:0005575 "cellular_component" evidence=ND

GO:0006139 "nucleobase-containing compound metabolic process" evidence=ISS

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

 Score = 92 (37.4 bits), Expect = 1.4e-06, Sum P(2) = 1.4e-06
 Identities = 18/45 (40%), Positives = 26/45 (57%)

Query:     3 KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPK 47
             +D+ +   RG GFITFA    V+ ++ DTH + G  V + R  PK
Sbjct:    52 RDRHTGQPRGFGFITFADPSVVDKVIEDTHVINGKQVEIKRTIPK 96

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 105 (42.0 bits), Expect = 0.00011, Sum P(2) = 0.00011
 Identities = 22/46 (47%), Positives = 30/46 (65%)

Query:     4 DQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKE 48
             D  ++  RG GFIT+ S ++VE +++ T HEL G  V V RA PKE
Sbjct:   142 DHNTQRPRGFGFITYDSEEAVEKVLLKTFHELNGKMVEVKRAVPKE 187

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005576 "extracellular region" evidence=ISM

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

 Score = 89 (36.4 bits), Expect = 2.2e-06, Sum P(2) = 2.2e-06
 Identities = 15/28 (53%), Positives = 23/28 (82%)

Query:   103 KIFVGRLPQEATAEDLRRYFSRFGRILD 130
             KIFVG + QEAT +D +++F +FGR++D
Sbjct:   195 KIFVGGVSQEATEQDFKQFFMQFGRVID 222

GO:0008150 "biological_process" evidence=ND

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	171
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	4e-14
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	6e-10
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	4e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	7e-09
smart00360	73	smart00360, RRM, RNA recognition motif	3e-08
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	7e-08
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-07
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-07
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	5e-07
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	5e-07
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	5e-07
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	6e-07
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	2e-06
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	4e-06
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	6e-06
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	6e-06
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	8e-06
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	8e-06
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	1e-05
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	1e-05
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	2e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	2e-05
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-05
cd12226	78	cd12226, RRM_NOL8, RNA recognition motif in nucleo	4e-05
cd12559	84	cd12559, RRM_SRSF10, RNA recognition motif in seri	5e-05
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	5e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	6e-05
cd12570	76	cd12570, RRM5_MRD1, RNA recognition motif 5 in yea	6e-05
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	6e-05
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	7e-05
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	9e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	9e-05
smart00360	73	smart00360, RRM, RNA recognition motif	1e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-04
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-04
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-04
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-04
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	2e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	2e-04
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	2e-04
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	2e-04
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	2e-04
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	2e-04
cd12337	70	cd12337, RRM1_SRSF4_like, RNA recognition motif 1	3e-04
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-04
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	5e-04
cd12588	71	cd12588, RRM1_p54nrb, RNA recognition motif 1 in v	5e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	6e-04
cd12632	87	cd12632, RRM1_CELF3_4_5_6, RNA recognition motif 1	6e-04
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	8e-04
cd12350	74	cd12350, RRM3_SHARP, RNA recognition motif 3 in SM	9e-04
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	0.001
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	0.001
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	0.001
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.001
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	0.001
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	0.001
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	0.001
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	0.001
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.001
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.002
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	0.002
cd12555	87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	0.002
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	0.003
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.003
cd12633	80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	0.003
cd12595	70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	0.003
cd12246	78	cd12246, RRM1_U1A_like, RNA recognition motif 1 in	0.003
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.003
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	0.003
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.003
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	0.003
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.003
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	0.003
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	0.004
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	0.004

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

 Score = 63.4 bits (155), Expect = 4e-14
 Identities = 22/36 (61%), Positives = 30/36 (83%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +K+FVGRL ++ T EDLR+YFS+FG + DVY+PK F
Sbjct: 1   RKVFVGRLTEDMTEEDLRQYFSQFGEVTDVYIPKPF 36

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

 Score = 52.7 bits (127), Expect = 6e-10
 Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

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

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

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

 Score = 50.3 bits (120), Expect = 4e-09
 Identities = 16/40 (40%), Positives = 28/40 (70%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHL 142
           K+FVG LP EAT +++R  F ++G++L+  + K + F H+
Sbjct: 2   KLFVGNLPPEATEQEIRSLFEQYGKVLECDIIKNYGFVHM 41

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

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

 Score = 49.5 bits (119), Expect = 7e-09
 Identities = 16/40 (40%), Positives = 25/40 (62%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHL 142
           K+FVG LP   T+E+LR  F ++G + +  V K + F H+
Sbjct: 1   KLFVGNLPDATTSEELRALFEKYGTVTECDVVKNYGFVHM 40

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

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

 Score = 48.0 bits (115), Expect = 3e-08
 Identities = 14/33 (42%), Positives = 22/33 (66%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            +FVG LP + T E+LR  FS+FG++  V + +
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVR 33

Length = 73

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

 Score = 47.0 bits (112), Expect = 7e-08
 Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 6/44 (13%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP------KRFWFC 140
           KIFVG L  E T E +R YF +FG I+++ +P      KR  FC
Sbjct: 1   KIFVGGLSPETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFC 44

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|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 = 46.4 bits (111), Expect = 1e-07
 Identities = 15/31 (48%), Positives = 22/31 (70%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           K+FVG+LP+ AT ED+R  F  +G I +V +
Sbjct: 1   KLFVGQLPKTATEEDVRALFEEYGNIEEVTI 31

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 16/32 (50%), Positives = 21/32 (65%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +FVG LP + T EDLR  FS+FG I  V + +
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVR 32

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

 Score = 44.9 bits (107), Expect = 5e-07
 Identities = 17/34 (50%), Positives = 21/34 (61%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            KIFVG LP   T + LR+YFS+FG I +  V  
Sbjct: 1   TKIFVGGLPYHTTDDSLRKYFSQFGEIEEAVVIT 34

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

 Score = 45.0 bits (107), Expect = 5e-07
 Identities = 19/33 (57%), Positives = 23/33 (69%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
            KKIFVG LP   T  DLR+YFS+FG + +V V
Sbjct: 2   TKKIFVGGLPPNVTETDLRKYFSQFGTVTEVVV 34

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|215696 pfam00076, RRM_1, RNA recognition motif

 Score = 44.5 bits (106), Expect = 5e-07
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +FVG LP + T EDL+  FS+FG I  + + +
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVR 32

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

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

 Score = 44.6 bits (106), Expect = 6e-07
 Identities = 16/29 (55%), Positives = 22/29 (75%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           +IFVG +P + T E+LR +FSRFG + DV
Sbjct: 4   RIFVGGIPPDTTEEELRDFFSRFGSVKDV 32

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

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 17/42 (40%), Positives = 26/42 (61%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCG 144
           KIFVG + ++ + E+LR  F  +G +L   V ++F F HL G
Sbjct: 2   KIFVGNVDEDTSQEELRALFEAYGAVLSCAVMRQFAFVHLRG 43

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

 Score = 42.7 bits (101), Expect = 4e-06
 Identities = 20/46 (43%), Positives = 26/46 (56%), Gaps = 1/46 (2%)

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

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

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

 Score = 42.0 bits (99), Expect = 6e-06
 Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

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

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

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

 Score = 41.8 bits (98), Expect = 6e-06
 Identities = 15/40 (37%), Positives = 24/40 (60%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHL 142
           KIFVG +    T+++LR  F  FGR+++    K + F H+
Sbjct: 2   KIFVGNVSATCTSDELRGLFEEFGRVVECDKVKDYAFVHM 41

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

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

 Score = 42.0 bits (99), Expect = 8e-06
 Identities = 12/29 (41%), Positives = 21/29 (72%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           ++FVG LP + T ++L+ +F  FG +L+V
Sbjct: 5   QLFVGNLPHDITEDELKEFFKEFGNVLEV 33

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

 Score = 41.7 bits (98), Expect = 8e-06
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+FVG L  E T E LRRYFS++G ++D  + K
Sbjct: 1   KLFVGGLSWETTQETLRRYFSQYGEVVDCVIMK 33

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

 Score = 41.6 bits (98), Expect = 1e-05
 Identities = 13/37 (35%), Positives = 22/37 (59%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW 138
             ++V  +      +DLRR F ++G I+DVY+P  F+
Sbjct: 1   TSLYVRNVADATRPDDLRRLFGKYGPIVDVYIPLDFY 37

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

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 15/28 (53%), Positives = 22/28 (78%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILD 130
           KIFVG LP + T E+ + YFS+FG+++D
Sbjct: 1   KIFVGGLPPDVTEEEFKEYFSQFGKVVD 28

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 40.6 bits (96), Expect = 2e-05
 Identities = 12/32 (37%), Positives = 20/32 (62%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           ++V  LP   T EDLR +FS +G++  V + +
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVR 32

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

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

 Score = 40.7 bits (96), Expect = 2e-05
 Identities = 12/33 (36%), Positives = 23/33 (69%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           ++FVG LP + T E+ +  FS++G + +V++ K
Sbjct: 3   RLFVGNLPNDITEEEFKELFSKYGEVSEVFLNK 35

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 17/33 (51%), Positives = 23/33 (69%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
           IFVG+L  + T E+L   FSR G+IL+V + KR
Sbjct: 6   IFVGQLSPDVTKEELNERFSRHGKILEVNLIKR 38

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

 Score = 39.8 bits (94), Expect = 4e-05
 Identities = 15/33 (45%), Positives = 19/33 (57%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
           +FVG L    T  DL   FSRFG + DV + K+
Sbjct: 2   LFVGGLSPSVTESDLEERFSRFGTVSDVEIIKK 34

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

 Score = 39.6 bits (92), Expect = 5e-05
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW 138
           +FV  +  +  +EDLRR F R+G I+DVYVP  F+
Sbjct: 3   LFVRNIADDTRSEDLRREFGRYGPIVDVYVPLDFY 37

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

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 14/29 (48%), Positives = 21/29 (72%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           KIFVG L    T +D+++YFS+FG++ D 
Sbjct: 1   KIFVGGLSANTTEDDVKKYFSQFGKVEDA 29

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

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 13/30 (43%), Positives = 19/30 (63%)

Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           V  L    T +DLRR F ++G + DVY+P+
Sbjct: 3   VDNLTYRTTPDDLRRVFEKYGEVGDVYIPR 32

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

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 18/35 (51%), Positives = 24/35 (68%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           KI V  LP EAT +D+R  FS +G++  V VPK+F
Sbjct: 2   KILVKNLPFEATKKDVRTLFSSYGQLKSVRVPKKF 36

This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRFWFC 140
           K++VG L   AT  +L   F ++G +  V+V   P  F F 
Sbjct: 1   KVYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPGFAFV 41

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

 Score = 41.5 bits (96), Expect = 7e-05
 Identities = 27/136 (19%), Positives = 44/136 (32%), Gaps = 26/136 (19%)

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

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

Query: 119 RRYFSRFGRILDVYVP 134
              F   G I+   +P
Sbjct: 243 ADLFKSRGDIVRASLP 258

Length = 306

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

 Score = 38.8 bits (90), Expect = 9e-05
 Identities = 18/33 (54%), Positives = 21/33 (63%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
           KKIFVG L  EAT E +R YF  FG I  + +P
Sbjct: 5   KKIFVGGLNPEATEEKIREYFGEFGEIEAIELP 37

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

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

 Score = 38.7 bits (91), Expect = 9e-05
 Identities = 10/32 (31%), Positives = 20/32 (62%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +++G LP      +LR+YFS+FG +  + + +
Sbjct: 2   VYIGHLPHGFYEPELRKYFSQFGTVTRLRLSR 33

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|214636 smart00360, RRM, RNA recognition motif

 Score = 38.3 bits (90), Expect = 1e-04
 Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 2/43 (4%)

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

Length = 73

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

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 13/32 (40%), Positives = 21/32 (65%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +F+G L  + T E LR YFS++G ++D  + K
Sbjct: 1   LFIGGLSWDTTEESLREYFSKYGEVVDCVIMK 32

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|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 = 38.7 bits (91), Expect = 1e-04
 Identities = 14/35 (40%), Positives = 21/35 (60%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G K+FV  L    T ++L   FS+FGR+ +V + K
Sbjct: 1   GNKLFVSGLSTRTTEKELEALFSKFGRVEEVLLMK 35

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

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

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

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           ++VG LP   T E+L+R FS FG I +V V
Sbjct: 3   VYVGNLPHGLTEEELQRTFSPFGAIEEVRV 32

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 15/29 (51%), Positives = 21/29 (72%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           K+FVG L ++ T EDLR YFS++G +  V
Sbjct: 1   KLFVGGLKEDVTEEDLREYFSQYGNVESV 29

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)

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

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

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 14/32 (43%), Positives = 22/32 (68%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
           K+FVG LP    +++L+ YFS+FG++    VP
Sbjct: 1   KLFVGNLPWTVGSKELKEYFSQFGKVKSCNVP 32

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|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 = 37.6 bits (88), Expect = 2e-04
 Identities = 16/36 (44%), Positives = 24/36 (66%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
            K+ V  +P EAT ++LR  FS FG++  V +PK+F
Sbjct: 1   TKLIVRNVPFEATKKELRELFSPFGQVKSVRLPKKF 36

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

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 12/32 (37%), Positives = 17/32 (53%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           K +FV RL  + T   LRR F  +G I  + +
Sbjct: 2   KTLFVARLNYDTTESKLRREFEEYGPIKRIRL 33

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

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
           I+VG++P + T  +LR+ F  FG I ++ +  R
Sbjct: 5   IYVGKIPIDTTRSELRQRFQPFGEIEEITLHFR 37

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

>gnl|CDD|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 = 37.7 bits (88), Expect = 2e-04
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKV 155
           +FVG L    T ++LR  F  FG I+ V +P  K   F     R+ + +   ++
Sbjct: 4   VFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCGFVQFVHRAAAEAAIQQL 57

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

 Score = 37.3 bits (87), Expect = 3e-04
 Identities = 13/37 (35%), Positives = 23/37 (62%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWF 139
           ++++GRLP  A   D+ R+F  +GRI ++ +   F F
Sbjct: 1   RVYIGRLPYRARERDVERFFKGYGRIREINLKNGFGF 37

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

 Score = 39.2 bits (90), Expect = 4e-04
 Identities = 14/34 (41%), Positives = 20/34 (58%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
             +FVG LP + T EDLR  F +FG +  V + +
Sbjct: 116 NTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVR 149

Length = 306

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

 Score = 37.4 bits (87), Expect = 4e-04
 Identities = 16/32 (50%), Positives = 17/32 (53%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           IFVG L  E   E LR  F+ FG I D  V K
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVK 33

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

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

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

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

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

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 11/33 (33%), Positives = 24/33 (72%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           ++FVG LP + T E++R+ F ++G+  ++++ K
Sbjct: 3   RLFVGNLPPDITEEEMRKLFEKYGKAGEIFIHK 35

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

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

 Score = 36.6 bits (85), Expect = 6e-04
 Identities = 17/41 (41%), Positives = 26/41 (63%), Gaps = 1/41 (2%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHL 142
           K +FVG LP+ AT E +R  F + G I+ + + K+  FCH+
Sbjct: 7   KTVFVGGLPENATEEIIREVFEQCGEIIAIRMSKKN-FCHI 46

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

>gnl|CDD|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 = 36.6 bits (85), Expect = 6e-04
 Identities = 14/33 (42%), Positives = 23/33 (69%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+FVG++P+    +DLR  F +FG+I ++ V K
Sbjct: 7   KLFVGQIPRNLEEKDLRPLFEQFGKIYELTVLK 39

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

 Score = 36.0 bits (84), Expect = 8e-04
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           ++VG L +E   + L   F  FG I D+ +P 
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPL 32

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

 Score = 36.2 bits (84), Expect = 9e-04
 Identities = 14/34 (41%), Positives = 21/34 (61%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + +F+G L +  T  DLR  F RFG I+D+ + K
Sbjct: 3   RTLFIGNLEKTTTYSDLREAFERFGEIIDIDIKK 36

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

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 15/33 (45%), Positives = 21/33 (63%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+F+G L  E T + L+ YFS++G I D  V K
Sbjct: 1   KLFIGGLSYETTDDSLKNYFSQWGEITDCVVMK 33

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

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

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

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 6/45 (13%)

Query: 1  MPKDQGSKAHRGIGFITFA----SADSVENLMVDTHELGGSTVVV 41
          +P D  ++ HRG  F+ F     +A +++N+  +  EL G T+ V
Sbjct: 30 IPLDYETQKHRGFAFVEFEEPEDAAAAIDNM--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|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 = 36.1 bits (84), Expect = 0.001
 Identities = 14/32 (43%), Positives = 20/32 (62%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
           ++FV  LP   T E+LR  F  FG I +V++P
Sbjct: 1   RLFVRNLPFTTTEEELRELFEAFGEISEVHLP 32

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

 Score = 36.1 bits (83), Expect = 0.001
 Identities = 17/35 (48%), Positives = 22/35 (62%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW 138
           +FV  +      EDLRR F R+G I+DVYVP  F+
Sbjct: 3   LFVRNVADATRPEDLRREFGRYGPIVDVYVPLDFY 37

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

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 3  KDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKED 49
          K  G K  RG GF+ F + DS +   +V  H + G  V V +A PKE+
Sbjct: 35 KQTGKK--RGFGFVYFQNHDSADKAAVVKFHPINGHRVEVKKAVPKEE 80

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

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

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 106 VGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           V  L ++A  +DLR  F  FG I  VY+ K
Sbjct: 4   VTNLSEDADEDDLRELFRPFGPISRVYLAK 33

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

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
             K+FVG L  + +   LRR+F+R+G++ +  V
Sbjct: 2   LCKLFVGGLNLKTSDSGLRRHFTRYGKLTECVV 34

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

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

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 13/31 (41%), Positives = 23/31 (74%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           K+FVG L ++AT +++   FS +GR+ D+Y+
Sbjct: 1   KLFVGCLNKQATEKEVEEVFSPYGRVEDIYM 31

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

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

 Score = 34.9 bits (81), Expect = 0.002
 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 103 KIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRS 150
           ++FVG L   + + EDL   FS++G+IL + + K + F        +R+
Sbjct: 2   RVFVGNLNTDKVSKEDLEEIFSKYGKILGISLHKGYGFVQFDNEEDARA 50

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

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

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 16/45 (35%), Positives = 22/45 (48%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPK 47
          +D  +   RG GF+TF    SV  +M   H L G  +   RA P+
Sbjct: 32 RDSATGRSRGFGFLTFKKPKSVNEVMKKEHILDGKIIDPKRAIPR 76

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

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

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 17/37 (45%), Positives = 21/37 (56%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           E  QR  + +F+G L    T  DLRR F RFG I +V
Sbjct: 1   EDDQRANRTLFLGNLDITVTETDLRRAFDRFGVITEV 37

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

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

 Score = 35.0 bits (81), Expect = 0.003
 Identities = 11/30 (36%), Positives = 17/30 (56%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           +FVG L   A  +DL  +F   G ++DV +
Sbjct: 2   LFVGNLSWSAEQDDLEEFFKECGEVVDVRI 31

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

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 11/27 (40%), Positives = 19/27 (70%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI 128
           + +F+  LP +AT E+L+  FS+FG +
Sbjct: 1   RTVFIRNLPFDATEEELKELFSQFGEV 27

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

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+FVG +P+  T +++R  F   G +L+V + K
Sbjct: 1   KLFVGSVPRTITEQEVRPMFEEHGNVLEVAIIK 33

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

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 14/37 (37%), Positives = 24/37 (64%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWF 139
           ++F+GRL   A  +D+ R+F  +GRI D+ + + F F
Sbjct: 1   RVFIGRLNPAAREKDVERFFKGYGRIRDIDLKRGFGF 37

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

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

 Score = 34.8 bits (81), Expect = 0.003
 Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 4/36 (11%)

Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
           +++  L ++   ++L+R     FS+FG +LD+   K
Sbjct: 2   LYINNLNEKIKKDELKRSLYALFSQFGPVLDIVASK 37

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

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 12/33 (36%), Positives = 20/33 (60%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP 134
            ++FV  LP     +DL + FS+FG + +V+V 
Sbjct: 3   GRLFVRNLPYSCKEDDLEKLFSKFGELSEVHVA 35

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

 Score = 34.7 bits (79), Expect = 0.003
 Identities = 14/29 (48%), Positives = 20/29 (68%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILD 130
           KKIFVG L      ED+++YF +FG++ D
Sbjct: 4   KKIFVGGLSANTVVEDVKQYFEQFGKVED 32

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

 Score = 34.4 bits (80), Expect = 0.003
 Identities = 10/35 (28%), Positives = 17/35 (48%), Gaps = 1/35 (2%)

Query: 102 KKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVPK 135
             + V  +P E      L  +FS+FG I+++ V  
Sbjct: 2   TTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNY 36

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

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

 Score = 34.9 bits (81), Expect = 0.003
 Identities = 14/27 (51%), Positives = 17/27 (62%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI 128
             +FVGRL  + T E LR  FSR+G I
Sbjct: 4   LTLFVGRLSLQTTEETLREVFSRYGDI 30

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

 Score = 34.5 bits (80), Expect = 0.003
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
            ++VG LP   T EDL+  F +FG +    V
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARV 31

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 12/32 (37%), Positives = 22/32 (68%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           ++V  LP+ AT E L+  FS++G ++ V +P+
Sbjct: 2   VYVECLPKNATHEWLKAVFSKYGTVVYVSLPR 33

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

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 14/28 (50%), Positives = 20/28 (71%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILD 130
           KIFVG L    T ED+++YF +FG++ D
Sbjct: 1   KIFVGGLSVNTTVEDVKQYFEQFGKVDD 28

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

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 6/44 (13%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP------KRFWFC 140
           K+FVG L  + T E ++ YF  FG I ++ +P      +R  FC
Sbjct: 1   KVFVGGLSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFC 44

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	171
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.96
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.93
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.91
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.9
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.9
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.89
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.88
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.88
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.87
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.86
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.86
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.85
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.84
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.84
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.82
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.81
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.81
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.8
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.78
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.78
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.77
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.75
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.75
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.73
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.72
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.71
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.7
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.61
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.53
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.53
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.48
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.47
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.46
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.44
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.43
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.41
PLN03120	260	nucleic acid binding protein; Provisional	99.39
PLN03121	243	nucleic acid binding protein; Provisional	99.37
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.35
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.3
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.28
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.24
KOG0122	270	consensus Translation initiation factor 3, subunit	99.24
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.24
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.23
PLN03213	759	repressor of silencing 3; Provisional	99.23
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.23
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.2
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.18
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.18
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.18
smart00362	72	RRM_2 RNA recognition motif.	99.18
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.15
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.15
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.14
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.13
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.08
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.08
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.07
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.06
smart00360	71	RRM RNA recognition motif.	99.04
smart00361	70	RRM_1 RNA recognition motif.	99.01
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.0
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.97
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	98.97
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.97
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	98.96
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.95
KOG4207	256	consensus Predicted splicing factor, SR protein su	98.91
COG0724	306	RNA-binding proteins (RRM domain) [General functio	98.89
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.85
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.84
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.84
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.82
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	98.8
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	98.76
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	98.75
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.73
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.73
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.67
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	98.63
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.63
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.61
KOG0151	877	consensus Predicted splicing regulator, contains R	98.58
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	98.58
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.57
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	98.53
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.53
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	98.5
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	98.5
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	98.48
smart00360	71	RRM RNA recognition motif.	98.46
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	98.43
KOG0226	290	consensus RNA-binding proteins [General function p	98.43
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.42
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.4
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.4
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.39
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.35
smart00361	70	RRM_1 RNA recognition motif.	98.34
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.31
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.31
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.3
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.29
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.24
KOG0226	290	consensus RNA-binding proteins [General function p	98.23
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.23
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.23
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.19
KOG4210	285	consensus Nuclear localization sequence binding pr	98.18
smart00362	72	RRM_2 RNA recognition motif.	98.17
PLN03120	260	nucleic acid binding protein; Provisional	98.1
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.1
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	98.01
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	98.0
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.99
PLN03213	759	repressor of silencing 3; Provisional	97.98
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.98
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	97.89
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	97.89
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.86
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.83
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.79
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.78
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	97.74
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	97.72
PLN03121	243	nucleic acid binding protein; Provisional	97.65
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.52
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.49
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.47
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.38
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	97.36
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.35
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.34
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	97.32
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	97.21
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.21
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.07
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.98
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.96
KOG1548	382	consensus Transcription elongation factor TAT-SF1	96.69
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	96.66
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.45
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	96.39
KOG3152	278	consensus TBP-binding protein, activator of basal	96.34
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.27
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	96.21
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	95.91
KOG1995	351	consensus Conserved Zn-finger protein [General fun	95.76
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	95.65
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	95.37
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	95.15
COG5175	480	MOT2 Transcriptional repressor [Transcription]	95.01
KOG2314	698	consensus Translation initiation factor 3, subunit	94.97
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	94.79
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.62
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	94.59
KOG1996	378	consensus mRNA splicing factor [RNA processing and	94.51
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	94.51
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.47
KOG2314	698	consensus Translation initiation factor 3, subunit	93.87
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	93.75
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.55
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	92.8
KOG4210	285	consensus Nuclear localization sequence binding pr	92.69
KOG1995	351	consensus Conserved Zn-finger protein [General fun	92.65
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	92.63
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	92.14
COG5175	480	MOT2 Transcriptional repressor [Transcription]	91.88
KOG4660	549	consensus Protein Mei2, essential for commitment t	91.32
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	91.11
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	90.54
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	89.91
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	89.14
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	89.07
KOG0533	243	consensus RRM motif-containing protein [RNA proces	88.65
KOG2135	526	consensus Proteins containing the RNA recognition	88.06
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	87.64
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	87.58
PF02714	325	DUF221: Domain of unknown function DUF221; InterPr	85.86
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	85.79
KOG2068	327	consensus MOT2 transcription factor [Transcription	84.26
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	81.82
KOG1996	378	consensus mRNA splicing factor [RNA processing and	80.87
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	80.62

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.96  E-value=1.1e-28  Score=182.12  Aligned_cols=129  Identities=22%  Similarity=0.340  Sum_probs=106.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |+||.+|++|||||||.|.+.++|++||..  +..|++|.|+..||+.|.....      .+...-..-++         
T Consensus        94 virD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n------~~~ltfdeV~N---------  158 (321)
T KOG0148|consen   94 VIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMN------GKPLTFDEVYN---------  158 (321)
T ss_pred             EeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccccCccccC------CCCccHHHHhc---------
Confidence            689999999999999999999999999995  7999999999999987742111      00000000000         


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVS  156 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai  156 (171)
                                       ...+..++|||||++..++|++|++.|++||+|.+|+|.+|  +.||+|...|+    |..||
T Consensus       159 -----------------Qssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~qGYaFVrF~tkEa----AahAI  217 (321)
T KOG0148|consen  159 -----------------QSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQGYAFVRFETKEA----AAHAI  217 (321)
T ss_pred             -----------------cCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEecccceEEEEecchhh----HHHHH
Confidence                             11456899999999999999999999999999999999987  56899999999    99999


Q ss_pred             HHHhHhCCC
Q 030822          157 RNLWTAGCN  165 (171)
Q Consensus       157 ~~l~~~~~~  165 (171)
                      ..||+..+.
T Consensus       218 v~mNntei~  226 (321)
T KOG0148|consen  218 VQMNNTEIG  226 (321)
T ss_pred             HHhcCceeC
Confidence            999998764

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.93  E-value=4.2e-26  Score=179.60  Aligned_cols=112  Identities=17%  Similarity=0.277  Sum_probs=99.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.||++||||||+|.++++|++||+.  +..|.+++|.|.++.+...                             
T Consensus       139 i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a~p~~~-----------------------------  189 (346)
T TIGR01659       139 IMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYARPGGE-----------------------------  189 (346)
T ss_pred             EEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeeccccccc-----------------------------
Confidence            578999999999999999999999999984  7899999999998754311                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                         ....++|||+|||+.+||++|+++|++||.|++|.|++|        ++||+|.++++   
T Consensus       190 -------------------~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~---  247 (346)
T TIGR01659       190 -------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREE---  247 (346)
T ss_pred             -------------------ccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHH---
Confidence                               123578999999999999999999999999999999977        57999999999   


Q ss_pred             HHHHHHHHHhHhCC
Q 030822          151 CFSKVSRNLWTAGC  164 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~  164 (171)
                       |++||+.||+..+
T Consensus       248 -A~~Ai~~lng~~~  260 (346)
T TIGR01659       248 -AQEAISALNNVIP  260 (346)
T ss_pred             -HHHHHHHhCCCcc
Confidence             9999999998754

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=99.91  E-value=3.9e-24  Score=177.26  Aligned_cols=123  Identities=15%  Similarity=0.305  Sum_probs=98.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..|+||.|.|.+.......+...                        
T Consensus       139 I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~~~p~a~~~~------------------------  194 (612)
T TIGR01645       139 MSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNMPQAQPII------------------------  194 (612)
T ss_pred             EeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeeccccccccccccc------------------------
Confidence            57899999999999999999999999998  4889999999998542210000000                        


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                   ..........++|||+|||+++++++|+++|+.||.|++|+|++|        ++||+|.+.++   
T Consensus       195 -------------~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~---  258 (612)
T TIGR01645       195 -------------DMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS---  258 (612)
T ss_pred             -------------ccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHH---
Confidence                         000000224579999999999999999999999999999999865        68999999999   


Q ss_pred             HHHHHHHHHhHhCC
Q 030822          151 CFSKVSRNLWTAGC  164 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~  164 (171)
                       |.+||..||+..+
T Consensus       259 -A~kAI~amNg~el  271 (612)
T TIGR01645       259 -QSEAIASMNLFDL  271 (612)
T ss_pred             -HHHHHHHhCCCee
Confidence             9999999998754

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.

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.90  E-value=9.3e-24  Score=165.13  Aligned_cols=159  Identities=21%  Similarity=0.313  Sum_probs=106.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCcc-CCeEEEEeecCC----------CCCCC----------------
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THEL-GGSTVVVDRATP----------KEDDF----------------   51 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i-~gr~i~v~~a~~----------~~~~~----------------   51 (171)
                      ||+|+.+|.+||||||+|.+.++|++||+.  .++| .||.|.|+.+..          |....                
T Consensus       115 LMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvd  194 (506)
T KOG0117|consen  115 LMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVD  194 (506)
T ss_pred             EeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeE
Confidence            689999999999999999999999999994  5666 689998887632          21100                


Q ss_pred             -----CCCCcCCCCCCCCccccchhh-----hhhhccCCCCccCCCC---CCCC---CCCCCCCCCceEEEeCCCCCCCH
Q 030822           52 -----RPVGRMSHGGYGAYNAYISAA-----TRYAALGAPTLYDHPG---SFYG---RGESSQRIGKKIFVGRLPQEATA  115 (171)
Q Consensus        52 -----~~~~~~~~~~~~~~~~~~~~~-----~~~~~~g~~~~~~~~~---~~~~---~~~~~~~~~~~lfV~nLp~~~te  115 (171)
                           .+..+....+.+ ...|.+..     .+....|.-.++.+..   ...+   .++.....-+-|||+||+.++|+
T Consensus       195 Vivy~~p~dk~KNRGFa-FveYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~ded~ms~VKvLYVRNL~~~tTe  273 (506)
T KOG0117|consen  195 VIVYPSPDDKTKNRGFA-FVEYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEPDEDTMSKVKVLYVRNLMESTTE  273 (506)
T ss_pred             EEEecCccccccccceE-EEEeecchhHHHHHhhccCCceeecCCcceeeccCcccCCChhhhhheeeeeeeccchhhhH
Confidence                 011111111111 01111110     0111111111222111   0111   11112455678999999999999


Q ss_pred             HHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          116 EDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       116 ~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +.|+++|++||.|+.|+.++|++||+|.++++    |.+|+++||+..+
T Consensus       274 E~lk~~F~~~G~veRVkk~rDYaFVHf~eR~d----avkAm~~~ngkel  318 (506)
T KOG0117|consen  274 ETLKKLFNEFGKVERVKKPRDYAFVHFAERED----AVKAMKETNGKEL  318 (506)
T ss_pred             HHHHHHHHhccceEEeecccceeEEeecchHH----HHHHHHHhcCcee
Confidence            99999999999999999999999999999999    9999999998654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.90  E-value=2.3e-23  Score=165.17  Aligned_cols=113  Identities=22%  Similarity=0.370  Sum_probs=100.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.||+|||||||+|.+.++|++||+.  +..|.|+.|.|.++.++..                             
T Consensus        35 i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~~~~-----------------------------   85 (352)
T TIGR01661        35 LVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARPSSD-----------------------------   85 (352)
T ss_pred             EEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeeccccc-----------------------------
Confidence            578999999999999999999999999984  7899999999998865422                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                         .....+|||+|||+.+++++|+++|++||.|..+.|+.|        ++||+|.+.++   
T Consensus        86 -------------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~---  143 (352)
T TIGR01661        86 -------------------SIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDE---  143 (352)
T ss_pred             -------------------ccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHH---
Confidence                               123578999999999999999999999999999999865        68999999999   


Q ss_pred             HHHHHHHHHhHhCCC
Q 030822          151 CFSKVSRNLWTAGCN  165 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~~  165 (171)
                       |++||+.||+....
T Consensus       144 -A~~ai~~l~g~~~~  157 (352)
T TIGR01661       144 -ADRAIKTLNGTTPS  157 (352)
T ss_pred             -HHHHHHHhCCCccC
Confidence             99999999987553

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.89  E-value=1.3e-22  Score=160.85  Aligned_cols=61  Identities=20%  Similarity=0.235  Sum_probs=56.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.+|||+|||+.+++++|+++|++||.|++|+|++|        ++||+|.+.++    |.+||..||+..+
T Consensus       268 ~~~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~----A~~Ai~~lnG~~~  336 (352)
T TIGR01661       268 AGYCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDE----AAMAILSLNGYTL  336 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHH----HHHHHHHhCCCEE
Confidence            4558999999999999999999999999999999976        57999999999    9999999998654

These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.88  E-value=3.2e-22  Score=163.73  Aligned_cols=124  Identities=21%  Similarity=0.324  Sum_probs=98.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      |++|+.||++||||||+|.+.++|++||. ++..+.|++|.|+.+.............                      
T Consensus       121 i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~----------------------  178 (457)
T TIGR01622       121 CIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQAEKNRAAKAATH----------------------  178 (457)
T ss_pred             EeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecchhhhhhhhcccc----------------------
Confidence            47899999999999999999999999999 4889999999998654321110000000                      


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                            .      ..  ..+..++|||+|||+.+++++|+++|++||.|..|.|++|        ++||+|.+.++    
T Consensus       179 ------~------~~--~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~----  240 (457)
T TIGR01622       179 ------Q------PG--DIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEE----  240 (457)
T ss_pred             ------c------CC--CCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH----
Confidence                  0      00  0123689999999999999999999999999999999864        57999999999    


Q ss_pred             HHHHHHHHhHhCC
Q 030822          152 FSKVSRNLWTAGC  164 (171)
Q Consensus       152 a~~Ai~~l~~~~~  164 (171)
                      |.+|+..||+..+
T Consensus       241 A~~A~~~l~g~~i  253 (457)
T TIGR01622       241 AKEALEVMNGFEL  253 (457)
T ss_pred             HHHHHHhcCCcEE
Confidence            9999999998554

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.88  E-value=8.5e-23  Score=150.51  Aligned_cols=111  Identities=23%  Similarity=0.358  Sum_probs=100.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      ++||+.||.|-|||||.|-++++|++|+.  ++..+..+.|+|.+|.|..+                             
T Consensus        73 LvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~-----------------------------  123 (360)
T KOG0145|consen   73 LVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSD-----------------------------  123 (360)
T ss_pred             eeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChh-----------------------------
Confidence            58999999999999999999999999999  48899999999999977533                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                         .....+|||.+||.++|..+|+++|++||.|..-+|..|        -+||.|+-+.|   
T Consensus       124 -------------------~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~E---  181 (360)
T KOG0145|consen  124 -------------------SIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIE---  181 (360)
T ss_pred             -------------------hhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhH---
Confidence                               345678999999999999999999999999999988766        57999999999   


Q ss_pred             HHHHHHHHHhHhC
Q 030822          151 CFSKVSRNLWTAG  163 (171)
Q Consensus       151 ~a~~Ai~~l~~~~  163 (171)
                       |++||+.|||..
T Consensus       182 -Ae~AIk~lNG~~  193 (360)
T KOG0145|consen  182 -AEEAIKGLNGQK  193 (360)
T ss_pred             -HHHHHHhccCCC
Confidence             999999999865

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.87  E-value=5.5e-22  Score=164.11  Aligned_cols=114  Identities=24%  Similarity=0.297  Sum_probs=97.0

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      +..++++||||||+|++.++|.+|++.    ...+.|+.|.|.|+.++.+....                          
T Consensus       175 ~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~~~d~~--------------------------  228 (578)
T TIGR01648       175 AADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEEEVDED--------------------------  228 (578)
T ss_pred             ccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeeccccccccc--------------------------
Confidence            345688999999999999999999984    24688999999998765332110                          


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcc--cceEEEEecCcceeEEecCCcccHHHHHHHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF--GRILDVYVPKRFWFCHLCGRSCSRSCFSKVSR  157 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~f--G~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~  157 (171)
                                       .....++|||+|||+++++++|+++|++|  |.|++|.++++++||+|.++++    |++|++
T Consensus       229 -----------------~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rgfAFVeF~s~e~----A~kAi~  287 (578)
T TIGR01648       229 -----------------VMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRDYAFVHFEDRED----AVKAMD  287 (578)
T ss_pred             -----------------ccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecCeEEEEeCCHHH----HHHHHH
Confidence                             02235789999999999999999999999  9999999999999999999999    999999


Q ss_pred             HHhHhCC
Q 030822          158 NLWTAGC  164 (171)
Q Consensus       158 ~l~~~~~  164 (171)
                      .||+..+
T Consensus       288 ~lnG~~i  294 (578)
T TIGR01648       288 ELNGKEL  294 (578)
T ss_pred             HhCCCEE
Confidence            9998654

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.

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

Probab=99.86  E-value=1.4e-21  Score=163.77  Aligned_cols=115  Identities=20%  Similarity=0.286  Sum_probs=97.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.|++|+|||||+|.+.++|++||+.  ...|.|+.|+|.|+.......                           
T Consensus        32 v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~~~~~---------------------------   84 (562)
T TIGR01628        32 VCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRDPSLR---------------------------   84 (562)
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccccccc---------------------------
Confidence            468999999999999999999999999985  577999999999874321100                           


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~  151 (171)
                                         .....+|||+|||.++++++|+++|+.||.|.+|+|++|       ++||+|.+.++    
T Consensus        85 -------------------~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~----  141 (562)
T TIGR01628        85 -------------------RSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEES----  141 (562)
T ss_pred             -------------------ccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHH----
Confidence                               112467999999999999999999999999999999865       67999999999    


Q ss_pred             HHHHHHHHhHhCCC
Q 030822          152 FSKVSRNLWTAGCN  165 (171)
Q Consensus       152 a~~Ai~~l~~~~~~  165 (171)
                      |.+|+..||+..++
T Consensus       142 A~~Ai~~lng~~~~  155 (562)
T TIGR01628       142 AKAAIQKVNGMLLN  155 (562)
T ss_pred             HHHHHHHhcccEec
Confidence            99999999887543

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]

Probab=99.86  E-value=5.3e-21  Score=141.08  Aligned_cols=156  Identities=21%  Similarity=0.241  Sum_probs=103.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCC--eEEEEeecCCCCCCC----------CCCCcCCCCCCCCcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGG--STVVVDRATPKEDDF----------RPVGRMSHGGYGAYN   66 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~g--r~i~v~~a~~~~~~~----------~~~~~~~~~~~~~~~   66 (171)
                      |..|+.||.|||.|||.|...++|++||+.  ++.-.|  -+|.|+++.......          .|..+..+.-+.+..
T Consensus       159 iL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~  238 (360)
T KOG0145|consen  159 ILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQ  238 (360)
T ss_pred             hhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhh
Confidence            467999999999999999999999999994  554444  579999986442211          112111111111111


Q ss_pred             cc---c-----hhhhhhhccCCCCccCCCCCCCCC-CCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-
Q 030822           67 AY---I-----SAATRYAALGAPTLYDHPGSFYGR-GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-  136 (171)
Q Consensus        67 ~~---~-----~~~~~~~~~g~~~~~~~~~~~~~~-~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-  136 (171)
                      ..   .     ....+..++.    .+......+. -+.....+++|||.||.++++|..|+++|++||.|.+|+|++| 
T Consensus       239 r~r~~~~~~~~~~~~rfsP~~----~d~m~~l~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpFGAv~nVKvirD~  314 (360)
T KOG0145|consen  239 RFRLDNLLNPHAAQARFSPMT----IDGMSGLAGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPFGAVTNVKVIRDF  314 (360)
T ss_pred             hhccccccchhhhhccCCCcc----ccccceeeeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcccceeeEEEEecC
Confidence            00   0     0011111111    1111111111 1112345899999999999999999999999999999999998 


Q ss_pred             -------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          137 -------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       137 -------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                             ++||.+.+++|    |..||..|||-..
T Consensus       315 ttnkCKGfgFVtMtNYdE----AamAi~sLNGy~l  345 (360)
T KOG0145|consen  315 TTNKCKGFGFVTMTNYDE----AAMAIASLNGYRL  345 (360)
T ss_pred             CcccccceeEEEecchHH----HHHHHHHhcCccc
Confidence                   56899999999    9999999998653

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.85  E-value=6.3e-22  Score=154.42  Aligned_cols=112  Identities=23%  Similarity=0.405  Sum_probs=94.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc---CCccCC--eEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhh
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD---THELGG--STVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRY   75 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~---~~~i~g--r~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   75 (171)
                      |+||+.||.|||||||+|.+.++|.+|+..   ...|.|  .+|.|++|....++                         
T Consensus        66 l~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er-------------------------  120 (510)
T KOG0144|consen   66 LIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER-------------------------  120 (510)
T ss_pred             eecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc-------------------------
Confidence            689999999999999999999999999884   344444  56777766432110                         


Q ss_pred             hccCCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCccc
Q 030822           76 AALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCS  148 (171)
Q Consensus        76 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~  148 (171)
                                            -...++||||-|+..+||.+++++|++||.|++|.|++|       ++||+|..++. 
T Consensus       121 ----------------------~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~-  177 (510)
T KOG0144|consen  121 ----------------------IVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEM-  177 (510)
T ss_pred             ----------------------cccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHH-
Confidence                                  123689999999999999999999999999999999986       68999999999 


Q ss_pred             HHHHHHHHHHHhHhC
Q 030822          149 RSCFSKVSRNLWTAG  163 (171)
Q Consensus       149 ~~~a~~Ai~~l~~~~  163 (171)
                         |..||+.||+.-
T Consensus       178 ---A~~Aika~ng~~  189 (510)
T KOG0144|consen  178 ---AVAAIKALNGTQ  189 (510)
T ss_pred             ---HHHHHHhhccce
Confidence               999999999864

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.84  E-value=7.2e-21  Score=152.25  Aligned_cols=138  Identities=21%  Similarity=0.387  Sum_probs=103.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      ++.++.++.+||||||+|+-.+++++|+..  ...+.||.|.|..+.++............                 ..
T Consensus        37 vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~R~r~e~~~~~e~~-----------------~v   99 (678)
T KOG0127|consen   37 VVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKKRARSEEVEKGENK-----------------AV   99 (678)
T ss_pred             EecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccccccchhcccccch-----------------hh
Confidence            467889999999999999999999999995  67799999999999876443310000000                 00


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~  151 (171)
                      -.|.....+.     ...-..+.++|.|+||||.+.+.+|+.+|+.||.|.+|.|++.       |+||+|....+    
T Consensus       100 eK~~~q~~~~-----k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k~dgklcGFaFV~fk~~~d----  170 (678)
T KOG0127|consen  100 EKPIEQKRPT-----KAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRKKDGKLCGFAFVQFKEKKD----  170 (678)
T ss_pred             hcccccCCcc-----hhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEcccCCCCCccceEEEEEeeHHH----
Confidence            0000000000     0001234799999999999999999999999999999999953       78999999999    


Q ss_pred             HHHHHHHHhHhCC
Q 030822          152 FSKVSRNLWTAGC  164 (171)
Q Consensus       152 a~~Ai~~l~~~~~  164 (171)
                      |++|++.||+..+
T Consensus       171 A~~Al~~~N~~~i  183 (678)
T KOG0127|consen  171 AEKALEFFNGNKI  183 (678)
T ss_pred             HHHHHHhccCcee
Confidence            9999999998654

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.84  E-value=4.7e-21  Score=134.39  Aligned_cols=113  Identities=22%  Similarity=0.402  Sum_probs=96.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      ||+|+.|..++|||||+|.++++|+-|++  ++..+.||+|+|..+.....                             
T Consensus        41 iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas~~~~-----------------------------   91 (203)
T KOG0131|consen   41 IPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKASAHQK-----------------------------   91 (203)
T ss_pred             cchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecccccc-----------------------------
Confidence            68999999999999999999999999999  68889999999997752111                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEE-EecCc--------ceeEEecCCcccH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKR--------FWFCHLCGRSCSR  149 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~d--------~~fv~f~~~~~~~  149 (171)
                                        ....+.+|||+||.+.++|..|.+.|+.||.+... +|++|        ++|+.|.+.+.  
T Consensus        92 ------------------nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfea--  151 (203)
T KOG0131|consen   92 ------------------NLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEA--  151 (203)
T ss_pred             ------------------cccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHH--
Confidence                              13346899999999999999999999999998874 45544        67899999999  


Q ss_pred             HHHHHHHHHHhHhCC
Q 030822          150 SCFSKVSRNLWTAGC  164 (171)
Q Consensus       150 ~~a~~Ai~~l~~~~~  164 (171)
                        +..||..||+...
T Consensus       152 --sd~ai~s~ngq~l  164 (203)
T KOG0131|consen  152 --SDAAIGSMNGQYL  164 (203)
T ss_pred             --HHHHHHHhccchh
Confidence              9999999988654

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.82  E-value=7.5e-20  Score=151.55  Aligned_cols=138  Identities=12%  Similarity=0.175  Sum_probs=94.5

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCc
Q 030822            5 QGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTL   83 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   83 (171)
                      ...++++|||||+|.+.++|..||. ++..|.|+.|.|.+..................   ....      .     +. 
T Consensus       217 ~~~~~~kg~afVeF~~~e~A~~Al~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~---~~~~------~-----~~-  281 (509)
T TIGR01642       217 VNINKEKNFAFLEFRTVEEATFAMALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKN---PDDN------A-----KN-  281 (509)
T ss_pred             EEECCCCCEEEEEeCCHHHHhhhhcCCCeEeeCceeEecCccccCCccccCCCCCCCC---Cccc------c-----cc-
Confidence            3456889999999999999999997 47889999999875432211000000000000   0000      0     00 


Q ss_pred             cCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHH
Q 030822           84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKV  155 (171)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~A  155 (171)
                         .... ..........++|||+|||+.+++++|+++|+.||.|..+.|++|        ++||+|.+.++    |..|
T Consensus       282 ---~~~~-~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~----a~~A  353 (509)
T TIGR01642       282 ---VEKL-VNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSV----TDVA  353 (509)
T ss_pred             ---cccc-cccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHH----HHHH
Confidence               0000 000001234689999999999999999999999999999999865        68999999999    9999


Q ss_pred             HHHHhHhCCC
Q 030822          156 SRNLWTAGCN  165 (171)
Q Consensus       156 i~~l~~~~~~  165 (171)
                      |..||+..+.
T Consensus       354 ~~~l~g~~~~  363 (509)
T TIGR01642       354 IAALNGKDTG  363 (509)
T ss_pred             HHHcCCCEEC
Confidence            9999987653

Members of this subfamily are found in plants, metazoa and fungi.

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

Probab=99.81  E-value=1.9e-19  Score=150.83  Aligned_cols=116  Identities=22%  Similarity=0.317  Sum_probs=97.4

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      ++| .+|++||||||+|++.++|++|++.  +..++|+.|.|....++.+...                           
T Consensus       121 ~~~-~~g~skg~afV~F~~~e~A~~Ai~~lng~~~~~~~i~v~~~~~~~~~~~---------------------------  172 (562)
T TIGR01628       121 ATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRFIKKHEREA---------------------------  172 (562)
T ss_pred             eec-CCCCcccEEEEEECCHHHHHHHHHHhcccEecCceEEEecccccccccc---------------------------
Confidence            456 4889999999999999999999984  7889999999976554422210                           


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCF  152 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a  152 (171)
                                      ......++|||+|||+++|+++|+++|+.||.|+++.|++|       ++||.|.+.++    |
T Consensus       173 ----------------~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~----A  232 (562)
T TIGR01628       173 ----------------APLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHED----A  232 (562)
T ss_pred             ----------------ccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHH----H
Confidence                            00234678999999999999999999999999999999865       68999999999    9


Q ss_pred             HHHHHHHhHhCCC
Q 030822          153 SKVSRNLWTAGCN  165 (171)
Q Consensus       153 ~~Ai~~l~~~~~~  165 (171)
                      .+|++.||+..+.
T Consensus       233 ~~Av~~l~g~~i~  245 (562)
T TIGR01628       233 AKAVEEMNGKKIG  245 (562)
T ss_pred             HHHHHHhCCcEec
Confidence            9999999987765

There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.81  E-value=4.4e-19  Score=146.09  Aligned_cols=116  Identities=11%  Similarity=0.130  Sum_probs=92.6

Q ss_pred             CccceEEEEECCHHHHHHHHh----cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCcc
Q 030822            9 AHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~----~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   84 (171)
                      ++||||||+|++.++|++||+    ++..|.|++|.|.++..+........   .                         
T Consensus        36 ~~k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v~~s~~~~~~~~~~~---~-------------------------   87 (481)
T TIGR01649        36 PGKRQALVEFEDEESAKACVNFATSVPIYIRGQPAFFNYSTSQEIKRDGNS---D-------------------------   87 (481)
T ss_pred             CCCCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEEEecCCcccccCCCC---c-------------------------
Confidence            367999999999999999998    36789999999999875432111000   0                         


Q ss_pred             CCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----ceeEEecCCcccHHHHHHHHHHHh
Q 030822           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                            .  .........+|||+||++.+|+++|+++|++||.|.+|.|+++    ++||+|.+.++    |.+|+..||
T Consensus        88 ------~--~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~~~afVef~~~~~----A~~A~~~Ln  155 (481)
T TIGR01649        88 ------F--DSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNVFQALVEFESVNS----AQHAKAALN  155 (481)
T ss_pred             ------c--cCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCceEEEEEECCHHH----HHHHHHHhc
Confidence                  0  0000123458999999999999999999999999999999866    58999999999    999999999


Q ss_pred             HhCC
Q 030822          161 TAGC  164 (171)
Q Consensus       161 ~~~~  164 (171)
                      +..+
T Consensus       156 g~~i  159 (481)
T TIGR01649       156 GADI  159 (481)
T ss_pred             CCcc
Confidence            9976

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).

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=99.80  E-value=5e-20  Score=142.01  Aligned_cols=111  Identities=35%  Similarity=0.613  Sum_probs=97.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      ||+|+.||++|||+||+|++++.+.++|.. .|.|+||.|.++.+.++.+.+....                        
T Consensus        38 vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~r~~~~~~~~------------------------   93 (311)
T KOG4205|consen   38 VMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVSREDQTKVGR------------------------   93 (311)
T ss_pred             EeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccCccccccccc------------------------
Confidence            589999999999999999999999999996 7999999999999999877655322                        


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                                        .....+|||++||..+++++|+++|.+||.|.++.++.|        ++||.|.+++.    
T Consensus        94 ------------------~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~s----  151 (311)
T KOG4205|consen   94 ------------------HLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDS----  151 (311)
T ss_pred             ------------------ccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccc----
Confidence                              224689999999999999999999999999999999977        57899999998    


Q ss_pred             HHHHHH
Q 030822          152 FSKVSR  157 (171)
Q Consensus       152 a~~Ai~  157 (171)
                      .++++.
T Consensus       152 Vdkv~~  157 (311)
T KOG4205|consen  152 VDKVTL  157 (311)
T ss_pred             cceecc
Confidence            665543

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]

Probab=99.78  E-value=4.1e-18  Score=136.63  Aligned_cols=153  Identities=20%  Similarity=0.297  Sum_probs=95.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCC-------CcC----------CCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPV-------GRM----------SHGG   61 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~-------~~~----------~~~~   61 (171)
                      ||+.+ .|+-.|||||.|.+..+|.+||+  ++++|+||+|.|.||.++.......       ...          ...+
T Consensus       149 IP~k~-dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~  227 (678)
T KOG0127|consen  149 IPRKK-DGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDG  227 (678)
T ss_pred             cccCC-CCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccc
Confidence            56654 56666999999999999999999  4899999999999998875432211       000          0000


Q ss_pred             CCCcc--ccchhhhhhhccC--------CCC-----ccCCCCCCCCCC-----------CCCCCCCceEEEeCCCCCCCH
Q 030822           62 YGAYN--AYISAATRYAALG--------APT-----LYDHPGSFYGRG-----------ESSQRIGKKIFVGRLPQEATA  115 (171)
Q Consensus        62 ~~~~~--~~~~~~~~~~~~g--------~~~-----~~~~~~~~~~~~-----------~~~~~~~~~lfV~nLp~~~te  115 (171)
                      .....  ....+.......|        ...     ..+. ....+..           ......+.+|||+|||+++|+
T Consensus       228 ~~~~~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd-~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tE  306 (678)
T KOG0127|consen  228 KDFDEEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDD-EESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTE  306 (678)
T ss_pred             cccchhcccccccccccccccchhhhcccccccccccccc-ccccccCcccchhccccccccccccceEEEecCCccccH
Confidence            00000  0000000000000        000     0000 0000000           011334689999999999999


Q ss_pred             HHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHH
Q 030822          116 EDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus       116 ~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      ++|.++|++||+|.++.|+.|        .+||+|.+..+    +.++|.+.
T Consensus       307 Eel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~----~~~ci~~A  354 (678)
T KOG0127|consen  307 EELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIA----AQNCIEAA  354 (678)
T ss_pred             HHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHH----HHHHHHhc
Confidence            999999999999999999976        46899999999    55555544

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family

Probab=99.78  E-value=4.1e-18  Score=140.37  Aligned_cols=141  Identities=16%  Similarity=0.202  Sum_probs=93.8

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCC
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~   87 (171)
                      ++|||||+|.+.++|++||..  +..|.|++|.|.++..+............+ ...+..+....  ...      ...+
T Consensus       312 ~~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~-~~~~~d~~~~~--~~r------~~~~  382 (481)
T TIGR01649       312 KKETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDG-LTSYKDYSSSR--NHR------FKKP  382 (481)
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCC-CcccccccCCc--ccc------CCCc
Confidence            479999999999999999984  789999999999875432211100000000 00000000000  000      0000


Q ss_pred             CCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccc--eEEEEecC------cceeEEecCCcccHHHHHHHHHHH
Q 030822           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVPK------RFWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus        88 ~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~--v~~v~i~~------d~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      .... . ..-.+++.+|||+|||+++++++|+++|+.||.  |..+++..      .++||+|.+.++    |.+||..|
T Consensus       383 ~~~~-~-~~~~~ps~~L~v~NLp~~~tee~L~~lF~~~G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~----A~~Al~~l  456 (481)
T TIGR01649       383 GSAN-K-NNIQPPSATLHLSNIPLSVSEEDLKELFAENGVHKVKKFKFFPKDNERSKMGLLEWESVED----AVEALIAL  456 (481)
T ss_pred             cccc-c-cccCCCCcEEEEecCCCCCCHHHHHHHHHhcCCccceEEEEecCCCCcceeEEEEcCCHHH----HHHHHHHh
Confidence            0000 0 001245789999999999999999999999998  88888863      468899999999    99999999


Q ss_pred             hHhCCC
Q 030822          160 WTAGCN  165 (171)
Q Consensus       160 ~~~~~~  165 (171)
                      |+..+.
T Consensus       457 n~~~l~  462 (481)
T TIGR01649       457 NHHQLN  462 (481)
T ss_pred             cCCccC
Confidence            998763

Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein ) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067).

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor

Probab=99.77  E-value=3.7e-18  Score=141.43  Aligned_cols=141  Identities=15%  Similarity=0.197  Sum_probs=96.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.||+++|||||+|.+.++|+.||.  ++..|+|+.|.|+++.............  +. .               
T Consensus       327 ~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~--~~-~---------------  388 (509)
T TIGR01642       327 LIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSN--GM-A---------------  388 (509)
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCccccc--cc-c---------------
Confidence            46788999999999999999999999998  4789999999999986432211110000  00 0               


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCC----------CHHHHHHHhhcccceEEEEecCc-----------c
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEA----------TAEDLRRYFSRFGRILDVYVPKR-----------F  137 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~----------te~~L~~~F~~fG~v~~v~i~~d-----------~  137 (171)
                        +.....+............+...|+|.||....          ..++|+++|++||.|+.|.|+++           +
T Consensus       389 --~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~  466 (509)
T TIGR01642       389 --PVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGK  466 (509)
T ss_pred             --ccccccccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcce
Confidence              000000000000000012346889999996421          13689999999999999999864           4


Q ss_pred             eeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          138 WFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       138 ~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .||+|.+.++    |++|+..|||..++
T Consensus       467 ~fV~F~~~e~----A~~A~~~lnGr~~~  490 (509)
T TIGR01642       467 VFLEYADVRS----AEKAMEGMNGRKFN  490 (509)
T ss_pred             EEEEECCHHH----HHHHHHHcCCCEEC
Confidence            5999999999    99999999987653

Members of this subfamily are found in plants, metazoa and fungi.

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family

Probab=99.75  E-value=2.9e-18  Score=142.14  Aligned_cols=104  Identities=23%  Similarity=0.351  Sum_probs=84.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCcc-CCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THEL-GGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAA   77 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i-~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (171)
                      ||+| .+|+|||||||+|.+.++|++||+.  +.+| .|+.|.|.++.                                
T Consensus        90 l~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~--------------------------------  136 (578)
T TIGR01648        90 LMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV--------------------------------  136 (578)
T ss_pred             EEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc--------------------------------
Confidence            5788 8999999999999999999999995  4555 46766655321                                


Q ss_pred             cCCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccc-eEEEEec---------CcceeEEecCCcc
Q 030822           78 LGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVP---------KRFWFCHLCGRSC  147 (171)
Q Consensus        78 ~g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~-v~~v~i~---------~d~~fv~f~~~~~  147 (171)
                                            ..++|||+|||+++++++|.++|++++. ++++.+.         +.++||+|.++++
T Consensus       137 ----------------------~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~ed  194 (578)
T TIGR01648       137 ----------------------DNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRA  194 (578)
T ss_pred             ----------------------cCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHH
Confidence                                  2578999999999999999999999964 4555442         3478999999999


Q ss_pred             cHHHHHHHHHHHhHhC
Q 030822          148 SRSCFSKVSRNLWTAG  163 (171)
Q Consensus       148 ~~~~a~~Ai~~l~~~~  163 (171)
                          |++|++.|+...
T Consensus       195 ----Aa~AirkL~~gk  206 (578)
T TIGR01648       195 ----AAMARRKLMPGR  206 (578)
T ss_pred             ----HHHHHHHhhccc
Confidence                999999986543

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.

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.75  E-value=1.9e-18  Score=129.22  Aligned_cols=99  Identities=20%  Similarity=0.404  Sum_probs=90.6

Q ss_pred             cceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCC
Q 030822           11 RGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPG   88 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~   88 (171)
                      |-||||+.++...++.||.+  +..|+|..|.|+-++.|                                         
T Consensus        36 KNYgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK-----------------------------------------   74 (346)
T KOG0109|consen   36 KNYGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK-----------------------------------------   74 (346)
T ss_pred             cccceEEeecccccHHHHhhcccceecceEEEEEecccc-----------------------------------------
Confidence            56999999999999999996  67999999999977655                                         


Q ss_pred             CCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        89 ~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                               ....++|+|+||.+.++.++|+..|++||+|++|+|++|++||+|.-.++    |..||+.|++..
T Consensus        75 ---------sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkdy~fvh~d~~ed----a~~air~l~~~~  136 (346)
T KOG0109|consen   75 ---------SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKDYAFVHFDRAED----AVEAIRGLDNTE  136 (346)
T ss_pred             ---------CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecceeEEEEeeccc----hHHHHhcccccc
Confidence                     23478999999999999999999999999999999999999999999999    999999998754

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=99.73  E-value=1.3e-17  Score=128.40  Aligned_cols=121  Identities=15%  Similarity=0.281  Sum_probs=95.8

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      ..|+.||++|||+||+|+-+|.|+.|++.  +..++||.|+|.+...-  .+.           ++--....        
T Consensus       146 SWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPsNm--pQA-----------QpiID~vq--------  204 (544)
T KOG0124|consen  146 SWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPSNM--PQA-----------QPIIDMVQ--------  204 (544)
T ss_pred             ccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCCCC--ccc-----------chHHHHHH--------
Confidence            47999999999999999999999999995  78999999998743211  000           00000000        


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                                      .......+|||..+.++.+|+||+.+|+.||+|++|.+.++        ++|++|.+...    
T Consensus       205 ----------------eeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs----  264 (544)
T KOG0124|consen  205 ----------------EEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQS----  264 (544)
T ss_pred             ----------------HHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccc----
Confidence                            00234689999999999999999999999999999999754        78999999999    


Q ss_pred             HHHHHHHHhHhC
Q 030822          152 FSKVSRNLWTAG  163 (171)
Q Consensus       152 a~~Ai~~l~~~~  163 (171)
                      ...||..||-..
T Consensus       265 ~~eAiasMNlFD  276 (544)
T KOG0124|consen  265 QSEAIASMNLFD  276 (544)
T ss_pred             hHHHhhhcchhh
Confidence            999999987654

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.72  E-value=2.4e-17  Score=130.88  Aligned_cols=103  Identities=19%  Similarity=0.303  Sum_probs=91.4

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      -+|. |  |-|||||.|.++++|++||..  -..+.|++|++.|+...                                
T Consensus        31 c~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd--------------------------------   75 (369)
T KOG0123|consen   31 CRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRD--------------------------------   75 (369)
T ss_pred             eecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccC--------------------------------
Confidence            4787 6  999999999999999999996  46899999999987532                                


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFS  153 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~  153 (171)
                                           ...|||.||++.++..+|.++|+.||+|++|+|..|      + ||+|.++++    |.
T Consensus        76 ---------------------~~~~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~----a~  129 (369)
T KOG0123|consen   76 ---------------------PSLVFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEES----AK  129 (369)
T ss_pred             ---------------------CceeeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHH----HH
Confidence                                 112999999999999999999999999999999976      4 999999999    99


Q ss_pred             HHHHHHhHhCCC
Q 030822          154 KVSRNLWTAGCN  165 (171)
Q Consensus       154 ~Ai~~l~~~~~~  165 (171)
                      +||..||+-..+
T Consensus       130 ~ai~~~ng~ll~  141 (369)
T KOG0123|consen  130 KAIEKLNGMLLN  141 (369)
T ss_pred             HHHHHhcCcccC
Confidence            999999986543

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.71  E-value=6.1e-17  Score=133.21  Aligned_cols=109  Identities=27%  Similarity=0.437  Sum_probs=89.9

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDH   86 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~   86 (171)
                      .|.|||||+|.++++|+.|++.  ++.|+|+.|.|+++..+....                                   
T Consensus       558 lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~-----------------------------------  602 (725)
T KOG0110|consen  558 LSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPAST-----------------------------------  602 (725)
T ss_pred             cccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCccccc-----------------------------------
Confidence            3679999999999999999996  799999999999886221100                                   


Q ss_pred             CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--------cceeEEecCCcccHHHHHHHHHH
Q 030822           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--------RFWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        87 ~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--------d~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                          .+...+.....++|.|+|||+.++-.+++.+|..||.|.+|+|++        .++||.|-++.+    |.+|+..
T Consensus       603 ----~gK~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~e----a~nA~~a  674 (725)
T KOG0110|consen  603 ----VGKKKSKKKKGTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPRE----AKNAFDA  674 (725)
T ss_pred             ----cccccccccccceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHH----HHHHHHh
Confidence                001111133468999999999999999999999999999999984        367999999999    9999999


Q ss_pred             Hh
Q 030822          159 LW  160 (171)
Q Consensus       159 l~  160 (171)
                      |+
T Consensus       675 l~  676 (725)
T KOG0110|consen  675 LG  676 (725)
T ss_pred             hc
Confidence            97

>TIGR01622 SF-CC1 splicing factor, CC1-like family

Probab=99.70  E-value=2.6e-16  Score=128.88  Aligned_cols=161  Identities=15%  Similarity=0.190  Sum_probs=98.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCC------cCCCCCCCCccccc-hh
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVG------RMSHGGYGAYNAYI-SA   71 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~------~~~~~~~~~~~~~~-~~   71 (171)
                      |++|+.+|+++|||||+|.+.++|.+|++.  +..|.|+.|.|.++...........      .....+........ ..
T Consensus       218 ~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  297 (457)
T TIGR01622       218 LHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQL  297 (457)
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHH
Confidence            467889999999999999999999999984  7899999999999753211110000      00000000000000 00


Q ss_pred             hhhh---h---ccCCCCc-----------------------cCCCC---CCCCCCCC---CCCCCceEEEeCCCCCCC--
Q 030822           72 ATRY---A---ALGAPTL-----------------------YDHPG---SFYGRGES---SQRIGKKIFVGRLPQEAT--  114 (171)
Q Consensus        72 ~~~~---~---~~g~~~~-----------------------~~~~~---~~~~~~~~---~~~~~~~lfV~nLp~~~t--  114 (171)
                      ....   .   ..+.+..                       +....   .......+   .......|+|.||....+  
T Consensus       298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~  377 (457)
T TIGR01622       298 MEKLDRDDGDGGLLIPGTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEE  377 (457)
T ss_pred             HHhhccCCCCccccCCCccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccc
Confidence            0000   0   0000000                       00000   00000000   135678999999955444  


Q ss_pred             --------HHHHHHHhhcccceEEEEec----CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          115 --------AEDLRRYFSRFGRILDVYVP----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       115 --------e~~L~~~F~~fG~v~~v~i~----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                              .+||++.|++||.|+.|.|.    ..+.||+|.+.++    |.+|++.|||..+.
T Consensus       378 ~~~~~~~~~~dv~~e~~k~G~v~~v~v~~~~~~G~~fV~F~~~e~----A~~A~~~lnGr~f~  436 (457)
T TIGR01622       378 EPNFDNEILDDVKEECSKYGGVVHIYVDTKNSAGKIYLKFSSVDA----ALAAFQALNGRYFG  436 (457)
T ss_pred             cchHHHHHHHHHHHHHHhcCCeeEEEEeCCCCceeEEEEECCHHH----HHHHHHHhcCcccC
Confidence                    37899999999999999997    3478999999999    99999999996653

A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the model.

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.61  E-value=4.2e-16  Score=125.22  Aligned_cols=125  Identities=22%  Similarity=0.328  Sum_probs=97.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      ||.|+.++++||.|||+|-+.+.+..||. .|..+.|-+|.|+........   .+.                       
T Consensus       211 iI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEaeknr---~a~-----------------------  264 (549)
T KOG0147|consen  211 IIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEAEKNR---AAN-----------------------  264 (549)
T ss_pred             eeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHHHHHH---HHh-----------------------
Confidence            57899999999999999999999999998 489999999999854321000   000                       


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                             .+...+... -..+..+|||+||.++.++++|+.+|++||.|+.|.+++|        ++|++|.+.++    
T Consensus       265 -------~s~a~~~k~-~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~----  332 (549)
T KOG0147|consen  265 -------ASPALQGKG-FTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKED----  332 (549)
T ss_pred             -------ccccccccc-cccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHH----
Confidence                   000000000 0223445999999999999999999999999999999987        68899999999    


Q ss_pred             HHHHHHHHhHhC
Q 030822          152 FSKVSRNLWTAG  163 (171)
Q Consensus       152 a~~Ai~~l~~~~  163 (171)
                      |.+|+.+||+..
T Consensus       333 ar~a~e~lngfe  344 (549)
T KOG0147|consen  333 ARKALEQLNGFE  344 (549)
T ss_pred             HHHHHHHhccce
Confidence            999999999854

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.53  E-value=1.6e-14  Score=100.89  Aligned_cols=63  Identities=22%  Similarity=0.356  Sum_probs=57.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.++|++|+++|++||+|.+|.|++|        ++||+|.+.++    |+.|++.||+..++
T Consensus        32 ~~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~----A~~Al~~lng~~i~  102 (144)
T PLN03134         32 LMSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGA----ATAAISEMDGKELN  102 (144)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            35789999999999999999999999999999999865        68999999999    99999999876543

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.53  E-value=3.4e-14  Score=112.99  Aligned_cols=117  Identities=24%  Similarity=0.366  Sum_probs=99.0

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      ++|. .| |||| ||+|+++++|++||+.  +..+.|++|.|.....+++...+...                       
T Consensus       109 ~~~~-~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~er~~~~~~-----------------------  162 (369)
T KOG0123|consen  109 ATDE-NG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEEREAPLGE-----------------------  162 (369)
T ss_pred             EEcC-CC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhhhcccccc-----------------------
Confidence            4553 45 9999 9999999999999994  88999999999988777665443221                       


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCF  152 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a  152 (171)
                                       .......+||.|++.+.+++.|..+|+.||.|..+.++.+       ++||.|.++++    |
T Consensus       163 -----------------~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~----a  221 (369)
T KOG0123|consen  163 -----------------YKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPED----A  221 (369)
T ss_pred             -----------------hhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhH----H
Confidence                             1334678999999999999999999999999999999865       78999999998    9


Q ss_pred             HHHHHHHhHhCCC
Q 030822          153 SKVSRNLWTAGCN  165 (171)
Q Consensus       153 ~~Ai~~l~~~~~~  165 (171)
                      ..|+..||+....
T Consensus       222 ~~av~~l~~~~~~  234 (369)
T KOG0123|consen  222 KKAVETLNGKIFG  234 (369)
T ss_pred             HHHHHhccCCcCC
Confidence            9999999998764

>PF00076 RRM_1: RNA recognition motif

Probab=99.48  E-value=5.2e-14  Score=85.96  Aligned_cols=58  Identities=31%  Similarity=0.547  Sum_probs=53.8

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       104 lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      |||+|||+.+++++|+++|++||.|..+.++.+       ++||+|.++++    |++|+..||+..++
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~----a~~a~~~l~g~~~~   65 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEED----AEKALEELNGKKIN   65 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHH----HHHHHHHHTTEEET
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHH----HHHHHHHcCCCEEC
Confidence            799999999999999999999999999999875       57899999999    99999999987654

(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 ....

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]

Probab=99.47  E-value=3.5e-14  Score=106.56  Aligned_cols=62  Identities=31%  Similarity=0.604  Sum_probs=58.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCCCc
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRF  167 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~  167 (171)
                      -+|||||||..+++.+|+.+|++||+|.+|.|+++++||++++...    ++.||++||+-.++-+
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNYgFVHiEdkta----aedairNLhgYtLhg~   64 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKNYGFVHIEDKTA----AEDAIRNLHGYTLHGV   64 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecccceEEeecccc----cHHHHhhcccceecce
Confidence            4799999999999999999999999999999999999999999999    9999999998766544

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.46  E-value=2.6e-12  Score=90.97  Aligned_cols=131  Identities=18%  Similarity=0.225  Sum_probs=94.4

Q ss_pred             CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDH   86 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~   86 (171)
                      ....||||+|+++.+|+.||.  ++..++|..|+|.++..-...  ...+   +++.             ..|.  .  .
T Consensus        43 g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprggr~s--~~~~---G~y~-------------gggr--g--G  100 (241)
T KOG0105|consen   43 GPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGGRSS--SDRR---GSYS-------------GGGR--G--G  100 (241)
T ss_pred             CCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCCCcc--cccc---cccC-------------CCCC--C--C
Confidence            346799999999999999999  489999999999987432100  0000   0000             0000  0  0


Q ss_pred             CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        87 ~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+....+.++...+..+|.|.+||++.+|+||+++...-|.|....+.+| .+-|.|...++    .+-|+++|.+....
T Consensus       101 gg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rDg~GvV~~~r~eD----MkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  101 GGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRDGVGVVEYLRKED----MKYAVRKLDDQKFR  176 (241)
T ss_pred             CCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecccceeeeeeehhh----HHHHHHhhcccccc
Confidence            01111122333556789999999999999999999999999999999998 45699999999    99999999776543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.44  E-value=2.6e-13  Score=107.26  Aligned_cols=63  Identities=21%  Similarity=0.325  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|+.||+|++|+|++|        ++||+|.++++    |++||+.||+..+
T Consensus       104 ~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~----A~~Ai~~LnG~~l  174 (346)
T TIGR01659       104 NNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEAD----SQRAIKNLNGITV  174 (346)
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHH----HHHHHHHcCCCcc
Confidence            556899999999999999999999999999999999876        58999999999    9999999998766

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).

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=99.43  E-value=2.5e-12  Score=95.80  Aligned_cols=63  Identities=22%  Similarity=0.263  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.+|+|||..||.+..+.+|.++|-+||.|++.+|..|        ++||.|+++..    |..||..|||.-+
T Consensus       282 GPeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~S----aQaAIqAMNGFQI  352 (371)
T KOG0146|consen  282 GPEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPAS----AQAAIQAMNGFQI  352 (371)
T ss_pred             CCCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchh----HHHHHHHhcchhh
Confidence            567999999999999999999999999999999999877        67899999999    9999999998743

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.41  E-value=2.1e-13  Score=99.61  Aligned_cols=59  Identities=31%  Similarity=0.497  Sum_probs=53.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      +...++||||||+|.+..+.|+++|++||+|+++.|+.|        ++||+|++.+.    |.+|.+..|
T Consensus         9 DT~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~a----a~rAc~dp~   75 (247)
T KOG0149|consen    9 DTTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEA----ATRACKDPN   75 (247)
T ss_pred             CceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHH----HHHHhcCCC
Confidence            446799999999999999999999999999999999977        67999999999    999887654

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.39  E-value=5.9e-13  Score=99.92  Aligned_cols=59  Identities=19%  Similarity=0.166  Sum_probs=54.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++|||+|||+.+|+++|+++|+.||+|++|.|++|     ++||+|.++++    |+.||. ||+..+
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~~~GfAFVtF~d~ea----Ae~All-LnG~~l   67 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENERSQIAYVTFKDPQG----AETALL-LSGATI   67 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEeCcHHH----HHHHHH-hcCCee
Confidence            579999999999999999999999999999999865     68999999999    999995 888755

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.37  E-value=1e-12  Score=97.29  Aligned_cols=60  Identities=22%  Similarity=0.190  Sum_probs=55.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.+|||+||++.+|+++|+++|+.||+|.+|.|++|     ++||+|.+++.    ++.|+ .||++.+
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~et~gfAfVtF~d~~a----aetAl-lLnGa~l   68 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGEYACTAYVTFKDAYA----LETAV-LLSGATI   68 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCCcceEEEEEECCHHH----HHHHH-hcCCCee
Confidence            4689999999999999999999999999999999987     57899999999    99998 7888754

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=99.35  E-value=1.5e-12  Score=91.22  Aligned_cols=62  Identities=27%  Similarity=0.375  Sum_probs=57.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec---CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~---~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+||+..+++.+|+.+|..||+|..|.|.   .+++||+|+++-+    |+.|+..|++..|+
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnPPGfAFVEFed~RD----A~DAvr~LDG~~~c   73 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNPPGFAFVEFEDPRD----AEDAVRYLDGKDIC   73 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecCCCceEEeccCccc----HHHHHhhcCCcccc
Confidence            37899999999999999999999999999999886   5689999999999    99999999998865

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=99.30  E-value=7e-12  Score=95.65  Aligned_cols=63  Identities=25%  Similarity=0.414  Sum_probs=57.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec------CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP------KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~------~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|+|-|||+.-.|.||+.+|.+||.|.+|.|+      +.|+||+|++.++    |++|-.+||+..+
T Consensus        93 ~~~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~d----adRARa~LHgt~V  161 (376)
T KOG0125|consen   93 KDTPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPAD----ADRARAELHGTVV  161 (376)
T ss_pred             CCCCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhh----HHHHHHHhhccee
Confidence            3446899999999999999999999999999999998      4589999999999    9999999999764

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=99.28  E-value=5e-12  Score=84.43  Aligned_cols=63  Identities=22%  Similarity=0.296  Sum_probs=57.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...+++|||+||++.++|++|.++|+..|+|..|.+-.|        +.||.|.++++    |+.|++-+++..+
T Consensus        33 ~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~d----A~~AlryisgtrL  103 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDD----AEDALRYISGTRL  103 (153)
T ss_pred             HhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchh----HHHHHHHhccCcc
Confidence            446899999999999999999999999999999988766        56899999999    9999999998764

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]

Probab=99.24  E-value=3.7e-12  Score=93.17  Aligned_cols=46  Identities=22%  Similarity=0.385  Sum_probs=42.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~   46 (171)
                      |+.|+.||||||||||+|++.+.|.+|+++ ...|+||+-.|+.|..
T Consensus        44 vitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   44 VITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            578999999999999999999999999998 6789999999998853

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]

Probab=99.24  E-value=2.2e-11  Score=89.63  Aligned_cols=62  Identities=24%  Similarity=0.392  Sum_probs=57.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|-|.||+.+++|++|+++|.+||.|..+.|.+|        |+||+|.++++    |.+||..|||..+.
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRdd----A~rAI~~LnG~gyd  257 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDD----AARAIADLNGYGYD  257 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHH----HHHHHHHccCcccc
Confidence            5688999999999999999999999999999999877        67899999999    99999999998764

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=99.24  E-value=8.7e-12  Score=91.40  Aligned_cols=126  Identities=21%  Similarity=0.299  Sum_probs=92.4

Q ss_pred             cceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCC
Q 030822           11 RGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPG   88 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~   88 (171)
                      .|||||+|.+.-+|+.|+..  +..|.|-.+.|.++......+   .    .+.++....     .             .
T Consensus        35 ~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~~~---g----~~~~g~r~~-----~-------------~   89 (216)
T KOG0106|consen   35 NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRRGR---G----RPRGGDRRS-----D-------------S   89 (216)
T ss_pred             cccceeccCchhhhhcccchhcCceecceeeeeeccccccccc---C----CCCCCCccc-----h-------------h
Confidence            48999999999999999984  566666667777665432222   0    000000000     0             0


Q ss_pred             CCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCCCcc
Q 030822           89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFS  168 (171)
Q Consensus        89 ~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~~  168 (171)
                      ..+   .+...+.+.|+|.+|+..+.+++|.++|.++|++.+..+++.+++|+|...++    |.+|+..|++...+...
T Consensus        90 ~~~---~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~~~~~~~v~Fs~~~d----a~ra~~~l~~~~~~~~~  162 (216)
T KOG0106|consen   90 RRY---RPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDARRNFAFVEFSEQED----AKRALEKLDGKKLNGRR  162 (216)
T ss_pred             hcc---CCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhhhccccceeehhhhh----hhhcchhccchhhcCce
Confidence            000   01134578999999999999999999999999999888899999999999999    99999999998876543

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=99.23  E-value=2.1e-10  Score=83.67  Aligned_cols=154  Identities=12%  Similarity=0.147  Sum_probs=99.8

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCC-----cCCCCCCCCccccchhhhhhhcc
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVG-----RMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      .|.+.||-|||.|.+.+.|..|+..  +..+.|+.+++.+|..+.+......     +......................
T Consensus        47 kt~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~  126 (221)
T KOG4206|consen   47 KTPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHF  126 (221)
T ss_pred             CCCCccCceEEEecChhHHHHHHHHhcCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccc
Confidence            5889999999999999999999995  7899999999999976543221100     00000000000000000000000


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec---CcceeEEecCCcccHHHHHHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRFWFCHLCGRSCSRSCFSKV  155 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~---~d~~fv~f~~~~~~~~~a~~A  155 (171)
                      ........+...   .....++...+|+.|||..++.+.|..+|.+|.....++++   .+.+||+|.+...    |..|
T Consensus       127 ~~~~~~~~p~p~---~~~~~ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~~~iAfve~~~d~~----a~~a  199 (221)
T KOG4206|consen  127 YNMNRMNLPPPF---LAQMAPPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPRSGIAFVEFLSDRQ----ASAA  199 (221)
T ss_pred             cccccccCCCCc---cccCCCCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCCCceeEEecchhhh----hHHH
Confidence            000000000001   02225678899999999999999999999999888888887   4678999999988    8888


Q ss_pred             HHHHhHhCCCC
Q 030822          156 SRNLWTAGCNR  166 (171)
Q Consensus       156 i~~l~~~~~~~  166 (171)
                      ...|.+.+|-.
T Consensus       200 ~~~lq~~~it~  210 (221)
T KOG4206|consen  200 QQALQGFKITK  210 (221)
T ss_pred             hhhhccceecc
Confidence            88888877653

>PLN03213 repressor of silencing 3; Provisional

Probab=99.23  E-value=1.8e-11  Score=98.07  Aligned_cols=63  Identities=19%  Similarity=0.266  Sum_probs=56.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----ceeEEecCC--cccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----FWFCHLCGR--SCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----~~fv~f~~~--~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .....+||||||++.+++++|+.+|+.||.|.+|.|+++    |+||.|...  .+    +.+||..||++..
T Consensus         7 ~~~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRETGRGFAFVEMssdddaE----eeKAISaLNGAEW   75 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTKGRSFAYIDFSPSSTNS----LTKLFSTYNGCVW   75 (759)
T ss_pred             CCcceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEecccCCceEEEEecCCcHHH----HHHHHHHhcCCee
Confidence            345689999999999999999999999999999999964    789999987  57    8999999998764

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.23  E-value=1.8e-11  Score=74.91  Aligned_cols=56  Identities=30%  Similarity=0.510  Sum_probs=49.0

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       104 lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      |||+|||+++++++|+++|+.||.|..+.+.++       .+||+|.+.++    |.+|++.+|+..
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~----a~~al~~~~~~~   63 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEED----AKRALELLNGKE   63 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHH----HHHHHHHHTTEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHH----HHHHHHHCCCcE
Confidence            799999999999999999999999999999876       46899999999    999999987543

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 ....

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]

Probab=99.20  E-value=1.3e-10  Score=94.00  Aligned_cols=156  Identities=17%  Similarity=0.243  Sum_probs=90.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcC--------CCCCCCCccccch
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRM--------SHGGYGAYNAYIS   70 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~--------~~~~~~~~~~~~~   70 (171)
                      +++|..||++||||||+|.+.++|++|+.  ++.+|.||.|+|..-+-+..........        .....+... ...
T Consensus       310 l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g-~~Q  388 (549)
T KOG0147|consen  310 LTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGG-RNQ  388 (549)
T ss_pred             eccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhcccccccccc-HHH
Confidence            46888899999999999999999999988  4899999999987654332221110000        000000000 000


Q ss_pred             hhhhhhccCC---C--------------CccCCCC-CCCCCCCCC------CCCCceEEEeCC--CCCCC--------HH
Q 030822           71 AATRYAALGA---P--------------TLYDHPG-SFYGRGESS------QRIGKKIFVGRL--PQEAT--------AE  116 (171)
Q Consensus        71 ~~~~~~~~g~---~--------------~~~~~~~-~~~~~~~~~------~~~~~~lfV~nL--p~~~t--------e~  116 (171)
                      .....+....   +              ......+ .......|.      ..++.++.+.|+  |.+.|        .+
T Consensus       389 l~~kla~~~~~~~~s~~~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~e  468 (549)
T KOG0147|consen  389 LMAKLAEGKGRSLPSTAISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIRE  468 (549)
T ss_pred             HHHHHhccCCccccchhhhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHH
Confidence            0000000000   0              0000000 000000110      145566667776  22222        26


Q ss_pred             HHHHHhhcccceEEEEecCcc-e--eEEecCCcccHHHHHHHHHHHhH
Q 030822          117 DLRRYFSRFGRILDVYVPKRF-W--FCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus       117 ~L~~~F~~fG~v~~v~i~~d~-~--fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      |+.+..++||.|..|.|-+.- +  +|+|.+.+.    |..|++.||+
T Consensus       469 dV~Eec~k~g~v~hi~vd~ns~g~VYvrc~s~~~----A~~a~~alhg  512 (549)
T KOG0147|consen  469 DVIEECGKHGKVCHIFVDKNSAGCVYVRCPSAEA----AGTAVKALHG  512 (549)
T ss_pred             HHHHHHHhcCCeeEEEEccCCCceEEEecCcHHH----HHHHHHHHhh
Confidence            788888999999999998764 3  588888888    9999999998

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=99.18  E-value=2.1e-10  Score=91.73  Aligned_cols=123  Identities=19%  Similarity=0.263  Sum_probs=89.2

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPT   82 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~   82 (171)
                      -+.+||..|=|||+|++++++++||+. ...+..|-|.|-.+.+.+.......                       ..|.
T Consensus        42 ~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~~e~d~~~~~-----------------------~g~~   98 (510)
T KOG4211|consen   42 PRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGGAEADWVMRP-----------------------GGPN   98 (510)
T ss_pred             eccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCCccccccccC-----------------------CCCC
Confidence            356899999999999999999999995 5678889999987765533211100                       0000


Q ss_pred             ccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEE-EEecCc-------ceeEEecCCcccHHHHHH
Q 030822           83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPKR-------FWFCHLCGRSCSRSCFSK  154 (171)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~-v~i~~d-------~~fv~f~~~~~~~~~a~~  154 (171)
                                    .......|-+++|||.||++||.++|+..=.|.. +.++.|       -+||+|.+.+.    |++
T Consensus        99 --------------s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~----ae~  160 (510)
T KOG4211|consen   99 --------------SSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFESQES----AEI  160 (510)
T ss_pred             --------------CCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecCHHH----HHH
Confidence                          0123567889999999999999999998855555 334444       36899999999    999


Q ss_pred             HHHHHhHhCCCCc
Q 030822          155 VSRNLWTAGCNRF  167 (171)
Q Consensus       155 Ai~~l~~~~~~~~  167 (171)
                      |+..-....-+||
T Consensus       161 Al~rhre~iGhRY  173 (510)
T KOG4211|consen  161 ALGRHRENIGHRY  173 (510)
T ss_pred             HHHHHHHhhccce
Confidence            9877554444443

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family

Probab=99.18  E-value=2.2e-11  Score=101.82  Aligned_cols=62  Identities=19%  Similarity=0.254  Sum_probs=56.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+++++++|+++|++||+|.+|.|++|        ++||.|.+.++    |.+|++.||+..+
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~----A~~Ai~~lnG~~i  174 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEA----AQLALEQMNGQML  174 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHH----HHHHHHhcCCeEE
Confidence            35689999999999999999999999999999999755        78999999999    9999999988654

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.

>PLN03134 glycine-rich RNA-binding protein 4; Provisional

Probab=99.18  E-value=9e-11  Score=82.01  Aligned_cols=49  Identities=22%  Similarity=0.458  Sum_probs=44.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|++.++|++||+.  ++.|+|+.|.|+++.++..
T Consensus        66 i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~~~~~  116 (144)
T PLN03134         66 VIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPANDRPS  116 (144)
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCCcCCC
Confidence            468999999999999999999999999984  7899999999999976543

>smart00362 RRM_2 RNA recognition motif

Probab=99.18  E-value=5.6e-11  Score=71.95  Aligned_cols=58  Identities=36%  Similarity=0.563  Sum_probs=52.5

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +|||+|||+.+++++|+++|++||+|.++.+..+      .+||.|.+.++    |+.|+..|++..+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~----a~~a~~~~~~~~~   64 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEED----AEKAIEALNGTKL   64 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHH----HHHHHHHhCCcEE
Confidence            5899999999999999999999999999999865      46899999999    9999999987543

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=99.15  E-value=8.4e-10  Score=87.44  Aligned_cols=155  Identities=19%  Similarity=0.198  Sum_probs=95.6

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCC-CcCCCC----------C-------
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPV-GRMSHG----------G-------   61 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~-~~~~~~----------~-------   61 (171)
                      ..| ..|++||||.|+|+++|.+++|++.  .+++.||+|.|+.....+..+... .+-..+          +       
T Consensus        78 l~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~  156 (608)
T KOG4212|consen   78 LFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGG  156 (608)
T ss_pred             ecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccCchhhhhhhheeeccCcccccCcceeccccccccc
Confidence            345 5899999999999999999999995  799999999998654322211100 000000          0       


Q ss_pred             --CCC--ccccchh-hhhhhcc----CCCCccCCC---------CCCC-CCCCCCCCCCceEEEeCCCCCCCHHHHHHHh
Q 030822           62 --YGA--YNAYISA-ATRYAAL----GAPTLYDHP---------GSFY-GRGESSQRIGKKIFVGRLPQEATAEDLRRYF  122 (171)
Q Consensus        62 --~~~--~~~~~~~-~~~~~~~----g~~~~~~~~---------~~~~-~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F  122 (171)
                        .+.  .+..... ..+....    .....|.+.         .+.. +.....++...++||.||.+.+....|++.|
T Consensus       157 g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvf  236 (608)
T KOG4212|consen  157 GGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVF  236 (608)
T ss_pred             CCCCccccCCCCcccccccccccCccccccccccchhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHh
Confidence              000  0000000 0000000    000001000         0000 0011124556799999999999999999999


Q ss_pred             hcccceEEEEecCcc-------eeEEecCCcccHHHHHHHHHHHhH
Q 030822          123 SRFGRILDVYVPKRF-------WFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus       123 ~~fG~v~~v~i~~d~-------~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      .-.|.|+.+.+-.|+       .-++|+.+-+    |.+||..|++
T Consensus       237 gmAGkv~~vdf~idKeG~s~G~~vi~y~hpve----avqaIsml~~  278 (608)
T KOG4212|consen  237 GMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVE----AVQAISMLDR  278 (608)
T ss_pred             ccceeeeeeceeeccccccCCeeEEEecchHH----HHHHHHhhcc
Confidence            999999999887663       3489988889    9999998874

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=99.15  E-value=8.2e-11  Score=84.76  Aligned_cols=63  Identities=25%  Similarity=0.394  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ......|-|-||.+.++.++|+.+|++||.|.+|.|++|        |+||.|.+..+    |+.|+..|.++.+
T Consensus        10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~d----aedA~damDG~~l   80 (256)
T KOG4207|consen   10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRD----AEDALDAMDGAVL   80 (256)
T ss_pred             cccceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecch----HHHHHHhhcceee
Confidence            455688999999999999999999999999999999987        78999999999    9999999988754

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.14  E-value=1.1e-10  Score=75.24  Aligned_cols=61  Identities=16%  Similarity=0.272  Sum_probs=54.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC-----cceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-----RFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~-----d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ...+-|||+|||+.+|.++..++|+.||+|..|+|--     .-+||.|++..+    |.+|..-|++-.
T Consensus        16 evnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~TrGTAFVVYedi~d----Ak~A~dhlsg~n   81 (124)
T KOG0114|consen   16 EVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKETRGTAFVVYEDIFD----AKKACDHLSGYN   81 (124)
T ss_pred             hhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccCcCceEEEEehHhhh----HHHHHHHhcccc
Confidence            3467899999999999999999999999999999974     457899999999    999999998854

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]

Probab=99.13  E-value=1.2e-10  Score=91.89  Aligned_cols=61  Identities=25%  Similarity=0.483  Sum_probs=56.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcc--------eeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF--------WFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~--------~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      +...-++||+-+|..|+|.||+++|++||.|.+|.|++|+        .||+|..+++    |.+|+..||.-
T Consensus        31 d~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~----a~~a~~Alhn~   99 (510)
T KOG0144|consen   31 DGSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKE----ADEAINALHNQ   99 (510)
T ss_pred             CchhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHH----HHHHHHHhhcc
Confidence            4567899999999999999999999999999999999994        5899999999    99999999864

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]

Probab=99.08  E-value=1.7e-10  Score=81.52  Aligned_cols=60  Identities=18%  Similarity=0.305  Sum_probs=55.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ...+|||+||+..++++.|+++|-+.|+|+++.|++|        ++|++|.++++    |+-||+-||..+
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eed----adYAikiln~Vk   75 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEED----ADYAIKILNMVK   75 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhh----hHHHHHHHHHHH
Confidence            4689999999999999999999999999999999987        68999999999    999999999543

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.08  E-value=5.3e-12  Score=89.09  Aligned_cols=61  Identities=26%  Similarity=0.352  Sum_probs=55.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +.-|||||||+..||.||--+|++||+|++|.+++|        |+|++|.+-..    ...|+.+|||..+.
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRS----TILAVDN~NGiki~  103 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRS----TILAVDNLNGIKIL  103 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccc----eEEEEeccCCceec
Confidence            466999999999999999999999999999999988        66899999888    88999999988753

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=99.07  E-value=1.9e-10  Score=85.91  Aligned_cols=60  Identities=23%  Similarity=0.335  Sum_probs=56.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      --.+||+-|...++-++|++.|.+||+|.+++|++|        ++||.|.+.++    ||+||..|||.=+
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~d----AEnAI~~MnGqWl  129 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKED----AENAIQQMNGQWL  129 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHH----HHHHHHHhCCeee
Confidence            457999999999999999999999999999999988        67999999999    9999999998644

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]

Probab=99.06  E-value=1.3e-09  Score=86.49  Aligned_cols=64  Identities=19%  Similarity=0.451  Sum_probs=59.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+.++.||||.||.++.|++|..+|++-|+|-+++||+|        ++||.|++.++    |.+||+.||...+.
T Consensus        80 p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~----Aq~Aik~lnn~Eir  151 (506)
T KOG0117|consen   80 PPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEE----AQEAIKELNNYEIR  151 (506)
T ss_pred             CCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHH----HHHHHHHhhCcccc
Confidence            356899999999999999999999999999999999987        67999999999    99999999988443

>smart00360 RRM RNA recognition motif

Probab=99.04  E-value=2.6e-10  Score=68.67  Aligned_cols=55  Identities=33%  Similarity=0.484  Sum_probs=49.7

Q ss_pred             EeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          106 VGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       106 V~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      |+|||+.+++++|+++|++||.|..+.+..+        ++||.|.+.++    |..|+..||+..+
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~----a~~a~~~~~~~~~   63 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEED----AEKALEALNGKEL   63 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHH----HHHHHHHcCCCee
Confidence            5799999999999999999999999999865        67899999999    9999999986544

>smart00361 RRM_1 RNA recognition motif

Probab=99.01  E-value=5.7e-10  Score=68.44  Aligned_cols=40  Identities=28%  Similarity=0.378  Sum_probs=35.6

Q ss_pred             CCCCCC--CCccceEEEEECCHHHHHHHHhc--CCccCCeEEEE
Q 030822            2 PKDQGS--KAHRGIGFITFASADSVENLMVD--THELGGSTVVV   41 (171)
Q Consensus         2 ~~D~~t--g~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v   41 (171)
                      +.|+.+  |++||||||+|.+.++|.+|++.  +..++||.|.+
T Consensus        26 ~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361       26 YIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             EeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            456666  99999999999999999999994  78999999876

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]

Probab=99.00  E-value=5.5e-10  Score=79.29  Aligned_cols=61  Identities=18%  Similarity=0.330  Sum_probs=54.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec-----CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||..+.+.+|+++|.+||.|..|.|.     ..++||+|++.-+    |+.||..-++-.+
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~g~ppfafVeFEd~RD----AeDAiygRdGYdy   70 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRPGPPPFAFVEFEDPRD----AEDAIYGRDGYDY   70 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCCCCCCeeEEEecCccc----hhhhhhccccccc
Confidence            46899999999999999999999999999999985     3478999999999    9999987665443

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.97  E-value=9.5e-10  Score=83.04  Aligned_cols=60  Identities=30%  Similarity=0.497  Sum_probs=55.1

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+|||+|||+.+++++|+++|.+||.|..+.|+.|        ++||.|.+.++    |..|+..|++..+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~----~~~a~~~~~~~~~  182 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEES----AEKAIEELNGKEL  182 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHH----HHHHHHHcCCCeE
Confidence            599999999999999999999999999999999866        57899999999    9999999986544

>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=98.97  E-value=1.6e-09  Score=65.79  Aligned_cols=57  Identities=33%  Similarity=0.546  Sum_probs=52.2

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      +|+|+|||+.+++++|+++|+.||.|..+.+..+       .++|.|.+.++    |..|+..|++..
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~----a~~a~~~~~~~~   64 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEED----AEKALEALNGKE   64 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHH----HHHHHHHhCCCe
Confidence            4899999999999999999999999999999865       46899999999    999999998864

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).

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.97  E-value=2.7e-10  Score=82.89  Aligned_cols=62  Identities=24%  Similarity=0.353  Sum_probs=57.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++||||+|..+++|.-|...|-+||.|.+|.|+.|        ++||+|.-.++    |..||.+||++.+
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aED----AaaAiDNMnesEL   77 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAED----AAAAIDNMNESEL   77 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccch----hHHHhhcCchhhh
Confidence            35789999999999999999999999999999999976        67999999999    9999999998764

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]

Probab=98.96  E-value=6.4e-10  Score=83.13  Aligned_cols=60  Identities=25%  Similarity=0.412  Sum_probs=55.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ..++||||-|...-.|+|++.+|++||.|++|.+.+.       .+||+|.+..|    |..||..||+..
T Consensus        18 ~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~e----AqaAI~aLHgSq   84 (371)
T KOG0146|consen   18 DDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAE----AQAAINALHGSQ   84 (371)
T ss_pred             cchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchH----HHHHHHHhcccc
Confidence            4689999999999999999999999999999999864       67999999999    999999999853

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=98.95  E-value=3e-08  Score=72.52  Aligned_cols=58  Identities=12%  Similarity=0.186  Sum_probs=42.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHhH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      .-.+|||.||..++||++|+++|+.|-.....+|.-. -.-|-|.+.++    .++|-..|+-
T Consensus       209 acstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~~~g~~vaf~~~~~----~~~at~am~~  267 (284)
T KOG1457|consen  209 ACSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRARGGMPVAFADFEE----IEQATDAMNH  267 (284)
T ss_pred             hhhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEecCCCcceEeecHHH----HHHHHHHHHH
Confidence            3468999999999999999999999987777777532 22355555555    5555555543

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]

Probab=98.91  E-value=1e-09  Score=79.14  Aligned_cols=45  Identities=24%  Similarity=0.471  Sum_probs=42.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      ||+|+.|+.+||||||-|.+..+|+.||+.  +.+++|+.|.|+.|.
T Consensus        45 IPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   45 IPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            799999999999999999999999999994  899999999998774

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]

Probab=98.89  E-value=1.3e-08  Score=76.73  Aligned_cols=108  Identities=24%  Similarity=0.415  Sum_probs=77.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCC----CCCCCCCCCcCCCCCCCCccccchhhhh
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATP----KEDDFRPVGRMSHGGYGAYNAYISAATR   74 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (171)
                      |+.|+.||++||||||+|.+.++|..|+..  +..|.|+.|.|.++.+    +......             ........
T Consensus       147 ~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~-------------~~~~~~~~  213 (306)
T COG0724         147 LVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNN-------------LDASFAKK  213 (306)
T ss_pred             eeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeeccccccccccccccc-------------cchhhhcc
Confidence            467889999999999999999999999995  6899999999998653    1111000             00000000


Q ss_pred             hhccCCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc
Q 030822           75 YAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR  136 (171)
Q Consensus        75 ~~~~g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d  136 (171)
                                     ..............+++.+++..++..++...|..+|.+....+...
T Consensus       214 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  260 (306)
T COG0724         214 ---------------LSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPPS  260 (306)
T ss_pred             ---------------ccccccccccccceeeccccccccchhHHHHhccccccceeeeccCC
Confidence                           00000111445788999999999999999999999999987777644

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.85  E-value=4e-09  Score=85.23  Aligned_cols=61  Identities=31%  Similarity=0.502  Sum_probs=57.6

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCNR  166 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~  166 (171)
                      +.|||||||+++++++|..+|+..|.|.+++++.|        ++|++|.+.++    ++.|+++||++..+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~----~~~a~~~lNg~~~~g   87 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEET----AERAIRNLNGAEFNG   87 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhh----HHHHHHhcCCcccCC
Confidence            89999999999999999999999999999999977        67899999999    999999999998764

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.84  E-value=4e-09  Score=79.83  Aligned_cols=62  Identities=19%  Similarity=0.285  Sum_probs=55.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.+||||+-|+++++|..|+..|+.||+|..+.|++|        ++||.|..+-+    ...|.+..++..+
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erd----m~~AYK~adG~~I  168 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERD----MKAAYKDADGIKI  168 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHH----HHHHHHhccCcee
Confidence            46899999999999999999999999999999999987        68999999999    8888887765443

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.84  E-value=4.3e-09  Score=71.15  Aligned_cols=63  Identities=22%  Similarity=0.222  Sum_probs=57.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++-|||.++...++|+++.+.|..||+|.++.+-.|        ++.|.|...++    |..||..||++.+
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~ke----Aq~A~~~~Ng~~l  139 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKE----AQAAIDALNGAEL  139 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHH----HHHHHHhccchhh
Confidence            456899999999999999999999999999999999876        34599999999    9999999998865

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=98.82  E-value=5.7e-09  Score=87.66  Aligned_cols=62  Identities=23%  Similarity=0.410  Sum_probs=56.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .-++|||||+|+..++|.||.++|+.||+|++|.++  +.++||++..+.+    |++|+.+|+...+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~R~cAfI~M~~Rqd----A~kalqkl~n~kv  482 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPPRGCAFIKMVRRQD----AEKALQKLSNVKV  482 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhcccceeEeeccCCceeEEEEeehhH----HHHHHHHHhcccc
Confidence            457899999999999999999999999999999998  5678999999999    9999999986554

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.80  E-value=4.3e-09  Score=76.68  Aligned_cols=47  Identities=36%  Similarity=0.627  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ||.|..++++||||||+|...|+|..||.+  ..++-||.|+|.+|.|.
T Consensus        42 iPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~AkP~   90 (298)
T KOG0111|consen   42 IPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAKPE   90 (298)
T ss_pred             cccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecCCc
Confidence            588999999999999999999999999997  57999999999999873

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]

Probab=98.76  E-value=8.6e-09  Score=78.09  Aligned_cols=44  Identities=18%  Similarity=0.407  Sum_probs=41.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      |++|+.||+|||||||+|+++-+...|.++  +..|+|+.|.|.+-
T Consensus       133 lV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen  133 LVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             EeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            589999999999999999999999999995  89999999999864

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]

Probab=98.75  E-value=1e-08  Score=81.41  Aligned_cols=64  Identities=17%  Similarity=0.159  Sum_probs=57.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec---CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~---~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+++||+.|++-|..||.|.++.|+   ++.+-|+|.++++    |+.|+..|++..+.
T Consensus       533 arKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime~GkskGVVrF~s~ed----AEra~a~Mngs~l~  599 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIMENGKSKGVVRFFSPED----AERACALMNGSRLD  599 (608)
T ss_pred             cccccEEEEecCCccccHHHHHHHHHhccceehhhhhccCCccceEEecCHHH----HHHHHHHhccCccc
Confidence            3467899999999999999999999999999999996   4567799999999    99999999987653

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]

Probab=98.73  E-value=2.8e-08  Score=72.65  Aligned_cols=60  Identities=23%  Similarity=0.362  Sum_probs=53.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHH----HhhcccceEEEEec-----CcceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          100 IGKKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVP-----KRFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~----~F~~fG~v~~v~i~-----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      +..+|||.||+..+..++|+.    +|++||.|.+|...     ++.+||.|++.+.    |..|+++|+|.-
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvFk~~~~----As~A~r~l~gfp   76 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVFKETEA----ASAALRALQGFP   76 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEecChhH----HHHHHHHhcCCc
Confidence            344999999999999999998    99999999999885     5689999999999    999999998753

>PF13893 RRM_5: RNA recognition motif

Probab=98.73  E-value=1.4e-08  Score=59.34  Aligned_cols=43  Identities=23%  Similarity=0.318  Sum_probs=38.2

Q ss_pred             HHHHhhcccceEEEEecC---cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          118 LRRYFSRFGRILDVYVPK---RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       118 L~~~F~~fG~v~~v~i~~---d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      |+++|++||+|.++.+.+   +.+||+|.+.++    |..|++.||+...
T Consensus         1 L~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~----A~~a~~~l~~~~~   46 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKKRGFAFVEFASVED----AQKAIEQLNGRQF   46 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTSTTEEEEEESSHHH----HHHHHHHHTTSEE
T ss_pred             ChHHhCCcccEEEEEEEeCCCCEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            789999999999999997   458999999999    9999999998764

(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 ....

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.67  E-value=3.4e-08  Score=80.69  Aligned_cols=136  Identities=15%  Similarity=0.219  Sum_probs=88.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      +++|..||-|+||+|.+|.++.....|+..  +..+.+++|.|..|.+-.....+.....+.     ..........   
T Consensus       321 lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~-----~~~~i~~~~~---  392 (500)
T KOG0120|consen  321 LVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQS-----QVPGIPLLMT---  392 (500)
T ss_pred             eecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCcccc-----ccccchhhhc---
Confidence            357889999999999999999999999994  788999999999886543222111110000     0000000000   


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCC----CCCCH------HHHHHHhhcccceEEEEecCcc-----------
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLP----QEATA------EDLRRYFSRFGRILDVYVPKRF-----------  137 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp----~~~te------~~L~~~F~~fG~v~~v~i~~d~-----------  137 (171)
                                      .....+...|...|+=    ...++      ++++..++.||.|..|.|++++           
T Consensus       393 ----------------q~~g~~t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~g~v~~v~ipr~~~~~~~~~G~Gk  456 (500)
T KOG0120|consen  393 ----------------QMAGIPTEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKFGAVRSVEIPRPYPDENPVPGTGK  456 (500)
T ss_pred             ----------------ccCCCcchhhhhhhcCCHHHhcchHHHHHHHHHHHHHhcccCceeEEecCCCCCCCCcCCCccc
Confidence                            0001223334444431    11111      6778888999999999999882           


Q ss_pred             eeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          138 WFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       138 ~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      -||+|.+.++    +++|..+|+|-.+
T Consensus       457 VFVefas~ed----~qrA~~~L~GrKF  479 (500)
T KOG0120|consen  457 VFVEFADTED----SQRAMEELTGRKF  479 (500)
T ss_pred             EEEEecChHH----HHHHHHHccCcee
Confidence            3899999999    9999999987543

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]

Probab=98.63  E-value=2.6e-08  Score=77.38  Aligned_cols=55  Identities=35%  Similarity=0.553  Sum_probs=48.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ..++|||++|+|.++++.|+++|++||+|.+|.|++|        ++||.|.+.++    ...++..
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~----v~~vl~~   67 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEG----VDAVLNA   67 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcc----hheeecc
Confidence            5789999999999999999999999999999999996        67899998888    5555544

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.63  E-value=1.2e-07  Score=79.20  Aligned_cols=60  Identities=27%  Similarity=0.373  Sum_probs=53.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC-----------cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-----------RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~-----------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++|||.||++.++.++|..+|..+|.|.++.|.+           .++||+|.+.+.    |..|++.|++..+
T Consensus       515 ~t~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~----A~~a~k~lqgtvl  585 (725)
T KOG0110|consen  515 ETKLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPES----AQAALKALQGTVL  585 (725)
T ss_pred             chhhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHH----HHHHHHHhcCcee
Confidence            34499999999999999999999999999998863           468999999999    9999999986544

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=98.61  E-value=4.5e-08  Score=70.67  Aligned_cols=45  Identities=13%  Similarity=0.220  Sum_probs=38.9

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATP   46 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~   46 (171)
                      .|++.||.|||||||+|++++.|.-|-+.  ...+.++.|.|.+--|
T Consensus        83 sRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vmpp  129 (214)
T KOG4208|consen   83 SRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVMPP  129 (214)
T ss_pred             ecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEeCc
Confidence            38899999999999999999999999885  5788899998886533

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]

Probab=98.58  E-value=1e-07  Score=79.72  Aligned_cols=68  Identities=19%  Similarity=0.259  Sum_probs=61.4

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC-----------cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           97 SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-----------RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        97 ~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~-----------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +.+..++|||+||++.++++.|-..|+.||+|..++|+-           ..+||-|-++.+    |+.|++.|++-.+-
T Consensus       170 gDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D----~era~k~lqg~iv~  245 (877)
T KOG0151|consen  170 GDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRAD----AERALKELQGIIVM  245 (877)
T ss_pred             CCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhh----HHHHHHHhcceeee
Confidence            466789999999999999999999999999999999983           368999999999    99999999998876


Q ss_pred             Ccc
Q 030822          166 RFS  168 (171)
Q Consensus       166 ~~~  168 (171)
                      +|.
T Consensus       246 ~~e  248 (877)
T KOG0151|consen  246 EYE  248 (877)
T ss_pred             eee
Confidence            653

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]

Probab=98.58  E-value=6.1e-08  Score=74.45  Aligned_cols=45  Identities=18%  Similarity=0.411  Sum_probs=39.2

Q ss_pred             CCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCC
Q 030822            7 SKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDF   51 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~   51 (171)
                      ..-|||||||+|++.++|++|-++  +..+.||+|+|+.++++....
T Consensus       132 ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATarV~n~  178 (376)
T KOG0125|consen  132 ERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATARVHNK  178 (376)
T ss_pred             cCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchhhccC
Confidence            346999999999999999999885  789999999999998874443

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.57  E-value=1.1e-07  Score=73.60  Aligned_cols=60  Identities=22%  Similarity=0.387  Sum_probs=52.1

Q ss_pred             CCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHH
Q 030822           96 SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus        96 ~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      +.+..-.+|||++|-..++|.+|+++|.+||+|.++.+...  .+||+|..++.    |+.|...+
T Consensus       223 PeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~~CAFv~ftTR~a----AE~Aae~~  284 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRKGCAFVTFTTREA----AEKAAEKS  284 (377)
T ss_pred             CcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecccccceeeehhhHH----HHHHHHhh
Confidence            34667789999999999999999999999999999999855  67999999999    77766553

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]

Probab=98.53  E-value=6e-08  Score=75.58  Aligned_cols=60  Identities=20%  Similarity=0.274  Sum_probs=55.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      --++||||.|.++..|+.|+..|.+||+|.++.+.-|        |+||+|+-++.    |..|+++||+.-
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEa----AqLAlEqMNg~m  179 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEA----AQLALEQMNGQM  179 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHH----HHHHHHHhcccc
Confidence            4689999999999999999999999999999998644        78899999999    999999999863

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=98.53  E-value=3.3e-07  Score=75.23  Aligned_cols=64  Identities=20%  Similarity=0.441  Sum_probs=57.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...+++|||-+|...+...+|+.+|++||.|+-++|+.+        ++||+|.+..+    |.+.|..||...++
T Consensus       402 s~~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~e----AtkCI~hLHrTELH  473 (940)
T KOG4661|consen  402 STLGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAE----ATKCIEHLHRTELH  473 (940)
T ss_pred             cccccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHH----HHHHHHHhhhhhhc
Confidence            345789999999999999999999999999999999965        78999999999    89999999876543

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]

Probab=98.50  E-value=1.4e-07  Score=76.44  Aligned_cols=47  Identities=21%  Similarity=0.452  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ++.|+.||++|||||++|.+++++++|++.  +.++.||+|+|.|+...
T Consensus        50 ~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   50 LVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             ecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            467999999999999999999999999995  79999999999998644

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.50  E-value=2.3e-08  Score=70.92  Aligned_cols=44  Identities=18%  Similarity=0.337  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      |+||+.||+|+||||+.|++..+.-.|+.+  +..|.||.|+|...
T Consensus        67 LiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   67 LIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             EEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            589999999999999999999999999985  88999999999864

>PF14259 RRM_6: RNA recognition motif (a

Probab=98.48  E-value=1.8e-07  Score=56.98  Aligned_cols=38  Identities=21%  Similarity=0.429  Sum_probs=33.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEE
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVV   40 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~   40 (171)
                      +++++ |+++|+|||+|.++++|++|++.  ++.++|+.|+
T Consensus        31 ~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen   31 IKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             Eeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            35666 89999999999999999999994  5899999874

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 ....

>smart00360 RRM RNA recognition motif

Probab=98.46  E-value=3.5e-07  Score=54.65  Aligned_cols=41  Identities=24%  Similarity=0.503  Sum_probs=35.0

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEe
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVD   42 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~   42 (171)
                      +.++.+++++|||||+|.+.++|.+|++.  +..++|+.|.|.
T Consensus        29 ~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360       29 VRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             EeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            45566899999999999999999999985  578889988763

>PF00076 RRM_1: RNA recognition motif

Probab=98.43  E-value=2.2e-07  Score=56.20  Aligned_cols=35  Identities=20%  Similarity=0.485  Sum_probs=31.9

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEE
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVV   40 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~   40 (171)
                      .+++++|||||+|++.++|++|++.  +..++|++|+
T Consensus        34 ~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen   34 SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            5789999999999999999999994  8899999874

(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 ....

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.43  E-value=1.2e-07  Score=70.58  Aligned_cols=45  Identities=16%  Similarity=0.402  Sum_probs=39.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      ++||+.||+|+|||||.|.++.++.+||++  +..++.|.|..+.+.
T Consensus       222 viRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS~  268 (290)
T KOG0226|consen  222 VIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKSE  268 (290)
T ss_pred             ccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhhh
Confidence            589999999999999999999999999996  678888888776543

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=98.42  E-value=5.5e-07  Score=67.60  Aligned_cols=63  Identities=19%  Similarity=0.207  Sum_probs=56.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcce-------eEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW-------FCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~-------fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....+|+|.|||+.++++||+++|..||.+..+.|.+|..       -|.|.-.++    |+.|++.+|+..+.
T Consensus        81 ~~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~D----A~~avk~~~gv~ld  150 (243)
T KOG0533|consen   81 TRSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDD----AERAVKKYNGVALD  150 (243)
T ss_pred             CCcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHh----HHHHHHHhcCcccC
Confidence            3458899999999999999999999999999999998853       499999999    99999999986543

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=98.40  E-value=3.2e-07  Score=71.35  Aligned_cols=61  Identities=25%  Similarity=0.360  Sum_probs=55.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      .++.+.|||=-|.+-++++||.-+|+.||.|.+|.|++|        ++||.|.+.++    .++|.=.|..+
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~es----cE~AyFKMdNv  304 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKES----CEQAYFKMDNV  304 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhh----HHHHHhhhcce
Confidence            567899999999999999999999999999999999998        57899999999    88888777543

>PF13893 RRM_5: RNA recognition motif

Probab=98.40  E-value=8.1e-07  Score=51.74  Aligned_cols=34  Identities=26%  Similarity=0.556  Sum_probs=31.6

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeec
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a   44 (171)
                      +|+|||+|.+.++|++|++  ++..++|++|.|.+|
T Consensus        21 ~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen   21 RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            6999999999999999999  588999999999875

(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 ....

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=98.39  E-value=3.7e-06  Score=65.23  Aligned_cols=142  Identities=16%  Similarity=0.140  Sum_probs=86.8

Q ss_pred             CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccC
Q 030822            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   85 (171)
                      |.-||=|.+.|--.++++.|++  ++..+.|++|+|..|.-.............+...........  +....+-     
T Consensus       180 G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~--q~k~~dw-----  252 (382)
T KOG1548|consen  180 GKLKGDALCCYIKRESVELAIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQ--QQKLLDW-----  252 (382)
T ss_pred             CCccCceEEEeecccHHHHHHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHH--HHhhccc-----
Confidence            7778999999999999999999  578899999999988642111110000000000000000000  0000000     


Q ss_pred             CCCCCCCCCCCCCCCCceEEEeCCC----CCCC-------HHHHHHHhhcccceEEEEec----CcceeEEecCCcccHH
Q 030822           86 HPGSFYGRGESSQRIGKKIFVGRLP----QEAT-------AEDLRRYFSRFGRILDVYVP----KRFWFCHLCGRSCSRS  150 (171)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~lfV~nLp----~~~t-------e~~L~~~F~~fG~v~~v~i~----~d~~fv~f~~~~~~~~  150 (171)
                        .... ..++.....++|.+.||=    +..+       +++|++-.++||.|.+|.|-    ..-.+|.|.+.++   
T Consensus       253 --~pd~-~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlkedl~eec~K~G~v~~vvv~d~hPdGvvtV~f~n~ee---  326 (382)
T KOG1548|consen  253 --RPDR-DDPSKARADRTVILKNMFTPEDFEKNPDLLNDLKEDLTEECEKFGQVRKVVVYDRHPDGVVTVSFRNNEE---  326 (382)
T ss_pred             --CCCc-cccccccCCcEEEeeecCCHHHhccCHHHHHHHHHHHHHHHHHhCCcceEEEeccCCCceeEEEeCChHH---
Confidence              0000 011124456889999982    2333       46778889999999999885    2245799999999   


Q ss_pred             HHHHHHHHHhHhC
Q 030822          151 CFSKVSRNLWTAG  163 (171)
Q Consensus       151 ~a~~Ai~~l~~~~  163 (171)
                       |..+|+.|+|-.
T Consensus       327 -A~~ciq~m~GR~  338 (382)
T KOG1548|consen  327 -ADQCIQTMDGRW  338 (382)
T ss_pred             -HHHHHHHhcCee
Confidence             999999998743

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]

Probab=98.35  E-value=1e-06  Score=72.18  Aligned_cols=127  Identities=20%  Similarity=0.244  Sum_probs=88.9

Q ss_pred             CCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCC
Q 030822            8 KAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDH   86 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~   86 (171)
                      ...+.|+|++|.+.++|..|+.. +..+.|+.+.+.................+                       .+..
T Consensus       220 n~~~nfa~ie~~s~~~at~~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~-----------------------~~~~  276 (500)
T KOG0120|consen  220 NLEKNFAFIEFRSISEATEAMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQ-----------------------LGKV  276 (500)
T ss_pred             cccccceeEEecCCCchhhhhcccchhhCCCCceecccccccCCccchhhhcc-----------------------cccc
Confidence            35688999999999999999984 77788998877643322111100000000                       0000


Q ss_pred             CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHH
Q 030822           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        87 ~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      +.  ...........++|||++||...++.+++++...||++....++.|        +.|.+|.+..-    ...|+..
T Consensus       277 ~~--~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsv----td~A~ag  350 (500)
T KOG0120|consen  277 GL--LPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSV----TDQAIAG  350 (500)
T ss_pred             CC--cccccCcccccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcc----hhhhhcc
Confidence            00  0000011345689999999999999999999999999999999876        56799999999    9999999


Q ss_pred             HhHhC
Q 030822          159 LWTAG  163 (171)
Q Consensus       159 l~~~~  163 (171)
                      |||-.
T Consensus       351 LnGm~  355 (500)
T KOG0120|consen  351 LNGMQ  355 (500)
T ss_pred             cchhh
Confidence            99854

>smart00361 RRM_1 RNA recognition motif

Probab=98.34  E-value=5.2e-07  Score=55.16  Aligned_cols=47  Identities=17%  Similarity=0.147  Sum_probs=39.4

Q ss_pred             HHHHHHHhh----cccceEEEE-ecC----------cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          115 AEDLRRYFS----RFGRILDVY-VPK----------RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       115 e~~L~~~F~----~fG~v~~v~-i~~----------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +++|+++|+    +||+|.++. |+.          .++||.|.+.++    |.+|++.||+..+.
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~d----A~~A~~~l~g~~~~   63 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSED----AARAIVDLNGRYFD   63 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            678999999    999999995 432          247899999999    99999999987543

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=98.31  E-value=8.8e-07  Score=72.34  Aligned_cols=61  Identities=16%  Similarity=0.243  Sum_probs=54.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      +.+..+|+|-|||.++++++|+++|+.||+|..|+.-+.   .-||+|.|.-+    |+.|+++|++-
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~~~~~~~v~FyDvR~----A~~Alk~l~~~  135 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPNKRGIVFVEFYDVRD----AERALKALNRR  135 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccccCceEEEEEeehHh----HHHHHHHHHHH
Confidence            556789999999999999999999999999999776543   45899999999    99999999864

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]

Probab=98.31  E-value=3.2e-07  Score=67.54  Aligned_cols=60  Identities=23%  Similarity=0.436  Sum_probs=56.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++||++||+.+.+.+|..+|..||.|.+|.+...++||.|.+..+    |+.||..||+..+.
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~gf~fv~fed~rd----a~Dav~~l~~~~l~   61 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMKNGFGFVEFEDPRD----ADDAVHDLDGKELC   61 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceeecccceeccCchhh----hhcccchhcCceec
Confidence            4699999999999999999999999999999999999999999999    99999999887654

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=98.30  E-value=1e-05  Score=64.16  Aligned_cols=135  Identities=16%  Similarity=0.157  Sum_probs=86.2

Q ss_pred             eEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCCCC
Q 030822           13 IGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSF   90 (171)
Q Consensus        13 fgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~   90 (171)
                      -|.|.|.+...|+-|++  +++.+.|++|+|.++.-..-. .+.......+...+ ...+...+.         ..|++-
T Consensus       337 ~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~vq-lp~egq~d~glT~d-y~~spLhrf---------kkpgsK  405 (492)
T KOG1190|consen  337 NALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTNVQ-LPREGQEDQGLTKD-YGNSPLHRF---------KKPGSK  405 (492)
T ss_pred             ceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcccc-CCCCCCcccccccc-CCCCchhhc---------cCcccc
Confidence            48999999999999999  489999999999876422111 11110000000000 000111111         111211


Q ss_pred             CCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--Cc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        91 ~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .....  -++..+|..-|+|.+++|++|+.+|..-|-.+....-  +|  .+.+.+.+.++    |..|+-.||....
T Consensus       406 N~~ni--~PpsatlHlsnip~svsee~lk~~f~~~g~~vkafkff~kd~kmal~q~~svee----A~~ali~~hnh~l  477 (492)
T KOG1190|consen  406 NYQNI--FPPSATLHLSNIPPSVSEEDLKNLFQEPGGQVKAFKFFQKDRKMALPQLESVEE----AIQALIDLHNHYL  477 (492)
T ss_pred             ccccc--CCchhheeeccCCcccchhHHHHhhhcCCceEEeeeecCCCcceeecccCChhH----hhhhccccccccC
Confidence            11111  3567899999999999999999999998887666543  34  45688999999    9999888876543

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation

Probab=98.29  E-value=3e-06  Score=55.99  Aligned_cols=57  Identities=19%  Similarity=0.216  Sum_probs=40.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      +-|.|.+++..++.++|++.|++||.|..|.+.++  .++|.|.+.+.    |..|+..+...
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~----A~~a~~~~~~~   60 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEA----AQKALEKLKEA   60 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS-------HHHHHHHHHHT
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcch----HHHHHHHHHhc
Confidence            46889899999999999999999999999999976  57899999999    99999998776

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=98.24  E-value=1.2e-06  Score=70.76  Aligned_cols=54  Identities=28%  Similarity=0.437  Sum_probs=47.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--------cceeEEecCCcccHHHHHHHHHH
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--------RFWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--------d~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ...|||+|||++++..+|++.|..||+|+...|..        -++||.|.+.++    +..||..
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~----~~~~i~A  349 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAA----VQNAIEA  349 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecch----hhhhhhc
Confidence            45599999999999999999999999999998874        367999999999    8888764

>KOG0226 consensus RNA-binding proteins [General function prediction only]

Probab=98.23  E-value=2.9e-06  Score=63.33  Aligned_cols=63  Identities=19%  Similarity=0.278  Sum_probs=57.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...-+||.+.|.-+++++.|-..|.+|-.-...++++|        ++||.|.+..+    +..|++.|++-.++
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad----~~rAmrem~gkyVg  258 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPAD----YVRAMREMNGKYVG  258 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHH----HHHHHHhhcccccc
Confidence            34678999999999999999999999988888899987        67999999999    99999999987764

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=98.23  E-value=6.3e-07  Score=65.49  Aligned_cols=63  Identities=13%  Similarity=0.201  Sum_probs=56.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|+...++|+.|.++|-+-|+|..|.|+.+      +++|.|.++-.    ..-|++-|||..+
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~s----v~~a~~L~ng~~l   74 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENS----VQLAGQLENGDDL   74 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccc----hhhhhhhcccchh
Confidence            345789999999999999999999999999999999865      57899999999    9999999988653

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=98.23  E-value=4.1e-07  Score=71.38  Aligned_cols=138  Identities=21%  Similarity=0.258  Sum_probs=85.5

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCcc
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   84 (171)
                      -.||..|=|||.|..+++|+.||.. ...|+-|-|++-+++..+-++. ..+........            ..+.|.. 
T Consensus       201 pdgrpTGdAFvlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqv-lnr~~s~pLi~------------~~~sp~~-  266 (508)
T KOG1365|consen  201 PDGRPTGDAFVLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQV-LNREVSEPLIP------------GLTSPLL-  266 (508)
T ss_pred             CCCCcccceEEEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHH-HHhhccccccC------------CCCCCCC-
Confidence            4789999999999999999999995 5667777777765543211110 00000000000            0000000 


Q ss_pred             CCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEE---EEecCc-------ceeEEecCCcccHHHHHH
Q 030822           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD---VYVPKR-------FWFCHLCGRSCSRSCFSK  154 (171)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~---v~i~~d-------~~fv~f~~~~~~~~~a~~  154 (171)
                        ++. ..+--+...+..+|-+++||++++-++|-.+|..|..-++   |.++.+       -+||+|.+.+.++.||.+
T Consensus       267 --p~~-p~~~~p~~~~kdcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk  343 (508)
T KOG1365|consen  267 --PGG-PARLVPPTRSKDCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQK  343 (508)
T ss_pred             --CCC-ccccCCCCCCCCeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHH
Confidence              000 0011122344678999999999999999999999864333   344432       469999999997777777


Q ss_pred             HHHHHh
Q 030822          155 VSRNLW  160 (171)
Q Consensus       155 Ai~~l~  160 (171)
                      .-+.+.
T Consensus       344 ~hk~~m  349 (508)
T KOG1365|consen  344 CHKKLM  349 (508)
T ss_pred             HHHhhc
Confidence            776665

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=98.19  E-value=1.6e-05  Score=64.67  Aligned_cols=57  Identities=25%  Similarity=0.359  Sum_probs=48.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhh-cccceEEEEecCccee--------EEecCCcccHHHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFS-RFGRILDVYVPKRFWF--------CHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~-~fG~v~~v~i~~d~~f--------v~f~~~~~~~~~a~~Ai~~  158 (171)
                      -.+.+|||||+||--++.++|-.+|. .||.|..+-|=.|..+        |+|.+...    -.+||..
T Consensus       367 lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqs----Yi~AIsa  432 (520)
T KOG0129|consen  367 IDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQA----YIKAISA  432 (520)
T ss_pred             cCccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHH----HHHHHhh
Confidence            34579999999999999999999999 7999999999888433        99999888    6666653

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.18  E-value=4.4e-06  Score=64.66  Aligned_cols=121  Identities=21%  Similarity=0.201  Sum_probs=82.7

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc-C-CccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD-T-HELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAP   81 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~-~-~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~   81 (171)
                      ......++||+.|.|+..+.+..|+.. + ..+.++.+.......+...  +..                          
T Consensus       123 ~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~~~~~~--~~n--------------------------  174 (285)
T KOG4210|consen  123 LEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNTRRGLR--PKN--------------------------  174 (285)
T ss_pred             hccccccccceeeccccHHHHHHHHHhhhccccccccccCccccccccc--ccc--------------------------
Confidence            355778999999999999999999985 3 4666666655444333200  000                          


Q ss_pred             CccCCCCCCCCCCCCCCCCCceEE-EeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHH
Q 030822           82 TLYDHPGSFYGRGESSQRIGKKIF-VGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCF  152 (171)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~lf-V~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a  152 (171)
                           +....     ......++| |++|+..+++++|+.+|..+|.|..++++.+        +++|.|....+    .
T Consensus       175 -----~~~~~-----~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~----~  240 (285)
T KOG4210|consen  175 -----KLSRL-----SSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNS----K  240 (285)
T ss_pred             -----hhccc-----ccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchh----H
Confidence                 00000     012234555 9999999999999999999999999999866        44588888777    6


Q ss_pred             HHHHHHHhHhCCCCc
Q 030822          153 SKVSRNLWTAGCNRF  167 (171)
Q Consensus       153 ~~Ai~~l~~~~~~~~  167 (171)
                      ..++.. .+..|-.+
T Consensus       241 ~~~~~~-~~~~~~~~  254 (285)
T KOG4210|consen  241 KLALND-QTRSIGGR  254 (285)
T ss_pred             HHHhhc-ccCcccCc
Confidence            666665 45444433

>smart00362 RRM_2 RNA recognition motif

Probab=98.17  E-value=4e-06  Score=50.11  Aligned_cols=35  Identities=26%  Similarity=0.552  Sum_probs=31.0

Q ss_pred             CCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEe
Q 030822            8 KAHRGIGFITFASADSVENLMVD--THELGGSTVVVD   42 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~   42 (171)
                      +.++|+|||+|.+.++|++|++.  +..++|+.|.|+
T Consensus        36 ~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362       36 GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            77899999999999999999984  678899988763

>PLN03120 nucleic acid binding protein; Provisional

Probab=98.10  E-value=5e-06  Score=62.91  Aligned_cols=42  Identities=17%  Similarity=0.362  Sum_probs=36.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~   45 (171)
                      |++|+.   ++|||||+|+++++|+.||. ++..|.|+.|.|.++.
T Consensus        36 I~~d~~---~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~   78 (260)
T PLN03120         36 MQSENE---RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAE   78 (260)
T ss_pred             EeecCC---CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEecc
Confidence            355653   67999999999999999998 4899999999999875

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]

Probab=98.10  E-value=3.3e-06  Score=57.37  Aligned_cols=45  Identities=20%  Similarity=0.271  Sum_probs=41.5

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      .|+.||-.|||+.|+|++.++|+.||..  +..|.|.+|.|.|+..+
T Consensus       106 LDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv~  152 (170)
T KOG0130|consen  106 LDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFVK  152 (170)
T ss_pred             cccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEec
Confidence            5899999999999999999999999994  78999999999999655

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]

Probab=98.01  E-value=8.9e-06  Score=54.80  Aligned_cols=43  Identities=21%  Similarity=0.323  Sum_probs=39.9

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      .|+.|...-|||||+|-+.++|+.||+  ++..++.|.|.+.|..
T Consensus        70 Ldr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D~  114 (153)
T KOG0121|consen   70 LDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWDA  114 (153)
T ss_pred             cccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeeccc
Confidence            688999999999999999999999999  5899999999999864

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=98.00  E-value=0.00022  Score=56.19  Aligned_cols=63  Identities=14%  Similarity=0.123  Sum_probs=54.3

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCcc---eeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRF---WFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d~---~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+++.+.|.+|.. ..+-+.|..+|..||.|+.|+.++-+   +-|++-+..+    .++|+.-||+.-+
T Consensus       284 ~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~gtamVemgd~~a----ver~v~hLnn~~l  350 (494)
T KOG1456|consen  284 GAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKPGTAMVEMGDAYA----VERAVTHLNNIPL  350 (494)
T ss_pred             CCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecccceeEEEcCcHHH----HHHHHHHhccCcc
Confidence            56789999999997 57789999999999999999999763   4599999999    9999999987543

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif

Probab=97.99  E-value=1e-05  Score=46.69  Aligned_cols=50  Identities=28%  Similarity=0.490  Sum_probs=40.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHH
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVS  156 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai  156 (171)
                      +.|-|.|.+....+. +..+|..||+|+.+.+.  .+..+++|.++.+    |++|+
T Consensus         2 ~wI~V~Gf~~~~~~~-vl~~F~~fGeI~~~~~~~~~~~~~l~y~~~~~----ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEE-VLEHFASFGEIVDIYVPESTNWMYLKYKSRKD----AEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHH-HHHHHHhcCCEEEEEcCCCCcEEEEEECCHHH----HHhhC
Confidence            457788888766655 45589999999999999  6677899999999    99885

>PLN03213 repressor of silencing 3; Provisional

Probab=97.98  E-value=7.6e-06  Score=66.42  Aligned_cols=40  Identities=18%  Similarity=0.402  Sum_probs=35.5

Q ss_pred             CCCCCccceEEEEECCH--HHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            5 QGSKAHRGIGFITFASA--DSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~--~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      +.||  ||||||+|.+.  .++++||.  ++..+.||.|+|..|.+
T Consensus        44 RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAKP   87 (759)
T PLN03213         44 RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAKE   87 (759)
T ss_pred             cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeeccH
Confidence            4577  99999999988  78999999  48999999999998865

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.98  E-value=3.3e-06  Score=72.07  Aligned_cols=92  Identities=15%  Similarity=0.175  Sum_probs=74.3

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCC
Q 030822            5 QGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPT   82 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~   82 (171)
                      .++|+-||+|||+|..++++.+||.-  .+.+.                                               
T Consensus       703 ~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g-----------------------------------------------  735 (881)
T KOG0128|consen  703 KNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG-----------------------------------------------  735 (881)
T ss_pred             hhccccccceeeEeecCCchhhhhhhhhhhhhh-----------------------------------------------
Confidence            35789999999999999999999862  22221                                               


Q ss_pred             ccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcce-------eEEecCCcccHHHHHHH
Q 030822           83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW-------FCHLCGRSCSRSCFSKV  155 (171)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~-------fv~f~~~~~~~~~a~~A  155 (171)
                                        ..++||.|+|+..|.+.|+.+++.+|.+.+.+++..++       +|.|.++.+    +.++
T Consensus       736 ------------------K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~----~s~~  793 (881)
T KOG0128|consen  736 ------------------KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEAD----ASRK  793 (881)
T ss_pred             ------------------hhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcch----hhhh
Confidence                              25599999999999999999999999999999876554       899999999    7777


Q ss_pred             HHHHhHhCCC
Q 030822          156 SRNLWTAGCN  165 (171)
Q Consensus       156 i~~l~~~~~~  165 (171)
                      +..+.....+
T Consensus       794 ~~s~d~~~~r  803 (881)
T KOG0128|consen  794 VASVDVAGKR  803 (881)
T ss_pred             cccchhhhhh
Confidence            6665544443

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=97.89  E-value=3.2e-05  Score=46.36  Aligned_cols=35  Identities=26%  Similarity=0.550  Sum_probs=30.8

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEee
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDR   43 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~   43 (171)
                      +++|+|||+|.+.++|+.|++.  +..++|+.+.|.+
T Consensus        38 ~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590          38 KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            6799999999999999999994  6678999998763

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).

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]

Probab=97.89  E-value=7.7e-05  Score=60.49  Aligned_cols=43  Identities=26%  Similarity=0.376  Sum_probs=36.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRAT   45 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~   45 (171)
                      +.| .-||+-|=|||.|++++.|++||.. ...|+.|-|.|-.+.
T Consensus       137 ~~d-~rgR~tGEAfVqF~sqe~ae~Al~rhre~iGhRYIEvF~Ss  180 (510)
T KOG4211|consen  137 PMD-QRGRPTGEAFVQFESQESAEIALGRHRENIGHRYIEVFRSS  180 (510)
T ss_pred             ecc-CCCCcccceEEEecCHHHHHHHHHHHHHhhccceEEeehhH
Confidence            344 4678999999999999999999995 778899999997663

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.86  E-value=1.1e-06  Score=69.89  Aligned_cols=100  Identities=15%  Similarity=0.215  Sum_probs=82.7

Q ss_pred             cceEEEEECCHHHHHHHHhc---CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCC
Q 030822           11 RGIGFITFASADSVENLMVD---THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHP   87 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~~---~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~   87 (171)
                      -||+||.+.+...|.+|++.   ..++.|+.+.+..+.++                                        
T Consensus        37 ~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~k----------------------------------------   76 (584)
T KOG2193|consen   37 SGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPK----------------------------------------   76 (584)
T ss_pred             cceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhH----------------------------------------
Confidence            48999999999999999994   47889999988876654                                        


Q ss_pred             CCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec-Cccee----EEecCCcccHHHHHHHHHHHhHh
Q 030822           88 GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KRFWF----CHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        88 ~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-~d~~f----v~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                                ...++++-|+|+|+...|+.|..+..+||.|+.|..+ .|..+    |+|...+.    +..||..|++.
T Consensus        77 ----------kqrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~etavvnvty~~~~~----~~~ai~kl~g~  142 (584)
T KOG2193|consen   77 ----------KQRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSETAVVNVTYSAQQQ----HRQAIHKLNGP  142 (584)
T ss_pred             ----------HHHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHHHHHHHHHHHHHH----HHHHHHhhcch
Confidence                      2235778899999999999999999999999999764 45443    77888888    89999888775


Q ss_pred             CC
Q 030822          163 GC  164 (171)
Q Consensus       163 ~~  164 (171)
                      -.
T Consensus       143 Q~  144 (584)
T KOG2193|consen  143 QL  144 (584)
T ss_pred             Hh
Confidence            43

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]

Probab=97.83  E-value=8.8e-05  Score=58.98  Aligned_cols=60  Identities=13%  Similarity=0.103  Sum_probs=52.9

Q ss_pred             CceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecC---cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPK---RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~---d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...|.|-||.. .+|.+.|.-+|+-||.|.+|+|..   |.+.|.|.+...    |..|+.-|+++.+
T Consensus       297 n~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkkd~ALIQmsd~~q----AqLA~~hL~g~~l  360 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKKDNALIQMSDGQQ----AQLAMEHLEGHKL  360 (492)
T ss_pred             ceEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCCcceeeeecchhH----HHHHHHHhhccee
Confidence            57888989875 699999999999999999999984   567899999999    9999999987654

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]

Probab=97.79  E-value=3.8e-05  Score=56.50  Aligned_cols=62  Identities=16%  Similarity=0.230  Sum_probs=52.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec---------CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---------KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~---------~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..-++|||-+||.++.-.+|..+|..|---+.+.|-         +-.+|++|.+..+    |..|+..|||...
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~----A~aamnaLNGvrF  102 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQF----ALAAMNALNGVRF  102 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHH----HHHHHHHhcCeee
Confidence            346899999999999999999999998666666554         2367999999999    9999999998754

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]

Probab=97.78  E-value=0.00023  Score=56.32  Aligned_cols=119  Identities=18%  Similarity=0.118  Sum_probs=80.0

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCcc
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   84 (171)
                      ..|+.-|.|.|.|.++|.-+-|++. .|.+.+|.|.|-.+...+--.-                                
T Consensus        97 ~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~ge~f~~i--------------------------------  144 (508)
T KOG1365|consen   97 AQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATGEEFLKI--------------------------------  144 (508)
T ss_pred             hhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCchhheEe--------------------------------
Confidence            4578889999999999999999995 7889999999987654321110                                


Q ss_pred             CCCCCCCC-CCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcc----cceEEEEec-C------cceeEEecCCcccHHHH
Q 030822           85 DHPGSFYG-RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF----GRILDVYVP-K------RFWFCHLCGRSCSRSCF  152 (171)
Q Consensus        85 ~~~~~~~~-~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~f----G~v~~v~i~-~------d~~fv~f~~~~~~~~~a  152 (171)
                       .++.+.. .........--|-+++||+++++.++.++|.+-    |.++.|-.+ +      .-+||.|..+++    |
T Consensus       145 -agg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvlfa~ee~----a  219 (508)
T KOG1365|consen  145 -AGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVLFACEED----A  219 (508)
T ss_pred             -cCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEEecCHHH----H
Confidence             0000000 000001223456779999999999999999742    234444443 3      257999999999    8


Q ss_pred             HHHHHHHhH
Q 030822          153 SKVSRNLWT  161 (171)
Q Consensus       153 ~~Ai~~l~~  161 (171)
                      ..|+..=..
T Consensus       220 q~aL~khrq  228 (508)
T KOG1365|consen  220 QFALRKHRQ  228 (508)
T ss_pred             HHHHHHHHH
Confidence            888875433

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]

Probab=97.74  E-value=3.1e-05  Score=54.87  Aligned_cols=39  Identities=23%  Similarity=0.463  Sum_probs=34.1

Q ss_pred             CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      ...|||||+|+++.+|+.|+.  ++..|.|..|.|..+.-+
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen   45 NPPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             cCCCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            568999999999999999999  588899999999987643

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]

Probab=97.72  E-value=8.7e-05  Score=53.92  Aligned_cols=60  Identities=15%  Similarity=0.363  Sum_probs=52.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcc-cceEEEEecC--------cceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRF-GRILDVYVPK--------RFWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~f-G~v~~v~i~~--------d~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      .....-+||..+|....+..|..+|.+| |.|..+++.+        .++||.|.+.+-    |+-|-..||+
T Consensus        46 ~~~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eV----A~IaAETMNN  114 (214)
T KOG4208|consen   46 QEIEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEV----AKIAAETMNN  114 (214)
T ss_pred             cCCccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHH----HHHHHHHhhh
Confidence            4556789999999999999999999998 8888888854        478999999999    9999999985

>PLN03121 nucleic acid binding protein; Provisional

Probab=97.65  E-value=8.4e-05  Score=55.59  Aligned_cols=42  Identities=14%  Similarity=0.226  Sum_probs=35.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~   45 (171)
                      |++|   ++++|||||+|++++.++.||. ++..|.++.|.|..+.
T Consensus        37 I~~D---~et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121         37 IIRS---GEYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             EecC---CCcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            3556   4567899999999999999998 5899999999998654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.52  E-value=0.00042  Score=58.62  Aligned_cols=133  Identities=11%  Similarity=0.073  Sum_probs=80.0

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCC--CCcCCCCCCCCccccchhhhhhhccC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRP--VGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      .|+..+-..|-++|+|....++++|++. ....-.|.+.+..+...+-...+  ....+....+            ..+|
T Consensus       344 ~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g~~~~~~a~~~~~~~~~~~~~------------~~hg  411 (944)
T KOG4307|consen  344 ENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPGNLGRNGAPPFQAGVPPPVIQ------------NNHG  411 (944)
T ss_pred             hhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCCccccccCccccccCCCCccc------------ccCC
Confidence            3444444588999999999999999996 45556788877755433222111  0000000000            0111


Q ss_pred             CCCccCCCCCCCCCC-CCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEE-EEecC---c----ceeEEecCCcc
Q 030822           80 APTLYDHPGSFYGRG-ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPK---R----FWFCHLCGRSC  147 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~-~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~-v~i~~---d----~~fv~f~~~~~  147 (171)
                      .+..........+.. ......+..|||..||..+++.++-++|...-.|++ |.|.+   |    -+||.|..+++
T Consensus       412 ~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~P~~~~~~~afv~F~~~~a  488 (944)
T KOG4307|consen  412 RPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRLPTDLLRPAAFVAFIHPTA  488 (944)
T ss_pred             CCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhhhhhhheeEeccCCcccccchhhheeccccc
Confidence            111111111111111 112456789999999999999999999999888888 55543   2    46899998777

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]

Probab=97.49  E-value=0.00029  Score=55.60  Aligned_cols=54  Identities=13%  Similarity=0.051  Sum_probs=47.0

Q ss_pred             eCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          107 GRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       107 ~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      -|--+.+|-+-|..+.-+.|+|.+|.|.+.   .+-|+|++-+.    |.+|-.+||||.+
T Consensus       128 lNp~YpItvDVly~Icnp~GkVlRIvIfkkngVQAmVEFdsv~~----AqrAk~alNGADI  184 (494)
T KOG1456|consen  128 LNPQYPITVDVLYTICNPQGKVLRIVIFKKNGVQAMVEFDSVEV----AQRAKAALNGADI  184 (494)
T ss_pred             ecCccccchhhhhhhcCCCCceEEEEEEeccceeeEEeechhHH----HHHHHhhcccccc
Confidence            444567999999999999999999999876   45699999888    9999999999864

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.47  E-value=0.00022  Score=46.24  Aligned_cols=45  Identities=18%  Similarity=0.290  Sum_probs=34.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccC----CeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELG----GSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~----gr~i~v~~a~   45 (171)
                      ||.|-.++.+.|||||.|.+++.|.+-.+.  +..+.    .+...|.+|.
T Consensus        35 LPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i~yAr   85 (97)
T PF04059_consen   35 LPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEISYAR   85 (97)
T ss_pred             eeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEEehhH
Confidence            578999999999999999999999998874  33332    3445555553

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.38  E-value=0.00021  Score=53.70  Aligned_cols=45  Identities=27%  Similarity=0.447  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~   45 (171)
                      |+.|+.+|.+|||+||+|.+.+.+++++. ++..|.|+.+.|.+..
T Consensus       133 i~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~~r  178 (231)
T KOG4209|consen  133 VPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTLKR  178 (231)
T ss_pred             eeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeeeee
Confidence            57899999999999999999999999999 7889999999987653

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=97.36  E-value=0.00017  Score=54.23  Aligned_cols=62  Identities=19%  Similarity=0.242  Sum_probs=54.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ......+||+|+.+.++-+++..+|+.+|.|..+.|+.|        +++|.|.+.+.    .++|++ |++..+
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~----~~~ay~-l~gs~i  167 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYEL----VEEAYK-LDGSEI  167 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhh----hHHHhh-cCCccc
Confidence            456789999999999999999999999999999988866        45799999999    999999 776554

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=97.35  E-value=0.00074  Score=42.33  Aligned_cols=57  Identities=14%  Similarity=0.264  Sum_probs=39.4

Q ss_pred             ceEEEeCCCCCCCH----HHHHHHhhcc-cceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATA----EDLRRYFSRF-GRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te----~~L~~~F~~f-G~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .-|||.|||.+.+.    ..|++++..+ |.|..|  ....+.+.|.+.+.    |++|.+.|++..+
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v--~~~tAilrF~~~~~----A~RA~KRmegEdV   64 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSV--SGGTAILRFPNQEF----AERAQKRMEGEDV   64 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE----TT-EEEEESSHHH----HHHHHHHHTT--S
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEE--eCCEEEEEeCCHHH----HHHHHHhhccccc
Confidence            46999999998885    5677787787 466554  57788899999999    9999999987654

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=97.34  E-value=0.00071  Score=43.92  Aligned_cols=63  Identities=14%  Similarity=0.266  Sum_probs=53.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhc--ccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCCCcc
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSR--FGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFS  168 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~--fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~~  168 (171)
                      ++|-|+|||-..|.++|.+++..  .|...-+.++.|        ++||-|.+++.    |.+-.+.+|+...+.+.
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~----~~~F~~~f~g~~w~~~~   74 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQA----AIRFYKAFNGKKWPNFN   74 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHH----HHHHHHHHcCCccccCC
Confidence            68999999999999999999875  378888888877        57999999999    88888888887766553

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]

Probab=97.32  E-value=0.00016  Score=56.61  Aligned_cols=46  Identities=17%  Similarity=0.262  Sum_probs=41.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~   46 (171)
                      |++|..||-|--||||+|++.+++++|.-.  ...|+.|.|.|.++..
T Consensus       271 VIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  271 VIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             EEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            589999999999999999999999999875  4689999999998753

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]

Probab=97.21  E-value=0.00013  Score=53.59  Aligned_cols=72  Identities=22%  Similarity=0.342  Sum_probs=55.8

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      +.+ ..+..| ||||.|+++-.+.-|++  ++..+.++.+.++                                     
T Consensus        42 p~~-~d~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~-------------------------------------   82 (267)
T KOG4454|consen   42 PSG-QDQEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRT-------------------------------------   82 (267)
T ss_pred             CCC-ccCCCc-eeeeecccccchhhhhhhcccchhccchhhcc-------------------------------------
Confidence            344 466777 99999999999999998  4666777776554                                     


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeC----CCCCCCHHHHHHHhhcccceEEEEecCc
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGR----LPQEATAEDLRRYFSRFGRILDVYVPKR  136 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~n----Lp~~~te~~L~~~F~~fG~v~~v~i~~d  136 (171)
                                              ++.|+    |...++++.+...|+.-|++..+++.++
T Consensus        83 ------------------------~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~  119 (267)
T KOG4454|consen   83 ------------------------LRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTD  119 (267)
T ss_pred             ------------------------cccCCCcchhhhhcchhhheeeecccCCCCCcccccc
Confidence                                    33344    6667888899999999999999888765

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.21  E-value=0.0025  Score=39.87  Aligned_cols=57  Identities=23%  Similarity=0.310  Sum_probs=41.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ..+..+|. .|.+|-..||.++|++||.|.---|----+||...+++.    +..|+..+.-
T Consensus         8 RdHVFhlt-FPkeWK~~DI~qlFspfG~I~VsWi~dTSAfV~l~~r~~----~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKTSDIYQLFSPFGQIYVSWINDTSAFVALHNRDQ----AKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--HHHHHHHCCCCCCEEEEEECTTEEEEEECCCHH----HHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhhhhHHHHhccCCcEEEEEEcCCcEEEEeecHHH----HHHHHHHhcc
Confidence            34555565 999999999999999999976555544578999999999    8888887753

; 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.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.07  E-value=0.00053  Score=59.40  Aligned_cols=63  Identities=16%  Similarity=0.190  Sum_probs=53.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....+.++|++|+..+....|..+|..||+|..|.+-..  +..+.|.+...    +..|...|-++-+
T Consensus       452 st~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~hgq~yayi~yes~~~----aq~a~~~~rgap~  516 (975)
T KOG0112|consen  452 STPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRHGQPYAYIQYESPPA----AQAATHDMRGAPL  516 (975)
T ss_pred             cccceeeccCCCCCCChHHHHHHHhhccCcceeeecccCCcceeeecccCcc----chhhHHHHhcCcC
Confidence            345789999999999999999999999999999887644  55689999988    8888888877643

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.98  E-value=0.0018  Score=48.72  Aligned_cols=54  Identities=22%  Similarity=0.260  Sum_probs=47.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHH
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      ..|||.||+..++-+.|.+-|+.||+|....+.-|       .+.|.|.....    |.+|...+
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~----a~~a~rr~   92 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPN----ARKAARRC   92 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchh----HHHHHHHh
Confidence            56999999999999999999999999999988866       35699999999    77777665

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.96  E-value=0.0009  Score=53.67  Aligned_cols=62  Identities=18%  Similarity=0.199  Sum_probs=52.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---------------------ceeEEecCCcccHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---------------------FWFCHLCGRSCSRSCFSKVS  156 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---------------------~~fv~f~~~~~~~~~a~~Ai  156 (171)
                      ..++++|.+-|||.+-.-+.|.++|+.+|.|..|+|.+.                     .++|+|...+.    |.+|.
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~----A~KA~  303 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEA----ARKAR  303 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHH----HHHHH
Confidence            457899999999999888999999999999999999743                     24588988888    99998


Q ss_pred             HHHhHhC
Q 030822          157 RNLWTAG  163 (171)
Q Consensus       157 ~~l~~~~  163 (171)
                      .-|+.+.
T Consensus       304 e~~~~e~  310 (484)
T KOG1855|consen  304 ELLNPEQ  310 (484)
T ss_pred             Hhhchhh
Confidence            8886553

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]

Probab=96.69  E-value=0.0039  Score=48.86  Aligned_cols=65  Identities=17%  Similarity=0.285  Sum_probs=49.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEE--------EEecCc-------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~--------v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ....+.|||.|||..+|-+++.++|+++|-|..        |+|-++       -+-+.|--+++    .+.|++-|+++
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ES----VeLA~~ilDe~  206 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRES----VELAIKILDED  206 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccH----HHHHHHHhCcc
Confidence            345677999999999999999999999997643        222222       12366666777    89999999988


Q ss_pred             CCCC
Q 030822          163 GCNR  166 (171)
Q Consensus       163 ~~~~  166 (171)
                      .+.-
T Consensus       207 ~~rg  210 (382)
T KOG1548|consen  207 ELRG  210 (382)
T ss_pred             cccC
Confidence            7653

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.66  E-value=0.002  Score=50.42  Aligned_cols=37  Identities=19%  Similarity=0.438  Sum_probs=33.6

Q ss_pred             ccceEEEEECCHHHHHHHHhc---CCccCCeEEEEeecCC
Q 030822           10 HRGIGFITFASADSVENLMVD---THELGGSTVVVDRATP   46 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~---~~~i~gr~i~v~~a~~   46 (171)
                      .+|+|||+|.+.+.|+.|...   ...|+|+.|.|.|..+
T Consensus       263 ~~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg~~  302 (377)
T KOG0153|consen  263 RKGCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWGRP  302 (377)
T ss_pred             ccccceeeehhhHHHHHHHHhhcceeeecceEEEEEeCCC
Confidence            467999999999999999985   5789999999999987

>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=96.45  E-value=0.0046  Score=40.35  Aligned_cols=53  Identities=19%  Similarity=0.237  Sum_probs=36.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEE-------------ecCcce--eEEecCCcccHHHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVY-------------VPKRFW--FCHLCGRSCSRSCFSKVSR  157 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~-------------i~~d~~--fv~f~~~~~~~~~a~~Ai~  157 (171)
                      ..+-|.|.+.|+. ....+-++|++||.|.+..             ++....  .++|.++.+    |.+|+.
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~----A~rAL~   72 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLS----AQRALQ   72 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHH----HHHHHT
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHH----HHHHHH
Confidence            3566999999988 4556778899999999885             333332  389999999    888875

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.

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]

Probab=96.39  E-value=0.012  Score=48.45  Aligned_cols=58  Identities=26%  Similarity=0.434  Sum_probs=43.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec-----------Cc---ceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-----------KR---FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-----------~d---~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ..-+++||||+||+.++|+.|...|..||.+. |..+           +.   +.|+-|+++..    ...-+...+
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~s----V~~Ll~aC~  327 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERS----VQSLLSACS  327 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHH----HHHHHHHHh
Confidence            34578999999999999999999999999864 4444           22   55788888777    444444433

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.34  E-value=0.0021  Score=48.29  Aligned_cols=59  Identities=14%  Similarity=0.282  Sum_probs=48.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcc--------------------eeEEecCCcccHHHHHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF--------------------WFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~--------------------~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      ...-||+.+||+..+-..|+++|++||.|-.|.+....                    +.|.|.+..-    |......|
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~Krv----AK~iAe~L  148 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRV----AKRIAELL  148 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHH----HHHHHHHh
Confidence            45679999999999999999999999999999997541                    2377777777    77777777


Q ss_pred             hHh
Q 030822          160 WTA  162 (171)
Q Consensus       160 ~~~  162 (171)
                      |+.
T Consensus       149 nn~  151 (278)
T KOG3152|consen  149 NNT  151 (278)
T ss_pred             CCC
Confidence            764

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.27  E-value=0.014  Score=34.64  Aligned_cols=54  Identities=11%  Similarity=0.175  Sum_probs=43.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcc---cceEEEEecCc-ceeEEecCCcccHHHHHHHHHHH
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRF---GRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~f---G~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      ..+|+|+|+. +.+.++++.+|..|   .....|..+-| ...|.|.+.+.    |.+|+..|
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtScNvvf~d~~~----A~~AL~~L   62 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTSCNVVFKDEET----AARALVAL   62 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCcEEEEECCHHH----HHHHHHcC
Confidence            4679999996 68889999999999   23457777777 45799999999    99998765

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.21  E-value=0.011  Score=38.64  Aligned_cols=42  Identities=17%  Similarity=0.252  Sum_probs=36.3

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      .|..-||-|||.|++-.+|.+|+..  +.-+.++.+.|-+..+.
T Consensus        52 ~~k~TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~~   95 (124)
T KOG0114|consen   52 NTKETRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQPE   95 (124)
T ss_pred             CccCcCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCHH
Confidence            4556789999999999999999995  78899999999887653

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=95.91  E-value=0.014  Score=37.18  Aligned_cols=71  Identities=17%  Similarity=0.241  Sum_probs=46.9

Q ss_pred             EEEEECCHHHHHHHHhcC---CccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCCCC
Q 030822           14 GFITFASADSVENLMVDT---HELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSF   90 (171)
Q Consensus        14 gFV~F~~~~~a~~Al~~~---~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~   90 (171)
                      |.|+|.++.-|++.++.+   ..+++..+.|...--.........              -                    
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~~~~k~q--------------v--------------------   46 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLGHLQKFQ--------------V--------------------   46 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecCCceEEE--------------E--------------------
Confidence            679999999999999952   356777776653311100000000              0                    


Q ss_pred             CCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhh
Q 030822           91 YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFS  123 (171)
Q Consensus        91 ~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~  123 (171)
                           ....+.++|-|.|||...++++|++..+
T Consensus        47 -----~~~vs~rtVlvsgip~~l~ee~l~D~Le   74 (88)
T PF07292_consen   47 -----FSGVSKRTVLVSGIPDVLDEEELRDKLE   74 (88)
T ss_pred             -----EEcccCCEEEEeCCCCCCChhhheeeEE
Confidence                 0134578999999999999999988654

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=95.76  E-value=0.012  Score=46.24  Aligned_cols=66  Identities=12%  Similarity=0.000  Sum_probs=53.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEE--------EecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV--------YVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v--------~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      .....+|||-+||..+++.+|.++|.+.|.|..=        .|-+|        .++|.|.+..+    |..||..+++
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~----akaai~~~ag  138 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPA----AKAAIEWFAG  138 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhh----hhhhhhhhcc
Confidence            4456799999999999999999999999876432        22233        35799999988    9999999988


Q ss_pred             hCCCCc
Q 030822          162 AGCNRF  167 (171)
Q Consensus       162 ~~~~~~  167 (171)
                      +..+.+
T Consensus       139 kdf~gn  144 (351)
T KOG1995|consen  139 KDFCGN  144 (351)
T ss_pred             ccccCC
Confidence            877653

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]

Probab=95.65  E-value=0.015  Score=48.61  Aligned_cols=44  Identities=23%  Similarity=0.397  Sum_probs=36.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      +++-.+---|-||||++.+.++|.+||++  .++|.||-|.|..+.
T Consensus       438 VTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  438 VTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             eecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            34444445678999999999999999997  568999999998775

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]

Probab=95.37  E-value=0.071  Score=43.56  Aligned_cols=39  Identities=28%  Similarity=0.550  Sum_probs=33.8

Q ss_pred             CCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCC
Q 030822            8 KAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATP   46 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~   46 (171)
                      +++..||||+|++.++++.||.. ...|+++++.|+.-.+
T Consensus       327 ~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  327 GKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             CCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccc
Confidence            45559999999999999999996 7899999999986554

>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=95.15  E-value=0.048  Score=34.33  Aligned_cols=35  Identities=14%  Similarity=0.256  Sum_probs=26.3

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      +.|-|+|.|.+++.|++|.+.  +..+.|.+|.|.+.
T Consensus        38 ~~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen   38 SGGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             -TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             eCCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEc
Confidence            457899999999999999994  77889999999976

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=95.01  E-value=0.042  Score=43.21  Aligned_cols=60  Identities=15%  Similarity=0.300  Sum_probs=47.6

Q ss_pred             CCCceEEEeCCCCCCCHHH------HHHHhhcccceEEEEecCcc---------e--eEEecCCcccHHHHHHHHHHHhH
Q 030822           99 RIGKKIFVGRLPQEATAED------LRRYFSRFGRILDVYVPKRF---------W--FCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~------L~~~F~~fG~v~~v~i~~d~---------~--fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....-+||-+||+.+..++      =.++|++||.|..|.|-+.-         .  .++|...++    |.++|.+..+
T Consensus       112 vQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~ked----AarcIa~vDg  187 (480)
T COG5175         112 VQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKED----AARCIAEVDG  187 (480)
T ss_pred             eecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHH----HHHHHHHhcc
Confidence            3456689999999876655      35789999999999887542         1  589999999    9999998866


Q ss_pred             h
Q 030822          162 A  162 (171)
Q Consensus       162 ~  162 (171)
                      .
T Consensus       188 s  188 (480)
T COG5175         188 S  188 (480)
T ss_pred             c
Confidence            4

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=94.97  E-value=0.031  Score=46.66  Aligned_cols=40  Identities=23%  Similarity=0.375  Sum_probs=29.6

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccC-CeEEEEe
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELG-GSTVVVD   42 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~-gr~i~v~   42 (171)
                      |-|..+| .+||.|++|+++.+|+.|+++  |+.|+ +++..|.
T Consensus        97 P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~v~  139 (698)
T KOG2314|consen   97 PIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFFVR  139 (698)
T ss_pred             ccCccCC-eeeEEEEEecChhhHHHHHHhcccceecccceEEee
Confidence            5566555 999999999999999999995  44443 3444443

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]

Probab=94.79  E-value=0.043  Score=47.48  Aligned_cols=39  Identities=21%  Similarity=0.341  Sum_probs=35.2

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      -+||||||.+...++|++||.+  .+.+.++.|+|.|+..+
T Consensus       455 ~~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  455 PPRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             cCCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            3799999999999999999996  68899999999999754

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.62  E-value=0.19  Score=42.14  Aligned_cols=64  Identities=9%  Similarity=0.240  Sum_probs=51.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhc--ccceEEEEecC-cceeEEecCCcccHHHHHHHHHHHhHhCCCCccc
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSR--FGRILDVYVPK-RFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRFSH  169 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~--fG~v~~v~i~~-d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~~~  169 (171)
                      -|-|.++-||.++..|+++.+|.-  +-++++|.... |-.+|+|.+..+    |..|.+-|. ..+|.|+.
T Consensus       175 RcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~nWyITfesd~D----AQqAykylr-eevk~fqg  241 (684)
T KOG2591|consen  175 RCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDNWYITFESDTD----AQQAYKYLR-EEVKTFQG  241 (684)
T ss_pred             eeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCceEEEeecchh----HHHHHHHHH-HHHHhhcC
Confidence            466777999999999999999975  77889998764 567899999999    999998883 34555544

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=94.59  E-value=0.0023  Score=55.36  Aligned_cols=56  Identities=23%  Similarity=0.161  Sum_probs=47.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--------CcceeEEecCCcccHHHHHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--------KRFWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--------~d~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      ...++||.||++.+.+.+|...|+++|.+..++|.        +..+.+.|...++    +.+||...
T Consensus       666 ~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~----~~aaV~f~  729 (881)
T KOG0128|consen  666 DLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEH----AGAAVAFR  729 (881)
T ss_pred             HHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCc----hhhhhhhh
Confidence            35789999999999999999999999999988876        3356789999999    77777654

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=94.51  E-value=0.04  Score=42.49  Aligned_cols=45  Identities=11%  Similarity=0.110  Sum_probs=38.1

Q ss_pred             HHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          115 AEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       115 e~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ++++++..++||+|..|.|.-+         +-||+|...++    |.+|+..|||-.
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~----aiKA~VdlnGRy  353 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVES----AIKAVVDLNGRY  353 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHH----HHHHHHhcCCce
Confidence            3677888999999999998754         34899999999    999999998743

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=94.51  E-value=0.0098  Score=51.94  Aligned_cols=66  Identities=17%  Similarity=0.226  Sum_probs=54.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCCCc
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCNRF  167 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~  167 (171)
                      .....+||++||+..+++.+|+..|..+|.|.+|.|-.-       ++||.|.+...    +-.|...|.+-.+-.+
T Consensus       369 ~~atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dm----tp~ak~e~s~~~I~~g  441 (975)
T KOG0112|consen  369 FRATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDM----TPSAKFEESGPLIGNG  441 (975)
T ss_pred             hhhhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhcccc----CcccchhhcCCccccC
Confidence            456789999999999999999999999999999998643       67899998888    7777776665555444

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.47  E-value=0.033  Score=40.21  Aligned_cols=59  Identities=15%  Similarity=0.125  Sum_probs=38.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhc-ccce---EEEE--ecC--------cceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSR-FGRI---LDVY--VPK--------RFWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~-fG~v---~~v~--i~~--------d~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ...+|.|++||+++||+++++..++ ++.-   .++.  ...        -++.+.|.+.++    +..-...++|.
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~----~~~F~~~~~g~   78 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPED----LLEFRDRFDGH   78 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHH----HHHHHHHCTTE
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHH----HHHHHHhcCCc
Confidence            4679999999999999999998887 6665   3333  111        145699999988    66666666654

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.

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=93.87  E-value=0.057  Score=45.16  Aligned_cols=62  Identities=19%  Similarity=0.320  Sum_probs=49.9

Q ss_pred             CCCceEEEeCCCCCCC------HHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEAT------AEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~t------e~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .-...|+|-|+|---.      ..-|..+|+++|+|+...++.|       +.|+.|.+..+    |+.|+++|||..+
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~----A~~aVK~l~G~~l  130 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRD----AKKAVKSLNGKRL  130 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhh----HHHHHHhccccee
Confidence            3457899999985322      2456789999999999999955       55899999999    9999999988654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=93.75  E-value=0.077  Score=42.52  Aligned_cols=46  Identities=15%  Similarity=0.314  Sum_probs=41.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----------ceeEEecCCcc
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----------FWFCHLCGRSC  147 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----------~~fv~f~~~~~  147 (171)
                      .-|-|.||.++++.++++-||...|.|.++.|...           -.||.|.+...
T Consensus         8 ~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~s   64 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQS   64 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcc
Confidence            47999999999999999999999999999998753           35899999887

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.55  E-value=0.16  Score=35.24  Aligned_cols=60  Identities=20%  Similarity=0.185  Sum_probs=45.5

Q ss_pred             CCCCceEEEeCCCCCCC-HHHHH---HHhhcccceEEEEec-CcceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEAT-AEDLR---RYFSRFGRILDVYVP-KRFWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~t-e~~L~---~~F~~fG~v~~v~i~-~d~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      .++-.+|.|+=|..++. .+||+   +..+.||+|.+|.+. +.-+-|.|.+...    |-+|+.+++.
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrqsavVvF~d~~S----AC~Av~Af~s  147 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQSAVVVFKDITS----ACKAVSAFQS  147 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCceEEEEehhhHH----HHHHHHhhcC
Confidence            55678899977766543 24444   455779999999887 4567799999999    9999988864

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=92.80  E-value=0.31  Score=33.97  Aligned_cols=53  Identities=9%  Similarity=0.104  Sum_probs=37.7

Q ss_pred             CCceEEEeCCCCC------CCH---HHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHH
Q 030822          100 IGKKIFVGRLPQE------ATA---EDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVS  156 (171)
Q Consensus       100 ~~~~lfV~nLp~~------~te---~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai  156 (171)
                      +..+|.|.=+.+.      .++   .+|-+.|.+||.|+-++++-+.-.|+|.+-..    |.+|+
T Consensus        26 pDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~~mwVTF~dg~s----ALaal   87 (146)
T PF08952_consen   26 PDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGDTMWVTFRDGQS----ALAAL   87 (146)
T ss_dssp             TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETTCEEEEESSCHH----HHHHH
T ss_pred             CCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCCeEEEEECccHH----HHHHH
Confidence            4567777655522      222   37888899999999999999999999999888    66554

; PDB: 1UFW_A 2DNR_A.

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=92.69  E-value=0.062  Score=41.82  Aligned_cols=47  Identities=21%  Similarity=0.571  Sum_probs=41.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      ++.++.+|.++|||||.|.+......++. ..+.+.++.+.+....++
T Consensus       217 ~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  264 (285)
T KOG4210|consen  217 LPTDEESGDSKGFAYVDFSAGNSKKLALNDQTRSIGGRPLRLEEDEPR  264 (285)
T ss_pred             cCCCCCccchhhhhhhhhhhchhHHHHhhcccCcccCcccccccCCCC
Confidence            46678899999999999999999999998 467899999999877665

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=92.65  E-value=0.091  Score=41.50  Aligned_cols=46  Identities=15%  Similarity=0.287  Sum_probs=40.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      -+|+.|+++||=|-|+|.++..|+.||.  +...+.|-+|.|..|..+
T Consensus       107 y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn~ikvs~a~~r  154 (351)
T KOG1995|consen  107 YTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGNTIKVSLAERR  154 (351)
T ss_pred             cccccccCcCCceeeeecChhhhhhhhhhhccccccCCCchhhhhhhc
Confidence            4789999999999999999999999999  477888888888877654

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=92.63  E-value=0.074  Score=44.77  Aligned_cols=63  Identities=10%  Similarity=0.150  Sum_probs=52.8

Q ss_pred             CCCCCceEEEeCCCCCCCHHHHHHHhh-cccceEEEEe--cCcceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           97 SQRIGKKIFVGRLPQEATAEDLRRYFS-RFGRILDVYV--PKRFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        97 ~~~~~~~lfV~nLp~~~te~~L~~~F~-~fG~v~~v~i--~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ....++.|+|.||-.-.|.-+|+.+.+ ..|.|++..|  ++-..||.|.+.++    |...+..||+..
T Consensus       440 R~~~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~WmDkIKShCyV~yss~eE----A~atr~AlhnV~  505 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEFWMDKIKSHCYVSYSSVEE----AAATREALHNVQ  505 (718)
T ss_pred             CCCccceEeeecccccchHHHHHHHHhhccCchHHHHHHHhhcceeEecccHHH----HHHHHHHHhccc
Confidence            356688999999999999999999999 5677777633  35678999999999    999999999864

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=92.14  E-value=0.16  Score=41.18  Aligned_cols=57  Identities=19%  Similarity=0.252  Sum_probs=44.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcc--cceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRF--GRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~f--G~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      .++|++||.+.++..+|+.+|...  |---.+-+...+.||...+..-    |.+||+.|++.
T Consensus         2 nklyignL~p~~~psdl~svfg~ak~~~~g~fl~k~gyafvd~pdq~w----a~kaie~~sgk   60 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLVKSGYAFVDCPDQQW----ANKAIETLSGK   60 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccccCCCCcceeeecceeeccCCchhh----hhhhHHhhchh
Confidence            469999999999999999999864  2222233445678898888888    99999988764

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=91.88  E-value=0.11  Score=40.85  Aligned_cols=31  Identities=16%  Similarity=0.368  Sum_probs=27.9

Q ss_pred             EEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822           15 FITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus        15 FV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      ||+|.+.|+|.+||.+  +..++||.|+..+.+
T Consensus       169 YITy~~kedAarcIa~vDgs~~DGr~lkatYGT  201 (480)
T COG5175         169 YITYSTKEDAARCIAEVDGSLLDGRVLKATYGT  201 (480)
T ss_pred             EEEecchHHHHHHHHHhccccccCceEeeecCc
Confidence            9999999999999995  899999999887654

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]

Probab=91.32  E-value=0.37  Score=40.32  Aligned_cols=37  Identities=22%  Similarity=0.402  Sum_probs=32.3

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEE
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVV   40 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~   40 (171)
                      ++.|-..+|-.||+|-|.-+|++|++.  ..+|.|+.|.
T Consensus       105 ir~t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen  105 IRETPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             hhcccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            356778899999999999999999995  6788888886

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=91.11  E-value=0.08  Score=36.82  Aligned_cols=84  Identities=15%  Similarity=0.193  Sum_probs=59.4

Q ss_pred             ccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPG   88 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~   88 (171)
                      ..|+..+.|.+.+++++++.. ...++|..+.++.-.|........                                  
T Consensus        54 ~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~~~~~~~----------------------------------   99 (153)
T PF14111_consen   54 GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDFNPSEVK----------------------------------   99 (153)
T ss_pred             CCCeEEEEEEeccceeEEEecccccccccchhhhhhcccccccccc----------------------------------
Confidence            467889999999999999986 566778777776554332110000                                  


Q ss_pred             CCCCCCCCCCCCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecC
Q 030822           89 SFYGRGESSQRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPK  135 (171)
Q Consensus        89 ~~~~~~~~~~~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~  135 (171)
                              -.....=|-|.|||.. ++++-|+.+-+.+|.+.++....
T Consensus       100 --------~~~~~vWVri~glP~~~~~~~~~~~i~~~iG~~i~vD~~t  139 (153)
T PF14111_consen  100 --------FEHIPVWVRIYGLPLHLWSEEILKAIGSKIGEPIEVDENT  139 (153)
T ss_pred             --------eeccchhhhhccCCHHHhhhHHHHHHHHhcCCeEEEEcCC
Confidence                    0111233566899986 88999999999999999998653

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=90.54  E-value=0.26  Score=42.03  Aligned_cols=58  Identities=21%  Similarity=0.225  Sum_probs=51.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhH
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ++.-++||+|+.+.+..+-++.+....|-|.++.... |+|..|..+.-    +..|+..|+-
T Consensus        38 ~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-fgf~~f~~~~~----~~ra~r~~t~   95 (668)
T KOG2253|consen   38 PPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-FGFCEFLKHIG----DLRASRLLTE   95 (668)
T ss_pred             CCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-hcccchhhHHH----HHHHHHHhcc
Confidence            4567899999999999999999999999999998877 99999999888    8888877754

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=89.91  E-value=0.12  Score=41.37  Aligned_cols=34  Identities=18%  Similarity=0.095  Sum_probs=31.4

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEec
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP  134 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~  134 (171)
                      .++|+|.+|+..|...++-++|..+|.|.+..+.
T Consensus       151 rRt~~v~sl~~~~~l~e~~e~f~r~Gev~ya~~a  184 (479)
T KOG4676|consen  151 RRTREVQSLISAAILPESGESFERKGEVSYAHTA  184 (479)
T ss_pred             Hhhhhhhcchhhhcchhhhhhhhhcchhhhhhhh
Confidence            3789999999999999999999999999988875

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=89.14  E-value=0.12  Score=39.05  Aligned_cols=43  Identities=14%  Similarity=0.215  Sum_probs=34.0

Q ss_pred             HHHHHHhh-cccceEEEEecCcc-------eeEEecCCcccHHHHHHHHHHHhHh
Q 030822          116 EDLRRYFS-RFGRILDVYVPKRF-------WFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       116 ~~L~~~F~-~fG~v~~v~i~~d~-------~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ++|...|+ +||+|++++|-.+.       ..|+|...++    |+.|+..||+-
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~----ae~a~~~lnnR  133 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDNLGDHLVGNVYVKFRSEED----AEAALEDLNNR  133 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcccchhhhhhhhhhcccHHH----HHHHHHHHcCc
Confidence            45555555 89999999886653       3599999999    99999999864

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=89.07  E-value=3.5  Score=35.92  Aligned_cols=57  Identities=12%  Similarity=0.130  Sum_probs=44.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEec-Cc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-KR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      .|-+.|+|++++-+||-++|..|-.+-.-.++ ++       -.-|-|++.++    |..|...|++-.
T Consensus       869 V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~e----Ar~A~~dl~~~~  933 (944)
T KOG4307|consen  869 VLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEE----ARRASMDLDGQK  933 (944)
T ss_pred             EEEecCCCccccHHHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHH----HHhhhhccccCc
Confidence            78899999999999999999999544333222 21       23499999999    999998887644

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]

Probab=88.65  E-value=0.94  Score=34.40  Aligned_cols=42  Identities=14%  Similarity=0.226  Sum_probs=36.7

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ..|+|.|.|=|.|...++|.+||+.  +..++|+.+.+....+.
T Consensus       119 ~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~~  162 (243)
T KOG0533|consen  119 RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISSP  162 (243)
T ss_pred             CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecCc
Confidence            4899999999999999999999994  78899999988766443

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=88.06  E-value=0.21  Score=41.05  Aligned_cols=59  Identities=17%  Similarity=0.135  Sum_probs=42.4

Q ss_pred             CceEEEeCCCCCCC-HHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEAT-AEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~t-e~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.|=+.-.|+..+ -.+|..+|.+||.|..|.|-.  +.+.|+|..+.+    |-+| ...|++.+
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~~a~vTF~t~ae----ag~a-~~s~~avl  433 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSLHAVVTFKTRAE----AGEA-YASHGAVL  433 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCchhhheeeeecccc----ccch-hcccccee
Confidence            34455555666544 589999999999999999865  478899999988    6444 23444444

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=87.64  E-value=1.2  Score=34.82  Aligned_cols=53  Identities=17%  Similarity=0.192  Sum_probs=39.7

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCccee--EEecCCcccHHHHHHHHHH
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWF--CHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~f--v~f~~~~~~~~~a~~Ai~~  158 (171)
                      ..=|-|.+.|+.... .|..+|++||.|++......-.+  |.|.++.+    |.+||..
T Consensus       197 D~WVTVfGFppg~~s-~vL~~F~~cG~Vvkhv~~~ngNwMhirYssr~~----A~KALsk  251 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQVS-IVLNLFSRCGEVVKHVTPSNGNWMHIRYSSRTH----AQKALSK  251 (350)
T ss_pred             cceEEEeccCccchh-HHHHHHHhhCeeeeeecCCCCceEEEEecchhH----HHHhhhh
Confidence            445677788876555 45677999999999887755444  88999999    8888753

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=87.58  E-value=1.1  Score=31.20  Aligned_cols=35  Identities=23%  Similarity=0.366  Sum_probs=28.4

Q ss_pred             eEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822           13 IGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus        13 fgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      -=.|+|.+-++|-+|++ ++..+.|+.|.|+.-.|.
T Consensus        72 ~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtpd  107 (146)
T PF08952_consen   72 TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTPD  107 (146)
T ss_dssp             CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE----
T ss_pred             eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCcc
Confidence            35799999999999999 599999999999987664

; PDB: 1UFW_A 2DNR_A.

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length

Probab=85.86  E-value=1.6  Score=34.31  Aligned_cols=31  Identities=23%  Similarity=0.164  Sum_probs=22.8

Q ss_pred             EEEEECCHHHHHHHHhcCCccCCeEEEEeec
Q 030822           14 GFITFASADSVENLMVDTHELGGSTVVVDRA   44 (171)
Q Consensus        14 gFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a   44 (171)
                      |||+|++..+|+.|++..+..+++.+.+..|
T Consensus         1 aFVtF~~~~~a~~~~q~~~~~~~~~~~v~~A   31 (325)
T PF02714_consen    1 AFVTFNSQKSAQIALQLLLSKRPNSWRVSPA   31 (325)
T ss_pred             CEEEECCHHHHHHHHHHHhcCCCCCceEeeC
Confidence            7999999999999998533344455566544

; GO: 0016020 membrane

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=85.79  E-value=5.1  Score=26.58  Aligned_cols=63  Identities=8%  Similarity=0.015  Sum_probs=46.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcc-cceEEEEecCcce------eEEecCCcccHHHHHHHHHHHhHhCCCCc
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRF-GRILDVYVPKRFW------FCHLCGRSCSRSCFSKVSRNLWTAGCNRF  167 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~f-G~v~~v~i~~d~~------fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~  167 (171)
                      ...+.+...|+-++-++|..+.+++ ..|..++|++|..      -++|.+...    |..=.+.+||...|-.
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~----Ad~Fy~~fNGk~Fnsl   82 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQES----ADEFYEEFNGKPFNSL   82 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHH----HHHHHHHhCCCccCCC
Confidence            3444445566667777887776766 5677889998843      389999999    8888899998877654

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=84.26  E-value=0.68  Score=36.47  Aligned_cols=59  Identities=17%  Similarity=0.229  Sum_probs=45.0

Q ss_pred             CCceEEEeCCCCCCCHH-HHH--HHhhcccceEEEEecCcc-----------eeEEecCCcccHHHHHHHHHHHhHh
Q 030822          100 IGKKIFVGRLPQEATAE-DLR--RYFSRFGRILDVYVPKRF-----------WFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~-~L~--~~F~~fG~v~~v~i~~d~-----------~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ...-+||-+|+....++ .|+  +.|.+||.|..|.+-++.           ..|+|...++    |..+|...++.
T Consensus        76 qknlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~ed----a~rci~~v~g~  148 (327)
T KOG2068|consen   76 QKNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEED----ADRCIDDVDGF  148 (327)
T ss_pred             hhhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHh----hhhHHHHhhhH
Confidence            45678888999875544 443  579999999999998875           2488888888    88888887664

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=81.82  E-value=0.98  Score=34.31  Aligned_cols=35  Identities=17%  Similarity=0.297  Sum_probs=30.9

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      -+|=.||.|...++|++|++.  +.++.|++|...+.
T Consensus       109 l~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~  145 (260)
T KOG2202|consen  109 LVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELS  145 (260)
T ss_pred             hhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeec
Confidence            467889999999999999995  78999999988765

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=80.87  E-value=1.9  Score=33.54  Aligned_cols=30  Identities=27%  Similarity=0.356  Sum_probs=26.0

Q ss_pred             EEEEECCHHHHHHHHhc--CCccCCeEEEEee
Q 030822           14 GFITFASADSVENLMVD--THELGGSTVVVDR   43 (171)
Q Consensus        14 gFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~   43 (171)
                      -||+|+..++|-+|+-+  +..|+||.+.-.+
T Consensus       332 iFveF~r~e~aiKA~VdlnGRyFGGr~v~A~F  363 (378)
T KOG1996|consen  332 IFVEFERVESAIKAVVDLNGRYFGGRVVSACF  363 (378)
T ss_pred             eeeeeccHHHHHHHHHhcCCceecceeeehee
Confidence            59999999999999884  8999999886554

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=80.62  E-value=3.1  Score=32.35  Aligned_cols=64  Identities=14%  Similarity=0.225  Sum_probs=53.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcc---------------eeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF---------------WFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~---------------~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ..+.|...|+..+++=..+-..|.+||+|++|.++.+.               --+.|-+++.|..+--..++.|+...
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK   92 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFK   92 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHH
Confidence            46778899999999888889999999999999999765               13888888888888888888876543

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	171
3d2w_A	89	Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Co		2e-06
2dnq_A	90	Solution Structure Of Rna Binding Domain 1 In Rna-B		3e-06
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		8e-05
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-04
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		4e-04
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-04
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		5e-04
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		5e-04
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		5e-04

>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex Wit Length = 89

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 30/37 (81%)
Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           G K+FVGR  ++ TAE+L+++F ++G ++DV++PK F
Sbjct: 11  GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47

>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding Protein 30 Length = 90

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNL 159
           K+F+G LP+EAT +++R  F ++G++L+  + K + F H+  ++ +        RNL
Sbjct: 10  KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAI----RNL 62

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 26/34 (76%)
Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +FVGR   + T ++LR +FS++G ++DV++PK F
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF 41

>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 = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 48  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 99
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 100 ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 125
Query: 122 FSRFGRI 128
           F ++G+I
Sbjct: 126 FEQYGKI 132

>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 = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 46  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 97
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 98  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 123
Query: 122 FSRFGRI 128
           F ++G+I
Sbjct: 124 FEQYGKI 130

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 47  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 98
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 99  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 124
Query: 122 FSRFGRI 128
           F ++G+I
Sbjct: 125 FEQYGKI 131

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 45  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 96
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 97  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 122
Query: 122 FSRFGRI 128
           F ++G+I
Sbjct: 123 FEQYGKI 129

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 47  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 98
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 99  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 124
Query: 122 FSRFGRI 128
           F ++G+I
Sbjct: 125 FEQYGKI 131

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 32/127 (25%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP        
Sbjct: 40  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRP-------- 91
Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                A+++                               KKIFVG + ++     LR Y
Sbjct: 92  ----GAHLTV------------------------------KKIFVGGIKEDTEEHHLRDY 117
Query: 122 FSRFGRI 128
           F ++G+I
Sbjct: 118 FEQYGKI 124

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	171
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-23
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	2e-11
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-08
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-20
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-11
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-08
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	5e-15
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	2e-11
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-14
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	3e-11
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	5e-14
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-06
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	2e-12
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-12
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	6e-10
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	8e-12
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	1e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-11
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-04
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-05
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	1e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	1e-10
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	2e-09
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-10
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-08
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	7e-08
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-10
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-05
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-04
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	4e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	1e-09
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-04
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-09
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	1e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-09
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	5e-08
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	2e-09
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	4e-09
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-08
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-09
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	9e-07
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-04
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	6e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	8e-09
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-05
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-04
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	1e-08
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	1e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	1e-08
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	4e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-08
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	2e-05
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-08
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-08
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-06
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-08
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	3e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-08
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	3e-08
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-08
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	5e-08
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	6e-07
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	6e-08
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	7e-05
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	3e-05
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	8e-08
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	3e-07
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-08
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-07
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	1e-07
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-07
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	2e-07
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-07
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	2e-07
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-07
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	8e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	3e-07
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	3e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-07
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	7e-04
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	4e-07
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	7e-06
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	4e-07
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	2e-04
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	5e-07
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	6e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	6e-07
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-06
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	8e-07
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-07
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-07
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	9e-07
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	1e-06
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-06
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-06
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-06
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	2e-06
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-04
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-06
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	3e-06
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	3e-06
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-06
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	3e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	3e-06
2dis_A	109	Unnamed protein product; structural genomics, RRM	5e-05
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-06
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	3e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	4e-06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	6e-04
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	4e-06
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	5e-06
1x4e_A	85	RNA binding motif, single-stranded interacting pro	5e-06
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	6e-06
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-06
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	7e-06
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	7e-06
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	1e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	8e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-05
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	1e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-05
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	2e-04
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	8e-04
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	1e-05
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	2e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	1e-05
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-04
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	2e-05
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	2e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-05
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-05
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	6e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-05
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	1e-04
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	3e-05
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	4e-05
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	4e-05
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	5e-05
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-05
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	5e-05
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	6e-05
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	6e-05
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	6e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	6e-05
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	4e-04
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	8e-05
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	9e-05
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	9e-05
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-04
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	1e-04
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	1e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	1e-04
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	2e-04
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-04
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-04
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	2e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-04
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-04
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	5e-04
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-04
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	3e-04
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	3e-04
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-04
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	3e-04
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	4e-04
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-04
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	5e-04
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	7e-04
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	7e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	8e-04
1x5o_A	114	RNA binding motif, single-stranded interacting pro	8e-04

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 89.5 bits (223), Expect = 3e-23
 Identities = 25/135 (18%), Positives = 46/135 (34%), Gaps = 48/135 (35%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           + KD  +   RG GF++F    SV+ ++   H L G  +   RA P+++  +        
Sbjct: 35  IMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKT------- 87

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
                                                     KIFVG +  +   ++   
Sbjct: 88  -----------------------------------------GKIFVGGIGPDVRPKEFEE 106

Query: 121 YFSRFGRILDVYVPK 135
           +FS++G I+D  +  
Sbjct: 107 FFSQWGTIIDAQLML 121

>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 = 58.3 bits (142), Expect = 2e-11
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK 47
           +  D+ +   RG GF+T+ SAD+V+ +      +     + + RA P+
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAEPR 166

>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 = 50.6 bits (122), Expect = 1e-08
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            K+F+G L  + T ++LR YF ++G + D+ + K
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMK 37

>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 = 82.7 bits (205), Expect = 2e-20
 Identities = 31/133 (23%), Positives = 51/133 (38%), Gaps = 43/133 (32%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
           +D  +K  RG GF+T+A+ + V+  M    H++ G  V   RA  +ED  RP   ++   
Sbjct: 47  RDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLT--- 103

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                   KKIFVG + ++     LR Y
Sbjct: 104 ---------------------------------------VKKIFVGGIKEDTEEHHLRDY 124

Query: 122 FSRFGRILDVYVP 134
           F ++G+I  + + 
Sbjct: 125 FEQYGKIEVIEIM 137

>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 = 59.2 bits (144), Expect = 1e-11
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGR 56
           +  D+GS   RG  F+TF   DSV+ +++   H + G    V +A  K++       
Sbjct: 136 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS 192

>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 = 50.8 bits (122), Expect = 2e-08
 Identities = 13/34 (38%), Positives = 21/34 (61%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +K+F+G L  E T E LR +F ++G + D  V +
Sbjct: 14  RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR 47

>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 = 65.7 bits (161), Expect = 5e-15
 Identities = 17/44 (38%), Positives = 30/44 (68%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
                  G K+FVGR  ++ TAE+L+++F ++G ++DV++PK F
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF 47

>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 = 56.5 bits (137), Expect = 2e-11
 Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDF 51
          +PK       R   F+TFA     ++L  +   + G +V +  A PK +  
Sbjct: 43 IPKP-----FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHNKL 88

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 63.4 bits (155), Expect = 3e-14
 Identities = 15/40 (37%), Positives = 26/40 (65%)

Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
                 +FVGR   + T ++LR +FS++G ++DV++PK F
Sbjct: 2   SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF 41

>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 = 3e-11
 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 3/53 (5%)

Query: 8  KAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
          K  R   F+TFA     ++L  +   + G +V +  A PK +        S G
Sbjct: 39 KPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNSG---PSSG 88

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 66.2 bits (162), Expect = 5e-14
 Identities = 19/137 (13%), Positives = 44/137 (32%), Gaps = 39/137 (28%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           M  D  +  H+G  F+ +   ++ +  +  +++  LGG  + V R +             
Sbjct: 60  MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQA-------- 111

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                             +     R   +I+V  + Q+ + +D+
Sbjct: 112 -----------------------------QPIIDQLAEEARAFNRIYVASVHQDLSDDDI 142

Query: 119 RRYFSRFGRILDVYVPK 135
           +  F  FG+I    + +
Sbjct: 143 KSVFEAFGKIKSATLAR 159

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 5/53 (9%)

Query: 88  GSFYGRGESSQRIGK-----KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G   GRG ++QR G      +++VG +  E   + +R+ F+ FG I  + +  
Sbjct: 10  GQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSW 62

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
           + +D  +  H+G GFI +  A S ++ +  ++  +LGG  + V +A   
Sbjct: 157 LARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTP 205

>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 = 58.8 bits (143), Expect = 2e-12
 Identities = 14/50 (28%), Positives = 25/50 (50%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           G   SS +   K+ VG +    T ++LR  F  +G +++  + K + F H
Sbjct: 1   GSSGSSGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVH 50

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 58.4 bits (142), Expect = 3e-12
 Identities = 17/48 (35%), Positives = 30/48 (62%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           G S      K+F+G LP+EAT +++R  F ++G++L+  + K + F H
Sbjct: 1   GSSGSSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVH 48

>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 = 58.0 bits (141), Expect = 7e-12
 Identities = 17/52 (32%), Positives = 25/52 (48%)

Query: 84  YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + H      RG      G K+F+G L  + T E LR YF +FG + +  V +
Sbjct: 8   HHHSSGLVPRGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMR 59

>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 = 53.0 bits (128), Expect = 6e-10
 Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
           +D  +K  RG GF+TF     V+ ++    HEL   T+    A P+  
Sbjct: 59  RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA 106

>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 = 57.6 bits (140), Expect = 8e-12
 Identities = 16/44 (36%), Positives = 22/44 (50%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G   SS     KIFVG +P      +LR YF +FG + +V +  
Sbjct: 1   GSSGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIY 44

>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 = 54.5 bits (132), Expect = 1e-10
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
          M  D   +  RG GFITF    SV+  + +  H++ G  V V RA P++ 
Sbjct: 42 MIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDS 91

>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 = 55.7 bits (135), Expect = 3e-11
 Identities = 17/46 (36%), Positives = 25/46 (54%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
            S     KIFVG +    T+++LR  F R GR+++  V K + F H
Sbjct: 4   GSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVH 49

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 57.7 bits (140), Expect = 5e-11
 Identities = 18/134 (13%), Positives = 35/134 (26%), Gaps = 29/134 (21%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
                   +   F+ F S D     M  D     G ++ + R    +         S   
Sbjct: 43  LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYV 102

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
            G  +  +  +                              K+F+G LP     + ++  
Sbjct: 103 PGVVSTVVPDS----------------------------AHKLFIGGLPNYLNDDQVKEL 134

Query: 122 FSRFGRILDVYVPK 135
            + FG +    + K
Sbjct: 135 LTSFGPLKAFNLVK 148

>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 = 44.3 bits (105), Expect = 4e-06
 Identities = 9/52 (17%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD 50
           + KD  +   +G  F  +   +  +  +   +  +LG   ++V RA+    +
Sbjct: 146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKN 197

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 7/34 (20%), Positives = 17/34 (50%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           ++++VG +P   T E +  +F+   R+  +    
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAP 38

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 54.6 bits (132), Expect = 8e-11
 Identities = 12/42 (28%), Positives = 18/42 (42%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G S     + +FV   P+   +  L  YF  FG +  V + K
Sbjct: 1   GSSGSSGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDK 42

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 15/61 (24%), Positives = 20/61 (32%), Gaps = 7/61 (11%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFRPVGRMSH 59
          M KD+G         +      + E  L    H LGG  + V     KE    P  +   
Sbjct: 40 MDKDKG-----VFAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEFQ-SPASKSPK 93

Query: 60 G 60
          G
Sbjct: 94 G 94

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 55.0 bits (132), Expect = 1e-10
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G S     +K+FVG LP +   +++   F RFG ++  +  K
Sbjct: 1   GSSGSSGSRKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHK 42

>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 = 53.7 bits (130), Expect = 1e-10
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           KIFVG L  +   E +R YF  FG +  + +P 
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPM 33

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 50.6 bits (122), Expect = 2e-09
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRA 44
          +P D  +   RG  FITF   + V+ +M    H +G S   +  A
Sbjct: 31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA 75

>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 = 54.2 bits (131), Expect = 2e-10
 Identities = 10/47 (21%), Positives = 18/47 (38%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED 49
          KD  +   +G GF+ F   ++   +M   H + G          K+ 
Sbjct: 49 KDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS 95

>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 = 48.8 bits (117), Expect = 2e-08
 Identities = 14/32 (43%), Positives = 19/32 (59%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
             + V  LP + T +DL+ YFS FG +L V V
Sbjct: 16  SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV 47

>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 = 55.3 bits (134), Expect = 2e-10
 Identities = 18/135 (13%), Positives = 41/135 (30%), Gaps = 46/135 (34%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDTHE--LGGSTVVVDRATPKEDDFRPVGRMSHG 60
           + Q     +G  F+TF +  +        H   +        +  P + +          
Sbjct: 39  RSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSE---------- 88

Query: 61  GYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRR 120
                                             +++    +K+F+G + ++ T  D+R 
Sbjct: 89  ----------------------------------KNNAVEDRKLFIGMISKKCTENDIRV 114

Query: 121 YFSRFGRILDVYVPK 135
            FS FG+I +  + +
Sbjct: 115 MFSSFGQIEECRILR 129

>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 = 48.8 bits (117), Expect = 7e-08
 Identities = 11/33 (33%), Positives = 23/33 (69%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+FVG++P+  + +DLR  F ++G + ++ V +
Sbjct: 5   KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLR 37

>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 = 54.9 bits (133), Expect = 4e-10
 Identities = 16/134 (11%), Positives = 30/134 (22%), Gaps = 49/134 (36%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
                   +   F+ F S D     M  D     G ++ + R    +             
Sbjct: 43  LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA-------- 94

Query: 62  YGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRY 121
                                                    K+F+G LP     + ++  
Sbjct: 95  ----------------------------------------HKLFIGGLPNYLNDDQVKEL 114

Query: 122 FSRFGRILDVYVPK 135
            + FG +    + K
Sbjct: 115 LTSFGPLKAFNLVK 128

>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 = 42.6 bits (101), Expect = 1e-05
 Identities = 9/47 (19%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRAT 45
           + KD  +   +G  F  +   +  +  +  ++  +LG   ++V RA+
Sbjct: 126 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS 172

>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 = 39.5 bits (93), Expect = 1e-04
 Identities = 7/30 (23%), Positives = 17/30 (56%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           ++++VG +P   T E +  +F+   R+  +
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGL 34

>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 = 54.1 bits (130), Expect = 4e-10
 Identities = 19/101 (18%), Positives = 37/101 (36%), Gaps = 8/101 (7%)

Query: 36  GSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGE 95
            +T  VD AT +    +   + ++            AT+   +   + + H         
Sbjct: 16  TTTEAVDAATAE----KVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHM----HR 67

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
            S  +  K++VG L       +L R F  +G +  V+V + 
Sbjct: 68  DSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN 108

>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 = 52.2 bits (126), Expect = 1e-09
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            G           + V  L    + + LRR F ++GR+ DVY+P+
Sbjct: 3   SGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPR 47

>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 = 37.2 bits (87), Expect = 3e-04
 Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 5/62 (8%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +P++  +KA RG  F+ F      ++    +D  EL G  + V  A     D       S
Sbjct: 45  IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGRRDLS---GPS 101

Query: 59  HG 60
            G
Sbjct: 102 SG 103

>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 = 54.6 bits (132), Expect = 1e-09
 Identities = 26/141 (18%), Positives = 44/141 (31%), Gaps = 49/141 (34%)

Query: 1   MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKEDDFRPVGR 56
           +P  + +   R   +I   S +     VE L  +  ++ G T+V   + P E        
Sbjct: 150 LPSLRFNT-SRRFAYIDVTSKEDARYCVEKL--NGLKIEGYTLVTKVSNPLEKS------ 200

Query: 57  MSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAE 116
                                               R +S+   G++I +  L  E   E
Sbjct: 201 -----------------------------------KRTDSATLEGREIMIRNLSTELLDE 225

Query: 117 D-LRRYFSRFGRILDVYVPKR 136
           + LR  F  FG I  + +P  
Sbjct: 226 NLLRESFEGFGSIEKINIPAG 246

>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 = 43.4 bits (103), Expect = 1e-05
 Identities = 9/32 (28%), Positives = 14/32 (43%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + V  LP+      + +YF   G I+ V V  
Sbjct: 44  VLVKNLPKSYNQNKVYKYFKHCGPIIHVDVAD 75

>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 = 51.9 bits (125), Expect = 2e-09
 Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 1/52 (1%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKEDDFRP 53
           +D  SK  RG GF+TF+S   V+  M    H + G  V   RA  +E+    
Sbjct: 61  RDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGSG 112

>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 = 48.0 bits (115), Expect = 5e-08
 Identities = 13/32 (40%), Positives = 21/32 (65%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           +K+F+G L  E T E LR Y+ ++G++ D  V
Sbjct: 28  RKLFIGGLSFETTEESLRNYYEQWGKLTDCVV 59

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 51.5 bits (124), Expect = 2e-09
 Identities = 12/54 (22%), Positives = 21/54 (38%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           GS     +  +    ++FV   P +    +L   F  FG + +V +   F F  
Sbjct: 18  GSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVE 71

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 50.7 bits (122), Expect = 3e-09
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 96  SSQRIGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
            +     ++F+G LP +  + EDL R FS +G I+ + +   F F  
Sbjct: 5   HNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQ 51

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 49.8 bits (120), Expect = 4e-09
 Identities = 14/33 (42%), Positives = 20/33 (60%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           KIFVG L    T ED++ YF +FG++ D  +  
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMF 33

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 47.1 bits (113), Expect = 5e-08
 Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRA 44
          +  D+ +  HRG GF+TF S D VE +     HE+    V   +A
Sbjct: 31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA 75

>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 = 51.8 bits (125), Expect = 4e-09
 Identities = 15/126 (11%), Positives = 36/126 (28%), Gaps = 47/126 (37%)

Query: 4   DQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGY 62
           D  +  +R  G++ F SA+ +E  L +   ++ G+ + +++   ++              
Sbjct: 47  DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRD-------------- 92

Query: 63  GAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYF 122
                                               R  + +    L    T ++L+  F
Sbjct: 93  --------------------------------SKKVRAARTLLAKNLSFNITEDELKEVF 120

Query: 123 SRFGRI 128
                I
Sbjct: 121 EDALEI 126

>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 = 45.7 bits (109), Expect = 9e-07
 Identities = 9/45 (20%), Positives = 16/45 (35%), Gaps = 1/45 (2%)

Query: 93  RGESSQRIG-KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
             E S+      +F+G L    +  +L+   S      D+ V   
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV 48

>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 = 39.1 bits (92), Expect = 2e-04
 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 2/39 (5%)

Query: 11  RGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
           +GI +I F S    E  +      E+ G +V +     K
Sbjct: 136 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEK 174

>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 = 50.0 bits (120), Expect = 6e-09
 Identities = 15/40 (37%), Positives = 21/40 (52%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           K +FV  L    T E L + FS+FG++  V   K + F H
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIH 51

>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 = 52.3 bits (126), Expect = 8e-09
 Identities = 16/138 (11%), Positives = 28/138 (20%), Gaps = 48/138 (34%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +   + +   +G GF  +   DS       +    LG  T+ V      +          
Sbjct: 127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQL--------- 177

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEAT-AED 117
                                                      + + V RLP      + 
Sbjct: 178 ----------------------------------TPALLH--SRCLCVDRLPPGFNDVDA 201

Query: 118 LRRYFSRFGRILDVYVPK 135
           L R  S         +  
Sbjct: 202 LCRALSAVHSPTFCQLAC 219

>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 = 42.3 bits (100), Expect = 2e-05
 Identities = 7/40 (17%), Positives = 12/40 (30%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
             Q     + V  LP   T +        FG +   ++  
Sbjct: 90  QLQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVY 129

>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 = 39.2 bits (92), Expect = 2e-04
 Identities = 10/51 (19%), Positives = 18/51 (35%), Gaps = 3/51 (5%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMVDTH--ELGGSTVVVDRATPKED 49
           +   Q  +  +G   + + +A+  E          LGGS + V    P   
Sbjct: 217 LACGQDGQ-LKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP 266

>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 = 49.2 bits (118), Expect = 1e-08
 Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 86  HPGSFYGRGESSQRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           H     G       +  ++F+G LP +  + EDL R FS +G I+ + +   F F  
Sbjct: 7   HHHHSSGLVPRGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQ 63

>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 = 49.6 bits (119), Expect = 1e-08
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS  G          K+F+G++P+    +DL+  F  FG+I ++ V K
Sbjct: 1   GS-SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLK 47

>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 = 49.2 bits (118), Expect = 1e-08
 Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKED 49
          KD+ +   RG GF+ F   + V  ++    H L G  +     TP+  
Sbjct: 50 KDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGM 97

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 48.0 bits (115), Expect = 4e-08
 Identities = 16/42 (38%), Positives = 22/42 (52%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           G   S      K+FVG L    T E LR YFS++G ++D  +
Sbjct: 7   GMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVI 48

>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 = 49.2 bits (118), Expect = 2e-08
 Identities = 13/35 (37%), Positives = 19/35 (54%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
             KI V  +P +A   ++R  FS FG +  V +PK
Sbjct: 15  TSKILVRNIPFQANQREIRELFSTFGELKTVRLPK 49

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 4/53 (7%)

Query: 1  MPKDQ-GSKAHRGIGFITFASADSVEN---LMVDTHELGGSTVVVDRATPKED 49
          +PK   G+ AHRG GF+ F +    +     +  +  L G  +V++ A  +  
Sbjct: 47 LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT 99

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 48.8 bits (117), Expect = 2e-08
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
           K++VG L   A   +L R FS +G +  V++ + 
Sbjct: 2   KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN 35

>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 = 48.3 bits (116), Expect = 2e-08
 Identities = 12/32 (37%), Positives = 22/32 (68%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
            K+FVG L  + + +DL+ YF++FG ++D  +
Sbjct: 12  GKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTI 43

>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 = 43.7 bits (104), Expect = 1e-06
 Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRA 44
           D  +   RG GFI F  A SVE ++    H L G  +   +A
Sbjct: 45 MDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA 87

>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 = 48.9 bits (117), Expect = 2e-08
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 98  QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           + I  ++F+G L        D+   FS++GR+    V K + F  
Sbjct: 24  KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQ 68

>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 = 48.4 bits (116), Expect = 3e-08
 Identities = 8/34 (23%), Positives = 18/34 (52%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
             +FVG +       ++R +F+R+G + +V +  
Sbjct: 10  NTVFVGGIDVRMDETEIRSFFARYGSVKEVKIIT 43

>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 = 48.0 bits (115), Expect = 3e-08
 Identities = 8/39 (20%), Positives = 19/39 (48%)

Query: 11 RGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED 49
          +G GF++F +   V+ ++       G  + +  A  K++
Sbjct: 50 KGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRKQN 88

>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 = 48.7 bits (116), Expect = 3e-08
 Identities = 17/67 (25%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSR 149
           G   SS R    I    LP    A +++  FSRFG +  V +P               +R
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 150 SCFSKVS 156
             F  ++
Sbjct: 61  KAFRHLA 67

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 49.0 bits (117), Expect = 3e-08
 Identities = 15/49 (30%), Positives = 23/49 (46%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
               YGR          + V  L    + + LRR F ++GR+ DVY+P+
Sbjct: 33  GSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 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 = 48.5 bits (116), Expect = 3e-08
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
            +     +I+VG LP +   +D+   F ++G I D+ +  R
Sbjct: 17  PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR 57

>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 = 48.0 bits (115), Expect = 3e-08
 Identities = 15/42 (35%), Positives = 23/42 (54%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            ES     +K+FVG L ++ + ED+ R F  FG I +  V +
Sbjct: 8   SESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLR 49

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 47.1 bits (113), Expect = 5e-08
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           K+F+G L  + T E LR YF +FG + +  V
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGEVKECLV 32

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 44.0 bits (105), Expect = 6e-07
 Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 3  KDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRA 44
          +D  +K  RG GF+TF     V+ ++    HEL   T+    A
Sbjct: 34 RDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA 76

>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 = 48.7 bits (117), Expect = 6e-08
 Identities = 16/137 (11%), Positives = 35/137 (25%), Gaps = 50/137 (36%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           + +D  +    G  F+ F S    +    +++   +    + V  A P            
Sbjct: 35  IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPG----------- 83

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                                        ++V  LP+  T + L
Sbjct: 84  -------------------------------------GESIKDTNLYVTNLPRTITDDQL 106

Query: 119 RRYFSRFGRILDVYVPK 135
              F ++G I+   + +
Sbjct: 107 DTIFGKYGSIVQKNILR 123

>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 = 40.2 bits (95), Expect = 7e-05
 Identities = 9/35 (25%), Positives = 14/35 (40%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
              + V  LPQ+ T  +L   F   G I    + +
Sbjct: 3   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR 37

>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 = 48.3 bits (116), Expect = 7e-08
 Identities = 21/135 (15%), Positives = 40/135 (29%), Gaps = 50/135 (37%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           + +D+ +    G GF+ +      E     ++   L   T+ V  A P     R      
Sbjct: 34  LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSASIR------ 87

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                                        ++V  LP+  T ++L
Sbjct: 88  ------------------------------------------DANLYVSGLPKTMTQKEL 105

Query: 119 RRYFSRFGRILDVYV 133
            + FS++GRI+   +
Sbjct: 106 EQLFSQYGRIITSRI 120

>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 = 41.4 bits (98), Expect = 3e-05
 Identities = 10/33 (30%), Positives = 14/33 (42%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            + V  LPQ  T E+ R  F   G I    + +
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVR 36

>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 = 47.3 bits (113), Expect = 8e-08
 Identities = 16/32 (50%), Positives = 18/32 (56%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
            KIFVG LP   T   LR+YF  FG I +  V
Sbjct: 18  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVV 49

>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 = 46.1 bits (110), Expect = 3e-07
 Identities = 14/66 (21%), Positives = 23/66 (34%), Gaps = 2/66 (3%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLMVDT-HELGGSTVVVDRATPKEDDFRPVGRMSHGG 61
            D+ +   RG GF+T A   + E    D    + G    V+ A       R +      G
Sbjct: 51  TDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAKP-RSLQTGFAIG 109

Query: 62  YGAYNA 67
               ++
Sbjct: 110 VSGPSS 115

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 46.9 bits (112), Expect = 8e-08
 Identities = 14/38 (36%), Positives = 17/38 (44%), Gaps = 2/38 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWF 139
            ++G +P  AT  DL   F  FG ILD      K   F
Sbjct: 30  AYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCF 67

>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 = 46.8 bits (112), Expect = 1e-07
 Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)

Query: 88  GSFYGRGESSQRI-GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS    G + +      I V  L ++    DL+  F  FG I  +Y+ K
Sbjct: 1   GSSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAK 49

>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 = 46.5 bits (111), Expect = 1e-07
 Identities = 14/43 (32%), Positives = 27/43 (62%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            GE +     ++FVG LP + T E++R+ F ++G+  +V++ K
Sbjct: 7   GGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHK 49

>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 = 46.5 bits (111), Expect = 1e-07
 Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 7/57 (12%)

Query: 92  GRGESSQRIG-------KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           G   SS +IG        +++VG L    +   L R F RFG I  +   K   F +
Sbjct: 1   GSSGSSGKIGYGKANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAY 57

>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 = 46.4 bits (111), Expect = 1e-07
 Identities = 12/42 (28%), Positives = 22/42 (52%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G S      ++FV  L   ++ EDL + FS +G + +++ P 
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPI 42

>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 = 37.2 bits (87), Expect = 3e-04
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGR 56
           P D  +K  +G  F+TF   +        VD     G  + V  +T K++  +    
Sbjct: 40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>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 = 45.7 bits (109), Expect = 2e-07
 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWF 139
             ++VG L    T  DLR +F +FG I  + V   ++  F
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAF 52

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 47.1 bits (112), Expect = 2e-07
 Identities = 13/44 (29%), Positives = 20/44 (45%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G    S    + ++VG L +E   + L   F  FG I D+ +P 
Sbjct: 54  GGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 97

>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 = 45.7 bits (109), Expect = 2e-07
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 2/50 (4%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRFWFCH 141
           G S      K+++G L    TA+DLR+ F      L   V     + F  
Sbjct: 1   GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVD 50

>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 = 47.1 bits (112), Expect = 2e-07
 Identities = 12/44 (27%), Positives = 20/44 (45%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
                       + V  L    + + LRR F ++GR+ DVY+P+
Sbjct: 61  HHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPR 104

>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 = 47.8 bits (114), Expect = 3e-07
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
             SF   GE +     ++FVG LP + T ED +R F R+G   +V++ +
Sbjct: 8   IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR 56

>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 = 46.6 bits (111), Expect = 8e-07
 Identities = 10/33 (30%), Positives = 15/33 (45%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           G  + V  L    + E L + FS+FG +    V
Sbjct: 96  GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV 128

>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 = 45.7 bits (109), Expect = 3e-07
 Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS    G ++ +  + ++VG L +E   + L   F  FG I D+ +P 
Sbjct: 1   GSSGSSGMATTK--RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 46

>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 = 42.6 bits (101), Expect = 4e-06
 Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 5/62 (8%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +P D  ++ HRG  F+ F  A+     +  ++  EL G T+ V+ A P           S
Sbjct: 44  IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI---KESGPS 100

Query: 59  HG 60
            G
Sbjct: 101 SG 102

>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 = 45.5 bits (108), Expect = 3e-07
 Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 3/60 (5%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKRFWFCHLCGRSCSRSCFSK 154
           SS      I V  LPQ++  +++      +  +   V   KR  F  L     +++    
Sbjct: 2   SSGS--SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQAQNAIQM 59

>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 = 45.2 bits (108), Expect = 3e-07
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + ++VG L +E   + L   F  FG I D+ +P 
Sbjct: 8   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPL 41

>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 = 36.0 bits (84), Expect = 7e-04
 Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRA 44
          +P D  ++ HRG  F+ F  A+     +  ++  EL G T+ V+ A
Sbjct: 39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84

>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 = 45.3 bits (108), Expect = 4e-07
 Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 2/48 (4%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS    G +S     K+FVG L  +   + L + FS++G+I +V V K
Sbjct: 1   GSSGSSGMASD--EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVK 46

>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 = 41.8 bits (99), Expect = 7e-06
 Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          + KD+ ++  RG GF+TF + D  ++ M  ++   + G  + VD+A    D
Sbjct: 44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD 94

>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 = 45.4 bits (108), Expect = 4e-07
 Identities = 11/33 (33%), Positives = 19/33 (57%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+F+G L +E   + L+  F + G I +V + K
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIK 41

>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 = 38.5 bits (90), Expect = 2e-04
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 2   PKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSH 59
            KD+ SK  RG  FITF +    +N    ++   L G  + V++A       +  GR   
Sbjct: 40  IKDRTSK-SRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSF--QSGGRRRP 96

Query: 60  GGYGAYNAY 68
                  + 
Sbjct: 97  PASSRNRSP 105

>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 = 45.0 bits (107), Expect = 5e-07
 Identities = 11/38 (28%), Positives = 22/38 (57%), Gaps = 2/38 (5%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWF 139
           ++ G +    T + +R+ FS FG+I+++ V   K + F
Sbjct: 28  VYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSF 65

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 45.1 bits (107), Expect = 6e-07
 Identities = 9/37 (24%), Positives = 20/37 (54%)

Query: 99  RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            + + +++  LP + TAE++   F ++G I  + V  
Sbjct: 6   EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGN 42

>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 = 45.0 bits (107), Expect = 6e-07
 Identities = 10/41 (24%), Positives = 18/41 (43%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
              +R  + +F  +L       DL  +FS  G++ DV +  
Sbjct: 19  SPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIIS 59

>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 = 43.8 bits (104), Expect = 2e-06
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKE 48
           +  D+ S+  +GI ++ F    SV   + +    L G  ++V  +  ++
Sbjct: 57  IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAEK 105

>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 = 45.1 bits (107), Expect = 8e-07
 Identities = 13/71 (18%), Positives = 22/71 (30%), Gaps = 4/71 (5%)

Query: 65  YNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSR 124
           Y+ Y   A           +  P       +      + + V  +P       LR+ F R
Sbjct: 10  YDPYGQTAQLQQLQQQQQQHIPPTQMNPEPDV----LRNLMVNYIPTTVDEVQLRQLFER 65

Query: 125 FGRILDVYVPK 135
           +G I  V +  
Sbjct: 66  YGPIESVKIVC 76

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 44.6 bits (106), Expect = 8e-07
 Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 4/56 (7%)

Query: 84  YDHPGSFYGRGESSQRI----GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + H      RG           K++ V  +P      DLR+ F +FG+ILDV +  
Sbjct: 8   HHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF 63

>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 = 44.1 bits (105), Expect = 9e-07
 Identities = 10/33 (30%), Positives = 19/33 (57%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K+ +GRL +  T + +   FS +G+I  + +P 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPV 38

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 44.2 bits (105), Expect = 9e-07
 Identities = 12/49 (24%), Positives = 19/49 (38%)

Query: 87  PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            GS      S+     K+F+  LP   T E+L       G + D+ +  
Sbjct: 3   SGSSGVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVT 51

>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 = 44.1 bits (105), Expect = 1e-06
 Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 2/48 (4%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS   R          + V  L    T  DLR  FS++G I DV +  
Sbjct: 4   GSSGNRANPDP--NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY 49

>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 = 44.2 bits (105), Expect = 1e-06
 Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 88  GSFYGRGESSQRI-GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS    G S  +   K++ V  +P      DLR+ F +FG+ILDV +  
Sbjct: 1   GSSGSSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIF 49

>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 = 44.7 bits (106), Expect = 1e-06
 Identities = 12/45 (26%), Positives = 19/45 (42%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +    ++      + V  L    T  DLR  FS++G I DV +  
Sbjct: 36  HVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVY 80

>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 = 43.7 bits (104), Expect = 1e-06
 Identities = 11/35 (31%), Positives = 18/35 (51%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            + I+VG +   ATAE+L  +F   G +  V +  
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILC 40

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 11/59 (18%), Positives = 17/59 (28%), Gaps = 2/59 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRN 158
             + +  L       DL      FG I  V V   KR           + +  +  + N
Sbjct: 22  PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADN 80

>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 = 43.4 bits (103), Expect = 2e-06
 Identities = 12/35 (34%), Positives = 20/35 (57%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
              ++V  LP   T  DL R FS++G+++ V + K
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMK 50

>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 = 43.5 bits (103), Expect = 2e-06
 Identities = 10/35 (28%), Positives = 16/35 (45%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GK +F+  L  ++  E L     +FG +  V V  
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVL 49

>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 = 38.5 bits (90), Expect = 1e-04
 Identities = 8/57 (14%), Positives = 22/57 (38%), Gaps = 8/57 (14%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--------VDTHELGGSTVVVDRATPKED 49
           +     ++  +G  F  F + ++ +  +            +L G  + VD A  +++
Sbjct: 47  VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE 103

>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 = 44.9 bits (106), Expect = 2e-06
 Identities = 16/138 (11%), Positives = 39/138 (28%), Gaps = 19/138 (13%)

Query: 8   KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAY 65
              +    +  A  +  +  M  ++ H+L G  + +  +  +       G+   G    Y
Sbjct: 38  FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDY 97

Query: 66  NAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF 125
                   +            P                + +  +P   + EDL+  FS  
Sbjct: 98  GNSPLHRFKKPGSKNFQNIFPPS-------------ATLHLSNIPPSVSEEDLKVLFSSN 144

Query: 126 GRILDVYV----PKRFWF 139
           G ++  +      ++   
Sbjct: 145 GGVVKGFKFFQKDRKMAL 162

>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 = 43.4 bits (102), Expect = 2e-06
 Identities = 11/49 (22%), Positives = 23/49 (46%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
           GS  G   S+    + I + +LP + T  ++      FG++ ++ + K 
Sbjct: 18  GSHMGDSRSAGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 66

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 43.0 bits (102), Expect = 3e-06
 Identities = 11/44 (25%), Positives = 18/44 (40%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G   + +   + +FVG L      E L   F + G +  V + K
Sbjct: 7   GMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICK 50

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 2/59 (3%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRN 158
             + V  L +     DL     +FG I  V +   KR           ++ C +  +  
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAADV 74

>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 = 42.5 bits (101), Expect = 3e-06
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + I+VG L   AT+E ++  FS+FG++ +V +  
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIY 35

>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 = 43.5 bits (103), Expect = 3e-06
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G  +FV  + +EAT ED+   F+ +G I ++++  
Sbjct: 22  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 56

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 42.9 bits (101), Expect = 3e-06
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKED 49
                   +RG  F+ + S  +       LM    +L G  + VD A P+ D
Sbjct: 42 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 94

>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 = 39.8 bits (93), Expect = 5e-05
 Identities = 8/35 (22%), Positives = 18/35 (51%), Gaps = 1/35 (2%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPKR 136
           ++F+G +P+    E++    ++    +LDV V   
Sbjct: 10  RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYAS 44

>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 = 43.0 bits (102), Expect = 3e-06
 Identities = 8/35 (22%), Positives = 20/35 (57%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G  +FV  + +EA  ++++  F  +G I ++++  
Sbjct: 26  GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNL 60

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 6/38 (15%), Positives = 21/38 (55%)

Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
               + +++   P +AT +D++ +    G++L++ + +
Sbjct: 8   DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR 45

>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 = 43.2 bits (102), Expect = 4e-06
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + ++VG +   +TA+DL  +FS  G I  + +  
Sbjct: 37  RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILC 70

>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 = 37.0 bits (86), Expect = 6e-04
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 1/57 (1%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFRPVGR 56
           +  D+ S   +G  +I FA  +SV+  + +D     G T+ V              R
Sbjct: 68  ILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISSTDR 124

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 42.3 bits (100), Expect = 4e-06
 Identities = 4/44 (9%), Positives = 13/44 (29%), Gaps = 2/44 (4%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVPK 135
           G         I +  +      + +    S +    + ++ + K
Sbjct: 2   GHHHHHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIK 45

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G  +FV  + +EAT ED+   F+ +G I ++++  
Sbjct: 23  GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNL 57

>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 = 41.7 bits (99), Expect = 5e-06
 Identities = 6/35 (17%), Positives = 14/35 (40%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
              +++  L    T +DL +    +G+I+      
Sbjct: 5   SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAIL 39

>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 = 43.3 bits (102), Expect = 6e-06
 Identities = 12/63 (19%), Positives = 26/63 (41%)

Query: 73  TRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVY 132
           TR A      + +        G      G  +FV  + +EA  ++++  F  +G I +++
Sbjct: 44  TREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIH 103

Query: 133 VPK 135
           +  
Sbjct: 104 LNL 106

>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 = 41.9 bits (99), Expect = 6e-06
 Identities = 13/40 (32%), Positives = 21/40 (52%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +  R  + +FVG +P EAT E L+  FS  G ++   +  
Sbjct: 3   AVDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVY 42

>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 = 41.8 bits (99), Expect = 7e-06
 Identities = 15/47 (31%), Positives = 19/47 (40%), Gaps = 1/47 (2%)

Query: 88  GSFYGRGESSQR-IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           GS    G+   R     ++V  L      E LR+ FS FG I    V
Sbjct: 1   GSSGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKV 47

>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 = 41.9 bits (99), Expect = 7e-06
 Identities = 7/34 (20%), Positives = 13/34 (38%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K ++V  L    + E + + F+         V K
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK 49

>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 = 41.5 bits (98), Expect = 1e-05
 Identities = 7/39 (17%), Positives = 12/39 (30%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV 131
                 R  + +    L    T ++L+  F     I  V
Sbjct: 8   CTSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV 46

>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 = 36.1 bits (84), Expect = 8e-04
 Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 11 RGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          +GI +I F S    E  +      E+ G +V +     K  
Sbjct: 53 KGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG 93

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 43.1 bits (101), Expect = 1e-05
 Identities = 16/138 (11%), Positives = 39/138 (28%), Gaps = 19/138 (13%)

Query: 8   KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAY 65
              +    +  A  +  +  M  ++ H+L G  + +  +  +       G+   G    Y
Sbjct: 69  FNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDY 128

Query: 66  NAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF 125
                   +            P                + +  +P   + EDL+  FS  
Sbjct: 129 GNSPLHRFKKPGSKNFQNIFPPS-------------ATLHLSNIPPSVSEEDLKVLFSSN 175

Query: 126 GRILDVYV----PKRFWF 139
           G ++  +      ++   
Sbjct: 176 GGVVKGFKFFQKDRKMAL 193

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 8/45 (17%), Positives = 17/45 (37%), Gaps = 1/45 (2%)

Query: 88  GSFYGRGE-SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV 131
           GS    G    ++  +K+ +  +P     E L     ++G +   
Sbjct: 1   GSSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESC 45

>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 = 41.0 bits (97), Expect = 1e-05
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
             ++VG L    T + LR  F  FG+I ++ + K
Sbjct: 6   SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMK 39

>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 = 37.5 bits (88), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 6/53 (11%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKED 49
          + KD  +   +G GFITF+ ++     +E L  +  EL G  + V   T + D
Sbjct: 37 LMKDSDTGRSKGYGFITFSDSECARRALEQL--NGFELAGRPMRVGHVTERLD 87

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 6/35 (17%), Positives = 14/35 (40%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            K++   RL        L+    ++G + +V +  
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILL 40

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 10/66 (15%), Positives = 23/66 (34%), Gaps = 6/66 (9%)

Query: 1   MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKEDDFRPVGR 56
           +     ++ H G+  + F S       V+NL      + G+ +        +   +    
Sbjct: 38  ILLHPRTRKHLGLARVLFTSTRGAKETVKNL--HLTSVMGNIIHAQLDIKGQQRMKYYEL 95

Query: 57  MSHGGY 62
           + +G Y
Sbjct: 96  IVNGSY 101

>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 = 41.1 bits (97), Expect = 1e-05
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 88  GSFYGRGESSQR-IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           GS    G  S+R     ++VG L ++ +   L   F + G +++ ++PK
Sbjct: 1   GSSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPK 49

>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 = 40.7 bits (96), Expect = 2e-05
 Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           MPKD+ +  H+G GF+ F S +  +  +  +D  +L G  + V++A+    +       S
Sbjct: 47  MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNKNLS---GPS 103

Query: 59  HG 60
            G
Sbjct: 104 SG 105

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 41.2 bits (97), Expect = 1e-05
 Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +  D+ +   +G   ++F    S +      D  E  G+ + V  AT +  DF   G   
Sbjct: 47  LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRA-DFNRGGGNG 105

Query: 59  HGGYGAYNAY 68
            GG   ++ +
Sbjct: 106 RGGLEHHHHH 115

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 10/27 (37%), Positives = 13/27 (48%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRI 128
             IFV  L +  T E +  YF + G I
Sbjct: 8   NTIFVQGLGENVTIESVADYFKQIGII 34

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 10/49 (20%), Positives = 22/49 (44%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
           GS +     S    + I + +LP + T  ++      FG++ ++ + K 
Sbjct: 3   GSHHHHHHGSGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG 51

>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 = 40.6 bits (95), Expect = 2e-05
 Identities = 7/36 (19%), Positives = 18/36 (50%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
            + + + +LP E T  ++      FG++ ++ + K 
Sbjct: 15  SRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG 50

>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 = 40.8 bits (96), Expect = 2e-05
 Identities = 16/33 (48%), Positives = 20/33 (60%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            +FVG L  E T ED++  F+ FGRI D  V K
Sbjct: 17  HVFVGDLSPEITTEDIKAAFAPFGRISDARVVK 49

>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 = 40.3 bits (95), Expect = 2e-05
 Identities = 6/34 (17%), Positives = 18/34 (52%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + +++G +P + T E +    S  G ++++ +  
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMF 36

>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 = 39.1 bits (92), Expect = 6e-05
 Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 6/54 (11%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKEDD 50
          M  D  +   +G  FI F   +S    V NL  + ++LG   +    ++  +  
Sbjct: 34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNL--NGYQLGSRFLKCGYSSNSDIS 85

>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 = 40.4 bits (95), Expect = 3e-05
 Identities = 11/33 (33%), Positives = 17/33 (51%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +++VG L    T + LR  F  FGRI  + +  
Sbjct: 28  RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMM 60

>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 = 38.8 bits (91), Expect = 1e-04
 Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
           +  D  +   +G GFITF+ ++  +  +  ++  EL G  + V   T + D
Sbjct: 58  LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTD 108

>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 = 40.4 bits (95), Expect = 3e-05
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           G  +F+  LPQE   +DL + F  FG ++   V
Sbjct: 25  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKV 57

>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 = 39.4 bits (93), Expect = 3e-05
 Identities = 11/33 (33%), Positives = 13/33 (39%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            +FVG L      E LR  F  F   L  +V  
Sbjct: 3   NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMW 35

>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 = 36.3 bits (85), Expect = 5e-04
 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 11 RGIGFITFASADSVENLMVDTH--ELGGSTVVVDRATPKE 48
          RG GF++F S D  +N M      +L G  + ++ A   E
Sbjct: 43 RGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE 82

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 40.0 bits (94), Expect = 4e-05
 Identities = 13/33 (39%), Positives = 17/33 (51%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
           G  +F+  LPQE T  DL   F  FG ++   V
Sbjct: 40  GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKV 72

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 41.2 bits (96), Expect = 4e-05
 Identities = 16/129 (12%), Positives = 33/129 (25%), Gaps = 13/129 (10%)

Query: 8   KAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAY 65
           K+  G   +  A   +V+  +  ++ + + G  + V  +            +  G     
Sbjct: 39  KSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYK 98

Query: 66  NAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRF 125
           +   S   R++                     Q     +     P E T E+        
Sbjct: 99  DFSESRNNRFSTPEQA-----------AKNRIQHPSNVLHFFNAPLEVTEENFFEICDEL 147

Query: 126 GRILDVYVP 134
           G      V 
Sbjct: 148 GVKRPTSVK 156

>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 = 40.0 bits (94), Expect = 4e-05
 Identities = 10/43 (23%), Positives = 16/43 (37%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            G      G K+ V  L    +  D++  F+ FG +    V  
Sbjct: 27  GGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDY 69

>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 = 39.9 bits (94), Expect = 5e-05
 Identities = 11/32 (34%), Positives = 14/32 (43%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
             IF+  L +    + L   FS FG IL   V
Sbjct: 6   GNIFIKNLDKSIDNKALYDTFSAFGNILSCKV 37

>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 = 39.6 bits (93), Expect = 5e-05
 Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 6/46 (13%)

Query: 94  GESSQRIGKK----IFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           G S +R   +    ++V     + T   LR  FS FG I+D+ +  
Sbjct: 4   GSSGERRAPRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDP 47

>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 = 39.2 bits (92), Expect = 5e-05
 Identities = 11/35 (31%), Positives = 14/35 (40%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRI 128
              S      IFV  L +  T E +  YF + G I
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGII 40

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 39.1 bits (92), Expect = 6e-05
 Identities = 13/54 (24%), Positives = 20/54 (37%), Gaps = 6/54 (11%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV------PKRFWFCH 141
           G S      +IFV  LP + T + L+  F+  G +L   +       K      
Sbjct: 1   GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVK 54

>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 = 39.2 bits (92), Expect = 6e-05
 Identities = 10/41 (24%), Positives = 17/41 (41%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
            G +    G K+ V  L    +  D++  F+ FG +    V
Sbjct: 21  GGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 61

>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 = 39.1 bits (92), Expect = 6e-05
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 11 RGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          +G   +   S  S + LM  +   EL G   VV  +   E 
Sbjct: 45 KGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLEH 85

>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 = 39.2 bits (92), Expect = 6e-05
 Identities = 7/34 (20%), Positives = 13/34 (38%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
            +F+G L    +  +L+   S      D+ V   
Sbjct: 19  NLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV 52

>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 = 37.2 bits (87), Expect = 4e-04
 Identities = 8/40 (20%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 11 RGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKED 49
          R  G++ F SA+ +E  L +   ++ G+ + +++   ++ 
Sbjct: 58 RKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDG 97

>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 = 38.7 bits (91), Expect = 8e-05
 Identities = 13/31 (41%), Positives = 16/31 (51%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
            +FVG L  E T   +   F+ FGRI D  V
Sbjct: 8   HVFVGDLSPEITTAAIAAAFAPFGRISDARV 38

>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 = 38.7 bits (91), Expect = 9e-05
 Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 4/38 (10%)

Query: 102 KKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
             I++  L ++   ++L++     FSRFG+ILD+ V +
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR 46

>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 = 38.8 bits (91), Expect = 1e-04
 Identities = 9/44 (20%), Positives = 19/44 (43%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
                + R+G  +FV  L  +   + L+  FS  G ++   + +
Sbjct: 6   SGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILE 49

>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 = 38.4 bits (90), Expect = 1e-04
 Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
          +  D+ + + +G GF+ F S +  +     ++  E+ G+ V +D A PK +
Sbjct: 44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE 94

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 17/83 (20%), Positives = 25/83 (30%), Gaps = 1/83 (1%)

Query: 52  RPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQR-IGKKIFVGRLP 110
           R  G   +    A       A        P  + H     G G       G K+ V  L 
Sbjct: 38  RGGGPRRNRPAIARGGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLD 97

Query: 111 QEATAEDLRRYFSRFGRILDVYV 133
              +  D++  F+ FG +    V
Sbjct: 98  FGVSDADIQELFAEFGTLKKAAV 120

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 6/49 (12%)

Query: 93  RGESSQRIGKKIFVGRLPQ------EATAEDLRRYFSRFGRILDVYVPK 135
           R + +  I   I V  +PQ      E     + + FS+FG+I + + P+
Sbjct: 7   RPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPE 55

>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 = 38.0 bits (89), Expect = 2e-04
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 2/41 (4%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRI 128
           GS      S +   K + +  L   AT E L+  F +   I
Sbjct: 4   GSSGNSTWSGE--SKTLVLSNLSYSATEETLQEVFEKATFI 42

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFR 52
          + +D+ +   +G  ++ F   DS++  L  D   LG  ++ VD A  ++ D  
Sbjct: 46 LVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQDKS 98

>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 = 38.0 bits (89), Expect = 2e-04
 Identities = 10/35 (28%), Positives = 15/35 (42%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
              +F+  L    T E L+  FS+ G I    + K
Sbjct: 5   SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISK 39

>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 = 38.0 bits (89), Expect = 2e-04
 Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)

Query: 11  RGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKED 49
           +G G+  F   DS+ + L ++   LG   + VD A   +D
Sbjct: 61  KGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQD 100

>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 = 38.3 bits (89), Expect = 2e-04
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 9/62 (14%)

Query: 96  SSQRIGKK--IFVGRLPQEATAEDLRR---YFSRFGRILDVYVPKRFWFCHLCGRSCSRS 150
           +S R+ +K  +FV  L Q     ++ +   YF +FG+I  V +            S   S
Sbjct: 8   ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNS----TSYAGSQGPS 63

Query: 151 CF 152
             
Sbjct: 64  AS 65

>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 = 38.2 bits (89), Expect = 2e-04
 Identities = 8/37 (21%), Positives = 13/37 (35%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRI 128
                       I+V  L    T +DL  +F + G +
Sbjct: 6   SGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVV 42

>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 = 38.6 bits (90), Expect = 2e-04
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 3/50 (6%)

Query: 89  SFYGRGESSQRI---GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
            F G  E  +++      ++VG L    T E +   FS+ G I  + +  
Sbjct: 24  HFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGL 73

>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 = 37.9 bits (88), Expect = 5e-04
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 3/64 (4%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           M  D+  K   G  F+ + S    EN M  ++   L    +  D     ++  R  GR  
Sbjct: 71  MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKEG-RQYGRGR 129

Query: 59  HGGY 62
            GG 
Sbjct: 130 SGGQ 133

>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 = 38.7 bits (91), Expect = 2e-04
 Identities = 15/136 (11%), Positives = 32/136 (23%), Gaps = 49/136 (36%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVEN--LMVDTHELGGSTVVVDRATPKEDDFRPVGRMS 58
           +  D+ +  +    F+ +  +         ++  ++  + V ++ A   +          
Sbjct: 32  IMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQSSSDDTF-- 88

Query: 59  HGGYGAYNAYISAATRYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDL 118
                                                        +FVG L      E L
Sbjct: 89  --------------------------------------------NLFVGDLNVNVDDETL 104

Query: 119 RRYFSRFGRILDVYVP 134
           R  F  F   L  +V 
Sbjct: 105 RNAFKDFPSYLSGHVM 120

>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 = 39.4 bits (91), Expect = 3e-04
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           K +FV R+  + T   LRR F  +G I  +++  
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136

>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 = 37.6 bits (88), Expect = 3e-04
 Identities = 7/34 (20%), Positives = 16/34 (47%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           + ++VG L ++ T   + + FS+ G      +  
Sbjct: 16  RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMIT 49

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 37.0 bits (86), Expect = 3e-04
 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 6/39 (15%)

Query: 104 IFVGRLPQ------EATAEDLRRYFSRFGRILDVYVPKR 136
           I V  +PQ      E     + + FS+FG+I + + P+ 
Sbjct: 4   IVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEE 42

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 38.0 bits (88), Expect = 3e-04
 Identities = 9/44 (20%), Positives = 15/44 (34%), Gaps = 4/44 (9%)

Query: 102 KKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPKRFWFCH 141
           + + +  +  E   E L+       S  G ILD+ V        
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSG 73

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 37.6 bits (87), Expect = 3e-04
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 1/41 (2%)

Query: 11 RGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDD 50
             G +TF      E  L    HEL G+ + +  A P+   
Sbjct: 47 GCGGVLTFREPADAERVLAQADHELHGAQLSLRPAPPRAPA 87

>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 = 38.4 bits (90), Expect = 3e-04
 Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)

Query: 93  RGESSQRIGK-KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           R  S ++ G   IF+  L +    + L   FS FG IL   V  
Sbjct: 94  RDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC 137

>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 = 37.2 bits (87), Expect = 4e-04
 Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 11 RGIGFITFASADSVEN-LMVDTHELGGSTVVVDRATPKEDDFR 52
          +G G+  F   DS+ + L ++   LG   + VD A   +D   
Sbjct: 57 KGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDKDS 99

>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 = 36.7 bits (85), Expect = 5e-04
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 88  GSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
            S    G  S+R   ++ V  LP   + +DL+ +    G +    V + 
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD 50

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 37.6 bits (87), Expect = 5e-04
 Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 3   KDQGSKAHRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPKED 49
           +++ +   +G   +  AS +SV  L+  +    L G  V V  AT +  
Sbjct: 91  ENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQNL 139

>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 = 36.5 bits (85), Expect = 7e-04
 Identities = 9/36 (25%), Positives = 14/36 (38%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR 136
            K +++  L    T  DL   F+RF       +  R
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFR 60

>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 = 37.9 bits (87), Expect = 7e-04
 Identities = 11/36 (30%), Positives = 23/36 (63%), Gaps = 4/36 (11%)

Query: 104 IFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK 135
           I++  L ++   ++L++     FS+FG+ILD+ V +
Sbjct: 12  IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR 47

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 5/36 (13%), Positives = 14/36 (38%)

Query: 100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK 135
           +     +         + L   FS+ G+++++  P 
Sbjct: 11  VNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPI 46

>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 = 36.5 bits (85), Expect = 8e-04
 Identities = 5/33 (15%), Positives = 14/33 (42%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV 133
              +++  LP     ++L      FG+++   +
Sbjct: 25  PTNLYISNLPLSMDEQELENMLKPFGQVISTRI 57

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	171
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.93
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.93
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.93
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.93
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.93
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.92
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.92
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.91
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.91
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.91
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.91
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.9
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.9
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.89
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.88
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.88
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.87
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.87
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.86
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.85
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.84
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.83
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.71
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.69
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.69
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.69
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.69
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.69
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.69
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.68
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.68
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.67
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.67
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.67
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.67
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.66
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.66
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.66
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.65
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.65
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.65
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.65
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.65
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.65
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.65
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.64
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.64
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.64
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.64
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.64
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.64
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.64
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.64
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.64
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.64
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.63
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.63
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.63
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.63
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.63
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.62
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.62
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.62
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.62
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.62
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.62
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.62
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.62
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.61
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.61
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.61
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.61
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.61
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.61
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.61
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.61
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.61
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.6
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.6
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.6
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.6
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.6
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.6
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.6
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.6
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.6
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.6
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.6
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.6
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.59
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.59
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.59
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.59
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.59
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.59
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.59
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.59
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.59
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.59
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.59
2div_A	99	TRNA selenocysteine associated protein; structural	99.58
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.58
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.58
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.58
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.58
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.58
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.58
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.58
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.58
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.57
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.57
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.57
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.56
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.56
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.56
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.56
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.56
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.56
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.56
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.55
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.55
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.55
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.55
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.55
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.55
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.55
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.55
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.54
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.54
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.54
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.53
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.53
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.53
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.53
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.53
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.53
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.53
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.52
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.52
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.52
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.52
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.52
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.51
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.51
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.51
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.51
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.51
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.5
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.5
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.5
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.5
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.5
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.49
1x5p_A	97	Negative elongation factor E; structure genomics,	99.49
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.49
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.49
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.48
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.48
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.48
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.47
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.47
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.47
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.47
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.47
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.47
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.46
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.46
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.46
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.46
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.46
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.45
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.17
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.44
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.44
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.43
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.43
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.42
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.41
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.41
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.41
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.41
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.4
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.4
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.4
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.39
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.39
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.38
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.38
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.38
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.37
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.37
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.37
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.34
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.34
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.33
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.31
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.29
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.28
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.28
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.26
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.26
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.26
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.25
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.24
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.24
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.23
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.23
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.23
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.23
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.22
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.21
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.21
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.21
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.21
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.21
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.2
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.2
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.2
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.2
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.2
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.19
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.19
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.19
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.18
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.18
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.18
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.18
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.18
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.18
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.18
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.18
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.18
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.17
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.17
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.17
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.17
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.16
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.16
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.16
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.16
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.15
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.15
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.14
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.14
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.14
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.14
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.14
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.13
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.13
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.13
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.13
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.13
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.13
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.12
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.12
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.12
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.12
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.12
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.11
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.11
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.1
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.1
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.1
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.09
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.09
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.08
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.08
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.06
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.06
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.05
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.05
2div_A	99	TRNA selenocysteine associated protein; structural	99.05
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.05
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.05
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.05
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.04
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.04
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.03
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.03
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.03
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.03
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.03
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.03
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.02
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.02
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.02
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.02
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.02
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.01
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.01
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.01
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	98.57
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.01
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.0
1x4e_A	85	RNA binding motif, single-stranded interacting pro	98.99
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	98.99
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	98.99
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.99
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	98.98
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	98.97
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	98.96
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	98.96
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	98.94
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	98.94
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	98.94
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	98.94
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	98.93
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	98.92
1x5o_A	114	RNA binding motif, single-stranded interacting pro	98.92
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	98.92
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	98.9
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.89
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	98.89
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	98.89
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	98.88
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	98.83
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	98.82
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	98.82
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	98.81
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	98.81
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	98.8
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	98.8
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	98.79
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	98.79
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.79
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	98.78
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	98.77
1x5p_A	97	Negative elongation factor E; structure genomics,	98.75
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	98.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	98.7
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	98.7
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.69
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	98.69
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	98.69
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	98.68
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	98.68
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	98.67
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	98.66
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	98.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	98.66
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	98.65
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	98.64
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	98.63
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	98.62
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	98.61
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	98.6
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	98.58
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	98.57
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	98.56
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	98.55
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	98.55
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	98.54
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	98.54
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	98.54
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	98.53
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	98.52
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	98.51
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	98.5
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	98.48
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	98.48
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	98.47
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	98.36
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	98.28
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	98.23
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	98.16
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	98.13
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	97.99
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.91
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.8
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.66
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	97.64
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.62
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	97.6
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.38
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	97.38
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.31
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.23
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	97.17
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	96.36
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	96.2
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.72
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.66
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	94.64
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	93.59
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	92.52
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	90.77
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	87.08

>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=99.93  E-value=1.2e-25  Score=158.96  Aligned_cols=113  Identities=17%  Similarity=0.263  Sum_probs=100.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.++..                             
T Consensus        35 i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-----------------------------   85 (168)
T 1b7f_A           35 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARPGGE-----------------------------   85 (168)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCSS-----------------------------
T ss_pred             EEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCCCcc-----------------------------
Confidence            56788899999999999999999999998  48899999999998865421                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                         ....++|||+|||+.+++++|+++|++||.|.++.|+++        ++||+|.+.++   
T Consensus        86 -------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~---  143 (168)
T 1b7f_A           86 -------------------SIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE---  143 (168)
T ss_dssp             -------------------TTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHH---
T ss_pred             -------------------cCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHH---
Confidence                               224689999999999999999999999999999999876        47999999999   


Q ss_pred             HHHHHHHHHhHhCCC
Q 030822          151 CFSKVSRNLWTAGCN  165 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~~  165 (171)
                       |.+|+..||+..+.
T Consensus       144 -A~~A~~~l~g~~~~  157 (168)
T 1b7f_A          144 -AQEAISALNNVIPE  157 (168)
T ss_dssp             -HHHHHHHHTTCCCT
T ss_pred             -HHHHHHHhcCCEec
Confidence             99999999998663

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.93  E-value=1.7e-26  Score=170.28  Aligned_cols=115  Identities=17%  Similarity=0.215  Sum_probs=99.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.||+++|||||+|.+.++|++||+.  +..+.|+.|.+.++.......                           
T Consensus        47 i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~~~~~~~---------------------------   99 (213)
T 4f02_A           47 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLR---------------------------   99 (213)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCTHHH---------------------------
T ss_pred             EecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccccccccc---------------------------
Confidence            478999999999999999999999999984  789999999998775431100                           


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCF  152 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a  152 (171)
                                         .....+|||+|||+.+|+++|+++|++||.|++|+|++|      ++||+|.+.++    |
T Consensus       100 -------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~----a  156 (213)
T 4f02_A          100 -------------------KSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA----A  156 (213)
T ss_dssp             -------------------HHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHH----H
T ss_pred             -------------------ccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHH----H
Confidence                               123578999999999999999999999999999999865      67999999999    9


Q ss_pred             HHHHHHHhHhCCC
Q 030822          153 SKVSRNLWTAGCN  165 (171)
Q Consensus       153 ~~Ai~~l~~~~~~  165 (171)
                      ++||+.||+..++
T Consensus       157 ~~Ai~~lng~~~~  169 (213)
T 4f02_A          157 ERAIEKMNGMLLN  169 (213)
T ss_dssp             HHHHHHHTTCEET
T ss_pred             HHHHHHhCCCEEC
Confidence            9999999987543

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.93  E-value=1.7e-25  Score=157.92  Aligned_cols=113  Identities=20%  Similarity=0.328  Sum_probs=100.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.+...                             
T Consensus        34 ~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~~~~-----------------------------   84 (167)
T 1fxl_A           34 LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARPSSA-----------------------------   84 (167)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCG-----------------------------
T ss_pred             EEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCCCcc-----------------------------
Confidence            35788899999999999999999999998  48899999999998865421                             


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                         ....++|||+|||+.+++++|+++|++||.|.++.|++|        ++||+|.+.++   
T Consensus        85 -------------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~---  142 (167)
T 1fxl_A           85 -------------------SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE---  142 (167)
T ss_dssp             -------------------GGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH---
T ss_pred             -------------------cCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHH---
Confidence                               224688999999999999999999999999999999865        47999999999   


Q ss_pred             HHHHHHHHHhHhCCC
Q 030822          151 CFSKVSRNLWTAGCN  165 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~~  165 (171)
                       |.+|++.||+..+.
T Consensus       143 -A~~A~~~l~g~~~~  156 (167)
T 1fxl_A          143 -AEEAIKGLNGQKPS  156 (167)
T ss_dssp             -HHHHHHHHTTCCCT
T ss_pred             -HHHHHHHhcCCccC
Confidence             99999999998664

>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=99.93  E-value=1.1e-26  Score=164.43  Aligned_cols=111  Identities=26%  Similarity=0.488  Sum_probs=97.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGA   80 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~   80 (171)
                      |++|+.||++||||||+|.+.++|++||+.++.++|+.|.|.++.++..                               
T Consensus        35 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~-------------------------------   83 (167)
T 2cjk_A           35 IMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDE-------------------------------   83 (167)
T ss_dssp             CCCCTTTSSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHH-------------------------------
T ss_pred             EEECCCCCCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhh-------------------------------
Confidence            5789999999999999999999999999998999999999988754311                               


Q ss_pred             CCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHH
Q 030822           81 PTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCF  152 (171)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a  152 (171)
                                       ....++|||+|||+.+++++|+++|++||.|.++.|++|        ++||+|.+.++    |
T Consensus        84 -----------------~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~----a  142 (167)
T 2cjk_A           84 -----------------QDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADA----V  142 (167)
T ss_dssp             -----------------HHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHH----H
T ss_pred             -----------------ccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHH----H
Confidence                             123578999999999999999999999999999999976        68999999999    9


Q ss_pred             HHHHHHHhHhCC
Q 030822          153 SKVSRNLWTAGC  164 (171)
Q Consensus       153 ~~Ai~~l~~~~~  164 (171)
                      .+|++ ||+..+
T Consensus       143 ~~A~~-~~~~~~  153 (167)
T 2cjk_A          143 DRVCQ-NKFIDF  153 (167)
T ss_dssp             HHHHH-CSEECS
T ss_pred             HHHHh-CCCEEe
Confidence            99997 776544

>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=99.93  E-value=7.5e-26  Score=163.96  Aligned_cols=112  Identities=30%  Similarity=0.552  Sum_probs=93.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      |++|+.||++||||||+|.+.++|++||+. ++.++|+.|.|.++.++.....+.                         
T Consensus        45 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~~~~~~~~~~~~-------------------------   99 (196)
T 1l3k_A           45 VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG-------------------------   99 (196)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC---------------------------------
T ss_pred             EEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeecccCcccccccc-------------------------
Confidence            467889999999999999999999999995 789999999999987653321100                         


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                                       .....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    
T Consensus       100 -----------------~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~----  158 (196)
T 1l3k_A          100 -----------------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS----  158 (196)
T ss_dssp             --------------------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHH----
T ss_pred             -----------------cCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHH----
Confidence                             1334689999999999999999999999999999999976        48999999999    


Q ss_pred             HHHHHHH
Q 030822          152 FSKVSRN  158 (171)
Q Consensus       152 a~~Ai~~  158 (171)
                      |.+|+..
T Consensus       159 A~~A~~~  165 (196)
T 1l3k_A          159 VDKIVIQ  165 (196)
T ss_dssp             HHHHHHC
T ss_pred             HHHHHHh
Confidence            9999975

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.92  E-value=1.2e-24  Score=153.39  Aligned_cols=112  Identities=15%  Similarity=0.211  Sum_probs=97.0

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      ++|+ +|+++|||||+|.+.++|++|++  ++..+.|+.|.|.++.++...                             
T Consensus        33 ~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~~~-----------------------------   82 (166)
T 3md3_A           33 MIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQQS-----------------------------   82 (166)
T ss_dssp             ECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCCCC-----------------------------
T ss_pred             EECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCCCC-----------------------------
Confidence            5665 57899999999999999999997  488999999999988654221                             


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                                       .....++|||+|||+.+++++|+++|++||.|.++.|++|        ++||+|.+.++    
T Consensus        83 -----------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~----  141 (166)
T 3md3_A           83 -----------------SSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD----  141 (166)
T ss_dssp             -----------------CCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHH----
T ss_pred             -----------------CCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHH----
Confidence                             1334689999999999999999999999999999999876        68999999999    


Q ss_pred             HHHHHHHHhHhCC
Q 030822          152 FSKVSRNLWTAGC  164 (171)
Q Consensus       152 a~~Ai~~l~~~~~  164 (171)
                      |.+|+..||+..+
T Consensus       142 A~~A~~~l~g~~~  154 (166)
T 3md3_A          142 AQNAMDSMQGQDL  154 (166)
T ss_dssp             HHHHHHHHTTCEE
T ss_pred             HHHHHHHhCCCcc
Confidence            9999999998764

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.92  E-value=1.7e-24  Score=159.04  Aligned_cols=124  Identities=17%  Similarity=0.317  Sum_probs=97.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.+|+++|||||+|.+.++|++||+  ++..|+|+.|.|.++........               .......    
T Consensus        60 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~~~~~~~~---------------~~~~~~~----  120 (216)
T 2qfj_A           60 MSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQP---------------IIDQLAE----  120 (216)
T ss_dssp             ECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCSCCGGGHH---------------HHHHHHH----
T ss_pred             EeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCCCccccch---------------hhhhhhc----
Confidence            46888999999999999999999999999  47899999999987654321100               0000000    


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~  150 (171)
                                        .....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++   
T Consensus       121 ------------------~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~---  179 (216)
T 2qfj_A          121 ------------------EARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQS---  179 (216)
T ss_dssp             ------------------HHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHH---
T ss_pred             ------------------ccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHH---
Confidence                              0234689999999999999999999999999999999876        57999999999   


Q ss_pred             HHHHHHHHHhHhCCC
Q 030822          151 CFSKVSRNLWTAGCN  165 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~~  165 (171)
                       |.+|+..||+..+.
T Consensus       180 -A~~A~~~l~g~~~~  193 (216)
T 2qfj_A          180 -SQDAVSSMNLFDLG  193 (216)
T ss_dssp             -HHHHHHHHTTCBCS
T ss_pred             -HHHHHHHccCCEeC
Confidence             99999999987653

>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=99.91  E-value=1.6e-24  Score=153.85  Aligned_cols=108  Identities=18%  Similarity=0.329  Sum_probs=94.0

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCc
Q 030822            5 QGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTL   83 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   83 (171)
                      ..++++||||||+|.++++|++|+. +++.++|+.|.|.++.+...                                  
T Consensus        45 ~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~~----------------------------------   90 (172)
T 2g4b_A           45 VQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQP----------------------------------   90 (172)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHGGGTTCEETTEECEEECCSSCCC----------------------------------
T ss_pred             eEecCCCCEEEEEeCCHHHHHHHHHhCCcEecCceeeecCCcccCC----------------------------------
Confidence            3467899999999999999999996 37899999999997643311                                  


Q ss_pred             cCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHH
Q 030822           84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKV  155 (171)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~A  155 (171)
                                    ....++|||+|||+.+++++|+++|++||.|.++.|++|        ++||+|.+.++    |.+|
T Consensus        91 --------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~A  152 (172)
T 2g4b_A           91 --------------LPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV----TDQA  152 (172)
T ss_dssp             --------------CTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTH----HHHH
T ss_pred             --------------CCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHH----HHHH
Confidence                          223688999999999999999999999999999999877        48999999999    9999


Q ss_pred             HHHHhHhCC
Q 030822          156 SRNLWTAGC  164 (171)
Q Consensus       156 i~~l~~~~~  164 (171)
                      +..||+..+
T Consensus       153 ~~~l~g~~~  161 (172)
T 2g4b_A          153 IAGLNGMQL  161 (172)
T ss_dssp             HHHHTTCEE
T ss_pred             HHHcCCCEE
Confidence            999998654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.91  E-value=4.9e-24  Score=154.60  Aligned_cols=129  Identities=17%  Similarity=0.261  Sum_probs=98.7

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPT   82 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~   82 (171)
                      +..++++||||||+|.+.++|++||. ++..|+|+.|.|.++.+.............                       
T Consensus        44 ~~~~~~~~g~afV~F~~~~~A~~Al~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~-----------------------  100 (198)
T 2yh0_A           44 AVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSV-----------------------  100 (198)
T ss_dssp             EEEEETTTTEEEEEESCSHHHHHHGGGTTEEETTEEEEEECCCCCCCCCCSSSCSSC-----------------------
T ss_pred             EeEecCCCCEEEEEeCCHHHHHHHHHhcCCEEcCceEEEeCCCCCCCCCCCcCCCcC-----------------------
Confidence            44568999999999999999999996 378999999999988654322111000000                       


Q ss_pred             ccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHH
Q 030822           83 LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSK  154 (171)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~  154 (171)
                        ..++.   .........++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++
T Consensus       101 --~~~~~---~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~----a~~  171 (198)
T 2yh0_A          101 --YVPGV---VSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV----TDQ  171 (198)
T ss_dssp             --CCTTS---SCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSH----HHH
T ss_pred             --CCCCC---ccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHH----HHH
Confidence              00000   00111346799999999999999999999999999999999976        57999999999    999


Q ss_pred             HHHHHhHhCC
Q 030822          155 VSRNLWTAGC  164 (171)
Q Consensus       155 Ai~~l~~~~~  164 (171)
                      |+..||+..+
T Consensus       172 A~~~l~g~~~  181 (198)
T 2yh0_A          172 AIAGLNGMQL  181 (198)
T ss_dssp             HHHHHTTCEE
T ss_pred             HHHHcCCCEE
Confidence            9999998654

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=99.91  E-value=2.4e-24  Score=153.15  Aligned_cols=114  Identities=18%  Similarity=0.329  Sum_probs=93.9

Q ss_pred             CCCCCCCC--CccceEEEEECCHHHHHHHHhc--CCccC---CeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhh
Q 030822            1 MPKDQGSK--AHRGIGFITFASADSVENLMVD--THELG---GSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAAT   73 (171)
Q Consensus         1 i~~D~~tg--~srGfgFV~F~~~~~a~~Al~~--~~~i~---gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (171)
                      |++|+.+|  ++||||||+|.+.++|++|++.  +..+.   ++.+.+.++.++...                       
T Consensus        35 i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------------------   91 (175)
T 3nmr_A           35 VLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQMKPADSEKNN-----------------------   91 (175)
T ss_dssp             EEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECGGGCCS-----------------------
T ss_pred             EEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceEEccccccccc-----------------------
Confidence            35677777  9999999999999999999984  44443   566777665432110                       


Q ss_pred             hhhccCCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCc
Q 030822           74 RYAALGAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRS  146 (171)
Q Consensus        74 ~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~  146 (171)
                                              ....++|||+|||+.+|+++|+++|++||.|.++.|+++       ++||+|.+.+
T Consensus        92 ------------------------~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~  147 (175)
T 3nmr_A           92 ------------------------AVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRA  147 (175)
T ss_dssp             ------------------------CGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHH
T ss_pred             ------------------------cCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHH
Confidence                                    234689999999999999999999999999999999876       5899999999


Q ss_pred             ccHHHHHHHHHHHhHhCCC
Q 030822          147 CSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       147 ~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +    |.+|++.||+..+.
T Consensus       148 ~----A~~A~~~l~g~~~~  162 (175)
T 3nmr_A          148 M----AQTAIKAMHQAQTM  162 (175)
T ss_dssp             H----HHHHHHHHTTSCCC
T ss_pred             H----HHHHHHHhcCCccc
Confidence            9    99999999987653

>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=99.91  E-value=1.4e-24  Score=154.83  Aligned_cols=114  Identities=16%  Similarity=0.212  Sum_probs=96.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      +++|..+|++||||||+|.+.++|++||+ ++..+.|+.|.|.++.++....                            
T Consensus        44 ~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~~~~~~~~----------------------------   95 (175)
T 1fje_B           44 AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDSKK----------------------------   95 (175)
T ss_dssp             CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCSSCST----------------------------
T ss_pred             EEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecCCCccccc----------------------------
Confidence            46778899999999999999999999997 4789999999999887542210                            


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEe---cCcceeEEecCCcccHHHHHHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRFWFCHLCGRSCSRSCFSKVS  156 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i---~~d~~fv~f~~~~~~~~~a~~Ai  156 (171)
                                        ....++|||+|||+.+++++|+++|++||.|..+..   .+.++||+|.+.++    |.+|+
T Consensus        96 ------------------~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~----A~~A~  153 (175)
T 1fje_B           96 ------------------VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD----AEKNL  153 (175)
T ss_dssp             ------------------TGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEECSSSSCCSEEEEECSSHHH----HHHHH
T ss_pred             ------------------cccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEecCCCCCceEEEEEECCHHH----HHHHH
Confidence                              234689999999999999999999999999988711   13478999999999    99999


Q ss_pred             HHHhHhCC
Q 030822          157 RNLWTAGC  164 (171)
Q Consensus       157 ~~l~~~~~  164 (171)
                      ..||+..+
T Consensus       154 ~~l~g~~~  161 (175)
T 1fje_B          154 EEKQGAEI  161 (175)
T ss_dssp             HHHTEEEE
T ss_pred             HHhCCCEE
Confidence            99998654

>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=99.90  E-value=7.7e-24  Score=161.94  Aligned_cols=115  Identities=15%  Similarity=0.095  Sum_probs=100.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.++....                           
T Consensus       127 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~~~~~~~---------------------------  179 (284)
T 3smz_A          127 LVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTDAGQLTP---------------------------  179 (284)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCGGGCCT---------------------------
T ss_pred             EEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCCCc---------------------------
Confidence            36788999999999999999999999997  4889999999999987542211                           


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCC-CHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEA-TAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRS  150 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~-te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~  150 (171)
                                        .....++|||+|||+.+ ++++|+++|++||.|.++.|++|       ++||+|.+.++   
T Consensus       180 ------------------~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~---  238 (284)
T 3smz_A          180 ------------------ALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETAEM---  238 (284)
T ss_dssp             ------------------TTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEEEEEECSSCCEEEEEEEECSSHHH---
T ss_pred             ------------------ccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEEEEEECCCCCcccEEEEEeCCHHH---
Confidence                              02356899999999995 99999999999999999999876       67999999999   


Q ss_pred             HHHHHHHHHhHhCC
Q 030822          151 CFSKVSRNLWTAGC  164 (171)
Q Consensus       151 ~a~~Ai~~l~~~~~  164 (171)
                       |.+|+..||+..+
T Consensus       239 -A~~A~~~l~g~~~  251 (284)
T 3smz_A          239 -AEEAQQQADGLSL  251 (284)
T ss_dssp             -HHHHHHHHTTCEE
T ss_pred             -HHHHHHHhCCCcc
Confidence             9999999998754

>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=99.90  E-value=8.8e-24  Score=155.10  Aligned_cols=139  Identities=14%  Similarity=0.089  Sum_probs=94.1

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchh-hhhhhccCCCCccCC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISA-ATRYAALGAPTLYDH   86 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~   86 (171)
                      +||||||+|.+.++|++||+  ++..+.|+.|.|.++..+............+... ...+... ..+         ...
T Consensus        41 ~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~-~~~~~~~~~~r---------~~~  110 (205)
T 3tyt_A           41 KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCS-YKDFSESRNNR---------FST  110 (205)
T ss_dssp             STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBS-EEECTTCTTCS---------CSS
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccCCccCCCcccccccCCcc-ccccCCCcccc---------ccC
Confidence            58999999999999999998  4899999999999986432210000000000000 0000000 000         000


Q ss_pred             CCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccce--EEEEecCc------ceeEEecCCcccHHHHHHHHHH
Q 030822           87 PGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRI--LDVYVPKR------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        87 ~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v--~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      +....  .....++.++|||+|||+++|+++|+++|++||.|  .+++|+.+      ++||+|.+.++    |.+||..
T Consensus       111 ~~~~~--~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~----A~~Ai~~  184 (205)
T 3tyt_A          111 PEQAA--KNRIQHPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSD----ALETLGF  184 (205)
T ss_dssp             HHHHT--TSCCCCCCSEEEEEEECTTCCHHHHHHHHHHHTCCCCSEEEECSCCSSSSEEEEEECSSHHH----HHHHHHH
T ss_pred             ccccc--ccccCCCcceEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEEcCCCCCceEEEEEeCCHHH----HHHHHHH
Confidence            00000  00012356899999999999999999999999999  89999875      68999999999    9999999


Q ss_pred             HhHhCC
Q 030822          159 LWTAGC  164 (171)
Q Consensus       159 l~~~~~  164 (171)
                      ||+..+
T Consensus       185 lng~~~  190 (205)
T 3tyt_A          185 LNHYQM  190 (205)
T ss_dssp             HTTCEE
T ss_pred             hCCCCc
Confidence            998754

>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=99.89  E-value=1.4e-22  Score=154.73  Aligned_cols=64  Identities=16%  Similarity=0.162  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|+|+.+   ++||+|.+.++    |.+|+..||+..+.
T Consensus       204 ~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~  270 (282)
T 3pgw_A          204 NPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQ----AGAARDALQGFKIT  270 (282)
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCCCcEEEEEeCCHHH----HHHHHHHcCCcEeC
Confidence            446789999999999999999999999999999999875   58999999999    99999999997654

>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=99.88  E-value=9.9e-23  Score=156.34  Aligned_cols=117  Identities=20%  Similarity=0.305  Sum_probs=91.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+. |+++|||||+|.+.++|++|++  ++..++|+.|.|.++.++......                         
T Consensus       150 i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~~~-------------------------  203 (292)
T 2ghp_A          150 LPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKSKRT-------------------------  203 (292)
T ss_dssp             CC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC-------------------------------
T ss_pred             EEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCcccccc-------------------------
Confidence            456654 8999999999999999999999  488999999999998765332211                         


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCccc
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCS  148 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~  148 (171)
                                      .......++|||+|||+. +++++|+++|++||.|.+|.|++|         ++||+|.+.++ 
T Consensus       204 ----------------~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~-  266 (292)
T 2ghp_A          204 ----------------DSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS-  266 (292)
T ss_dssp             -------------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHH-
T ss_pred             ----------------cccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHH-
Confidence                            001345789999999999 999999999999999999999876         37999999999 


Q ss_pred             HHHHHHHHHHHhHhCC
Q 030822          149 RSCFSKVSRNLWTAGC  164 (171)
Q Consensus       149 ~~~a~~Ai~~l~~~~~  164 (171)
                         |.+|+ .||+..+
T Consensus       267 ---A~~A~-~l~g~~~  278 (292)
T 2ghp_A          267 ---AERAL-QMNRSLL  278 (292)
T ss_dssp             ---HHHHG-GGTTEEE
T ss_pred             ---HHHHH-HhcCCEE
Confidence               99999 9998754

>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=99.88  E-value=7.9e-23  Score=143.94  Aligned_cols=118  Identities=19%  Similarity=0.233  Sum_probs=85.0

Q ss_pred             CCccceEEEEECCHHHHHHHHhc---CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCcc
Q 030822            8 KAHRGIGFITFASADSVENLMVD---THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~---~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   84 (171)
                      .+++|||||+|.+.++|++|++.   ...++|... +..............                             
T Consensus        10 ~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~-----------------------------   59 (158)
T 2kn4_A           10 KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWT-YDDATKTFTVTEGSH-----------------------------   59 (158)
T ss_dssp             SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEE-EETTTTEEEEECCCC-----------------------------
T ss_pred             ccccchhHHHHHHHHhHHHHHHhhcccCCCCCccc-ccCcccccccccccc-----------------------------
Confidence            37999999999999999999974   233444332 221111000000000                             


Q ss_pred             CCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHH
Q 030822           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVS  156 (171)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai  156 (171)
                            ...........++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+
T Consensus        60 ------~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~----a~~A~  129 (158)
T 2kn4_A           60 ------HHHHHMDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD----AEDAM  129 (158)
T ss_dssp             ------CSSCCCCCCBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHH----HHHHH
T ss_pred             ------ccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHH----HHHHH
Confidence                  0000001345789999999999999999999999999999999987        58999999999    99999


Q ss_pred             HHHhHhCCC
Q 030822          157 RNLWTAGCN  165 (171)
Q Consensus       157 ~~l~~~~~~  165 (171)
                      ..||+..+.
T Consensus       130 ~~l~g~~~~  138 (158)
T 2kn4_A          130 DAMDGAVLD  138 (158)
T ss_dssp             HHSTTEESS
T ss_pred             HHhCCCEEC
Confidence            999987653

>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=99.87  E-value=9.9e-22  Score=146.24  Aligned_cols=138  Identities=14%  Similarity=0.213  Sum_probs=95.8

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPG   88 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~   88 (171)
                      +|||||+|.+.++|++||+  ++..+.|+.|.|.++.++.............   ....+....        ......+.
T Consensus        72 ~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~---~~~~~~~~~--------~~~~~~~~  140 (229)
T 2adc_A           72 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQG---LTKDYGNSP--------LHRFKKPG  140 (229)
T ss_dssp             SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTT---TEEECTTCS--------SCCCCSTT
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCccccCccccccccc---cccccccCc--------ccccCCcc
Confidence            8999999999999999998  4889999999999987653321110000000   000000000        00000000


Q ss_pred             CCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhccc-ceEEEEec---CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVP---KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        89 ~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG-~v~~v~i~---~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...  .....++.++|||+|||+.+++++|+++|++|| .|.+|.|+   +.++||+|.+.++    |.+|+..||+..+
T Consensus       141 ~~~--~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~g~afV~f~~~~~----A~~Ai~~l~g~~~  214 (229)
T 2adc_A          141 SKN--FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE----AVQALIDLHNHDL  214 (229)
T ss_dssp             SGG--GTTCCCSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHH----HHHHHHHHTTCBS
T ss_pred             ccc--cccCCCCCCEEEEeCCCccCCHHHHHHHHHHcCCCeeEEEEEECCCcEEEEEECCHHH----HHHHHHHHCCCcc
Confidence            000  001134579999999999999999999999999 99999995   3588999999999    9999999999876


Q ss_pred             C
Q 030822          165 N  165 (171)
Q Consensus       165 ~  165 (171)
                      .
T Consensus       215 ~  215 (229)
T 2adc_A          215 G  215 (229)
T ss_dssp             S
T ss_pred             C
Confidence            5

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.87  E-value=9.7e-22  Score=142.80  Aligned_cols=138  Identities=14%  Similarity=0.210  Sum_probs=96.3

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccCCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYDHPG   88 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~   88 (171)
                      +|||||+|.+.++|++|++  ++..++|+.|.|.++.++............   .....+....        ......++
T Consensus        41 ~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~---~~~~~~~~~~--------~~r~~~~~  109 (198)
T 1qm9_A           41 KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQ---GLTKDYGNSP--------LHRFKKPG  109 (198)
T ss_dssp             SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSS---SCEEESSCCC--------TTSSSSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccc---cccccccCCc--------hhhccCcc
Confidence            8999999999999999998  488999999999998765432211100000   0000000000        00000000


Q ss_pred             CCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhccc-ceEEEEecC---cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           89 SFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPK---RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        89 ~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG-~v~~v~i~~---d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...  .....++.++|||+|||+.+++++|+++|++|| .|.++.|++   .++||+|.+.++    |.+|+..||+..+
T Consensus       110 ~~~--~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~~v~~v~i~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~  183 (198)
T 1qm9_A          110 SKN--FQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE----AVQALIDLHNHDL  183 (198)
T ss_dssp             CCC--CSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTSCCCEEEESSTTSSCEEEECSSHHH----HHHHHHHHTSSCC
T ss_pred             ccc--cccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCCCceEEEEEeCCCcEEEEEeCCHHH----HHHHHHHhcCCcc
Confidence            000  001134579999999999999999999999999 999999954   578999999999    9999999999776


Q ss_pred             C
Q 030822          165 N  165 (171)
Q Consensus       165 ~  165 (171)
                      .
T Consensus       184 ~  184 (198)
T 1qm9_A          184 G  184 (198)
T ss_dssp             S
T ss_pred             C
Confidence            4

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.86  E-value=2.2e-21  Score=147.04  Aligned_cols=96  Identities=24%  Similarity=0.255  Sum_probs=88.0

Q ss_pred             CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccC
Q 030822            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   85 (171)
                      +++||||||+|.+.++|++|+.  ++..|.|+.|.|.++.+                                       
T Consensus        55 ~~~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a~~---------------------------------------   95 (261)
T 3sde_A           55 NRDRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATH---------------------------------------   95 (261)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC---------------------------------------
T ss_pred             eCCCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeeccc---------------------------------------
Confidence            4679999999999999999998  48899999999997642                                       


Q ss_pred             CCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHH
Q 030822           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                                     ..+|||+|||+.+|+++|+++|++||.|.+|.|++|       ++||+|.+.++    |.+|+..
T Consensus        96 ---------------~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~----A~~A~~~  156 (261)
T 3sde_A           96 ---------------GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPP----ARKALER  156 (261)
T ss_dssp             ---------------SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHH----HHHHHHH
T ss_pred             ---------------CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHH----HHHHHHH
Confidence                           478999999999999999999999999999999866       67999999999    9999999


Q ss_pred             HhH
Q 030822          159 LWT  161 (171)
Q Consensus       159 l~~  161 (171)
                      ||+
T Consensus       157 l~~  159 (261)
T 3sde_A          157 CGD  159 (261)
T ss_dssp             HHH
T ss_pred             hcC
Confidence            965

>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=99.85  E-value=2.2e-21  Score=135.57  Aligned_cols=122  Identities=19%  Similarity=0.220  Sum_probs=94.6

Q ss_pred             CCCccceEEEEECCHHHHHHHHh---cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCc
Q 030822            7 SKAHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTL   83 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~---~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~   83 (171)
                      ..+.+|+++|+|.+.++|++|++   ++..++| .|.+.++..+.........                           
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~---------------------------   60 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHH---------------------------   60 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSS---------------------------
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCcccccccccc---------------------------
Confidence            45679999999999999999997   4678999 9999977643211100000                           


Q ss_pred             cCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHh
Q 030822           84 YDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                           .............++|||+|||+.+++++|+++|++||.|.+|.|++|   ++||+|.+.++    |.+|+..||
T Consensus        61 -----~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~----a~~A~~~l~  131 (150)
T 2i2y_A           61 -----HHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRD----AADAVRELD  131 (150)
T ss_dssp             -----CCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSSSCSEEEEEESSHHH----HHHHHHHHS
T ss_pred             -----ccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeCCCcEEEEEECCHHH----HHHHHHHcC
Confidence                 000000111445799999999999999999999999999999999965   88999999999    999999999


Q ss_pred             HhCCC
Q 030822          161 TAGCN  165 (171)
Q Consensus       161 ~~~~~  165 (171)
                      +..+.
T Consensus       132 g~~~~  136 (150)
T 2i2y_A          132 GRTLC  136 (150)
T ss_dssp             SSCSS
T ss_pred             CCEEC
Confidence            87653

>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=99.84  E-value=1.1e-20  Score=144.45  Aligned_cols=99  Identities=14%  Similarity=0.276  Sum_probs=89.5

Q ss_pred             CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCccC
Q 030822            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLYD   85 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~   85 (171)
                      ++++|||||+|.+.++|++|++  ++..+.|+.|.|.++.                                        
T Consensus        54 ~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~----------------------------------------   93 (284)
T 3smz_A           54 DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP----------------------------------------   93 (284)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC----------------------------------------
T ss_pred             ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC----------------------------------------
Confidence            6789999999999999999998  4788999999998642                                        


Q ss_pred             CCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHH
Q 030822           86 HPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSR  157 (171)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~  157 (171)
                                    ..++|||+|||+.+++++|+++|++||.|.++.|++|        ++||+|.+.++    |.+|+.
T Consensus        94 --------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~  155 (284)
T 3smz_A           94 --------------TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDS----AARAKS  155 (284)
T ss_dssp             --------------CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHH
T ss_pred             --------------CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHH----HHHHHH
Confidence                          2478999999999999999999999999999999865        58999999999    999999


Q ss_pred             HHhHhCC
Q 030822          158 NLWTAGC  164 (171)
Q Consensus       158 ~l~~~~~  164 (171)
                      .||+..+
T Consensus       156 ~l~~~~~  162 (284)
T 3smz_A          156 DLLGKPL  162 (284)
T ss_dssp             HHTTCEE
T ss_pred             HhCCCEe
Confidence            9998654

>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=99.83  E-value=1.2e-20  Score=144.74  Aligned_cols=103  Identities=13%  Similarity=0.203  Sum_probs=89.4

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGA   80 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~   80 (171)
                      ++|+.+  ++|||||+|.+.++|++||+ ++..++|+.|.|.++                                    
T Consensus        74 ~~~~~~--~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~------------------------------------  115 (292)
T 2ghp_A           74 ADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL------------------------------------  115 (292)
T ss_dssp             EECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC------------------------------------
T ss_pred             EECCCC--CcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC------------------------------------
Confidence            455533  68999999999999999997 478999999999854                                    


Q ss_pred             CCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhccc-ceEEEEecCc-------ceeEEecCCcccHHHH
Q 030822           81 PTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKR-------FWFCHLCGRSCSRSCF  152 (171)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG-~v~~v~i~~d-------~~fv~f~~~~~~~~~a  152 (171)
                                         ..++|||+|||+.+++++|+++|++|| .|.+|.|+++       ++||.|.+.++    |
T Consensus       116 -------------------~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~----a  172 (292)
T 2ghp_A          116 -------------------TECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED----A  172 (292)
T ss_dssp             -------------------CSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHH----H
T ss_pred             -------------------CCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHH----H
Confidence                               258899999999999999999999999 9999999865       58999999999    9


Q ss_pred             HHHHHHHhHhCCC
Q 030822          153 SKVSRNLWTAGCN  165 (171)
Q Consensus       153 ~~Ai~~l~~~~~~  165 (171)
                      .+|+..||+..+.
T Consensus       173 ~~A~~~l~g~~~~  185 (292)
T 2ghp_A          173 RYCVEKLNGLKIE  185 (292)
T ss_dssp             HHHHHHHTTCEET
T ss_pred             HHHHHHhCCCEeC
Confidence            9999999986553

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.9e-17  Score=106.13  Aligned_cols=63  Identities=21%  Similarity=0.379  Sum_probs=59.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+++++||+|.+.++    |++|+..||+..+
T Consensus         7 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~~~afV~f~~~~~----a~~A~~~l~g~~~   69 (92)
T 2dgt_A            7 GKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAED----AVEAIRGLDNTEF   69 (92)
T ss_dssp             CCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECSSEEEEEESCHHH----HHHHHHHHTTEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEECCEEEEEECCHHH----HHHHHHHhCCCee
Confidence            45679999999999999999999999999999999999999999999999    9999999998754

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=4.2e-17  Score=104.12  Aligned_cols=63  Identities=27%  Similarity=0.377  Sum_probs=59.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+++++||+|.+.++    |++|+..||+..+
T Consensus         6 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~~~afV~f~~~~~----a~~A~~~l~g~~~   68 (90)
T 2dnp_A            6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEAD----AKAAIAQLNGKEV   68 (90)
T ss_dssp             SCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESCHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEECCEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            45679999999999999999999999999999999999999999999999    9999999998654

>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=99.69  E-value=3e-17  Score=106.90  Aligned_cols=61  Identities=21%  Similarity=0.325  Sum_probs=56.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+++|||+|||+++|+++|+++|++||+|.+|+|++|        ++||+|.+.++    |++|++.||+..+
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~----A~~Ai~~lng~~~   86 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKD----AERAINTLNGLRL   86 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHH----HHHHHHHhCCCEE
Confidence            4689999999999999999999999999999999876        57999999999    9999999998654

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=3.7e-17  Score=107.15  Aligned_cols=60  Identities=13%  Similarity=0.187  Sum_probs=55.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      +.+.++|||+|||+++|+++|+++|++||.|.+|.|+++  ++||+|.+.++    |+.|+..|++
T Consensus        13 ~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~kGfaFVeF~~~~~----A~~Ai~~l~~   74 (105)
T 1sjq_A           13 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEA----ANTMVNYYTS   74 (105)
T ss_dssp             CCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHH----HHHHHHHhcc
Confidence            346799999999999999999999999999999999975  67999999999    9999999875

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=7.6e-17  Score=102.93  Aligned_cols=64  Identities=28%  Similarity=0.542  Sum_probs=59.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++.++||+|.+.++    |++|+..||+..++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   68 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTA----AEDAIRNLHHYKLH   68 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEETTEEEEEESSHHH----HHHHHHHHTTCBCS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCEEEEEECCHHH----HHHHHHHhcCCccC
Confidence            44679999999999999999999999999999999999999999999999    99999999987654

>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=99.69  E-value=5.1e-17  Score=106.31  Aligned_cols=64  Identities=27%  Similarity=0.303  Sum_probs=59.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.|+++++||+|.+.++    |++|+..||+..++
T Consensus         8 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~afV~f~~~~~----a~~A~~~l~g~~~~   71 (103)
T 2dgu_A            8 MAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDG----AVKAMEEMNGKDLE   71 (103)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEECSSCEEEEESSHHH----HHHHHHHHTTEEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEeCCHHH----HHHHHHHHCCCccC
Confidence            44579999999999999999999999999999999999999999999999    99999999987543

>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=99.69  E-value=3.1e-17  Score=109.55  Aligned_cols=61  Identities=21%  Similarity=0.258  Sum_probs=56.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...+|||+|||+++|+++|+++|++||.|.+|+|++|      ++||+|.+.++    |++||+.||+..+
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~----A~~Ai~~l~~~~~   70 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA----AERAIEKMNGMLL   70 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHH----HHHHHHHHTTCEE
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHH----HHHHHHHcCCCEE
Confidence            3578999999999999999999999999999999976      68999999999    9999999998754

>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=99.68  E-value=8.5e-17  Score=105.15  Aligned_cols=61  Identities=10%  Similarity=0.079  Sum_probs=56.5

Q ss_pred             CCCceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           99 RIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        99 ~~~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      .+.++|||+|||+ .+++++|+++|++||.|.+|.|+++  ++||+|.+.++    |+.||..||+..
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~----A~~Ai~~l~~~~   76 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTED----AQAAVDYYTTTP   76 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHH----HHHHHHHHHHSC
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcCCCEEEEEECCHHH----HHHHHHHHcCCC
Confidence            3579999999999 9999999999999999999999986  68999999999    999999999753

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.68  E-value=1.2e-16  Score=103.73  Aligned_cols=62  Identities=15%  Similarity=0.048  Sum_probs=57.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      .+++++|||+|||+.+|+++|+++|++||+|.+|.|++  .++||+|.+.++    |..|+..||+..
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~~kg~AFVef~~~~~----A~~Av~~ln~~~   81 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLG----ACNAVNYAADNQ   81 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHHHSC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEcCCCEEEEEECCHHH----HHHHHHHhcCCC
Confidence            45689999999999999999999999999999999984  578999999999    999999999864

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.7e-16  Score=102.75  Aligned_cols=64  Identities=25%  Similarity=0.400  Sum_probs=58.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   81 (103)
T 2dnm_A           10 VDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRD----AQDAEAAMDGAELD   81 (103)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSH----HHHHHHHHSSCCBT
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            556799999999999999999999999999999999865        68999999999    99999999987654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.67  E-value=8.3e-17  Score=106.72  Aligned_cols=62  Identities=13%  Similarity=0.134  Sum_probs=57.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ++.++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++||+.||+..+
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~----A~~Ai~~lng~~~   73 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRG----AKETVKNLHLTSV   73 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            45789999999999999999999999999999999866        57999999999    9999999998754

>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=99.67  E-value=9.1e-17  Score=106.06  Aligned_cols=63  Identities=16%  Similarity=0.193  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC-cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~-d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++++++|+++|++||+|.+|.|++ .++||+|.+.++    |++||+.||+..+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~g~afV~f~~~~~----a~~Ai~~l~g~~~   75 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKED----MTYAVRKLDNTKF   75 (108)
T ss_dssp             CSCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETTTEEEEEESSHHH----HHHHHHHSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecCCEEEEEECCHHH----HHHHHHHHCcCCc
Confidence            45679999999999999999999999999999999999 589999999999    9999999998755

>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=99.67  E-value=3.2e-16  Score=102.30  Aligned_cols=61  Identities=15%  Similarity=0.202  Sum_probs=55.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.|+++  ++||+|.+.++    |++|+..|++.
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~kg~aFVef~~~~~----A~~Ai~~l~~~   74 (101)
T 2cq1_A           12 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEA----AITMVNYYSAV   74 (101)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHHHS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECCCCEEEEEECCHHH----HHHHHHHhccC
Confidence            456789999999999999999999999999999999975  68999999999    99999988753

>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=99.66  E-value=4.4e-16  Score=100.69  Aligned_cols=64  Identities=19%  Similarity=0.250  Sum_probs=59.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.|+++  ++||+|.+.++    |++|++.||+..++
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   79 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDA----AQAACAKMRGFPLG   79 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHH----HHHHHHHHTTCBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCCCCEEEEEECCHHH----HHHHHHHHCCCEeC
Confidence            345789999999999999999999999999999999976  88999999999    99999999998765

>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=99.66  E-value=4.3e-16  Score=102.21  Aligned_cols=62  Identities=13%  Similarity=0.059  Sum_probs=56.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      .++.++|||+|||+.+++++|+++|++||.|.+|.|+++  ++||+|.+.++    |++|++.||+..
T Consensus        12 ~~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~kg~aFVef~~~~~----A~~Ai~~l~~~~   75 (104)
T 1wex_A           12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDS----AKECVTFAADVP   75 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHHHSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECCCCEEEEEECCHHH----HHHHHHHhccCC
Confidence            456799999999999999999999999999999999864  78999999999    999999998753

>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=99.66  E-value=2e-16  Score=106.03  Aligned_cols=61  Identities=13%  Similarity=0.184  Sum_probs=56.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      .++.++|||+|||+++++++|+++|++||.|++|.|+++  ++||+|.+.++    |++|++.|++.
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~kG~AFVeF~~~e~----A~~Ai~~l~~~   90 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEA----ANTMVNYYTSV   90 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGGGTEEEEECSCHHH----HHHHHHHHHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEECCHHH----HHHHHHHhccC
Confidence            456789999999999999999999999999999999965  78999999999    99999999864

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=3.4e-16  Score=100.51  Aligned_cols=64  Identities=22%  Similarity=0.366  Sum_probs=58.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++.++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|++.||+..+.
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   84 (94)
T 2e5h_A           13 APSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS----AQNCTRAINNKQLF   84 (94)
T ss_dssp             CCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHH----HHHHHHHTTTEEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHH----HHHHHHHcCCCeeC
Confidence            456799999999999999999999999999999999875        68999999999    99999999986543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.65  E-value=7.5e-17  Score=110.70  Aligned_cols=64  Identities=23%  Similarity=0.379  Sum_probs=58.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        44 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~----A~~Ai~~l~g~~i~  115 (135)
T 2lea_A           44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD----AEDAMDAMDGAVLD  115 (135)
T ss_dssp             GGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHH----HHHHHTTTTTCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            445789999999999999999999999999999999876        68999999999    99999999987754

>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=99.65  E-value=4.4e-16  Score=101.72  Aligned_cols=64  Identities=25%  Similarity=0.400  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|      ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   81 (103)
T 2cq3_A           12 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD----ADRAREKLHGTVVE   81 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            456799999999999999999999999999999999965      78999999999    99999999987643

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.65  E-value=3.3e-16  Score=98.79  Aligned_cols=63  Identities=17%  Similarity=0.273  Sum_probs=58.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+.++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|+..||+..+.
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   73 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSA----AQKAVTALKASGVQ   73 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHH----HHHHHHHHHHHTCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHH----HHHHHHHhcCCeEe
Confidence            35789999999999999999999999999999999876        68999999999    99999999998654

>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=2.5e-16  Score=104.18  Aligned_cols=63  Identities=19%  Similarity=0.316  Sum_probs=58.8

Q ss_pred             CCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+. +++++|+++|++||.|.+|.|.+.++||+|.+.++    |++|+..||+..++
T Consensus        25 ~~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~----A~~A~~~l~g~~~~   88 (110)
T 1wf1_A           25 SINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERH----ARAAVLGENGRVLA   88 (110)
T ss_dssp             TCSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEEETTEEEEECSSSHH----HHHHHHHHTTCEET
T ss_pred             CCCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEeCCEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            34689999999999 99999999999999999999999999999999999    99999999987653

>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=99.65  E-value=9.3e-16  Score=101.22  Aligned_cols=64  Identities=20%  Similarity=0.327  Sum_probs=58.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+.+     ++||+|.+.++    |++|++.||+..++
T Consensus        19 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   87 (109)
T 1x4a_A           19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRD----AEDAVYGRDGYDYD   87 (109)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            456799999999999999999999999999999999865     78999999999    99999999987543

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.65  E-value=2.1e-16  Score=102.08  Aligned_cols=63  Identities=22%  Similarity=0.364  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++.++|||+|||+ .+++++|+++|++||.|.+|.|.+.++||+|.+.++    |++|+..||+..+
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~~g~afV~f~~~~~----A~~A~~~l~g~~~   70 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQS----VRDAIECESQEMN   70 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEETTEEEEEESCHHH----HHHHHHHHTCSSC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHH----HHHHHHHcCCCee
Confidence            45689999999999 999999999999999999999999999999999999    9999999998765

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.64  E-value=1.7e-16  Score=100.11  Aligned_cols=61  Identities=13%  Similarity=0.111  Sum_probs=55.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+..|||+||++.+||++|+++|.+||+|.+++++.  .++||+|.++++    |++|++.||+..+
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~~kGfaFVey~~~~e----A~~Ai~~Ln~~~l   68 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYLNQGIALCKYTTREE----ANKAQMALNNCVL   68 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHTTEEE
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcCCCcEEEEEECCHHH----HHHHHHHhcCCEE
Confidence            467899999999999999999999999999999874  578899999999    9999999998543

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=5.6e-16  Score=100.56  Aligned_cols=64  Identities=17%  Similarity=0.211  Sum_probs=59.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcc--cceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRF--GRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~f--G~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++|  |.|.+|.++++++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   77 (99)
T 2cpd_A           12 MSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNRED----AVEAMKALNGKVLD   77 (99)
T ss_dssp             SSCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHH----HHHHHHHHSSEEET
T ss_pred             cCCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEeCCeEEEEeCCHHH----HHHHHHHhCCCEeC
Confidence            4567999999999999999999999999  9999999999999999999999    99999999987553

>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=99.64  E-value=8.1e-16  Score=100.76  Aligned_cols=64  Identities=23%  Similarity=0.323  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|       ++||+|.+.++    |++||..||+..+.
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~   82 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTE----AQAAIHALHGSQTM   82 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHH----HHHHHHHHSSCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHH----HHHHHHHHcCCccC
Confidence            345799999999999999999999999999999999965       68999999999    99999999987654

>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=99.64  E-value=3.9e-16  Score=100.42  Aligned_cols=64  Identities=22%  Similarity=0.222  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|       ++||+|.+.++    |++|+..||+..++
T Consensus        13 ~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   83 (95)
T 2ywk_A           13 EEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPES----VSYAIALLNGIRLY   83 (95)
T ss_dssp             TTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            456799999999999999999999999999999999876       68999999999    99999999986543

>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=99.64  E-value=4.5e-16  Score=100.82  Aligned_cols=63  Identities=22%  Similarity=0.418  Sum_probs=59.5

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+..++|||+|||+ .+++++|+++|++||.|.+|.|.+.++||+|.+.++    |.+|+..||+..+
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~~g~afV~f~~~~~----A~~Ai~~l~g~~~   82 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQS----VRDAIEXESQEMN   82 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEECSSEEEEEESSHHH----HHHHHHHHTTSEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEeCCEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            45689999999999 999999999999999999999999999999999999    9999999998764

>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=99.64  E-value=6.7e-16  Score=101.14  Aligned_cols=64  Identities=14%  Similarity=0.226  Sum_probs=58.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   83 (105)
T 1x5u_A           12 RNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED----ADYAIKIMDMIKLY   83 (105)
T ss_dssp             CCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHH----HHHHHHHSSSCBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHH----HHHHHHHhCCCeEC
Confidence            456799999999999999999999999999999999876        68999999999    99999999987654

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=7.8e-16  Score=101.11  Aligned_cols=64  Identities=27%  Similarity=0.450  Sum_probs=58.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHH-hHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNL-WTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l-~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+++         ++||+|.+.++    |++|+..| |+..++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~~~~~~~   85 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD----AKKAFNALCHSTHLY   85 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHH----HHHHHHHHHTCCBSS
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHH----HHHHHHHhccCCeEC
Confidence            456899999999999999999999999999999999877         67999999999    99999999 776654

>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=99.64  E-value=2.5e-16  Score=105.14  Aligned_cols=63  Identities=16%  Similarity=0.187  Sum_probs=57.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC-cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK-RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~-d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+++++++|+++|++||+|.+|.|++ .++||+|.+.++    |++||+.||+..++
T Consensus        14 r~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~----a~~Ai~~l~g~~~~   77 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKED----MTYAVRKLDNTKFR   77 (115)
T ss_dssp             ---CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHH----HHHHHHHHTTCBCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecCCEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            4578999999999999999999999999999999999 689999999999    99999999987664

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=6.8e-16  Score=99.29  Aligned_cols=63  Identities=22%  Similarity=0.346  Sum_probs=58.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   73 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSEC----ARRALEQLNGFELA   73 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHH----HHHHHHHHTTCCSS
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHH----HHHHHHHhCCCeeC
Confidence            35789999999999999999999999999999999876        68999999999    99999999987654

>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=99.64  E-value=5.2e-16  Score=102.91  Aligned_cols=62  Identities=15%  Similarity=0.247  Sum_probs=56.4

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ..++++|||+|||++ +++++|+++|++||.|.+|.|++  .++||+|.+.++    |+.|+..||+..
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~~kg~aFVef~~~~~----A~~Ai~~l~~~~   86 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETRED----AMAMVDHCLKKA   86 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHH----HHHHHHHHHHSC
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCHHH----HHHHHHHhccCC
Confidence            446899999999998 99999999999999999999986  478999999999    999999998743

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.5e-16  Score=100.61  Aligned_cols=64  Identities=22%  Similarity=0.232  Sum_probs=58.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|      ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   81 (103)
T 2d9p_A           12 RYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEE----ATKAVTEMNGRIVA   81 (103)
T ss_dssp             CSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHH----HHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHH----HHHHHHHhCCCEeC
Confidence            456899999999999999999999999999999999965      78999999999    99999999987654

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=1e-15  Score=99.48  Aligned_cols=64  Identities=17%  Similarity=0.206  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+.|       ++||+|.+.++    |++|+..||+..++
T Consensus        14 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   84 (100)
T 2do4_A           14 SLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQ----ASQAVMKMDGMTIK   84 (100)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHH----HHHHHHHHTTEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            456789999999999999999999999999999999874       68999999999    99999999987654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.63  E-value=6.7e-16  Score=100.64  Aligned_cols=64  Identities=23%  Similarity=0.336  Sum_probs=58.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|++.||+..++
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   80 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD----AKDAMMAMNGKSVD   80 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHH----HHHHHHHHTTCCTT
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            446799999999999999999999999999999999876        78999999999    99999999987654

>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=99.63  E-value=5.6e-16  Score=100.11  Aligned_cols=62  Identities=13%  Similarity=0.133  Sum_probs=57.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHH----HHhhcccceEEEEec-----CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVP-----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~----~~F~~fG~v~~v~i~-----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+.+++++|+    ++|++||+|.+|.|+     +.++||+|.+.++    |++||..||+..+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~rg~afV~f~~~~~----A~~Ai~~l~g~~~   77 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQD----AIGAVNSLHRYKI   77 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHH----HHHHHHHHTTEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCCCeEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            457899999999999999999    999999999999999     4578999999999    9999999998754

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.63  E-value=3.4e-16  Score=103.40  Aligned_cols=63  Identities=17%  Similarity=0.337  Sum_probs=59.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++.++||+|.+.++    |++|+..||+..+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~kg~afV~f~~~~~----A~~Ai~~l~g~~~   90 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAES----AAKAIEEVHGKSF   90 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEETTEEEEECSSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEECCEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            45679999999999999999999999999999999999999999999999    9999999998765

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.63  E-value=9.4e-16  Score=99.44  Aligned_cols=63  Identities=24%  Similarity=0.440  Sum_probs=57.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+. ||+..++
T Consensus         7 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~-~~~~~~~   77 (99)
T 2dgs_A            7 GSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQS----VDQAVN-MHFHDIM   77 (99)
T ss_dssp             CSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHH----HHHHHH-HCCCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHH----HHHHHH-hCCCEEC
Confidence            456799999999999999999999999999999999865        68999999999    999998 8877654

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.62  E-value=8.6e-16  Score=102.28  Aligned_cols=63  Identities=27%  Similarity=0.348  Sum_probs=58.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~   82 (115)
T 2dgo_A           12 TSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD----AENAIQQMGGQWL   82 (115)
T ss_dssp             STTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHTTTCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            456899999999999999999999999999999999976        68999999999    9999999998654

>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=99.62  E-value=6e-16  Score=97.49  Aligned_cols=64  Identities=22%  Similarity=0.297  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||+|.++.|++|        ++||+|.+.++    |++|++.||+..++
T Consensus         4 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   75 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED----AAAAIDNMNESELF   75 (85)
T ss_dssp             CCCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            346799999999999999999999999999999999765        68999999999    99999999987653

>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=99.62  E-value=9.7e-16  Score=100.07  Aligned_cols=64  Identities=13%  Similarity=0.180  Sum_probs=58.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|      ++||+|.+.++    |++|+..||+..+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   81 (103)
T 2cqi_A           12 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRD----AAAALAAMNGRKIL   81 (103)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHH----HHHHHHHHTTEEET
T ss_pred             CCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHH----HHHHHHHhCCCCcC
Confidence            456799999999999999999999999999999999875      78999999999    99999999987543

>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=99.62  E-value=5.4e-16  Score=98.09  Aligned_cols=62  Identities=24%  Similarity=0.291  Sum_probs=56.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..+
T Consensus         4 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~   73 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWD----AENAIQQMGGQWL   73 (87)
T ss_dssp             --CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            35789999999999999999999999999999999876        68999999999    9999999998654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=9.5e-16  Score=98.54  Aligned_cols=64  Identities=22%  Similarity=0.156  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   83 (95)
T 2cqc_A           12 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD----AKEAKERANGMELD   83 (95)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHH----HHHHHHHHTTEEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            456799999999999999999999999999999999865        67999999999    99999999986543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=6.2e-16  Score=101.01  Aligned_cols=64  Identities=23%  Similarity=0.362  Sum_probs=58.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   83 (103)
T 2cq0_A           12 ADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED----AARAIAGVSGFGYD   83 (103)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHH----HHHHHHHTTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHH----HHHHHHHcCCCeeC
Confidence            456799999999999999999999999999999999976        68999999999    99999999987543

>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=99.62  E-value=1.6e-15  Score=98.36  Aligned_cols=64  Identities=27%  Similarity=0.467  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|+++  ++||+|.+.++    |++|++.||+..++
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~kg~afV~f~~~~~----a~~a~~~l~g~~~~   77 (99)
T 2cpj_A           12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTL----AEIAKVELDNMPLR   77 (99)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHH----HHHHHHHHTTCCBT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecCCCEEEEEECCHHH----HHHHHHHhCCCEeC
Confidence            456789999999999999999999999999999999974  77899999999    99999999987654

>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=99.62  E-value=1e-15  Score=99.19  Aligned_cols=64  Identities=20%  Similarity=0.269  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   76 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH----AVKAYAEVDGQVFQ   76 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHH----HHHHHHHTTTEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            345799999999999999999999999999999999875        58999999999    99999999987654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.61  E-value=6.2e-16  Score=99.83  Aligned_cols=61  Identities=13%  Similarity=0.195  Sum_probs=55.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccc--eEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR--ILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~--v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ...-.+|||+|||+++|+++|+++|++||.  |.+|+|++|        ++||+|.+.++    |++|++.||+.
T Consensus         6 ~~~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~----A~~Ai~~lng~   76 (95)
T 2lkz_A            6 HHHMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMD----ASQLLQILQSL   76 (95)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHH----HHHHHHHHHSS
T ss_pred             CCccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHH----HHHHHHHhcCC
Confidence            345689999999999999999999999995  679999876        67999999999    99999999985

>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=99.61  E-value=1.3e-15  Score=99.96  Aligned_cols=63  Identities=27%  Similarity=0.501  Sum_probs=58.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|++.||+..+
T Consensus        10 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~A~~~l~g~~~   80 (106)
T 2dgp_A           10 DHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERES----ALKAQSALHEQKT   80 (106)
T ss_dssp             CTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHH----HHHHHHHHTTTCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHH----HHHHHHHhcCCcc
Confidence            456799999999999999999999999999999999875        67999999999    9999999999765

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.61  E-value=1.4e-15  Score=97.17  Aligned_cols=64  Identities=17%  Similarity=0.154  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC------cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK------RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++      .++||+|.+.++    |++|+..||+..++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~----a~~a~~~l~g~~~~   74 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEV----AERACRMMNGMKLS   74 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHH----HHHHHHHHTTCCBT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            44679999999999999999999999999999999986      478999999999    99999999987653

>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=99.61  E-value=7.6e-16  Score=102.16  Aligned_cols=63  Identities=24%  Similarity=0.279  Sum_probs=57.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++  .++||+|.+.++    |++||..||+..+.
T Consensus         8 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~   72 (111)
T 1whx_A            8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLE----ARKAFRHLAYSKFH   72 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHH----HHHHHHHHTTCBSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCCCCEEEEEeCCHHH----HHHHHHHhCCCEEC
Confidence            3468999999999999999999999999999999975  478999999999    99999999987654

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.61  E-value=4.1e-16  Score=103.43  Aligned_cols=63  Identities=11%  Similarity=0.002  Sum_probs=57.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhccc-ceEEEEec----CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVP----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG-~v~~v~i~----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++++++|+++|++|| .|..+.|+    +.++||+|.+.++    |++||..||+..+
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~~~rGfaFV~F~~~e~----A~~Ai~~lng~~l   92 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEI----LVEALERLNNIEF   92 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSCSSSCCEEEEESSHHH----HHHHHHHTTTEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcCCCCCEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            34578999999999999999999999999 99999996    5689999999999    9999999998654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=6.6e-16  Score=100.67  Aligned_cols=64  Identities=22%  Similarity=0.297  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|++|.|++|        ++||+|.+.++    |++|++.||+..++
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   80 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED----AAAAIDNMNESELF   80 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHH----HHHHHHHHTTEEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            446799999999999999999999999999999999866        68999999999    99999999986543

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.7e-15  Score=100.69  Aligned_cols=64  Identities=14%  Similarity=0.089  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|       ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   82 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIE----AVQAISMFNGQLLF   82 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHH----HHHHHHHhCCCEeC
Confidence            445789999999999999999999999999999999976       78999999999    99999999987553

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.61  E-value=6.1e-16  Score=102.76  Aligned_cols=62  Identities=13%  Similarity=0.169  Sum_probs=57.1

Q ss_pred             CCCceEEE--eCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFV--GRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV--~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.++|||  +||++.+++++|+++|++||.|.+|.|+.+  ++||+|.+.++    |++|+..||+..+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~~rgfaFV~f~~~~~----A~~Ai~~lnG~~~   88 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEE----SKRAYVTLNGKEV   88 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHH----HHHHHHHTTTCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            45788999  779999999999999999999999999865  88999999999    9999999999765

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=1.8e-15  Score=97.51  Aligned_cols=64  Identities=11%  Similarity=0.073  Sum_probs=57.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEE-EecCcc----eeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKRF----WFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~d~----~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+| .|++|.    +||+|.+.++    |.+|+..||+..+.
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~afV~f~~~~~----a~~Ai~~l~g~~~~   80 (96)
T 2e44_A           12 RQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQ----ARQALDKLNGFQLE   80 (96)
T ss_dssp             CCSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEEEEEEESSHHH----HHHHHHHHTTCBCS
T ss_pred             CCCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            3457899999999999999999999999999999 588774    8999999999    99999999997664

>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=99.61  E-value=2.1e-15  Score=100.41  Aligned_cols=63  Identities=22%  Similarity=0.276  Sum_probs=57.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..+
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~   92 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS----AQAAIQSMNGFQI   92 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHH----HHHHHHHcCCCEE
Confidence            456789999999999999999999999999999999876        57999999999    9999999998654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.2e-15  Score=100.91  Aligned_cols=64  Identities=25%  Similarity=0.393  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|      ++||+|.+.++    |++|+..||+..++
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~----A~~Ai~~l~g~~~~   95 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD----ADRAREKLHGTVVE   95 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            456799999999999999999999999999999999955      78999999999    99999999987543

>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=99.60  E-value=2.1e-15  Score=102.65  Aligned_cols=64  Identities=22%  Similarity=0.156  Sum_probs=58.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++||..||+..++
T Consensus        43 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~----A~~Ai~~lng~~i~  114 (129)
T 2kxn_B           43 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD----AKEAKERANGMELD  114 (129)
T ss_dssp             CCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHH----HHHHHHHHTTCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            456799999999999999999999999999999999865        68999999999    99999999987654

>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=99.60  E-value=1.6e-15  Score=95.59  Aligned_cols=63  Identities=22%  Similarity=0.303  Sum_probs=56.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHH-hHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNL-WTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l-~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++  .++||+|.+.++    |++|+..| |+..+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~kg~afV~f~~~~~----A~~a~~~l~~~~~~   74 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQA----AEVAAEKSFNKLIV   74 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHH----HHHHHHTTTTTCEE
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECCCCEEEEEECCHHH----HHHHHHHhcCCeeE
Confidence            45679999999999999999999999999999999997  478999999999    99999998 76543

>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=99.60  E-value=1.3e-15  Score=98.26  Aligned_cols=61  Identities=16%  Similarity=0.297  Sum_probs=56.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|++.||+..++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~   70 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLES----SASAVRNLNGYQLG   70 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHH----HHHHHHHhCCCeEC
Confidence            589999999999999999999999999999999865        67999999999    99999999986543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.7e-15  Score=101.02  Aligned_cols=60  Identities=30%  Similarity=0.509  Sum_probs=56.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....++|||+|||+.+++++|+++|++||.|++|.|++|        ++||+|.+.++    |++||..||+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~Ai~~~~~   81 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA----AERACKDPNP   81 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHH----HHHHHTCSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHH----HHHHHHhCCC
Confidence            556899999999999999999999999999999999976        68999999999    9999999886

>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=99.60  E-value=3.6e-15  Score=98.40  Aligned_cols=64  Identities=23%  Similarity=0.326  Sum_probs=58.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+++        ++||.|.+.++    |++|++.||+..+.
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~----A~~Ai~~l~g~~i~   94 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSEC----AKKALEQLNGFELA   94 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHH----HHHHHHHHTTCCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            446789999999999999999999999999999999865        78999999999    99999999987654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.60  E-value=3.1e-15  Score=99.97  Aligned_cols=63  Identities=24%  Similarity=0.282  Sum_probs=57.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|++.||+..+
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~----A~~A~~~l~g~~~  107 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDS----AQVAIKAMNGFQV  107 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHH----HHHHHHHCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            456799999999999999999999999999999999866        67999999999    9999999988654

>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=99.60  E-value=1.6e-15  Score=96.09  Aligned_cols=62  Identities=18%  Similarity=0.334  Sum_probs=56.2

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC---------cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---------RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~---------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++++++|+++|++||.|.++.|++         .++||+|.+.++    |++|+..||+..+.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   73 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDE----AEKALKHMDGGQID   73 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHH----HHHHHHHcCCCeEC
Confidence            468999999999999999999999999999999964         467999999999    99999999987653

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.2e-15  Score=99.92  Aligned_cols=62  Identities=13%  Similarity=0.281  Sum_probs=55.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|++||+|.+|.|++|       ++||+|.+.++    |.+||. ||+..+
T Consensus         8 ~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~----a~~Ai~-~~~~~~   76 (103)
T 1s79_A            8 DVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIES----AKKFVE-TPGQKY   76 (103)
T ss_dssp             CSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHH----HHHHHT-SSCCCC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHH----HHHHHH-cCCCEE
Confidence            345789999999999999999999999999999999864       68999999999    999998 776554

>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=99.60  E-value=2.6e-15  Score=99.20  Aligned_cols=59  Identities=20%  Similarity=0.260  Sum_probs=55.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~A~~~~~   78 (111)
T 1x4h_A           12 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA----AQKCLAAAS   78 (111)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHH----HHHHHHHHC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHH----HHHHHHHhc
Confidence            456789999999999999999999999999999999865        68999999999    999999998

>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=99.60  E-value=1.4e-15  Score=95.36  Aligned_cols=60  Identities=22%  Similarity=0.252  Sum_probs=55.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+|||+|||+.+++++|+++|++||+|.++.|++|        ++||+|.+.++    |++|+..||+..+.
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~----a~~a~~~l~g~~~~   69 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDD----AQNAMDSMQGQDLN   69 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHH----HHHHHHHHTTCEET
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHH----HHHHHHHhcCCeeC
Confidence            68999999999999999999999999999999866        67999999999    99999999987543

>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=99.60  E-value=1.7e-15  Score=99.57  Aligned_cols=64  Identities=17%  Similarity=0.195  Sum_probs=58.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|.+|.|+++       ++||+|.+.++    |++|++.||+..+.
T Consensus        26 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   96 (107)
T 3ulh_A           26 VETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKAD----ALKAMKQYNGVPLD   96 (107)
T ss_dssp             CCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHH----HHHHHHHhCCCEeC
Confidence            456899999999999999999999999999999999955       78999999999    99999999987543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.59  E-value=7.9e-16  Score=96.29  Aligned_cols=61  Identities=20%  Similarity=0.343  Sum_probs=55.4

Q ss_pred             CceEEEeCCCCCC------CHHHHHHHhhcccceEEEEecC------cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEA------TAEDLRRYFSRFGRILDVYVPK------RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~------te~~L~~~F~~fG~v~~v~i~~------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +++|||+|||+.+      ++++|+++|++||+|.+|.|++      .++||+|.+.++    |++|+..||+..+.
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~----A~~Ai~~lng~~~~   73 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAH----AVDAVKNADGYKLD   73 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHH----HHHHHTTSSSCCCS
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHH----HHHHHHHhcCcccC
Confidence            3789999999999      7799999999999999999984      478999999999    99999999987654

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.59  E-value=3e-15  Score=97.11  Aligned_cols=64  Identities=16%  Similarity=0.114  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEE--------EEecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~--------v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+        +.|++|        ++||+|.+.++    |++|++.||+
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~----a~~Ai~~l~g   85 (99)
T 2la6_A           10 HSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS----AKAAIDWFDG   85 (99)
T ss_dssp             CCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHH----HHHHHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHH----HHHHHHHhCC
Confidence            556899999999999999999999999999999        999866        67999999999    9999999998


Q ss_pred             hCCC
Q 030822          162 AGCN  165 (171)
Q Consensus       162 ~~~~  165 (171)
                      ..+.
T Consensus        86 ~~~~   89 (99)
T 2la6_A           86 KEFS   89 (99)
T ss_dssp             CBSS
T ss_pred             CEeC
Confidence            7654

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=2.9e-15  Score=98.26  Aligned_cols=64  Identities=19%  Similarity=0.208  Sum_probs=58.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        20 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   91 (106)
T 1p27_B           20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE----AQAAMEGLNGQDLM   91 (106)
T ss_dssp             BTTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHH----HHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHH----HHHHHHHhcCCEEC
Confidence            445789999999999999999999999999999999855        67999999999    99999999987654

>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=99.59  E-value=3e-15  Score=101.19  Aligned_cols=64  Identities=19%  Similarity=0.208  Sum_probs=58.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        19 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   90 (126)
T 3ex7_B           19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE----AQAAMEGLNGQDLM   90 (126)
T ss_dssp             CSSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHH----HHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHhCCCeeC
Confidence            456789999999999999999999999999999999855        78999999999    99999999997764

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.59  E-value=5.8e-16  Score=99.79  Aligned_cols=62  Identities=21%  Similarity=0.251  Sum_probs=57.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEE-EecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.++|||+|||+.+++++|+++|++||.|.++ .|++|        ++||+|.+.++    |++|+..||+..+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~----A~~A~~~l~g~~~   73 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA----SDAAIEAMNGQYL   73 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHH----HHHHHHTTTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            357999999999999999999999999999999 99876        78999999999    9999999998754

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.59  E-value=2.3e-15  Score=98.38  Aligned_cols=62  Identities=15%  Similarity=0.134  Sum_probs=57.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhc-ccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSR-FGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~-fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ..+.++|||+|||+.+++++|+++|++ ||.|.+|.|++|       ++||.|.+.++    |++|+..||+..
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~   75 (104)
T 2dhg_A            6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELE----QKRALTECQGAV   75 (104)
T ss_dssp             SSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHH----HHHHHHHTTTCC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHH----HHHHHHHccCCc
Confidence            446799999999999999999999999 999999999865       78999999999    999999999876

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.59  E-value=1.5e-15  Score=98.27  Aligned_cols=63  Identities=22%  Similarity=0.283  Sum_probs=56.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+.++|||+|||+.+++++|+++|++||+|.+|.|++|           ++||+|.+.++    |++|+..||+..++
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   76 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ----AQKALKQLQGHTVD   76 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHH----HHHHHHHSTTCEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHH----HHHHHHHhCCCeeC
Confidence            35789999999999999999999999999999999853           67899999999    99999999987543

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.59  E-value=1.6e-15  Score=98.75  Aligned_cols=60  Identities=25%  Similarity=0.355  Sum_probs=55.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++|||+|||+.+++++|+++|++||+|.+|.|+++   ++||+|.+.++    |++|+..||+..++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   63 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRD----AEDAVRGLDGKVIC   63 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESSSSSEEEEECSSHHH----HHHHHHHHHHSCSS
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCEEEEEECCHHH----HHHHHHHHCCCeEC
Confidence            47999999999999999999999999999999866   88999999999    99999999997654

>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=99.59  E-value=8.2e-16  Score=98.14  Aligned_cols=60  Identities=20%  Similarity=0.246  Sum_probs=53.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhccc--ceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG--~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+|||+|||+++++++|+++|++||  .|.++.|++|        ++||+|.+.++    |++|++.||+..+.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~----a~~Ai~~l~g~~~~   71 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEAS----SKKLMDLLPKRELH   71 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHH----HHHHHHHGGGSCSS
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHH----HHHHHHHcCCCeeC
Confidence            4799999999999999999999999  9999999876        58999999999    99999999997654

>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=99.59  E-value=2.6e-15  Score=99.16  Aligned_cols=63  Identities=16%  Similarity=0.222  Sum_probs=57.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..||+..+
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~Ai~~l~g~~~   93 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ----ALAAKEALNGAEI   93 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            456789999999999999999999999999999999865        68999999999    9999999998754

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=3.5e-15  Score=97.74  Aligned_cols=62  Identities=31%  Similarity=0.487  Sum_probs=56.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++||.. |+..+
T Consensus        13 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~a~~~-~~~~~   82 (105)
T 2dh8_A           13 ADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNC----VGTVLAS-RPHTL   82 (105)
T ss_dssp             SSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTH----HHHHHHH-CSEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHH----HHHHHHh-CCCeE
Confidence            456799999999999999999999999999999999976        68999999999    9999988 76543

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=1.3e-15  Score=98.70  Aligned_cols=64  Identities=13%  Similarity=0.247  Sum_probs=57.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceE-EEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL-DVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~-~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|. +|.|++|        ++||+|.+.++    |++|+..||+..+.
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   78 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLAT----AEKCLHKINGKPLP   78 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHH----HHHHHHTTTTSEES
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHH----HHHHHHHHcCCccC
Confidence            34579999999999999999999999999999 9999876        57899999999    99999999986543

>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=99.58  E-value=7.1e-16  Score=102.89  Aligned_cols=75  Identities=16%  Similarity=0.327  Sum_probs=39.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhcc
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAAL   78 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (171)
                      |++|+  +++||||||+|.+.++|++||+.  ++.|+|+.|.|.++.++........                       
T Consensus        37 i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~~~~~~~~~-----------------------   91 (115)
T 4f25_A           37 VVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELG-----------------------   91 (115)
T ss_dssp             EEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCCCC-----------------------------
T ss_pred             EeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCccccccccc-----------------------
Confidence            35664  45899999999999999999984  8999999999999876543221100                       


Q ss_pred             CCCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHH
Q 030822           79 GAPTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAED  117 (171)
Q Consensus        79 g~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~  117 (171)
                                       ......++|||+|||+++|++.
T Consensus        92 -----------------~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           92 -----------------ARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             ---------------------------------------
T ss_pred             -----------------cccCCCCceEeCCCCCCccccc
Confidence                             0023457899999999999864

>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=99.58  E-value=2.1e-15  Score=106.67  Aligned_cols=63  Identities=16%  Similarity=0.222  Sum_probs=57.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|..|.|+++        ++||+|.+.++    |.+||..||+..+
T Consensus        69 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g~~~  139 (165)
T 1rk8_A           69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ----ALAAKEALNGAEI  139 (165)
T ss_dssp             CC-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            445789999999999999999999999999999999865        78999999999    9999999998654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.58  E-value=9.7e-16  Score=99.77  Aligned_cols=62  Identities=18%  Similarity=0.292  Sum_probs=57.0

Q ss_pred             CCceEEEeCCCC------CCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQ------EATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~------~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+      .+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++||+.||+..+.
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~----A~~Ai~~lng~~~~   80 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMND----AKKIIKSFHGKRLD   80 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHH----HHHHHHHHTTCBSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHH----HHHHHHHhCCcccC
Confidence            468999999999      9999999999999999999999855        67999999999    99999999987654

>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=99.58  E-value=8.9e-15  Score=97.16  Aligned_cols=64  Identities=11%  Similarity=0.245  Sum_probs=59.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|       ++||.|.+.++    |++|+..||+..+.
T Consensus        22 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   92 (114)
T 1x5o_A           22 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK----CEAVIGHFNGKFIK   92 (114)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHH----HHHHHHHHBTCCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHH----HHHHHHHhCCCEEc
Confidence            345789999999999999999999999999999999876       78999999999    99999999998763

>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=99.58  E-value=3.5e-15  Score=97.62  Aligned_cols=61  Identities=20%  Similarity=0.377  Sum_probs=55.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+.++|||+|||+.+++++|+++|++|| |.+|.|++|         ++||+|.+.++    |++|| .||+..+
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~----a~~A~-~l~g~~~   81 (104)
T 1wi8_A           12 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS----LLSAL-SLNEESL   81 (104)
T ss_dssp             SSSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHH----HHHHH-GGGTCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHH----HHHHH-hcCCCEe
Confidence            44579999999999999999999999999 999999865         68999999999    99999 9998654

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.58  E-value=4.7e-16  Score=99.59  Aligned_cols=56  Identities=20%  Similarity=0.279  Sum_probs=51.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhccc-ceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHh
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG-~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      +++|||+|||+++|+++|+++|++|| +|.+|+|++|        ++||+|.+.++    |++|++.|+
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~----A~~Ai~~~~   65 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQD----ATRWMEANQ   65 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHH----HHHHHHTTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHH----HHHHHHhcC
Confidence            36899999999999999999999999 8999999876        57899999999    999998773

>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=99.58  E-value=5.1e-15  Score=98.50  Aligned_cols=64  Identities=16%  Similarity=0.244  Sum_probs=58.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+++     ++||+|.+.++    |..|+..||+..+.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   73 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFD----AKNAVDHLSGFNVS   73 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTCEEEEESSHHH----HHHHHHHHTTCBSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCcEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            345789999999999999999999999999999999764     78999999999    99999999997664

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.58  E-value=5e-15  Score=97.15  Aligned_cols=63  Identities=21%  Similarity=0.348  Sum_probs=56.7

Q ss_pred             CCCceEEEeCCCCCC------CHHHHHHHhhcccceEEEEecC------cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEA------TAEDLRRYFSRFGRILDVYVPK------RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~------te~~L~~~F~~fG~v~~v~i~~------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+      ++++|+++|++||.|.+|.|++      .++||+|.+.++    |.+|+..||+..+.
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~----A~~Ai~~l~g~~~~   87 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAH----AVDAVKNADGYKLD   87 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSH----HHHHHHHCSSEECS
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHH----HHHHHHHhCCcccC
Confidence            346899999999999      7899999999999999999983      588999999999    99999999987553

>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=99.57  E-value=3e-15  Score=98.77  Aligned_cols=63  Identities=16%  Similarity=0.287  Sum_probs=57.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|+++  ++||+|.+.++    |++|+..||+..+
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~----a~~A~~~l~g~~~   86 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHES----AAHAIVSVNGTTI   86 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            446789999999999999999999999999999999964  78999999999    9999999998654

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.57  E-value=6.8e-15  Score=100.96  Aligned_cols=63  Identities=22%  Similarity=0.318  Sum_probs=57.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||+|.++.|++|        ++||+|.+.++    |++|++.||+..+
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~  130 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED----AAAAIDNMNESEL  130 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHH----HHHHHHHSTEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            456899999999999999999999999999999999866        68999999999    9999999998654

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.57  E-value=3e-15  Score=97.37  Aligned_cols=64  Identities=23%  Similarity=0.211  Sum_probs=57.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.++.|+  +.++||.|.+.++    |++|+..||+..++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~   89 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKGCCFIKYDTHEQ----AAVCIVALANFPFQ   89 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEETTTTEEEEECSSHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEecCCCEEEEEECCHHH----HHHHHHHhCCCeEC
Confidence            3457899999999999999999999999999999997  4578999999999    99999999987543

>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=99.57  E-value=4.4e-15  Score=95.80  Aligned_cols=63  Identities=25%  Similarity=0.410  Sum_probs=57.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH----HHhhcccceEEEEec-----CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVP-----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~----~~F~~fG~v~~v~i~-----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++.++|||+|||+.+++++|+    ++|++||.|.+|.|+     +.++||+|.+.++    |++|+..||+..+
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~   76 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS----ATNALRSMQGFPF   76 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcCCCcCcEEEEEeCCHHH----HHHHHHHhCCCEE
Confidence            4567999999999999999999    999999999999998     4689999999999    9999999998654

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=6.7e-15  Score=95.10  Aligned_cols=63  Identities=21%  Similarity=0.373  Sum_probs=56.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec----CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|. +.++    +.++||.|.+.++    |++|+..||+..++
T Consensus        16 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   82 (97)
T 2e5j_A           16 APLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQGPRRRAFLHYPDSAA----AQQAVSCLQGLRLG   82 (97)
T ss_dssp             SCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEETTTTEEEEECSSHHH----HHHHHHHHTTCCSS
T ss_pred             CCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcCCCCcEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            44578999999999999999999999999997 6666    4589999999999    99999999988664

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.56  E-value=4.5e-15  Score=98.46  Aligned_cols=64  Identities=13%  Similarity=0.064  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceE--------EEEecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL--------DVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~--------~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....++|||+|||+.+++++|+++|++||.|.        .|.|++|        ++||+|.+.++    |++||..||+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g   87 (113)
T 2cpe_A           12 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT----AKAAVEWFDG   87 (113)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHH----HHHHHHHHTT
T ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHH----HHHHHHHcCC
Confidence            45679999999999999999999999999999        6999876        68999999999    9999999998


Q ss_pred             hCCC
Q 030822          162 AGCN  165 (171)
Q Consensus       162 ~~~~  165 (171)
                      ..++
T Consensus        88 ~~~~   91 (113)
T 2cpe_A           88 KDFQ   91 (113)
T ss_dssp             CEET
T ss_pred             CccC
Confidence            7543

>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=99.56  E-value=2.7e-15  Score=99.40  Aligned_cols=63  Identities=16%  Similarity=0.198  Sum_probs=57.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH---HHhhcccceEEEEecCc-----------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLR---RYFSRFGRILDVYVPKR-----------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~---~~F~~fG~v~~v~i~~d-----------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ....++|||+|||+.+++++|+   ++|++||+|.+|.|++|           ++||+|.+.++    |++||+.||+..
T Consensus        12 ~~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~----A~~Ai~~lng~~   87 (111)
T 2cpi_A           12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED----ALRAIQCVNNVV   87 (111)
T ss_dssp             CCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHH----HHHHHHHHTTEE
T ss_pred             ccCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHH----HHHHHHHhCCCE
Confidence            4457899999999999999999   99999999999999865           67899999999    999999999875


Q ss_pred             C
Q 030822          164 C  164 (171)
Q Consensus       164 ~  164 (171)
                      +
T Consensus        88 ~   88 (111)
T 2cpi_A           88 V   88 (111)
T ss_dssp             E
T ss_pred             E
Confidence            4

>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=99.56  E-value=8.1e-15  Score=96.00  Aligned_cols=62  Identities=13%  Similarity=0.199  Sum_probs=54.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEE-EEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD-VYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~-v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+ |.|++|       ++||+|.++++    |++||.. |+..+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~----a~~A~~~-~~~~~   81 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI----AEKALKK-HKERI   81 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHH----HHHHHTT-TTCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHH----HHHHHHh-Ccchh
Confidence            456799999999999999999999999999998 888754       68999999999    9999987 76554

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.56  E-value=4.7e-15  Score=101.06  Aligned_cols=60  Identities=17%  Similarity=0.196  Sum_probs=55.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEE--EEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--VYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~--v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ....++|||+|||+.+|+++|+++|++||.|..  |+|++|        ++||+|.+. +    |.+|+..||+.
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~----a~~Ai~~l~g~   89 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-E----AAQLLQILQAL   89 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-H----HHHHHHHHTTC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-H----HHHHHHHhcCC
Confidence            345789999999999999999999999999977  999876        579999999 9    99999999987

>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=99.56  E-value=3.7e-15  Score=99.56  Aligned_cols=63  Identities=21%  Similarity=0.333  Sum_probs=57.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+++++++|+++|++||.|++|.|++|       ++||+|.+.++    |++|++.||+..++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~----A~~Ai~~l~g~~~~   74 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPAD----AKNAAKDMNGKSLH   74 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHH----HHHHHHHCSSCBCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            35689999999999999999999999999999999974       68999999999    99999999987664

>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=99.56  E-value=1.1e-14  Score=96.83  Aligned_cols=62  Identities=19%  Similarity=0.325  Sum_probs=56.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|| .||+..++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~-~l~g~~~~   92 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS----VPLAI-GLTGQRLL   92 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGG----HHHHH-HHTTEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHH----HHHHH-HcCCCEeC
Confidence            34689999999999999999999999999999999854        68999999999    99999 99987543

>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=99.55  E-value=4.3e-15  Score=94.28  Aligned_cols=61  Identities=21%  Similarity=0.262  Sum_probs=55.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+.+++++|+++|++||.|.++.|++|        ++||+|.+.++    |++|+ .||+..++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~a~-~~~g~~~~   73 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKES----VRTSL-ALDESLFR   73 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHH----HHHHG-GGTTCEET
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHH----HHHHH-hcCCCEEC
Confidence            3589999999999999999999999999999999876        68999999999    99999 99887543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.55  E-value=1.7e-14  Score=97.24  Aligned_cols=64  Identities=19%  Similarity=0.212  Sum_probs=58.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|       ++||+|.+.++    |++|+..||+..++
T Consensus        32 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~  102 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD----ALKAMKQYKGVPLD  102 (124)
T ss_dssp             CSSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHH----HHHHHHHHTTEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            456799999999999999999999999999999999864       78999999999    99999999987654

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.55  E-value=1e-14  Score=98.95  Aligned_cols=63  Identities=14%  Similarity=0.139  Sum_probs=56.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH----HHhhcccceEEEEecC-----cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVPK-----RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~----~~F~~fG~v~~v~i~~-----d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+.++|||+|||+.+++++|+    ++|++||.|++|.+.+     .++||+|.+.++    |..|+..||+..+
T Consensus        26 ~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~~~~rG~aFV~F~~~~~----A~~Ai~~lng~~l   97 (127)
T 2a3j_A           26 TEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDNSGKAYIVFATQES----AQAFVEAFQGYPF   97 (127)
T ss_dssp             CSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCCCSSCCCEEEEESSHHH----HHHHHHHSTTCCC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccCCCcCCEEEEEECCHHH----HHHHHHHHCCCEe
Confidence            3457899999999999999876    6999999999999974     589999999999    9999999998765

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.55  E-value=7.1e-15  Score=95.98  Aligned_cols=61  Identities=16%  Similarity=0.219  Sum_probs=55.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++|| |.+|.|++|        ++||+|.+.++    |++|+ .||+..+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~-~l~g~~~   80 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDS----LKEAL-TYDGALL   80 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHH----HHHHG-GGTTCEE
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHH----HHHHH-hhCCCeE
Confidence            45679999999999999999999999997 999999966        67999999999    99999 8988654

>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=99.55  E-value=1.9e-15  Score=98.74  Aligned_cols=63  Identities=29%  Similarity=0.454  Sum_probs=57.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+++++|+++|++||.|.+|.|+++        ++||+|.+.++    |++|++.||+..++
T Consensus         6 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   76 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET----ALSAMRNLNGREFS   76 (104)
T ss_dssp             HHHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHH----HHHHHHHSSSBSCS
T ss_pred             CCccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHH----HHHHHHHhCCCeeC
Confidence            35689999999999999999999999999999999855        68999999999    99999999987664

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.55  E-value=1.1e-14  Score=100.04  Aligned_cols=64  Identities=19%  Similarity=0.275  Sum_probs=58.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|+.||.|++|.|++|        ++||+|.+.++    |++|+..||+..++
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~~  110 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS----AQQAIAGLNGFNIL  110 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHH----HHHHHHHTTTEECS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            456799999999999999999999999999999999865        68999999999    99999999987654

>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=99.55  E-value=1.1e-14  Score=95.09  Aligned_cols=58  Identities=33%  Similarity=0.445  Sum_probs=53.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|+.++
T Consensus        12 ~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~~~   77 (103)
T 2cqg_A           12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET----QVKVMSQR   77 (103)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHH----HHHHHHSC
T ss_pred             cCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHH----HHHHHHcC
Confidence            456789999999999999999999999999999999876        68999999999    99999863

>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=99.55  E-value=6.8e-15  Score=96.12  Aligned_cols=61  Identities=16%  Similarity=0.130  Sum_probs=53.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|++||. ++|.|++|       ++||+|.+.++    |++|| .||+..+
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~-~~v~i~~d~~g~~~G~afV~F~~~~~----a~~Al-~~~~~~~   79 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHED----AVAAM-AKDKANM   79 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHH----HHHHH-TTSSCCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCc-eEEEEEECCCCCEeeEEEEEECCHHH----HHHHH-HhCCCeE
Confidence            456789999999999999999999999995 59999866       68999999999    99999 4776544

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.54  E-value=4.1e-15  Score=91.88  Aligned_cols=58  Identities=29%  Similarity=0.492  Sum_probs=53.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ++|||+|||+++++++|+++|++||+|.++.|++|        ++||.|.+.++    |++|+..|| ..+
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~a~~~~~-~~~   66 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG----VDKVLAQSR-HEL   66 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTH----HHHHHHTTT-CCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHH----HHHHHHhCC-Ccc
Confidence            47999999999999999999999999999999875        67899999999    999999988 443

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.54  E-value=5e-15  Score=103.94  Aligned_cols=61  Identities=11%  Similarity=0.146  Sum_probs=55.5

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhccc--ceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG--~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||+.+++++|+++|++||  .|.+|.|++|        ++||+|.+.++    |++||..||+..+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~----A~~Ai~~lng~~~  124 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENS----VHKLLELLPGKVL  124 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHH----HHHHHHHSTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHcCCCEE
Confidence            468999999999999999999999999  9999999876        68999999999    9999999998654

>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=99.54  E-value=1.1e-14  Score=92.04  Aligned_cols=57  Identities=28%  Similarity=0.535  Sum_probs=52.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|++.
T Consensus         8 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~~   72 (87)
T 3s7r_A            8 EEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAAS----VEKVLDQ   72 (87)
T ss_dssp             CSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHH----HHHHHHS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHH----HHHHHHh
Confidence            456799999999999999999999999999999999865        68999999999    9999965

>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=99.53  E-value=4.1e-15  Score=95.33  Aligned_cols=63  Identities=17%  Similarity=0.221  Sum_probs=55.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccc-eEEEEec-CcceeEEecCCcccHHHHHHHHHHHhH-hCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVP-KRFWFCHLCGRSCSRSCFSKVSRNLWT-AGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~-v~~v~i~-~d~~fv~f~~~~~~~~~a~~Ai~~l~~-~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||. |..+.+. +.++||+|.+.++    |++|+..||+ ..+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   70 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNW----AIRAIETLSGKVEL   70 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHH----HHHHHHHHTTTCEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEcCCCEEEEEECCHHH----HHHHHHHccCCeeE
Confidence            345789999999999999999999999999 6666654 6689999999999    9999999998 543

>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=99.53  E-value=3.2e-15  Score=96.70  Aligned_cols=63  Identities=13%  Similarity=0.055  Sum_probs=55.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.++.++.+        ++||+|.+.++    |++|++.||+..+
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~----a~~Ai~~l~g~~~   82 (98)
T 2cqp_A           12 KPGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE----ATAAVIDLNDRPI   82 (98)
T ss_dssp             CCSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHH----HHHHHHHTTTCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHH----HHHHHHHhCCCee
Confidence            445789999999999999999999999999988777643        68999999999    9999999998644

>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=99.53  E-value=2.1e-15  Score=97.00  Aligned_cols=62  Identities=13%  Similarity=0.050  Sum_probs=54.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +..++|||+|||+.+++++|+++|++||.|..+.++.+        ++||+|.+.++    |++|++.||+..+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~----a~~Ai~~l~g~~~   82 (95)
T 2ek1_A           13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE----ATAAVIDLNDRPI   82 (95)
T ss_dssp             --CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHH----HHHHHHHhCCCeE
Confidence            44689999999999999999999999999998887753        68999999999    9999999998654

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.53  E-value=6e-15  Score=98.85  Aligned_cols=62  Identities=15%  Similarity=0.071  Sum_probs=55.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccc---eEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR---ILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~---v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|++||.   |..|+|++|       ++||+|.+.++    |++||+ ||+..+
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~----a~~Al~-~~g~~~   85 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDD----VKLALK-KDRESM   85 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHH----HHHHGG-GTTEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHH----HHHHHh-cCCCeE
Confidence            445789999999999999999999999999   899999865       68999999999    999999 887654

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.53  E-value=1.6e-14  Score=97.43  Aligned_cols=59  Identities=14%  Similarity=0.084  Sum_probs=54.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC--cc-eeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK--RF-WFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~--d~-~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      -.|||+||++.+++++|+++|++||.|.+|.|+.  .+ +||+|.+.++    |..|+..||+..+
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~~Gf~aFVef~~~~~----A~~A~~~LnG~~i   87 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKRNGIQAMVEFESVLC----AQKAKAALNGADI   87 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEESSSEEEEEEESSHHH----HHHHHHHHTTCCC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHH----HHHHHHHhCCCEe
Confidence            4578999999999999999999999999999875  34 8999999999    9999999999876

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.53  E-value=1e-14  Score=107.10  Aligned_cols=62  Identities=18%  Similarity=0.183  Sum_probs=55.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.++|||+|||+++|+++|+++|++||+|++|+|++|        ++||+|.+.++    |++|+..||+..+
T Consensus        13 ~p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~----A~~Ai~~~~~~~~   82 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD----AERALDTMNFDVI   82 (213)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHH----HHHHHHHhhhhhc
Confidence            35689999999999999999999999999999999976        57999999999    9999999987654

>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=99.53  E-value=2.7e-15  Score=103.27  Aligned_cols=61  Identities=16%  Similarity=0.126  Sum_probs=53.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|++|| |++|.|++|       ++||+|.+.++    |++|| .||+..+
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~----A~~Al-~~~g~~l  110 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEE----AVAAM-SKDRANM  110 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHH----HHHHT-TCCSCSS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHH----HHHHH-hhCCCEE
Confidence            34578999999999999999999999999 779999865       68999999999    99999 7776544

>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=99.52  E-value=1.3e-14  Score=101.68  Aligned_cols=64  Identities=20%  Similarity=0.292  Sum_probs=58.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|++|.|++|        ++||+|.+.++    |++||..||+..++
T Consensus        36 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~  107 (156)
T 1h2v_Z           36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD----AENAMRYINGTRLD  107 (156)
T ss_dssp             TTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHTTTSEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            346799999999999999999999999999999999865        67999999999    99999999987553

>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=99.52  E-value=1.6e-14  Score=92.05  Aligned_cols=50  Identities=36%  Similarity=0.830  Sum_probs=44.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC---cceeEEecCCcc
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RFWFCHLCGRSC  147 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~---d~~fv~f~~~~~  147 (171)
                      ..+.++|||+|||+++|+++|+++|++||.|.+|.|++   .++||+|.++++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~srGfaFV~F~~~~~   60 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKV   60 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSSCCSEEEEEESCHHH
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeCCCCEEEEEECCHHH
Confidence            45689999999999999999999999999999999995   489999999988

>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=99.52  E-value=6.9e-15  Score=95.63  Aligned_cols=62  Identities=19%  Similarity=0.373  Sum_probs=53.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+++++++|+++|++|| |.+|.|++|         ++||+|.+.++    |++|+ .||+..++
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~----a~~Ai-~l~g~~~~   86 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS----LLSAL-SLNEESLG   86 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHH----HHHHH-HTTTCCBT
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHH----HHHHH-hcCCCEEC
Confidence            45679999999999999999999999999 999999865         67999999999    99999 99987654

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.52  E-value=5.2e-15  Score=91.03  Aligned_cols=58  Identities=33%  Similarity=0.536  Sum_probs=52.4

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +|||+|||+++++++|+++|++||+|.+|.|+++        ++||+|.+.++    |++|+. ||+..++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~a~~-~~~~~~~   66 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI----VEKVCE-IHFHEIN   66 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHH----HHHHHS-SSCCCSS
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHH----HHHHHH-CCCCEEC
Confidence            5999999999999999999999999999999865        57899999999    999987 8776654

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.52  E-value=1.5e-14  Score=95.61  Aligned_cols=59  Identities=31%  Similarity=0.521  Sum_probs=51.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ....++|||+|||+++++++|+++|++||.|.+|.|++|        ++||.|.+.++    |++|+..++
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~----A~~Ai~~~~   88 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG----VDKVLAQSR   88 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHH----HHHHHHSSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHH----HHHHHHHCC
Confidence            446799999999999999999999999999999999876        68999999999    999998764

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.51  E-value=1.2e-14  Score=92.73  Aligned_cols=61  Identities=5%  Similarity=0.151  Sum_probs=55.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++++++|+++|++| .|.+|.|++|       ++||.|.+.++    |.+|+. ||+..+
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~----a~~A~~-~~g~~~   74 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEE----VKQALK-CNREYM   74 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHH----HHHHHH-SCSEEE
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHH----HHHHHH-hCCcee
Confidence            4467999999999999999999999999 9999999876       78999999999    999999 988654

>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=99.51  E-value=1.6e-14  Score=101.59  Aligned_cols=62  Identities=18%  Similarity=0.162  Sum_probs=56.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....+|||+||++.+|+++|+++|++||.|.+|.|..+    ++||+|.+.++    |+.|++.||+..+
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~~rgfAFVeF~d~~~----A~~Ai~~LnG~~i  109 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS----AQHAKLSLDGQNI  109 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESSSCEEEEEEESCHHH----HHHHHHHSTTBCS
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCEEEEEECCHHH----HHHHHHHhCCCEe
Confidence            34578999999999999999999999999999999733    68999999999    9999999999876

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.51  E-value=2e-14  Score=92.31  Aligned_cols=61  Identities=20%  Similarity=0.286  Sum_probs=53.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+.+++++|+++|++||.|.+|.+-++   ++||+|.+.++    |++|+. ||+..+
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v~~~~~~g~~afV~f~~~~~----a~~ai~-l~g~~~   69 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKGVFAIVEMGDVGA----REAVLS-QSQHSL   69 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEEEECSSSCCEEEEEESSHHH----HHHHHT-CSCCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEcCCCCcEEEEEECCHHH----HHHHHh-cCCeEE
Confidence            34689999999999999999999999999999843332   79999999999    999999 987654

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.51  E-value=1.6e-14  Score=97.99  Aligned_cols=61  Identities=20%  Similarity=0.218  Sum_probs=55.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---c-eeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---F-WFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~-~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .--+|||+||++.+|+++|+++|++||+|.+|.|+.+   + +||+|.+.++    |++|++.|||..+
T Consensus        27 ~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~~gfqAFVef~~~~~----A~~Ai~~LnG~~i   91 (130)
T 3zzy_A           27 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS----AQHAKLSLDGQNI   91 (130)
T ss_dssp             SEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEETTEEEEEEEESCHHH----HHHHHHHHTTCEE
T ss_pred             ceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCCCCcEEEEEECCHHH----HHHHHHHcCCCee
Confidence            4567899999999999999999999999999999854   3 8999999999    9999999999765

>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=99.51  E-value=2.4e-14  Score=104.73  Aligned_cols=61  Identities=11%  Similarity=0.091  Sum_probs=56.4

Q ss_pred             CCceEEEeCCC-CCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp-~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+++|||+||| +.+++++|+++|++||.|.+|+|+++   ++||+|.+.++    |+.||+.||+..+
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~g~afV~f~~~~~----A~~Ai~~lng~~~   67 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYA----VDRAITHLNNNFM   67 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTSTTCEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCCCEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            46899999999 89999999999999999999999864   79999999999    9999999998654

>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=99.50  E-value=8.9e-15  Score=100.37  Aligned_cols=63  Identities=14%  Similarity=0.059  Sum_probs=56.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccc---eEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR---ILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~---v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+++|+++|+++|++||.   |.+|.|++|       ++||+|.+.++    |++||+ ||+..++
T Consensus        41 ~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~----a~~Al~-~~g~~l~  113 (136)
T 2hgl_A           41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDD----VKMALK-KDRESMG  113 (136)
T ss_dssp             CCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHH----HHHHHT-TTEEESS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHH----HHHHHh-cCCCEEC
Confidence            445789999999999999999999999999   899999866       68999999999    999999 9886553

>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=99.50  E-value=1.8e-14  Score=107.12  Aligned_cols=62  Identities=19%  Similarity=0.221  Sum_probs=56.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhccc--ceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFG--RILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG--~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+.+|+++|+++|++||  .|++|+|++|        ++||+|.+.++    |++||+.||+..+.
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~----a~~Ai~~lng~~~~  138 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEAS----SKKLMDLLPKRELH  138 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTH----HHHHHTTSTTSCBT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHH----HHHHHHHcCCCeEC
Confidence            467999999999999999999999999  9999999977        58999999999    99999999987654

>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=99.50  E-value=1.7e-14  Score=94.97  Aligned_cols=58  Identities=21%  Similarity=0.350  Sum_probs=53.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccc-eEEEEec-C--------cceeEEecCCcccHHHHHHHHHHHh
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVP-K--------RFWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~-v~~v~i~-~--------d~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ...++|||+|||+.+++++|+++|++||. |.+|.|+ .        .++||+|.+.++    |++|+..||
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~----A~~A~~~l~   73 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA----AAMARRKLM   73 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHH----HHHHHTTTT
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHH----HHHHHHHhh
Confidence            45789999999999999999999999999 9999998 2        378999999999    999999996

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=1.4e-14  Score=95.72  Aligned_cols=60  Identities=15%  Similarity=0.056  Sum_probs=53.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....+|||+|||+++++++|+++|++| .|.+|.|++|       ++||+|.+.++    |++|| .||+..+
T Consensus        14 ~~~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~----a~~Al-~~~~~~~   80 (109)
T 2dnn_A           14 PDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQD----TFEAL-KRNRMLM   80 (109)
T ss_dssp             HHHHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHH----HHHHH-HTTTEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHH----HHHHH-hcCCCeE
Confidence            346899999999999999999999999 8999999865       68999999999    99999 6887543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.50  E-value=2.7e-14  Score=92.79  Aligned_cols=61  Identities=18%  Similarity=0.198  Sum_probs=53.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|   .|+++       ++||+|.+.++    |++|+..||+..++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~----A~~A~~~l~g~~~~   79 (101)
T 2fc9_A           12 SGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFED----AKEALNSCNKREIE   79 (101)
T ss_dssp             SCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHH----HHHHHHHTSSEEET
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHH----HHHHHHHhCCCEeC
Confidence            4568999999999999999999999999988   45443       78999999999    99999999986543

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=6.5e-14  Score=89.13  Aligned_cols=59  Identities=14%  Similarity=0.247  Sum_probs=51.7

Q ss_pred             CCce-EEEeCCCCCCCHHH----HHHHhhcc-cceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKK-IFVGRLPQEATAED----LRRYFSRF-GRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~-lfV~nLp~~~te~~----L~~~F~~f-G~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +..+ |||+|||+.+++++    |+++|++| |+|.+|  ...++||.|.+.++    |.+|++.||+..+
T Consensus         7 p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V--tgG~AfV~F~~~es----A~~A~~~l~G~~l   71 (96)
T 2diu_A            7 GCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI--TGCSAILRFINQDS----AERAQKRMENEDV   71 (96)
T ss_dssp             CSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC--CTTCEEEEESSHHH----HHHHHHHHTTCCS
T ss_pred             CcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE--ecCEEEEEECCHHH----HHHHHHHhcCCcc
Confidence            3444 99999999999987    55899999 599988  45999999999999    9999999999765

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.49  E-value=6.6e-14  Score=90.38  Aligned_cols=61  Identities=23%  Similarity=0.285  Sum_probs=55.0

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+||  .+++++|+++|++||.|.+|.|.  +.++||+|.+.++    |++||..||+..+
T Consensus        12 ~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~~~~g~afV~f~~~~~----a~~Ai~~l~g~~~   74 (97)
T 1x5p_A           12 PRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES----ADQAVAELNGTQV   74 (97)
T ss_dssp             CCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHTTTEEE
T ss_pred             CCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEecCCCCEEEEEECCHHH----HHHHHHHhCCCeE
Confidence            446789999996  89999999999999999999997  4588999999999    9999999998754

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.49  E-value=2.7e-14  Score=95.00  Aligned_cols=58  Identities=24%  Similarity=0.465  Sum_probs=51.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ...++|||+|||+.+++++|+++|++||+|. +.++.+           ++||+|.+.++    |++||+.||.
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~----a~~Ai~~~~~   74 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESS----VQALIDACLE   74 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHH----HHHHHHHSEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHH----HHHHHHhhhh
Confidence            4578999999999999999999999999999 777643           67999999999    9999999843

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.49  E-value=1.3e-14  Score=97.75  Aligned_cols=60  Identities=18%  Similarity=0.277  Sum_probs=55.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||+.+++++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+ .||+..+
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~A~-~l~g~~~  102 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNS----VDAAV-AMDETVF  102 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHH----HHHHH-TTTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHH----HHHHH-hcCCCeE
Confidence            4689999999999999999999999999999999865        68999999999    99999 8988654

>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=99.48  E-value=1.8e-14  Score=94.80  Aligned_cols=63  Identities=14%  Similarity=-0.052  Sum_probs=56.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccc---eEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGR---ILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~---v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+++|+++|+++|++||.   |.+|.|++|       ++||+|.+.++    |++||. ||+..+.
T Consensus         8 ~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~----a~~Al~-~~~~~~~   80 (107)
T 2lmi_A            8 VDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD----VQKALE-KHRMYMG   80 (107)
T ss_dssp             CSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHH----HHHHHT-TTTCCSS
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHH----HHHHHH-hCcceeC
Confidence            446789999999999999999999999998   999999866       68999999999    999999 8886654

>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=99.48  E-value=2.2e-14  Score=96.82  Aligned_cols=63  Identities=13%  Similarity=0.154  Sum_probs=54.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--------CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--------KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--------~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|.++.++        +.++||+|.+.++    |++||. ||+..+.
T Consensus        22 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~----a~~Al~-~~g~~~~   92 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD----YKAALC-RHKQYMG   92 (124)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHH----HHHHHT-SCSBCST
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHH----HHHHHH-hCCCeEC
Confidence            4457899999999999999999999999999885444        2378999999999    999999 9887654

>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=99.48  E-value=2.8e-14  Score=90.13  Aligned_cols=61  Identities=18%  Similarity=0.304  Sum_probs=55.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcc----c-------ceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRF----G-------RILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~f----G-------~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+.+++++|+++|++|    |       .|.++.++++  ++||+|.+.++    |++|+ .||+..+
T Consensus         4 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~kg~afV~f~~~~~----a~~A~-~l~g~~~   77 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE----TTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSSSSEEEEEESSHHH----HHHHG-GGTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCCCcEEEEEcCCHHH----HHHHH-hcCCCEE
Confidence            357899999999999999999999999    8       9999999965  77899999999    99999 9998754

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.47  E-value=2.2e-14  Score=93.35  Aligned_cols=63  Identities=17%  Similarity=0.409  Sum_probs=55.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHH---HHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSR---NLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~---~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|.+|.|++|       ++||.|.+.++    |++|+.   .|++..+
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~----a~~Ai~~~~~~~g~~l   78 (102)
T 2xs2_A            6 KIMPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVD----VQKIVESQINFHGKKL   78 (102)
T ss_dssp             EEEEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCC----HHHHTTCCCEETTEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHH----HHHHHhCCCeECCEEE
Confidence            345689999999999999999999999999999999874       78999999999    999998   5555443

>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=99.47  E-value=2.5e-14  Score=95.18  Aligned_cols=61  Identities=11%  Similarity=-0.003  Sum_probs=53.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccce-EEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRI-LDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v-~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ....++|||+|||+.+++++|+++|++||.| ..|.|++|       ++||+|.+.++    |++||.. |+..
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~----a~~Al~~-~~~~   80 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDD----ARKSERL-HRKK   80 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHH----HHHHGGG-CSEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHH----HHHHHHh-CCCc
Confidence            3457899999999999999999999999999 88999754       78999999999    9999876 6643

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.47  E-value=2.9e-14  Score=92.67  Aligned_cols=61  Identities=15%  Similarity=0.127  Sum_probs=53.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+++++++|+++|++||.|.. .++.|        ++||+|.+.++    |++|++ ||+..+.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~----a~~A~~-l~g~~~~   83 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAED----LEKALE-LTGLKVF   83 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHH----HHHHHH-GGGCCBT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHH----HHHHHh-cCCcEEC
Confidence            35789999999999999999999999999888 55543        78999999999    999998 9987654

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.47  E-value=7.6e-14  Score=99.85  Aligned_cols=64  Identities=19%  Similarity=0.212  Sum_probs=58.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.|++|.|+.|       ++||+|.+.++    |++|++.||+..++
T Consensus        85 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~----A~~Ai~~lng~~l~  155 (177)
T 2f3j_A           85 VETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRAD----ALKAMKQYKGVPLD  155 (177)
T ss_dssp             CTTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHH----HHHHHHHSTTCBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHH----HHHHHHHhCCCEEC
Confidence            456799999999999999999999999999999999865       68999999999    99999999987654

>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=99.47  E-value=3.1e-14  Score=90.35  Aligned_cols=60  Identities=18%  Similarity=0.266  Sum_probs=54.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||+.+++++|+++|++| .|.++.|.  +.++||+|.+.++    |++|++.||+..+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~~~~g~afV~f~~~~~----a~~Ai~~l~g~~~   65 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQ----AQNAIQMFHQYSF   65 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEEGGGTEEEECCSCHHH----HHHHHHHHTTEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEeCCCcEEEEEECCHHH----HHHHHHHhCCCeE
Confidence            46899999999999999999999999 99999986  4578999999999    9999999998654

>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=99.47  E-value=1.2e-13  Score=91.77  Aligned_cols=64  Identities=14%  Similarity=0.130  Sum_probs=56.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccce----EEEEec----CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRI----LDVYVP----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v----~~v~i~----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|    ..+.++    +.++||+|.+.++    |++|+..||+..+.
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~----a~~Ai~~l~g~~~~   93 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI----AWQALHLVNGYKLY   93 (115)
T ss_dssp             CSCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHH----HHHHHHHSTTCBCS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHH----HHHHHHHhCCCEeC
Confidence            3457899999999999999999999999999    566665    3588999999999    99999999987653

>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=99.46  E-value=9.4e-14  Score=98.08  Aligned_cols=62  Identities=23%  Similarity=0.431  Sum_probs=56.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|+++          ++||+|.+.++    |++|+..||+..+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~~~~~~   73 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKA----ALEAQNALHNMKVL   73 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHH----HHHHHHHHTTTCCC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHH----HHHHHHHhcCcEEc
Confidence            3689999999999999999999999999999999865          57999999999    99999999987653

>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=99.46  E-value=4e-14  Score=89.74  Aligned_cols=52  Identities=31%  Similarity=0.685  Sum_probs=47.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKV  155 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~A  155 (171)
                      ..++|||+|||+++++++|+++|++||+|.+|.|+++   ++||+|.+.++    |++|
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~----a~~~   58 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQI----AQSL   58 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHH----HHHT
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecCCCCEEEEEECCHHH----HHHH
Confidence            4699999999999999999999999999999999854   88999999998    7654

>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=99.46  E-value=2.3e-14  Score=88.05  Aligned_cols=55  Identities=29%  Similarity=0.531  Sum_probs=50.0

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      +|||+|||+.+++++|+++|++||+|.++.|++|        ++||.|.+.++    |++|+.. ++.
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----a~~Ai~~-~~~   63 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP----VKKIMEK-KYH   63 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHH----HHHHHTT-SSC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHH----HHHHHHh-CCC
Confidence            5999999999999999999999999999999865        68999999999    9999985 443

>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=99.46  E-value=1.3e-13  Score=93.26  Aligned_cols=56  Identities=18%  Similarity=0.266  Sum_probs=50.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceE--EEEecCc-------ceeEEecCCcccHHHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL--DVYVPKR-------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~--~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ....++|||+|||+++|+++|+++|++| .|+  +|.|++|       ++||+|.+.++    |++||+.
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~----A~~Al~~  103 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQEL----AEKALGK  103 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTH----HHHHHTT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHH----HHHHHHH
Confidence            4457899999999999999999999999 677  8999865       68999999999    9999985

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.46  E-value=2.8e-14  Score=95.09  Aligned_cols=60  Identities=25%  Similarity=0.445  Sum_probs=54.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ...++|||+|||+.+++++|+++|++||.|..|.|++|        ++||+|.+.++    |++||.. |+..
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~Ai~~-~~~~   92 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE----VDAAMAA-RPHS   92 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHH----HHHHHTS-CSEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHH----HHHHHHh-CCcE
Confidence            34689999999999999999999999999999999976        78999999999    9999987 6543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.45  E-value=1.5e-13  Score=87.87  Aligned_cols=49  Identities=20%  Similarity=0.415  Sum_probs=43.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc---CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD---THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~---~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+.   +..++||+|.|.++.|+..
T Consensus        34 i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~~~~~   85 (91)
T 2lxi_A           34 LMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSDPKPK   85 (91)
T ss_dssp             SSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCCSCCC
T ss_pred             EEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcCCCCC
Confidence            589999999999999999999999999984   3579999999999987643

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.17  E-value=7.3e-15  Score=97.97  Aligned_cols=64  Identities=16%  Similarity=0.111  Sum_probs=57.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEE--------EEecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILD--------VYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~--------v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ..+.++|||+|||+.+++++|+++|++||.|.+        |.|++|        ++||+|.+.++    |++|+..||+
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g   79 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPS----AKAAIDWFDG   79 (116)
Confidence            345789999999999999999999999999999        888866        68999999999    9999999998


Q ss_pred             hCCC
Q 030822          162 AGCN  165 (171)
Q Consensus       162 ~~~~  165 (171)
                      ..+.
T Consensus        80 ~~~~   83 (116)
T 2lcw_A           80 KEFS   83 (116)
Confidence            7653

>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=99.44  E-value=1.4e-13  Score=96.43  Aligned_cols=60  Identities=22%  Similarity=0.293  Sum_probs=55.6

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++|||+|||+++++++|+++|++||+|.++.|+++        ++||+|.+.++    |.+|+..||+..+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~----A~~a~~~l~~~~~   69 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKD----AEKAINTLNGLRL   69 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHH----HHHHHHHcCCCcc
Confidence            589999999999999999999999999999999876        47999999999    9999999998654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.44  E-value=1.9e-13  Score=88.80  Aligned_cols=63  Identities=21%  Similarity=0.192  Sum_probs=51.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec-----CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|+.|+.|.-+.-.     +.++||+|.+.++    |++||..||+..+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~   79 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEED----AKAAKEAMEDGEI   79 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCSEEEEEECSSSCSEEEEEEEECSSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCeEEEEEecCCCCCcCcEEEEEECCHHH----HHHHHHHhCCCeE
Confidence            4568999999999999999999999998654333222     2378999999999    9999999998654

>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=99.43  E-value=1.3e-13  Score=96.78  Aligned_cols=61  Identities=18%  Similarity=0.256  Sum_probs=56.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +.++|||+|||+++++++|+++|++||+|.+|.|+++        ++||+|.+.++    |.+|+..||+..+
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~a~~~l~~~~~   70 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMD----SQRAIKVLNGITV   70 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHH----HHHHHHhcCCCEe
Confidence            3689999999999999999999999999999999865        68999999999    9999999998654

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A

Probab=99.43  E-value=2.7e-13  Score=100.50  Aligned_cols=64  Identities=13%  Similarity=0.083  Sum_probs=58.5

Q ss_pred             CCCCceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+..++|||+|||+ ++++++|+++|++||.|.+|+|++|   ++||+|.+.++    |++|+..||+..+.
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~g~afV~F~~~~~----A~~Ai~~l~g~~~~   98 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQ----AQLAMSHLNGHKLH   98 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHH----HHHHHHHHTTCBCS
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCCCEEEEEECCHHH----HHHHHHHhCCCeEC
Confidence            45679999999999 9999999999999999999999955   68999999999    99999999987653

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.42  E-value=1.4e-13  Score=102.56  Aligned_cols=63  Identities=16%  Similarity=0.202  Sum_probs=58.0

Q ss_pred             CCCCceEEEeCCCCCC---------CHHHHHHHhhcccceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEA---------TAEDLRRYFSRFGRILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~---------te~~L~~~F~~fG~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+         ++++|+++|++||+|++|+|+.  .++||+|.++++    |+.|+..||+..+
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 RKKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVESKNCGFVKFKYQAN----AEFAKEAMSNQTL  204 (240)
T ss_dssp             CCCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEGGGTEEEEEESSHHH----HHHHHHHHTTCCC
T ss_pred             ccCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEECCCCEEEEEeCCHHH----HHHHHHHhCCCEE
Confidence            4568999999999998         7999999999999999999985  578999999999    9999999999876

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.41  E-value=8.4e-14  Score=89.57  Aligned_cols=63  Identities=16%  Similarity=0.103  Sum_probs=54.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEe---cCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV---PKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i---~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||.|..+..   .+.++||+|.+.++    |.+|+..||+..+
T Consensus        13 ~~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~   78 (96)
T 1fjc_A           13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD----AEKNLEEKQGAEI   78 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHH----HHHHHHHTTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEeCCCCCcceEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            445799999999999999999999999999987722   13478999999999    9999999998654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.41  E-value=1.7e-13  Score=92.09  Aligned_cols=63  Identities=11%  Similarity=0.107  Sum_probs=53.0

Q ss_pred             ceEEEeCC----CCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecC----CcccHHHHHHHHH--HHhHhC
Q 030822          102 KKIFVGRL----PQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCG----RSCSRSCFSKVSR--NLWTAG  163 (171)
Q Consensus       102 ~~lfV~nL----p~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~----~~~~~~~a~~Ai~--~l~~~~  163 (171)
                      .+|||+||    |+.+++++|+++|++||+|.+|.++.|        ++||+|.+    ++++..+|.+|+.  .||+..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    999999999999999999999999977        57899997    6665666888888  666654


Q ss_pred             C
Q 030822          164 C  164 (171)
Q Consensus       164 ~  164 (171)
                      +
T Consensus        83 I   83 (136)
T 2j8a_A           83 I   83 (136)
T ss_dssp             E
T ss_pred             e
Confidence            3

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.41  E-value=8.1e-14  Score=93.97  Aligned_cols=60  Identities=17%  Similarity=0.115  Sum_probs=52.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccce----EEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRI----LDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v----~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ....+|||+|||+++|+++|+++|++||.|    .+|.|++|       ++||+|.+.++    |++||.. |+..
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~----A~~Al~~-~~~~   91 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEY----AQNALRK-HKDL   91 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHH----HHHHHTT-TTEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHH----HHHHHHh-CCCe
Confidence            356899999999999999999999999975    68888864       67999999999    9999986 6643

>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=99.41  E-value=3.5e-14  Score=98.02  Aligned_cols=64  Identities=17%  Similarity=0.129  Sum_probs=54.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEE--------Eec-----CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV--------YVP-----KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v--------~i~-----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+.++|||+|||+.+|+++|+++|++||.|..|        .+.     +.++||.|.+.++    |.+|+..||+..+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~----A~~Ai~~lng~~~  117 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA----AAKALKEANGYVL  117 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHH----HHHHHHHHTTBEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHH----HHHHHHHhCCCEe
Confidence            3457899999999999999999999999998764        332     3478999999999    9999999998765


Q ss_pred             C
Q 030822          165 N  165 (171)
Q Consensus       165 ~  165 (171)
                      .
T Consensus       118 ~  118 (143)
T 3egn_A          118 F  118 (143)
T ss_dssp             T
T ss_pred             C
Confidence            3

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.40  E-value=2.2e-13  Score=95.27  Aligned_cols=59  Identities=19%  Similarity=0.267  Sum_probs=54.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ++|||+|||+++|+++|+++|++||+|.+|.|+++       ++||+|.+.++    |.+|+..||+..+
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~~~~~   66 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHD----ANIALQTLNGKQI   66 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHH----HHHHHHHcCCCcc
Confidence            58999999999999999999999999999999865       48999999999    9999999998754

>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=99.40  E-value=2.4e-13  Score=109.81  Aligned_cols=63  Identities=19%  Similarity=0.234  Sum_probs=57.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+|+++|+++|++||.|+.|.|+.|        ++||+|.+.++    |..||..||+..++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~----A~~Ai~~lng~~i~  170 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERD----MHSAYKHADGKKID  170 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHH----HHHHHHHcCCCEEC
Confidence            34689999999999999999999999999999999865        68999999999    99999999987654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.39  E-value=3.6e-13  Score=94.52  Aligned_cols=55  Identities=29%  Similarity=0.550  Sum_probs=51.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|++|        ++||+|.+.++    |++|+..
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----a~~A~~~   64 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSS----VDEVVKT   64 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHH----HHHHHHS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHH----HHHHHhc
Confidence            3689999999999999999999999999999999976        68999999999    9999987

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.39  E-value=6.6e-13  Score=96.89  Aligned_cols=62  Identities=18%  Similarity=0.251  Sum_probs=56.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++|+++|+++|++||.|.+|.|++|        ++||+|.+.++    |.+|+..||+..+.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~A~~~l~~~~~~   96 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEA----AQLALEQMNSVMLG   96 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHH----HHHHHHHHSSCCCC
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHH----HHHHHHHccCCeeC
Confidence            4689999999999999999999999999999999865        58999999999    99999999987654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.38  E-value=5.1e-13  Score=86.07  Aligned_cols=46  Identities=28%  Similarity=0.463  Sum_probs=41.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--C----CccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--T----HELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~----~~i~gr~i~v~~a~~   46 (171)
                      |++|+.||+|||||||+|.+.++|++||+.  +    +.|+||+|.|.+|..
T Consensus        43 i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           43 LIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKS   94 (95)
T ss_dssp             CCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEEEEECCC
T ss_pred             EEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEEEEEccC
Confidence            589999999999999999999999999984  3    369999999999853

>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=99.38  E-value=1.3e-13  Score=87.70  Aligned_cols=59  Identities=29%  Similarity=0.470  Sum_probs=52.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++|||+|||+++++++|+++|++||+|.+|.|++|        ++||+|.+.+     |++|+..||+..++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-----a~~a~~~l~g~~~~   68 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-----VSEAIAKLDNTDFM   68 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-----HHHHHHTSCSSCCS
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-----HHHHHHHhCCCEEC
Confidence            68999999999999999999999999999999865        6789998753     68889999887654

>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=99.38  E-value=3.8e-13  Score=96.75  Aligned_cols=57  Identities=26%  Similarity=0.395  Sum_probs=52.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|++|        ++||+|.+.++    |.+|+..
T Consensus        10 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~----A~~A~~~   74 (196)
T 1l3k_A           10 PEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE----VDAAMNA   74 (196)
T ss_dssp             CGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHT
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHH----HHHHHhc
Confidence            446799999999999999999999999999999999875        68999999999    9999976

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.37  E-value=7e-13  Score=95.80  Aligned_cols=61  Identities=13%  Similarity=0.120  Sum_probs=56.6

Q ss_pred             CceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +++|||+|||+ .+++++|+++|++||.|.+|.|+++   ++||+|.+.++    |.+|+..||+..+.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~afV~f~~~~~----a~~A~~~l~~~~~~   67 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQ----AQLAMSHLNGHKLH   67 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCSSCCEEECTTTHH----HHHHHHHHTTCCCS
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCCCEEEEEECCHHH----HHHHHHHhCCCeec
Confidence            58999999999 9999999999999999999999965   68999999999    99999999987653

>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=99.37  E-value=3.9e-13  Score=87.24  Aligned_cols=46  Identities=24%  Similarity=0.420  Sum_probs=42.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.||++||||||+|.+.++|++|++  ++..|+|++|.|.+|.|
T Consensus        51 i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~AkP   98 (99)
T 4fxv_A           51 LIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYARP   98 (99)
T ss_dssp             EEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCB
T ss_pred             eeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46899999999999999999999999998  48999999999999875

>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=99.37  E-value=3.7e-13  Score=105.22  Aligned_cols=63  Identities=13%  Similarity=0.156  Sum_probs=57.3

Q ss_pred             CCCCceEEEeC--CCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGR--LPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~n--Lp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++.+|||+|  |++.+||++|+++|++||+|.+|.|+  +.++||+|.+.++    |++||+.||+..+
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~~kgfaFV~f~~~~~----A~~Ai~~lnG~~~   81 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEE----SKRAYVTLNGKEV   81 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCTTCSEEEEEESSHHH----HHHHHHHTTTCEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeCCCCEEEEEECCHHH----HHHHHHHhCCCcc
Confidence            45678999999  57899999999999999999999986  5578999999999    9999999999876

>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=99.34  E-value=1.4e-12  Score=98.47  Aligned_cols=63  Identities=29%  Similarity=0.468  Sum_probs=57.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|++||.|.+|.|.++  ++||.|.+.++    |..|+..||+..+
T Consensus        19 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~kg~afV~f~~~~~----A~~A~~~l~g~~i   83 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTL----AEIAKAELDGTIL   83 (261)
T ss_dssp             SCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTTTEEEEECSSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCCcEEEEEECCHHH----HHHHHHHcCCcEE
Confidence            455789999999999999999999999999999999965  67899999999    9999999998754

>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=99.34  E-value=1.6e-12  Score=98.80  Aligned_cols=63  Identities=24%  Similarity=0.393  Sum_probs=57.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHH----HHhhcccceEEEEecC-----cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLR----RYFSRFGRILDVYVPK-----RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~----~~F~~fG~v~~v~i~~-----d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+.++|||+|||+.+++++|+    ++|++||.|.+|.|++     .++||+|.+.++    |.+|+..||+..+
T Consensus         6 ~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f~~~~~----a~~A~~~l~g~~~   77 (282)
T 3pgw_A            6 TRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSS----ATNALRSMQGFPF   77 (282)
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEECCHHH----HHHHHHHhcCCee
Confidence            4568999999999999999977    9999999999999986     588999999999    9999999998654

>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=99.33  E-value=2.1e-12  Score=84.05  Aligned_cols=51  Identities=20%  Similarity=0.352  Sum_probs=46.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDF   51 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~~~   51 (171)
                      |++|+.||++||||||+|.+.++|++||++++.|+|+.|.|.++.++.+..
T Consensus        47 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~l~v~~a~~~~~~~   97 (103)
T 2cqg_A           47 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQD   97 (103)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCCCC
T ss_pred             EEecCCCCCccceEEEEECCHHHHHHHHHcCCeeCCeEEEEEecCCCCcCC
Confidence            467889999999999999999999999999999999999999998875543

>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=99.31  E-value=5.8e-13  Score=84.73  Aligned_cols=48  Identities=23%  Similarity=0.339  Sum_probs=40.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..++||.|.|.++.++.
T Consensus        35 i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~~~~   84 (90)
T 3p5t_L           35 FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSNKLE   84 (90)
T ss_dssp             EEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC----
T ss_pred             EEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECCCCc
Confidence            46789999999999999999999999998  4789999999999987653

>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=99.29  E-value=2.5e-12  Score=93.10  Aligned_cols=57  Identities=14%  Similarity=0.332  Sum_probs=52.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHh
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ..++|||+|||+++++++|+++|++||+|.+|+|+++       ++||+|.+.++    |++|+..++
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~----A~~A~~~~~  171 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIES----AKKFVETPG  171 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHH----HHHHHHCTT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHH----HHHHHHhCC
Confidence            3589999999999999999999999999999999853       78999999999    999998764

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.28  E-value=2.9e-12  Score=84.68  Aligned_cols=47  Identities=11%  Similarity=0.188  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||+|||||||+|++.++|++||+  ++..|+|+.|.|.++...
T Consensus        38 i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~~~   86 (110)
T 3s8s_A           38 ILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDIKG   86 (110)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSTT
T ss_pred             EEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            57899999999999999999999999999  488999999999998644

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.28  E-value=1.4e-12  Score=84.70  Aligned_cols=47  Identities=13%  Similarity=0.261  Sum_probs=43.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCC-eEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG-STVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~g-r~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..|+| +.|.|.++.++
T Consensus        44 i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l~V~~a~~~   93 (100)
T 3ns6_A           44 FPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDV   93 (100)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEESHHH
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEEEEEECchh
Confidence            68899999999999999999999999998  4889999 99999998764

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.26  E-value=9.2e-12  Score=82.01  Aligned_cols=49  Identities=31%  Similarity=0.549  Sum_probs=44.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+. ++.++|+.|.|.++.++..
T Consensus        57 i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~a~~~~~  106 (109)
T 2rs2_A           57 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVAFPRRA  106 (109)
T ss_dssp             ECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEECCCCCC
T ss_pred             EEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEccCCCC
Confidence            478999999999999999999999999996 6899999999999987644

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.26  E-value=1.3e-11  Score=79.68  Aligned_cols=49  Identities=37%  Similarity=0.613  Sum_probs=44.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+ +++.|+|+.|.|.++.++..
T Consensus        42 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a~~~~~   91 (99)
T 2dgs_A           42 MIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRAEPRDS   91 (99)
T ss_dssp             ECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEECCCCCC
T ss_pred             EEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEECCCCcc
Confidence            47889999999999999999999999998 57899999999999987644

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.26  E-value=8.1e-12  Score=83.46  Aligned_cols=61  Identities=15%  Similarity=0.056  Sum_probs=55.3

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecCc--ceeEEecC-CcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCG-RSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~-~~~~~~~a~~Ai~~l~~~  162 (171)
                      -++++-|||+||++. +++++|+++|++||+|.+|.+++|  .+||.|.+ ..+    |+.|++.||.-
T Consensus        15 ~~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~tgfVrf~~~~~~----A~~av~~ln~~   79 (121)
T 1owx_A           15 EKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKE----ALGKAKDANNG   79 (121)
T ss_dssp             CCCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHH----HHHHHHHTTTS
T ss_pred             ccCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCEEEEEECCChHH----HHHHHHHhhcC
Confidence            457899999999999 999999999999999999999987  57899999 688    99999999643

>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=99.25  E-value=7e-12  Score=78.19  Aligned_cols=48  Identities=29%  Similarity=0.495  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.+++
T Consensus        33 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   82 (83)
T 3md1_A           33 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKLE   82 (83)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             EEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcCC
Confidence            46788899999999999999999999999  4889999999999998763

>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=99.24  E-value=3e-11  Score=77.88  Aligned_cols=49  Identities=24%  Similarity=0.358  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        40 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (99)
T 1whw_A           40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             CCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             EEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCcc
Confidence            57888899999999999999999999997  47899999999999987644

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.24  E-value=1.9e-11  Score=78.29  Aligned_cols=49  Identities=24%  Similarity=0.388  Sum_probs=44.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|+++|||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        38 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   88 (96)
T 1x5t_A           38 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   88 (96)
T ss_dssp             ECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             EEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEecccCC
Confidence            47888999999999999999999999999  47899999999999987643

>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=99.23  E-value=2.7e-11  Score=79.70  Aligned_cols=51  Identities=16%  Similarity=0.349  Sum_probs=45.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--c------CCccCCeEEEEeecCCCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--D------THELGGSTVVVDRATPKEDDF   51 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~------~~~i~gr~i~v~~a~~~~~~~   51 (171)
                      |++|+.||++||||||+|.+.++|++||+  +      ++.|+|+.|.|.++.++....
T Consensus        47 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~l~v~~a~~~~~~~  105 (111)
T 1x4h_A           47 VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAA  105 (111)
T ss_dssp             CCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCCCC
T ss_pred             EEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEEEEEEECCCCccCC
Confidence            57899999999999999999999999998  4      789999999999998775443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.23  E-value=9e-12  Score=76.28  Aligned_cols=44  Identities=36%  Similarity=0.594  Sum_probs=40.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a   44 (171)
                      |++|+.+|++||||||+|.+.++|++|++ +++.++|+.|.|++|
T Consensus        31 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A           31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            57888899999999999999999999998 478999999999875

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.23  E-value=1.3e-11  Score=80.20  Aligned_cols=49  Identities=22%  Similarity=0.479  Sum_probs=43.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||. ++..|+|+.|.|.++.++..
T Consensus        46 i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2dng_A           46 LVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIAEGRKQ   95 (103)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEECCCCCC
T ss_pred             EeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEecCCCC
Confidence            46788999999999999999999999995 37899999999999987643

>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=99.23  E-value=1.4e-11  Score=81.48  Aligned_cols=63  Identities=16%  Similarity=0.097  Sum_probs=53.4

Q ss_pred             CCCCceEEEeCCCCCCC-----------HHHHHHHhhcccceEEEEec----CcceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEAT-----------AEDLRRYFSRFGRILDVYVP----KRFWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~t-----------e~~L~~~F~~fG~v~~v~i~----~d~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ..++++|+|.||....+           +++|+++|++||+|.+|.|.    +.++||+|.+.++    |++|+..||+.
T Consensus        12 ~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i~~~~~~G~afV~f~~~~~----A~~Ai~~lng~   87 (112)
T 2dit_A           12 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEE----ADYCIQTLDGR   87 (112)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHH----HHHHHHHSTTC
T ss_pred             CCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEEecCCCCEEEEEEECCHHH----HHHHHHHcCCC
Confidence            45689999999954432           58999999999999999775    4588999999999    99999999986


Q ss_pred             CC
Q 030822          163 GC  164 (171)
Q Consensus       163 ~~  164 (171)
                      .+
T Consensus        88 ~~   89 (112)
T 2dit_A           88 WF   89 (112)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.22  E-value=1.3e-11  Score=79.98  Aligned_cols=49  Identities=27%  Similarity=0.559  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++.+
T Consensus        44 ~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2fc8_A           44 IVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAKPKGE   94 (102)
T ss_dssp             EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCCCS
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEecCCCC
Confidence            46788999999999999999999999998  48899999999999987644

>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=99.21  E-value=2.6e-11  Score=77.81  Aligned_cols=48  Identities=19%  Similarity=0.298  Sum_probs=43.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.++.
T Consensus        34 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   83 (96)
T 2x1f_A           34 MMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSNSD   83 (96)
T ss_dssp             CCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCSS
T ss_pred             EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCCCC
Confidence            57888999999999999999999999998  4889999999999998763

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.21  E-value=2.4e-11  Score=79.53  Aligned_cols=62  Identities=10%  Similarity=0.034  Sum_probs=53.1

Q ss_pred             CCCceEEEeCCCC-----CCCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQ-----EATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~-----~~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++++|+|+||..     ..++++|+++|++||+|.+|.|++|         ++||+|.+.++    |.+|+..||+..+
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~----A~~Ai~~lnG~~~   81 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVES----AIKAVVDLNGRYF   81 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHH----HHHHHHHHCCCEE
Confidence            4578999999963     2378999999999999999999864         56899999999    9999999998654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.21  E-value=3.2e-11  Score=78.15  Aligned_cols=49  Identities=31%  Similarity=0.497  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|+++|||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        44 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~   94 (102)
T 2cqb_A           44 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPMRI   94 (102)
T ss_dssp             CCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCCCC
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeCCCCCC
Confidence            57899999999999999999999999998  48899999999999987643

>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=99.21  E-value=9.2e-12  Score=87.65  Aligned_cols=60  Identities=18%  Similarity=0.314  Sum_probs=53.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcc----c-------ceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRF----G-------RILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~f----G-------~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||+++|+++|+++|++|    |       .|.++.+.++  ++||+|.+.++    |.+|+ .||+..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~g~afV~f~~~~~----A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE----TTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTTTEEEEEESSHHH----HHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCCCEEEEEeCCHHH----HHHHH-HhCCcEe
Confidence            36899999999999999999999999    7       8899988754  78899999999    99999 8987654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.21  E-value=3.9e-11  Score=79.21  Aligned_cols=49  Identities=16%  Similarity=0.263  Sum_probs=44.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        55 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  105 (113)
T 2cpe_A           55 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP  105 (113)
T ss_dssp             CCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCCC
T ss_pred             EEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCCCEEEEEECCCCCC
Confidence            57888999999999999999999999999  58899999999999987643

>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=99.20  E-value=1.2e-11  Score=77.84  Aligned_cols=47  Identities=30%  Similarity=0.451  Sum_probs=41.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.++
T Consensus        38 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~k   86 (87)
T 3bs9_A           38 VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK   86 (87)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC--
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecCCC
Confidence            46788899999999999999999999999  488999999999998764

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.20  E-value=1.7e-11  Score=79.35  Aligned_cols=39  Identities=23%  Similarity=0.351  Sum_probs=35.8

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      ++|||||+|.+.++|++|++.  +..++|+.|.|.++.++.
T Consensus        36 ~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   76 (101)
T 2hvz_A           36 PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMP   76 (101)
T ss_dssp             SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCC
T ss_pred             CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCC
Confidence            899999999999999999994  788999999999998764

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.20  E-value=2.4e-11  Score=80.67  Aligned_cols=50  Identities=36%  Similarity=0.626  Sum_probs=45.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDD   50 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~   50 (171)
                      |++|+.||++||||||+|.+.++|++||+. ++.|+|+.|.|.++.++...
T Consensus        59 i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~~  109 (116)
T 1x4b_A           59 VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREES  109 (116)
T ss_dssp             EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCCC
T ss_pred             EEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCCCccC
Confidence            468889999999999999999999999995 78999999999999887554

>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=99.20  E-value=3.8e-11  Score=78.22  Aligned_cols=49  Identities=29%  Similarity=0.527  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|++||||||+|.+.++|++||+.  ++.|+|+.|.|.++.++..
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (105)
T 1x5u_A           47 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   97 (105)
T ss_dssp             CCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             EEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCCc
Confidence            578888999999999999999999999994  7899999999999987644

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.20  E-value=1.5e-11  Score=80.03  Aligned_cols=50  Identities=24%  Similarity=0.411  Sum_probs=43.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCc-cCCeEEEEeecCCCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THE-LGGSTVVVDRATPKEDDF   51 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~-i~gr~i~v~~a~~~~~~~   51 (171)
                      |++|+ +|++||||||+|.+.++|++||+.  +.. |+|+.|.|.++.++....
T Consensus        42 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           42 VVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKASRV   94 (104)
T ss_dssp             EEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCCBCCCCCSCC
T ss_pred             EEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEEEccCCCcCC
Confidence            46788 999999999999999999999994  677 999999999998765443

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.19  E-value=3.4e-11  Score=76.99  Aligned_cols=49  Identities=29%  Similarity=0.517  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||+++|||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        37 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   87 (95)
T 2dnz_A           37 LMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVTERLD   87 (95)
T ss_dssp             EECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESSCCCC
T ss_pred             EeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcccccC
Confidence            46788899999999999999999999999  48899999999999987643

>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=99.19  E-value=1.3e-11  Score=75.54  Aligned_cols=44  Identities=32%  Similarity=0.561  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      |++|+.||++||||||+|.+.++|++|++. ++.++|+.|.|++|
T Consensus        31 i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A           31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             EEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            578999999999999999999999999995 78999999999865

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.19  E-value=5.8e-11  Score=78.63  Aligned_cols=50  Identities=28%  Similarity=0.414  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (171)
                      |++|+.+|++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++...
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~~   98 (115)
T 2dgo_A           47 VVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPA   98 (115)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCCC
T ss_pred             EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccCCCCC
Confidence            46788899999999999999999999998  478999999999999876443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=8.7e-11  Score=77.94  Aligned_cols=49  Identities=24%  Similarity=0.331  Sum_probs=43.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+. ...|+|+.|.|.++.++..
T Consensus        49 i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~~~~   98 (116)
T 2cqd_A           49 VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGAK   98 (116)
T ss_dssp             ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTTCC
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHhCCCcCCCEEEEEEEcccCCC
Confidence            578899999999999999999999999995 3489999999999976533

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.18  E-value=1.3e-11  Score=79.87  Aligned_cols=48  Identities=17%  Similarity=0.385  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~   48 (171)
                      +++|+.+|++||||||+|.+.++|++||+ ++..|+|+.|.|.++.++.
T Consensus        48 ~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~   96 (101)
T 1fj7_A           48 AVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGRD   96 (101)
T ss_dssp             CCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCSCCC
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcCCCC
Confidence            57788899999999999999999999998 4688999999999998764

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.18  E-value=1e-11  Score=86.96  Aligned_cols=47  Identities=26%  Similarity=0.333  Sum_probs=43.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..|+|+.|.|.++.++
T Consensus        89 i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~a~~~  137 (156)
T 3n9u_C           89 FAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRPATRQ  137 (156)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEECCHH
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEEcCCC
Confidence            468999999999999999999999999995  78999999999998754

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.18  E-value=3.3e-11  Score=78.29  Aligned_cols=49  Identities=18%  Similarity=0.382  Sum_probs=44.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|+++|||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   97 (103)
T 2cq0_A           47 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPSTN   97 (103)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCCC
T ss_pred             EeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEECCCCCC
Confidence            46788899999999999999999999999  47899999999999987643

>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=99.18  E-value=2.6e-11  Score=78.52  Aligned_cols=48  Identities=23%  Similarity=0.514  Sum_probs=42.6

Q ss_pred             CCCCC-CCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQ-GSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~-~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+ .+|++||||||+|.+.++|++||. ++..|+|+.|.|.++.++.
T Consensus        50 i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~~a~~~~   99 (100)
T 2j76_E           50 LPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVDVADQAQ   99 (100)
T ss_dssp             CSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCEECCCSC
T ss_pred             EEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEEeccCCC
Confidence            57787 699999999999999999999995 3789999999999987653

>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=99.18  E-value=1.8e-11  Score=77.09  Aligned_cols=44  Identities=34%  Similarity=0.578  Sum_probs=40.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      |++|+.||+++|||||+|.+.++|++||+. ++.|+|+.|.|++|
T Consensus        43 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A           43 IKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKKA   87 (87)
T ss_dssp             EEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEEC
T ss_pred             EeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            467889999999999999999999999985 78899999999875

>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=99.18  E-value=6.1e-11  Score=77.17  Aligned_cols=50  Identities=24%  Similarity=0.533  Sum_probs=44.2

Q ss_pred             CCCCCCC-CCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCCC
Q 030822            1 MPKDQGS-KAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKEDD   50 (171)
Q Consensus         1 i~~D~~t-g~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~~   50 (171)
                      |++|+.| |++||||||+|.+.++|++||. ++..|+|+.|.|.++.++...
T Consensus        46 i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~~~~   97 (104)
T 1wi8_A           46 LPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQDK   97 (104)
T ss_dssp             CCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCCC
T ss_pred             EecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEccCCCCC
Confidence            5788888 9999999999999999999995 378999999999999876443

>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=99.18  E-value=1e-10  Score=76.68  Aligned_cols=47  Identities=23%  Similarity=0.365  Sum_probs=42.7

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      +|+.||++||||||+|.+.++|++|++.    +..++|+.|.|.++.++..
T Consensus        44 ~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~V~~a~~~~~   94 (109)
T 2dis_A           44 SAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   94 (109)
T ss_dssp             SSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             cCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEEEEEcCCCCC
Confidence            7899999999999999999999999994    3789999999999987654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.18  E-value=2e-11  Score=87.78  Aligned_cols=60  Identities=18%  Similarity=0.341  Sum_probs=52.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcc----c-------ceEEEEecC--cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRF----G-------RILDVYVPK--RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~f----G-------~v~~v~i~~--d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||+++++++|+++|++|    |       .|.++.+.+  .++||+|.+.++    |++|+ .||+..+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~g~afV~F~~~~~----A~~Al-~l~g~~~   75 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE----TTQAM-AFDGIIF   75 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTTTEEEEEESCSHH----HHHHG-GGTTEEE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCCCEEEEEeCCHHH----HHHHH-HhcCCEE
Confidence            36899999999999999999999999    5       788888874  578999999999    99999 8988654

>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=99.17  E-value=1.3e-11  Score=80.42  Aligned_cols=47  Identities=13%  Similarity=0.099  Sum_probs=41.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+ +|++||||||+|++.++|++||+ +++.|+||.|.|.++.+..
T Consensus        46 i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~~~~   93 (102)
T 1wez_A           46 IEIGP-DGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             EEESS-SSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCC
T ss_pred             EEECC-CCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCCCC
Confidence            46787 99999999999999999999997 4789999999999887553

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.17  E-value=2.6e-11  Score=82.31  Aligned_cols=48  Identities=23%  Similarity=0.396  Sum_probs=43.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CC----ccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--TH----ELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~----~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+. +|.+||..  +.    .|+||.|.|+++.++..
T Consensus        57 i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           57 VIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKTINVEFAKGSKR  110 (131)
T ss_dssp             CCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCCCCCEECCCSCC
T ss_pred             EEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEEEEEEECCCCCC
Confidence            689999999999999999999 99999994  67    99999999999987543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=4.2e-11  Score=77.76  Aligned_cols=47  Identities=28%  Similarity=0.474  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++
T Consensus        45 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~   93 (103)
T 2dnm_A           45 IPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYG   93 (103)
T ss_dssp             CCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEECSSC
T ss_pred             EEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEECCcC
Confidence            57899999999999999999999999999  488999999999999765

>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=99.17  E-value=3.5e-11  Score=79.76  Aligned_cols=49  Identities=16%  Similarity=0.325  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        57 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~  107 (115)
T 2cpz_A           57 VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  107 (115)
T ss_dssp             EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             EEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCc
Confidence            46788899999999999999999999998  48899999999999987644

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.16  E-value=4.3e-11  Score=77.53  Aligned_cols=49  Identities=31%  Similarity=0.607  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        44 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   94 (102)
T 1x5s_A           44 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   94 (102)
T ss_dssp             ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             EEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            46888999999999999999999999998  47899999999999987644

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=1.9e-11  Score=79.67  Aligned_cols=49  Identities=27%  Similarity=0.552  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|++||||||+|.+.++|++||+ +++.|+|+.|.|.++.++..
T Consensus        48 i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~a~~~~~   97 (105)
T 2dh8_A           48 IMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKPCTPRGM   97 (105)
T ss_dssp             EEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCCSCCSSC
T ss_pred             EeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEccCCCC
Confidence            46788999999999999999999999999 58899999999999987654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.16  E-value=3.1e-11  Score=79.56  Aligned_cols=46  Identities=22%  Similarity=0.241  Sum_probs=40.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+. |++||||||+|.+.++|++||. +++.|+||.|.|..+.++
T Consensus        47 i~~d~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~~   93 (109)
T 2dnn_A           47 LLKDHV-GRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER   93 (109)
T ss_dssp             ECCCTT-CCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCHH
T ss_pred             EEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCcc
Confidence            478875 9999999999999999999997 478999999999887543

>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=99.16  E-value=5e-11  Score=78.31  Aligned_cols=48  Identities=17%  Similarity=0.248  Sum_probs=43.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.+|+++|||||+|.+.++|++||.  ++..|+|+.|.|.++.++.
T Consensus        58 i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  107 (110)
T 1oo0_B           58 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKG  107 (110)
T ss_dssp             CCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEESS
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEcccCC
Confidence            57889999999999999999999999999  4889999999999997653

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.15  E-value=2.4e-11  Score=79.28  Aligned_cols=47  Identities=15%  Similarity=0.298  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||+++|||||+|.+.++|++||+  +++.|+|+.|.|.++.++
T Consensus        55 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~  103 (106)
T 1p27_B           55 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVR  103 (106)
T ss_dssp             EEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEESEES
T ss_pred             EEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEeecCC
Confidence            46788999999999999999999999998  488999999999998765

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.15  E-value=2.5e-11  Score=78.35  Aligned_cols=45  Identities=22%  Similarity=0.342  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+.||++||||||+|.+.++|++|++  ++..++|+.|.|.+|.
T Consensus        53 i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           53 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFAT   99 (99)
T ss_dssp             EEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             EEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEecC
Confidence            46788999999999999999999999998  4889999999999873

>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=99.14  E-value=2.1e-11  Score=80.82  Aligned_cols=46  Identities=17%  Similarity=0.212  Sum_probs=42.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+ ||++||||||+|.+.++|++||+. ++.|+||.|.|.++.++
T Consensus        48 i~~d~-~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a~~~   94 (114)
T 2cpy_A           48 VLVDN-NGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTLE   94 (114)
T ss_dssp             ECCCT-TSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECHH
T ss_pred             EEECC-CCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEECCHH
Confidence            47888 999999999999999999999985 78999999999998764

>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=99.14  E-value=8.6e-11  Score=76.60  Aligned_cols=47  Identities=21%  Similarity=0.371  Sum_probs=42.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~   48 (171)
                      |++| .+|++||||||+|.++++|++||+. +..|+||.|.|.++.+++
T Consensus        48 i~~~-~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~~~~~   95 (104)
T 1wg5_A           48 LPVD-FQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAE   95 (104)
T ss_dssp             CCBC-SSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTT
T ss_pred             EEEC-CCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEECCHHH
Confidence            5677 7999999999999999999999995 889999999999887653

>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=99.14  E-value=2.2e-11  Score=80.04  Aligned_cols=48  Identities=25%  Similarity=0.487  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.+|++||||||+|.+.++|++|++  ++..|+|+.|.|.++.++.
T Consensus        58 i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~k~  107 (108)
T 2jrs_A           58 LMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERT  107 (108)
T ss_dssp             EEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECSCSSC
T ss_pred             EEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcccCC
Confidence            46788899999999999999999999998  5889999999999998763

>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=99.14  E-value=4.3e-11  Score=74.89  Aligned_cols=44  Identities=32%  Similarity=0.532  Sum_probs=40.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a   44 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++
T Consensus        39 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A           39 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             EEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            56888999999999999999999999997  488999999999986

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.14  E-value=4.3e-11  Score=75.98  Aligned_cols=46  Identities=17%  Similarity=0.373  Sum_probs=41.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++| .+|+++|||||+|.+.++|++||+ ++..|+|+.|.|.++.++
T Consensus        41 i~~~-~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~~~   87 (91)
T 2dgw_A           41 IVRN-AHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKSG   87 (91)
T ss_dssp             EEEC-TTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEESSC
T ss_pred             EEEC-CCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECCcC
Confidence            4677 799999999999999999999999 467999999999999766

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.13  E-value=6.9e-11  Score=80.85  Aligned_cols=49  Identities=20%  Similarity=0.367  Sum_probs=43.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..|+|+.|.|.++.++..
T Consensus        74 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  124 (139)
T 1u6f_A           74 IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             EEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            467888999999999999999999999994  7899999999999987644

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=5.7e-11  Score=76.72  Aligned_cols=47  Identities=6%  Similarity=0.282  Sum_probs=42.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+ +|++||||||+|.+.++|++||+  ++..++|+.|.|.++.++.
T Consensus        49 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   97 (100)
T 2do4_A           49 LVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAISNSGP   97 (100)
T ss_dssp             EEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCCCS
T ss_pred             EEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            35677 99999999999999999999998  4789999999999998764

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.13  E-value=7.1e-11  Score=75.33  Aligned_cols=45  Identities=27%  Similarity=0.458  Sum_probs=41.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..|+|+.|.|.++.
T Consensus        48 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~ak   94 (94)
T 2e5h_A           48 IMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIAI   94 (94)
T ss_dssp             ECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             EEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEecC
Confidence            46888999999999999999999999998  4789999999999873

>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=99.13  E-value=1.1e-10  Score=77.60  Aligned_cols=47  Identities=28%  Similarity=0.491  Sum_probs=42.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+ +|+++|||||+|.+.++|++||+  ++..|+|+.|.|.++.++.
T Consensus        39 i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~   87 (116)
T 2fy1_A           39 LIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPS   87 (116)
T ss_dssp             EECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEECCCSS
T ss_pred             EEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCCC
Confidence            45777 99999999999999999999998  4789999999999997654

>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=99.13  E-value=1.5e-10  Score=75.49  Aligned_cols=49  Identities=18%  Similarity=0.282  Sum_probs=43.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCcc---CCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THEL---GGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i---~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..+   .|+.|.|.++.++..
T Consensus        45 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v~~a~~~~~   98 (106)
T 2dgp_A           45 VLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESR   98 (106)
T ss_dssp             CCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEEEECCCCSC
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEEEECCcccc
Confidence            578999999999999999999999999984  6666   889999999987643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.13  E-value=1.7e-10  Score=75.32  Aligned_cols=49  Identities=29%  Similarity=0.585  Sum_probs=43.9

Q ss_pred             CCCC-CCCCCccceEEEEECCHHHHHHHHh---cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKD-QGSKAHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D-~~tg~srGfgFV~F~~~~~a~~Al~---~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++| +.+|++||||||+|.+.++|++||+   ++..|+|+.|.|.++.++..
T Consensus        47 i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v~~a~~~~~   99 (107)
T 2cph_A           47 LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   99 (107)
T ss_dssp             CCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             EecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEEEeCCCCCC
Confidence            5677 7899999999999999999999998   47899999999999987644

>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=99.12  E-value=5.4e-11  Score=76.51  Aligned_cols=46  Identities=17%  Similarity=0.249  Sum_probs=41.5

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ++|+.+|++||||||+|.+.++|++||+.  +..|+|+.|.|.++..+
T Consensus        48 ~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (98)
T 2cqp_A           48 LKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGP   95 (98)
T ss_dssp             EEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEESSCS
T ss_pred             EEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEcCCC
Confidence            56788999999999999999999999984  78999999999998654

>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=99.12  E-value=1.3e-10  Score=81.18  Aligned_cols=47  Identities=30%  Similarity=0.473  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++
T Consensus       102 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  150 (158)
T 2kn4_A          102 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  150 (158)
T ss_dssp             CCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCS
T ss_pred             EeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            57899999999999999999999999998  478999999999999765

>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=99.12  E-value=5.6e-11  Score=80.60  Aligned_cols=47  Identities=30%  Similarity=0.458  Sum_probs=43.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..|+|++|.|.++.++
T Consensus        78 i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a~~~  126 (129)
T 2kxn_B           78 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITK  126 (129)
T ss_dssp             EECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCCSSS
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            46788999999999999999999999999  488999999999999765

>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=99.12  E-value=1.5e-11  Score=83.01  Aligned_cols=46  Identities=22%  Similarity=0.374  Sum_probs=41.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+. |++||||||+|.++++|++||+. +..|+||.|.|.++.++
T Consensus        75 i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a~~~  121 (126)
T 2hgm_A           75 LPVDPE-GKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE  121 (126)
T ss_dssp             CCCCSS-SSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEECHH
T ss_pred             EEECCC-CCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCHH
Confidence            578887 99999999999999999999995 78999999999987643

>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=99.12  E-value=2.3e-11  Score=85.97  Aligned_cols=63  Identities=16%  Similarity=0.181  Sum_probs=52.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec-------CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-------KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-------~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||.+..+.|.       +.++||+|.+.++    |.+|+ .||+..+.
T Consensus        10 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~----a~~A~-~l~g~~~~   79 (175)
T 1fje_B           10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED----LEKAL-ELTGLKVF   79 (175)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHH----HHHHH-HGGGEEET
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHH----HHHHH-hcCCCEeC
Confidence            4568999999999999999999999999977652221       3478999999999    99999 59987553

>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=99.11  E-value=5.9e-11  Score=74.89  Aligned_cols=47  Identities=21%  Similarity=0.321  Sum_probs=41.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.+|+++|||||+|.+.++|++|+. ++..++|+.|.|.++.++
T Consensus        38 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~~   85 (89)
T 3ucg_A           38 ILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTN   85 (89)
T ss_dssp             EEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTTT
T ss_pred             EEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccCC
Confidence            46788899999999999999999999995 378999999999998653

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.11  E-value=6.2e-11  Score=75.71  Aligned_cols=46  Identities=26%  Similarity=0.442  Sum_probs=41.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..|+|+.|.|.++.+
T Consensus        47 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~   94 (95)
T 2cqc_A           47 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGPSS   94 (95)
T ss_dssp             EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCSC
T ss_pred             EEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecCC
Confidence            46788999999999999999999999999  47899999999998753

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.10  E-value=3.3e-11  Score=73.98  Aligned_cols=44  Identities=32%  Similarity=0.549  Sum_probs=40.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      |++|+.+|++||||||+|.+.++|++|++. .+.++|++|.|++|
T Consensus        32 i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~a   76 (77)
T 1uaw_A           32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             EECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             EecCCCCCCcCceEEEEEcCHHHHHHHHHhCCCccCCEEEEEEec
Confidence            467889999999999999999999999995 47899999999986

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.10  E-value=4.9e-11  Score=77.78  Aligned_cols=45  Identities=18%  Similarity=0.282  Sum_probs=40.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~   46 (171)
                      |++|+. |++||||||+|.+.++|++||.. ++.++|+.|.|+++..
T Consensus        43 i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~~   88 (103)
T 1s79_A           43 MRRTLH-KAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD   88 (103)
T ss_dssp             EECCCT-TSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHHH
T ss_pred             EEECCC-CCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEchH
Confidence            467877 99999999999999999999994 7899999999998743

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.10  E-value=2.5e-10  Score=73.80  Aligned_cols=47  Identities=21%  Similarity=0.514  Sum_probs=41.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++| .+|++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++.
T Consensus        44 ~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (101)
T 2fc9_A           44 VPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQGPRG   92 (101)
T ss_dssp             CCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEECSSCC
T ss_pred             EEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEcCCCC
Confidence            4566 789999999999999999999999  4789999999999998763

>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=99.09  E-value=4.5e-11  Score=75.69  Aligned_cols=47  Identities=26%  Similarity=0.513  Sum_probs=40.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.||++||||||+|.+.+ |++|+..  +..++|+.|.|++|.++.
T Consensus        33 i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~~   81 (90)
T 2ki2_A           33 LIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPKK   81 (90)
T ss_dssp             ECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC----
T ss_pred             EEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            4688899999999999999999 9999994  789999999999997653

>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=99.09  E-value=2.3e-11  Score=80.57  Aligned_cols=65  Identities=12%  Similarity=0.226  Sum_probs=55.2

Q ss_pred             CCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccCCCCcc
Q 030822            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALGAPTLY   84 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~   84 (171)
                      +++++|||||+|.+.++|++|++  ++..++|+.|.|.++.++..                                   
T Consensus        43 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~-----------------------------------   87 (115)
T 3lqv_A           43 TPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYNANRA-----------------------------------   87 (115)
T ss_dssp             STTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECCHHHH-----------------------------------
T ss_pred             CCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCChh-----------------------------------
Confidence            46779999999999999999999  48899999999999865311                                   


Q ss_pred             CCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccc
Q 030822           85 DHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGR  127 (171)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~  127 (171)
                                      .     .+++...++++|+++|++||-
T Consensus        88 ----------------~-----~~~~~~~~~~~l~~~~~~~g~  109 (115)
T 3lqv_A           88 ----------------F-----QKMDTKKKEEQLKLLKEKYGI  109 (115)
T ss_dssp             ----------------T-----TTSCHHHHHHHHHHHHHHHCC
T ss_pred             ----------------h-----hhhhHhHhHHHHHHHHHHhCC
Confidence                            0     567888899999999999984

>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=99.08  E-value=7.5e-11  Score=75.35  Aligned_cols=45  Identities=16%  Similarity=0.278  Sum_probs=40.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+.+|++||||||+|.+.++|++||+  +++.|+|+.|.|.++.
T Consensus        47 ~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           47 CLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             EEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             EEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            35678899999999999999999999998  4889999999999775

>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=99.08  E-value=1.3e-10  Score=78.08  Aligned_cols=49  Identities=14%  Similarity=0.276  Sum_probs=44.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||+++|||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        54 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  104 (126)
T 3ex7_B           54 LNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP  104 (126)
T ss_dssp             CCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEESEESSS
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEecCCCC
Confidence            57888999999999999999999999998  58899999999999976543

>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=99.08  E-value=5.4e-11  Score=77.31  Aligned_cols=48  Identities=21%  Similarity=0.429  Sum_probs=43.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.+|+++|||||+|.+.++|++|++  ++..++|+.|.|.++.++.
T Consensus        40 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   89 (104)
T 1p1t_A           40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASEK   89 (104)
T ss_dssp             EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCTT
T ss_pred             EEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCCCcc
Confidence            35788899999999999999999999998  4789999999999997653

>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=99.06  E-value=3.4e-11  Score=82.43  Aligned_cols=46  Identities=17%  Similarity=0.272  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+. |++||||||+|.+.++|++||+ ++..|+||.|.|.++.++
T Consensus        79 i~~d~~-g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~~a~~~  125 (136)
T 2hgl_A           79 FIYTRE-GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRT  125 (136)
T ss_dssp             EEECSS-SCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEEECCHH
T ss_pred             EEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEEECChH
Confidence            467876 9999999999999999999999 468999999999988654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.06  E-value=2e-10  Score=77.04  Aligned_cols=47  Identities=26%  Similarity=0.341  Sum_probs=41.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.+|+++|||||+|.+.++|++||+ +++.|+|+.|.|.++.+.
T Consensus        68 i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  115 (124)
T 2jwn_A           68 ILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRTN  115 (124)
T ss_dssp             EEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSCC
T ss_pred             EEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCCC
Confidence            35788899999999999999999999995 378999999999998754

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.05  E-value=1.2e-10  Score=74.84  Aligned_cols=48  Identities=15%  Similarity=0.344  Sum_probs=41.3

Q ss_pred             CCCCC---CCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            2 PKDQG---SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~---tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      ++|+.   ||++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        38 ~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   90 (98)
T 2cpf_A           38 SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERATK   90 (98)
T ss_dssp             EEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCSSC
T ss_pred             EecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEccCCCC
Confidence            34544   77999999999999999999999  47899999999999976543

>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=99.05  E-value=9.4e-11  Score=76.81  Aligned_cols=46  Identities=17%  Similarity=0.218  Sum_probs=41.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+. |++||||||+|.+.++|++||+ +++.|+||.|.|.++.++
T Consensus        46 i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~~   92 (107)
T 2lmi_A           46 FLLNRD-GKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNE   92 (107)
T ss_dssp             CCCCTT-STTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCEECCHH
T ss_pred             EEECCC-CCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEEECCHH
Confidence            578887 9999999999999999999999 478899999999988654

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.05  E-value=9.7e-11  Score=75.45  Aligned_cols=47  Identities=21%  Similarity=0.299  Sum_probs=42.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeE----EEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGST----VVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~----i~v~~a~~~   47 (171)
                      |++|+.||+++|||||+|.+.++|++|++.  +..++|+.    |.|.++.+.
T Consensus        42 i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l~v~~a~~~   94 (99)
T 2div_A           42 IIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYS   94 (99)
T ss_dssp             EEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEECCEEETTCC
T ss_pred             EeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeEEEeecCCC
Confidence            467889999999999999999999999994  78999999    999988754

>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=99.05  E-value=2.3e-10  Score=74.88  Aligned_cols=62  Identities=18%  Similarity=0.251  Sum_probs=51.8

Q ss_pred             CCCceEEEeCC--CCCCC--------HHHHHHHhhcccceEEEEecCc----------ceeEEecCCcccHHHHHHHHHH
Q 030822           99 RIGKKIFVGRL--PQEAT--------AEDLRRYFSRFGRILDVYVPKR----------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        99 ~~~~~lfV~nL--p~~~t--------e~~L~~~F~~fG~v~~v~i~~d----------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      .+++.|.+.|+  |....        +++|+++|++||+|++|.|+++          ++||+|.+.++    |.+|++.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~----A~~Ai~~   78 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFD----CQKAMQG   78 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHH----HHHHHHH
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHH----HHHHHHH
Confidence            35788999998  33433        3799999999999999999865          46899999999    9999999


Q ss_pred             HhHhCC
Q 030822          159 LWTAGC  164 (171)
Q Consensus       159 l~~~~~  164 (171)
                      ||+..+
T Consensus        79 lnG~~f   84 (105)
T 3v4m_A           79 LTGRKF   84 (105)
T ss_dssp             HTTCEE
T ss_pred             hCCCEe
Confidence            998653

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.05  E-value=1.4e-10  Score=75.91  Aligned_cols=46  Identities=17%  Similarity=0.164  Sum_probs=40.2

Q ss_pred             CCCCCCC-CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            1 MPKDQGS-KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~t-g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.+ +++||||||+|.+.++|++|++  ++..++||.|.|.++.+
T Consensus        45 i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i~v~~a~~   93 (105)
T 2pe8_A           45 IFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFYNL   93 (105)
T ss_dssp             EEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             EecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcCH
Confidence            4567654 7999999999999999999999  48999999999998853

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.05  E-value=1.2e-10  Score=77.38  Aligned_cols=44  Identities=18%  Similarity=0.336  Sum_probs=40.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      |++|+.+|++||||||+|.+.++|++||+.  +..|+|+.|.|.++
T Consensus        72 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a  117 (118)
T 2khc_A           72 VFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQLK  117 (118)
T ss_dssp             ECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEEC
T ss_pred             EEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            468889999999999999999999999994  78999999999876

>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=99.04  E-value=6.8e-11  Score=81.21  Aligned_cols=47  Identities=11%  Similarity=0.085  Sum_probs=41.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+. |++||||||+|++.++|++||+ +++.|+||.|.|.++.++.
T Consensus        77 i~~d~~-g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~  124 (139)
T 2hgn_A           77 IEIGPD-GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTG  124 (139)
T ss_dssp             CCCSSS-SCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSC
T ss_pred             EEECCC-CCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCC
Confidence            578876 9999999999999999999996 3789999999999887653

>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=99.04  E-value=2.5e-10  Score=75.21  Aligned_cols=47  Identities=11%  Similarity=0.180  Sum_probs=40.4

Q ss_pred             CCCCCCC---CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            2 PKDQGSK---AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         2 ~~D~~tg---~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      ++|+.++   ++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++.
T Consensus        51 ~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~k~  102 (111)
T 2cpi_A           51 NNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY  102 (111)
T ss_dssp             ECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEESCCCCS
T ss_pred             ecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEEEEEeccccc
Confidence            5666654   566999999999999999999  4889999999999998763

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.04  E-value=2.9e-10  Score=73.78  Aligned_cols=47  Identities=19%  Similarity=0.365  Sum_probs=41.7

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD   50 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~   50 (171)
                      ++|  +|+++|||||+|.+.++|++||+  ++..|+|+.|.|.++.++...
T Consensus        48 ~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~~~   96 (103)
T 2d9p_A           48 MME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEER   96 (103)
T ss_dssp             EEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECSSCCCC
T ss_pred             EcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEecccccC
Confidence            455  89999999999999999999999  488999999999999876543

>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=99.03  E-value=2e-10  Score=74.95  Aligned_cols=43  Identities=9%  Similarity=0.258  Sum_probs=38.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a   44 (171)
                      |++|+ +|++||||||+|.++++|++|++  ++..++||.|.|.++
T Consensus        59 i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~v~~s  103 (104)
T 1jmt_A           59 VCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             ECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             EEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            45665 48999999999999999999999  489999999999875

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.03  E-value=4.5e-11  Score=77.48  Aligned_cols=48  Identities=19%  Similarity=0.421  Sum_probs=42.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+ +|++||||||+|.+.++|++|+++++.++|+.|.|.++.++..
T Consensus        41 i~~~~-~g~~~g~afV~f~~~~~a~~Ai~~~~~~~g~~l~v~~a~~~~~   88 (102)
T 2xs2_A           41 IITDR-TGVSKGYGFVSFYNDVDVQKIVESQINFHGKKLKLGPAIRKQN   88 (102)
T ss_dssp             EEECT-TSCEEEEEEEEESSCCCHHHHTTCCCEETTEECEEEEEEECC-
T ss_pred             EEECC-CCCccceEEEEECCHHHHHHHHhCCCeECCEEEEEEECCcCcc
Confidence            46787 9999999999999999999999988899999999999976643

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.03  E-value=2.4e-10  Score=78.01  Aligned_cols=47  Identities=30%  Similarity=0.473  Sum_probs=43.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.+|++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++
T Consensus        79 i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~  127 (135)
T 2lea_A           79 IPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYG  127 (135)
T ss_dssp             CCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCC
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            57888999999999999999999999998  478999999999999764

>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=99.03  E-value=1.7e-10  Score=76.33  Aligned_cols=47  Identities=21%  Similarity=0.418  Sum_probs=42.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||. +++.|+|+.|.|.++.++
T Consensus        57 i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~~  104 (114)
T 2cq4_A           57 IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQAE  104 (114)
T ss_dssp             ECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHHH
T ss_pred             EEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCCC
Confidence            46899999999999999999999999995 378999999999998654

>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=99.03  E-value=2e-10  Score=72.22  Aligned_cols=47  Identities=17%  Similarity=0.415  Sum_probs=41.6

Q ss_pred             CCCCCCCCC-ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKA-HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~-srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.++. ++|||||+|.+.++|++|++  ++..++|+.|.|.++.++
T Consensus        36 i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   85 (88)
T 4a8x_A           36 MPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVLAP   85 (88)
T ss_dssp             CCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEECCC
T ss_pred             EEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEECCCC
Confidence            466777766 99999999999999999999  589999999999998764

>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=99.03  E-value=2.9e-10  Score=73.95  Aligned_cols=48  Identities=17%  Similarity=0.297  Sum_probs=41.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCC---eEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG---STVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~g---r~i~v~~a~~~~~   49 (171)
                      |++|+ +|++||||||+|.+.++|++||+  ++..+.|   +.|.|.++.++..
T Consensus        47 i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V~~a~~~~~   99 (105)
T 2dnh_A           47 VLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTDKE   99 (105)
T ss_dssp             EEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEEEESCSSCC
T ss_pred             EEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEEEECccCcc
Confidence            35676 89999999999999999999998  4777887   9999999987644

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.02  E-value=1.6e-10  Score=77.05  Aligned_cols=46  Identities=17%  Similarity=0.263  Sum_probs=40.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+. |++||||||+|.+.++|++||+ +++.|+||.|.|.++.++
T Consensus        52 i~~~~~-g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~~   98 (118)
T 2db1_A           52 FIYTRE-GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSHRT   98 (118)
T ss_dssp             EEECSS-SCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEEEECHH
T ss_pred             EEECCC-CCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCHH
Confidence            357776 9999999999999999999999 478999999999988654

>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=99.02  E-value=3.8e-10  Score=75.34  Aligned_cols=61  Identities=11%  Similarity=0.089  Sum_probs=51.8

Q ss_pred             CCceEEEeCCCC--CC---CHHHHHHHhhcccceEEEEecCc------------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          100 IGKKIFVGRLPQ--EA---TAEDLRRYFSRFGRILDVYVPKR------------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       100 ~~~~lfV~nLp~--~~---te~~L~~~F~~fG~v~~v~i~~d------------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      +++.|++.|+-.  ++   -+++|++.|++||+|.+|.|++|            ++||+|.+.++    |.+|+..||+.
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~----A~~Ai~~LnGr   94 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASE----THKAIQALNGR   94 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHH----HHHHHHHHTTC
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHH----HHHHHHHHCCC
Confidence            578999999942  22   36999999999999999999865            36899999999    99999999986


Q ss_pred             CC
Q 030822          163 GC  164 (171)
Q Consensus       163 ~~  164 (171)
                      .+
T Consensus        95 ~f   96 (118)
T 3ue2_A           95 WF   96 (118)
T ss_dssp             EE
T ss_pred             EE
Confidence            43

>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=99.02  E-value=5.9e-11  Score=79.77  Aligned_cols=46  Identities=17%  Similarity=0.252  Sum_probs=41.4

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      +.|..||++||||||+|.+.++|++||+ +++.|+||.|.|.++.++
T Consensus        58 ~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~~~  104 (124)
T 1wel_A           58 IAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKK  104 (124)
T ss_dssp             EEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECHH
T ss_pred             EEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECCHH
Confidence            4567899999999999999999999999 478999999999998754

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.02  E-value=4.6e-10  Score=75.31  Aligned_cols=47  Identities=15%  Similarity=0.156  Sum_probs=42.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+ +|++||||||+|.+.++|++|++  ++..|+|+.|.|.++.+..
T Consensus        67 i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~  115 (124)
T 2kt5_A           67 VDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQI  115 (124)
T ss_dssp             EECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEECCTT
T ss_pred             EEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCC
Confidence            45787 99999999999999999999999  4889999999999997653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.02  E-value=8.8e-10  Score=71.40  Aligned_cols=59  Identities=10%  Similarity=0.058  Sum_probs=48.7

Q ss_pred             CceEEEeCCC-------CCCCHHHHHHHhhcccceEEEEec---CcceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          101 GKKIFVGRLP-------QEATAEDLRRYFSRFGRILDVYVP---KRFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       101 ~~~lfV~nLp-------~~~te~~L~~~F~~fG~v~~v~i~---~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ..+|-|.-..       ..+++++|+++|++||.|.+|.|+   +.++||+|.+.++    |+.|++.+++..
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te~~L~~~F~~~G~V~~v~i~~~~rGfaFVeF~~~~~----A~~Ai~~~~~~~   78 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSKDVLLRLLQKYGEVLNLVLSSKKPGTAVVEFATVKA----AELAVQNEVGLV   78 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCHHHHHHHHHTTSCEEEEEEESSSSSEEEEEESCHHH----HHHHHHTCCBCS
T ss_pred             cceEEEeeeccCccCcCCCCCHHHHHHHHHhcCCEEEEEEccCCCCEEEEEECCHHH----HHHHHHhcCCCC
Confidence            4456665443       458999999999999999999996   5689999999999    999999876643

>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=99.01  E-value=1.1e-10  Score=86.68  Aligned_cols=46  Identities=22%  Similarity=0.312  Sum_probs=42.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.||++||||||+|.+.++|++||+.  ++.|+|+.|.|.++.+
T Consensus       102 i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~a~~  149 (229)
T 3q2s_C          102 FFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPVNK  149 (229)
T ss_dssp             EEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEECCH
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEECCC
Confidence            578999999999999999999999999994  7899999999999864

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.01  E-value=4.5e-11  Score=80.44  Aligned_cols=46  Identities=20%  Similarity=0.240  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~   47 (171)
                      |++| .+|++||||||+|.+.++|++||+. ++.|+||.|.|..+.++
T Consensus        59 i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~~a~~~  105 (123)
T 2dha_A           59 FVTY-PDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAA  105 (123)
T ss_dssp             EEEC-TTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCEEECHH
T ss_pred             EEEC-CCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEEECCHH
Confidence            3567 4999999999999999999999995 78999999999987654

>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=99.01  E-value=3.5e-10  Score=78.83  Aligned_cols=49  Identities=22%  Similarity=0.282  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        71 i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  121 (156)
T 1h2v_Z           71 MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFKE  121 (156)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCCCT
T ss_pred             EEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            46788999999999999999999999999  47899999999999986543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=98.57  E-value=3.5e-11  Score=79.93  Aligned_cols=49  Identities=22%  Similarity=0.358  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        47 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           47 LYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFATRRAD   97 (116)
Confidence            46788999999999999999999999999  47899999999999987643

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.01  E-value=9.2e-10  Score=72.60  Aligned_cols=46  Identities=20%  Similarity=0.248  Sum_probs=40.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+ +|++||||||+|.+.++|++||+  +++.|+|+.|.|.++...
T Consensus        47 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~   94 (114)
T 2do0_A           47 ILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMDERA   94 (114)
T ss_dssp             EEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSCC
T ss_pred             EEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEcccC
Confidence            35676 69999999999999999999999  488999999999998653

>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=99.00  E-value=7.4e-10  Score=71.02  Aligned_cols=44  Identities=9%  Similarity=0.134  Sum_probs=38.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.+   ||||||+|.+.++|++||+.  +..++||.|.|.++.++
T Consensus        45 i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~~   90 (96)
T 2dgx_A           45 LSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATGA   90 (96)
T ss_dssp             ECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCS
T ss_pred             EEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            4677766   89999999999999999994  78999999999999765

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.99  E-value=9.9e-11  Score=73.29  Aligned_cols=44  Identities=14%  Similarity=0.277  Sum_probs=38.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      |++|+.+|++||||||+|.+.++|++|++.  +..++|+.|++.++
T Consensus        37 i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A           37 AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             EEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            467889999999999999999999999994  77899998877654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=98.99  E-value=1.4e-10  Score=77.96  Aligned_cols=44  Identities=16%  Similarity=0.018  Sum_probs=36.8

Q ss_pred             CCCCCCCCCccceEEEEECC----HHH----HHHHHh----cCCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFAS----ADS----VENLMV----DTHELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~----~~~----a~~Al~----~~~~i~gr~i~v~~a   44 (171)
                      ++.|+.||+|||||||+|.+    +++    |.+|+.    ++..|+||+|+|...
T Consensus        38 li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~I~Gr~irV~ln   93 (136)
T 2j8a_A           38 AFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCFIMGFKFEVILN   93 (136)
T ss_dssp             EEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEEETTEEEEEEEC
T ss_pred             EEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCeecCcEEEEEEC
Confidence            46899999999999999996    433    888988    588999999999864

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A

Probab=98.99  E-value=3.6e-10  Score=73.76  Aligned_cols=44  Identities=18%  Similarity=0.203  Sum_probs=40.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+ +|+++|||||+|.+.++|++||+  ++..|+|+.|.|.++.
T Consensus        61 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~  106 (107)
T 3ulh_A           61 VHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT  106 (107)
T ss_dssp             EEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEeC
Confidence            45777 99999999999999999999999  5889999999999874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.99  E-value=2.8e-10  Score=71.74  Aligned_cols=62  Identities=15%  Similarity=0.150  Sum_probs=53.1

Q ss_pred             CCCceEEEeCCC----CCCCH----HHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLP----QEATA----EDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp----~~~te----~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++..+|+|.-++    .++-+    .+|.+.|++||.|..++|+.|++||+|.+.++    |.+||. ||+..+.
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~~fVtF~d~~s----AlaAi~-mnG~~v~   74 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDKMWVTFLEGSS----ALNVLS-LNGKELL   74 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSSEEEEESSHHH----HHHGGG-GTTCEET
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCCEEEEECChHH----HHHHHh-cCCeEeC
Confidence            456889998776    23433    78999999999999999999999999999988    999998 9998764

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=98.98  E-value=5.6e-10  Score=72.81  Aligned_cols=44  Identities=18%  Similarity=0.215  Sum_probs=39.4

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHhc--CCccCCe-EEEEeecCCCC
Q 030822            5 QGSKAHRGIGFITFASADSVENLMVD--THELGGS-TVVVDRATPKE   48 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr-~i~v~~a~~~~   48 (171)
                      +.||++||||||+|.+.++|++||..  +..|+|+ .|.|.++...+
T Consensus        55 ~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           55 EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEEEEECSCCCC
T ss_pred             CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceEEEEEcchHh
Confidence            46899999999999999999999994  7899998 99999987543

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens}

Probab=98.97  E-value=4e-10  Score=71.92  Aligned_cols=44  Identities=23%  Similarity=0.397  Sum_probs=39.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+. |++||||||+|.+.++|++||+  +++.++|+.|.|.++.
T Consensus        48 i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   93 (95)
T 2ywk_A           48 ICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGPS   93 (95)
T ss_dssp             EEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             EEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEcC
Confidence            356765 9999999999999999999999  4889999999999874

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=6.6e-10  Score=73.43  Aligned_cols=46  Identities=22%  Similarity=0.298  Sum_probs=40.8

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +..+|++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        60 ~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~~  107 (115)
T 2cpx_A           60 RMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  107 (115)
T ss_dssp             EEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             EcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEccCCCC
Confidence            44589999999999999999999998  47899999999999987643

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=98.96  E-value=7.3e-10  Score=74.89  Aligned_cols=43  Identities=19%  Similarity=0.340  Sum_probs=39.1

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      .+|++||||||+|.+.++|++|++.  +..|.|++|.|.++.++.
T Consensus        67 ~~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~~a~~~~  111 (127)
T 2a3j_A           67 LSDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVITFSETPQ  111 (127)
T ss_dssp             CCCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEEECCCCC
T ss_pred             cCCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEEEccCcc
Confidence            4789999999999999999999984  889999999999997653

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.94  E-value=9.3e-10  Score=72.80  Aligned_cols=45  Identities=22%  Similarity=0.319  Sum_probs=39.0

Q ss_pred             CCCCCCC---CCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecC
Q 030822            1 MPKDQGS---KAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~t---g~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~   45 (171)
                      +++|+.|   |++||||||+|.+.++|++||+..+.++|+.+.+..+.
T Consensus        39 ~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~~~~   86 (114)
T 2dnl_A           39 WPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCVSSP   86 (114)
T ss_dssp             CTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEECCS
T ss_pred             EeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEeccCC
Confidence            4667777   89999999999999999999998778899999887554

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=2e-09  Score=69.72  Aligned_cols=46  Identities=15%  Similarity=0.238  Sum_probs=39.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      ++|+.  .+||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        48 ~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   95 (103)
T 2cqi_A           48 ITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPSS   95 (103)
T ss_dssp             ECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTTC
T ss_pred             EecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEECCCCcc
Confidence            45643  479999999999999999999  47899999999999987543

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A

Probab=98.94  E-value=1.2e-09  Score=71.32  Aligned_cols=45  Identities=18%  Similarity=0.265  Sum_probs=39.5

Q ss_pred             CCCCCCC--CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGS--KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~t--g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+.+  ++++|||||+|+++++|++|++  ++..++||.|.|.++.
T Consensus        47 i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~f~GR~i~v~~~~   95 (105)
T 3v4m_A           47 IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   95 (105)
T ss_dssp             CCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEeC
Confidence            5677655  5799999999999999999999  4899999999999864

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=98.94  E-value=5.5e-10  Score=78.65  Aligned_cols=49  Identities=16%  Similarity=0.239  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||+++|||||+|.+.++|++||.  ++..|+|+.|.|.++.++..
T Consensus       104 i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~  154 (165)
T 1rk8_A          104 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGP  154 (165)
T ss_dssp             EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-
T ss_pred             EEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCC
Confidence            46788999999999999999999999998  48899999999999976543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=98.93  E-value=7.1e-10  Score=70.30  Aligned_cols=43  Identities=19%  Similarity=0.301  Sum_probs=38.9

Q ss_pred             CCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      .+|++||||||+|.+.++|++|++  ++..++|+.|.|.++.++.
T Consensus        43 ~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   87 (92)
T 2dgv_A           43 ENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDRNAS   87 (92)
T ss_dssp             SSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECSCCS
T ss_pred             cCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCCC
Confidence            389999999999999999999999  4789999999999987653

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=98.92  E-value=1.3e-09  Score=68.54  Aligned_cols=37  Identities=11%  Similarity=0.342  Sum_probs=34.2

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      .|||||||+|.++++|++|++.  +..++||+|.|+.|.
T Consensus        41 ~~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A           41 LNQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4899999999999999999994  789999999999883

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.92  E-value=9e-10  Score=72.69  Aligned_cols=46  Identities=20%  Similarity=0.384  Sum_probs=39.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCcc--------CCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THEL--------GGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i--------~gr~i~v~~a~~~   47 (171)
                      |++|+ +|++||||||+|.+.++|++||+.  +..|        .+++|.|+++.|+
T Consensus        57 i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           57 ILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             EEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSCBEEEECCCS
T ss_pred             EEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCCCceeEEccCCC
Confidence            46787 999999999999999999999994  6677        5788999988754

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3

Probab=98.92  E-value=1e-10  Score=76.44  Aligned_cols=55  Identities=9%  Similarity=0.143  Sum_probs=47.9

Q ss_pred             EeCCCCCCCHHHHHHHh------------hcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          106 VGRLPQEATAEDLRRYF------------SRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       106 V~nLp~~~te~~L~~~F------------~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +.|||+.+++++|+++|            ++||+|.+|.|+++       ++||+|.+.++    |.+|+..||+..+
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~----A~~A~~~lng~~~   93 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREED----AEKAVIDLNNRWF   93 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHH----HHHHHHHHTTCEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHH----HHHHHHHHCCCEE
Confidence            67888888988888777            99999999999965       67899999999    9999999998653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=98.90  E-value=1.5e-09  Score=69.37  Aligned_cols=43  Identities=23%  Similarity=0.375  Sum_probs=39.0

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      .+|++||||||+|.+.++|++|++.  +..|+|+.|.|.++.++.
T Consensus        48 ~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   92 (96)
T 1fjc_A           48 QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKG   92 (96)
T ss_dssp             ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSC
T ss_pred             CCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCCCC
Confidence            5789999999999999999999994  689999999999997653

>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=98.89  E-value=1.2e-09  Score=69.13  Aligned_cols=65  Identities=9%  Similarity=0.073  Sum_probs=55.2

Q ss_pred             CCCCceEEEeCCCCC-----CCH----HHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCCCCc
Q 030822           98 QRIGKKIFVGRLPQE-----ATA----EDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCNRF  167 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~-----~te----~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~~~  167 (171)
                      .++..+|+|.-++..     +-+    .+|.+.|++||.|+.++++.|..||+|.+.++    |.+||. ||+..++.-
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~~fVtF~d~~s----Al~AI~-ldG~~v~Gr   85 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHS----ALSVLD-VDGMKVKGR   85 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHH----HHHHHH-GGGSEETTE
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCcEEEEEcChHH----HHHHHh-cCCeeeCCe
Confidence            345789999888743     322    67999999999999999999999999999999    999998 999877643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.89  E-value=2.6e-09  Score=69.12  Aligned_cols=41  Identities=12%  Similarity=0.185  Sum_probs=37.2

Q ss_pred             CCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCC
Q 030822            8 KAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~   48 (171)
                      +++||||||+|++.++|++||+.+..+.|++|.|.++.++.
T Consensus        51 ~~~rGfaFVeF~~~~~A~~Ai~~~~~~~g~~l~V~~a~~~~   91 (100)
T 2d9o_A           51 SKKPGTAVVEFATVKAAELAVQNEVGLVDNPLKISWLEGQP   91 (100)
T ss_dssp             SSSSSEEEEEESCHHHHHHHHHTCCBCSSSBCEEECSSCCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHhcCCCCCCeEEEEEccCCC
Confidence            57999999999999999999998777899999999987653

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.89  E-value=4e-09  Score=68.26  Aligned_cols=46  Identities=20%  Similarity=0.356  Sum_probs=39.3

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      ++|+.  .++|||||+|.+.++|++||+  +++.|+|+.|.|.++.++..
T Consensus        48 ~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~   95 (103)
T 2cq3_A           48 IFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARVM   95 (103)
T ss_dssp             ECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSCC
T ss_pred             EecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcccCCC
Confidence            45543  499999999999999999998  47899999999999987643

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=98.88  E-value=9.9e-10  Score=68.13  Aligned_cols=37  Identities=19%  Similarity=0.266  Sum_probs=33.4

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHhc--CCccCCe-EEEE
Q 030822            5 QGSKAHRGIGFITFASADSVENLMVD--THELGGS-TVVV   41 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr-~i~v   41 (171)
                      +.||++||||||+|.+.++|++|++.  +..++|+ +|.|
T Consensus        41 ~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A           41 EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            46899999999999999999999994  7889999 8866

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.83  E-value=7.9e-09  Score=67.58  Aligned_cols=43  Identities=14%  Similarity=0.276  Sum_probs=38.1

Q ss_pred             CCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      .++++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++.
T Consensus        56 ~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~  100 (109)
T 1x4a_A           56 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRSGR  100 (109)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCCCC
T ss_pred             ECCCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcccCC
Confidence            356799999999999999999997  4789999999999987653

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.82  E-value=3.2e-09  Score=69.63  Aligned_cols=44  Identities=20%  Similarity=0.437  Sum_probs=38.5

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      ++|+  +++||||||+|.+.++|++|++  ++..|+|+.|.|.++.++
T Consensus        62 ~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  107 (109)
T 2err_A           62 IFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATAR  107 (109)
T ss_dssp             CCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEECCCS
T ss_pred             EECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            4564  4599999999999999999999  488999999999998765

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=98.82  E-value=5.3e-09  Score=68.99  Aligned_cols=39  Identities=23%  Similarity=0.450  Sum_probs=35.5

Q ss_pred             CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      +++||||||+|++.++|++||+  ++..|+||.|.|.++..
T Consensus        64 ~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a~~  104 (111)
T 2jvr_A           64 RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN  104 (111)
T ss_dssp             CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEESCC
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            4699999999999999999998  48899999999998864

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*

Probab=98.81  E-value=8.8e-09  Score=83.16  Aligned_cols=49  Identities=20%  Similarity=0.323  Sum_probs=44.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||+++|||||+|.+.++|++||..  +..|+|+.|.|.++.++..
T Consensus       134 i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a~~~~~  184 (437)
T 3pgw_S          134 MVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV  184 (437)
T ss_pred             eeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            578999999999999999999999999984  7899999999999987543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=98.81  E-value=2.2e-09  Score=73.73  Aligned_cols=43  Identities=19%  Similarity=0.233  Sum_probs=39.4

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            5 QGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ..||++||||||+|.+.++|++||..  +..|+|+.|.|.++.+.
T Consensus        86 ~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~  130 (143)
T 3egn_A           86 MKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMVVQFARSA  130 (143)
T ss_dssp             EEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEECEEEECCCS
T ss_pred             ccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCC
Confidence            46899999999999999999999994  88999999999999764

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.80  E-value=3.8e-09  Score=67.71  Aligned_cols=41  Identities=17%  Similarity=0.275  Sum_probs=37.5

Q ss_pred             CCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      +++++|||||+|.+.++|++|++  ++..|+|+.|.|.++.++
T Consensus        52 ~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   94 (97)
T 2e5j_A           52 WQGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALARQQ   94 (97)
T ss_dssp             EETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECCCC
T ss_pred             cCCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCCC
Confidence            56899999999999999999998  488999999999999775

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=98.80  E-value=4.4e-09  Score=74.95  Aligned_cols=46  Identities=15%  Similarity=0.179  Sum_probs=41.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+ +|+++|||||+|.+.++|++||+  ++..|+|+.|.|.++.+.
T Consensus       120 i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~~~  167 (177)
T 2f3j_A          120 VDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVASQ  167 (177)
T ss_dssp             ECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEESSG
T ss_pred             EEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            46787 99999999999999999999999  478999999999998764

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A

Probab=98.79  E-value=1.8e-09  Score=72.04  Aligned_cols=39  Identities=15%  Similarity=0.133  Sum_probs=35.9

Q ss_pred             CCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            7 SKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      +++++||+||+|.+.++|++|++.  +..++||.|.|.++.
T Consensus        67 ~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~GR~i~v~~~~  107 (118)
T 3ue2_A           67 DAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  107 (118)
T ss_dssp             TCEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CCcceEEEEEEECCHHHHHHHHHHHCCCEECCcEEEEEEcC
Confidence            678999999999999999999994  899999999999864

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=98.79  E-value=2.7e-09  Score=68.24  Aligned_cols=42  Identities=19%  Similarity=0.267  Sum_probs=38.2

Q ss_pred             CCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            7 SKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      +|++||||||+|.+.++|++|++  ++..++|+.|.|.++.++.
T Consensus        47 ~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~   90 (97)
T 1nu4_A           47 SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   90 (97)
T ss_dssp             HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEEEEccCCC
Confidence            67899999999999999999998  4889999999999998753

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.79  E-value=1.3e-08  Score=67.38  Aligned_cols=62  Identities=11%  Similarity=0.105  Sum_probs=51.3

Q ss_pred             CCCceEEEeCCCCCCC----------HHHHHHHhhcccceEEEEecCc----ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEAT----------AEDLRRYFSRFGRILDVYVPKR----FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~t----------e~~L~~~F~~fG~v~~v~i~~d----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+++.|.+.|+=....          +++|+++|++||.|.+|.|.++    ++||+|.+.++    |.+|++.|||..+
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~~~G~~fV~f~~~e~----A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAA----AIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTCTTCCEEEECSSHHH----HHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCCCcEEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            3567899999843222          3689999999999999999864    68999999999    9999999998653

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.78  E-value=8.1e-09  Score=68.02  Aligned_cols=42  Identities=12%  Similarity=0.249  Sum_probs=37.4

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKEDD   50 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~~   50 (171)
                      .+||||||+|.+.++|++|++.  +..++||+|.|.++.++...
T Consensus        62 ~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l~v~~a~~~~~~  105 (112)
T 2dit_A           62 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTDY  105 (112)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCCS
T ss_pred             CCCEEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeCCCCCc
Confidence            3899999999999999999984  78999999999999876543

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=98.77  E-value=8.2e-09  Score=65.26  Aligned_cols=40  Identities=28%  Similarity=0.483  Sum_probs=31.8

Q ss_pred             ccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +||||||+|++.++|+++....+.+.|+.|.|.++.++..
T Consensus        47 srGfaFV~F~~~~~A~~~~~~~~~~~g~~v~v~~a~~k~~   86 (89)
T 3d2w_A           47 FRAFAFVTFADDKVAQSLCGEDLIIKGISVHISNAEPKHN   86 (89)
T ss_dssp             CCSEEEEEESCHHHHHHHTTCEEEETTEEEEEEECC----
T ss_pred             CCCEEEEEECCHHHHHHHcCCCcccCCEEEEEEEcCCCCc
Confidence            8999999999999999765555677899999999987643

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.75  E-value=2.3e-08  Score=63.95  Aligned_cols=41  Identities=15%  Similarity=0.319  Sum_probs=36.8

Q ss_pred             CCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            8 KAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      +++||||||+|.+.++|++||+  ++..|+|+.|.|.++.++.
T Consensus        46 ~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~~~~   88 (97)
T 1x5p_A           46 DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQP   88 (97)
T ss_dssp             ETTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCSSCC
T ss_pred             cCCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECCCCC
Confidence            3789999999999999999998  4789999999999997763

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.75  E-value=7.6e-09  Score=67.44  Aligned_cols=40  Identities=18%  Similarity=0.287  Sum_probs=34.8

Q ss_pred             ccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      .||||||+|++.++|++||+.    +..|+||+|.|.++.++..
T Consensus        51 ~kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~A~~~~~   94 (105)
T 1sjq_A           51 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL   94 (105)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCCCSSSSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEcCCCCC
Confidence            389999999999999999983    4789999999999976643

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=2.4e-08  Score=63.27  Aligned_cols=41  Identities=20%  Similarity=0.286  Sum_probs=36.6

Q ss_pred             CccceEEEEECCHHHHHHHHh--cC-CccCCeEEEEeecCCCCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DT-HELGGSTVVVDRATPKED   49 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~-~~i~gr~i~v~~a~~~~~   49 (171)
                      .++|||||+|.+.++|++|++  ++ ..++|+.|.|.++.++..
T Consensus        42 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~~~   85 (93)
T 2cqh_A           42 LKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   85 (93)
T ss_dssp             EETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEEccCccc
Confidence            479999999999999999998  47 899999999999987643

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.70  E-value=3.2e-08  Score=64.11  Aligned_cols=40  Identities=15%  Similarity=0.252  Sum_probs=34.9

Q ss_pred             ccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      .||||||+|++.++|++|++.    +..++||+|.|.++.++..
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   93 (101)
T 2cq1_A           50 GKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKEL   93 (101)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEcCcccC
Confidence            389999999999999999983    5689999999999976543

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.69  E-value=1.9e-08  Score=66.40  Aligned_cols=41  Identities=15%  Similarity=0.205  Sum_probs=35.7

Q ss_pred             CccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      ++||||||+|++.++|++||+.    +..|+||+|.|.++..+..
T Consensus        60 ~~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~~~~  104 (112)
T 1x4f_A           60 RMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKYKK  104 (112)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSCSS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEECccccc
Confidence            5799999999999999999983    4579999999999976543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=98.69  E-value=2.8e-08  Score=64.18  Aligned_cols=39  Identities=13%  Similarity=0.181  Sum_probs=34.0

Q ss_pred             CccceEEEEECCHHHHHHHHhc--C--CccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--T--HELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~--~~i~gr~i~v~~a~~~   47 (171)
                      ++||||||+|++.++|++|++.  +  ..|.||+|.|.++.++
T Consensus        55 ~~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S~~k   97 (100)
T 3r27_A           55 PKKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYSTSQ   97 (100)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEECSCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEecccc
Confidence            4689999999999999999994  3  3589999999999765

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=98.69  E-value=1.2e-08  Score=65.65  Aligned_cols=39  Identities=13%  Similarity=0.320  Sum_probs=35.4

Q ss_pred             CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      ++||||||+|.+.++|++|+.  ++..++|+.|.|.++.++
T Consensus        61 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  101 (101)
T 2la4_A           61 PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGKER  101 (101)
T ss_dssp             TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCCCC
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEeccCC
Confidence            689999999999999999998  488999999999998753

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.68  E-value=2.5e-08  Score=63.47  Aligned_cols=45  Identities=20%  Similarity=0.323  Sum_probs=38.6

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +.|+.+|+   ||||+|.+.++|++||+ +++.|+|+.|.|+++.++..
T Consensus        39 ~~~~~~g~---~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~~~~   84 (94)
T 2e5g_A           39 VMDKDKGV---FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQKEF   84 (94)
T ss_dssp             EECSSSCC---EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCCSCC
T ss_pred             EEcCCCCc---EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCcCCC
Confidence            46777777   99999999999999999 47899999999998876543

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=98.68  E-value=1.8e-08  Score=63.35  Aligned_cols=38  Identities=13%  Similarity=0.308  Sum_probs=34.9

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATP   46 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~   46 (171)
                      ++||||||+|.+.++|++|++.  +..++|+.|.|.++..
T Consensus        38 ~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~   77 (88)
T 1wg1_A           38 RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPT   77 (88)
T ss_dssp             GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCC
Confidence            6899999999999999999994  7899999999999854

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.67  E-value=3.8e-08  Score=64.32  Aligned_cols=39  Identities=21%  Similarity=0.423  Sum_probs=35.5

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      ||||||+|.+.++|++||+  ++..|+|+.|.|.++.++..
T Consensus        61 ~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  101 (109)
T 1x4g_A           61 KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKESPD  101 (109)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCCCS
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEecCCCCC
Confidence            8999999999999999998  48899999999999987643

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.66  E-value=5.7e-08  Score=62.29  Aligned_cols=41  Identities=24%  Similarity=0.413  Sum_probs=36.4

Q ss_pred             CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      .+||||||+|.+.++|++||.  ++..|+|+.|.|.++.++..
T Consensus        49 ~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   91 (99)
T 2cpd_A           49 KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   91 (99)
T ss_dssp             ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EeCCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEECCCCCC
Confidence            468999999999999999999  48899999999999987643

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.66  E-value=4.7e-08  Score=63.41  Aligned_cols=40  Identities=15%  Similarity=0.127  Sum_probs=34.3

Q ss_pred             ccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      .||||||+|++.++|++||+.    +..|+||+|.|.++..+..
T Consensus        51 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a~~~~~   94 (102)
T 1x4d_A           51 KINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKYKR   94 (102)
T ss_dssp             SSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCCTT
T ss_pred             CCCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEECCCCCC
Confidence            469999999999999999994    3569999999999976533

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A

Probab=98.66  E-value=8e-08  Score=62.09  Aligned_cols=42  Identities=21%  Similarity=0.370  Sum_probs=36.7

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCCCC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDDF   51 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~~~   51 (171)
                      .||||||+|.+.++|++||+  +++.|+|+.|.|.++.++....
T Consensus        44 ~~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~~   87 (103)
T 2dgu_A           44 LKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKR   87 (103)
T ss_dssp             CSSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCCCCCC
T ss_pred             ECCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCCCcccc
Confidence            37899999999999999999  4789999999999998765443

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.65  E-value=6.9e-08  Score=62.82  Aligned_cols=40  Identities=15%  Similarity=0.227  Sum_probs=34.6

Q ss_pred             ccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      +||||||+|++.++|++|++.    +..|+|++|.|.++.++..
T Consensus        50 ~kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a~~~~~   93 (104)
T 1wex_A           50 FKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSKRI   93 (104)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSSSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEccCccc
Confidence            489999999999999999983    3569999999999976543

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.64  E-value=2.8e-08  Score=62.37  Aligned_cols=40  Identities=28%  Similarity=0.480  Sum_probs=35.3

Q ss_pred             ccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +||||||+|.+.++|++|+...+.++|+.|.|.++.++..
T Consensus        41 ~~g~afV~f~~~~~a~~~~~~~~~~~g~~l~v~~a~~~~~   80 (88)
T 1wf0_A           41 FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHN   80 (88)
T ss_dssp             CCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCC
T ss_pred             CCCEEEEEECCHHHHHHHhcCCceeCCEEEEEEecCCCCC
Confidence            8999999999999999887766778999999999987644

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.63  E-value=3.3e-08  Score=63.40  Aligned_cols=40  Identities=25%  Similarity=0.350  Sum_probs=35.9

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      ++||||||+|.+.++|++|++.  ++.|+|+.|.|.++.++.
T Consensus        49 ~~kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~~   90 (99)
T 2cpj_A           49 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA   90 (99)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCCS
T ss_pred             cCCCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEcCCCC
Confidence            4689999999999999999984  788999999999998753

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.61  E-value=8.1e-08  Score=60.47  Aligned_cols=39  Identities=18%  Similarity=0.382  Sum_probs=35.0

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      ||||||+|.+.++|++|++  ++..++|+.|.|.++.++..
T Consensus        42 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~   82 (90)
T 2dnq_A           42 KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKNKSK   82 (90)
T ss_dssp             TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSSCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECCCCCC
Confidence            7999999999999999998  47889999999999987643

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.60  E-value=5.1e-08  Score=64.95  Aligned_cols=40  Identities=18%  Similarity=0.287  Sum_probs=35.1

Q ss_pred             ccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822           10 HRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      .||||||+|++.++|++|++.    +..|+|++|.|.++.++..
T Consensus        66 ~kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a~~k~~  109 (119)
T 2ad9_A           66 GKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKEL  109 (119)
T ss_dssp             GGTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEECSSSSC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEccCCCC
Confidence            489999999999999999983    4689999999999977643

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=98.58  E-value=7.7e-08  Score=61.64  Aligned_cols=38  Identities=18%  Similarity=0.397  Sum_probs=34.5

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      +||||||+|.+.++|++|++.  +..++|+.|.|.++.++
T Consensus        56 ~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   95 (97)
T 2xnq_A           56 KNAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEVSSSN   95 (97)
T ss_dssp             CSSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEECCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCCC
Confidence            489999999999999999994  78999999999998754

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.57  E-value=5.8e-08  Score=61.83  Aligned_cols=45  Identities=16%  Similarity=0.172  Sum_probs=37.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.+|+    |||+|.+.++|++||+  ++..|+|+.|.|.++.+++.
T Consensus        48 i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~~~   94 (96)
T 2e44_A           48 VNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAYIPDEMA   94 (96)
T ss_dssp             ECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECCCCCS
T ss_pred             eecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcCcccc
Confidence            356665554    9999999999999998  48899999999999988743

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.56  E-value=1.2e-07  Score=60.16  Aligned_cols=38  Identities=16%  Similarity=0.285  Sum_probs=34.7

Q ss_pred             ceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822           12 GIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus        12 GfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |||||.|.+.++|++|+++  +..+.||+|+|.+|..+.+
T Consensus        47 G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~A~~~sd   86 (96)
T 2diu_A           47 CSAILRFINQDSAERAQKRMENEDVFGNRIIVSFTPKNRE   86 (96)
T ss_dssp             TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEESSCCSCC
T ss_pred             CEEEEEECCHHHHHHHHHHhcCCccCCceEEEEecCCCcc
Confidence            9999999999999999994  8999999999999976644

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=98.55  E-value=8.1e-08  Score=62.81  Aligned_cols=38  Identities=18%  Similarity=0.444  Sum_probs=34.7

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      +||||||+|.+.++|++||+  ++..|+|+.|.|.++.++
T Consensus        61 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~  100 (110)
T 1wf1_A           61 HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGEP  100 (110)
T ss_dssp             ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCCC
Confidence            68999999999999999998  488999999999998754

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=98.55  E-value=6e-08  Score=64.15  Aligned_cols=36  Identities=8%  Similarity=0.113  Sum_probs=33.6

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      +||||||+|.+.++|++|++  ++..++||.|.|.++.
T Consensus        54 ~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~   91 (114)
T 3s6e_A           54 AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVP   91 (114)
T ss_dssp             TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEc
Confidence            69999999999999999999  4899999999999874

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.54  E-value=1.6e-07  Score=59.08  Aligned_cols=38  Identities=13%  Similarity=0.331  Sum_probs=34.5

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      +|||||+|.+.++|++||+  ++..++|+.|.|.++.++.
T Consensus        43 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~   82 (90)
T 2dnp_A           43 KDYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELSTKGQ   82 (90)
T ss_dssp             SSCEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEECCCCC
Confidence            6799999999999999999  4889999999999997763

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.54  E-value=7.9e-08  Score=59.73  Aligned_cols=35  Identities=20%  Similarity=0.287  Sum_probs=32.3

Q ss_pred             ccceEEEEECCHHHHHHHHh---cCCccCCeEEEEeec
Q 030822           10 HRGIGFITFASADSVENLMV---DTHELGGSTVVVDRA   44 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~---~~~~i~gr~i~v~~a   44 (171)
                      +||||||+|.+.++|++|++   ++..++|+.|.|.++
T Consensus        47 ~kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           47 RQQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             GGTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            68999999999999999998   468999999999986

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=98.54  E-value=2.3e-07  Score=58.60  Aligned_cols=38  Identities=18%  Similarity=0.347  Sum_probs=34.5

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      +|||||+|.+.++|++|++  +++.|+|+.|.|.++.++.
T Consensus        44 ~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~   83 (92)
T 2dgt_A           44 KDYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTSRL   83 (92)
T ss_dssp             SSEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESSCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEccCCC
Confidence            6799999999999999998  4889999999999998763

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=98.53  E-value=4.6e-08  Score=62.45  Aligned_cols=39  Identities=18%  Similarity=0.387  Sum_probs=35.1

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      +||||||+|.+.++|++|++  ++..+.|+.|.|.++.++.
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~~~   84 (96)
T 2kvi_A           44 KNAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVSSSNA   84 (96)
T ss_dssp             ETTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEEECCC
T ss_pred             eCCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEcCcCC
Confidence            58999999999999999999  4788999999999997653

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.52  E-value=1.3e-07  Score=60.42  Aligned_cols=37  Identities=22%  Similarity=0.334  Sum_probs=34.3

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccC--CeEEEEeecCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELG--GSTVVVDRATPK   47 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~--gr~i~v~~a~~~   47 (171)
                      ||||||+|.+.++|++|++  ++..|+  |+.|.|.++.++
T Consensus        53 ~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~a~~~   93 (97)
T 1why_A           53 DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEECCCC
Confidence            8999999999999999999  478899  999999999876

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=98.51  E-value=1.2e-07  Score=62.03  Aligned_cols=37  Identities=16%  Similarity=0.302  Sum_probs=34.4

Q ss_pred             cceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822           11 RGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      ||||||+|.+.++|++|++  ++..++|+.|.|.++.++
T Consensus        65 kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~  103 (108)
T 2jvo_A           65 NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSKLP  103 (108)
T ss_dssp             TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEESCSCC
T ss_pred             CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEecCC
Confidence            8999999999999999998  488999999999998765

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.50  E-value=1.4e-07  Score=61.44  Aligned_cols=38  Identities=13%  Similarity=0.333  Sum_probs=34.0

Q ss_pred             ceEEEEECCHHHHHHHHhc--CCccCC-----eEEEEeecCCCCC
Q 030822           12 GIGFITFASADSVENLMVD--THELGG-----STVVVDRATPKED   49 (171)
Q Consensus        12 GfgFV~F~~~~~a~~Al~~--~~~i~g-----r~i~v~~a~~~~~   49 (171)
                      |||||+|.+.++|++||+.  +..|+|     +.|.|.++.++..
T Consensus        51 g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V~~a~~~~~   95 (108)
T 1x4c_A           51 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPRSP   95 (108)
T ss_dssp             TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEEEESSCCSC
T ss_pred             CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEEEeCCCCCC
Confidence            9999999999999999994  678888     9999999987643

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=98.48  E-value=1.1e-07  Score=62.36  Aligned_cols=39  Identities=5%  Similarity=-0.008  Sum_probs=35.1

Q ss_pred             CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      ++||||||+|.+.++|++||+  ++..++|+.|.|.++...
T Consensus        44 ~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A           44 EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            478999999999999999999  488999999999998643

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A

Probab=98.48  E-value=1.8e-07  Score=58.31  Aligned_cols=36  Identities=22%  Similarity=0.448  Sum_probs=31.6

Q ss_pred             CCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEee
Q 030822            8 KAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDR   43 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~   43 (171)
                      .++||||||+|.+.++|++|+. ++..++|+.|.|++
T Consensus        50 ~~~kg~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~r   86 (87)
T 2hzc_A           50 NQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   86 (87)
T ss_dssp             CSSSSEEEEEESSHHHHHHHGGGTTCEETTEECEEEC
T ss_pred             cCCCcEEEEEcCCHHHHHHHHhcCCCEECCeEEEEeC
Confidence            3569999999999999999994 37899999999874

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A

Probab=98.47  E-value=2.3e-07  Score=65.07  Aligned_cols=42  Identities=12%  Similarity=0.133  Sum_probs=36.1

Q ss_pred             CCccceEEEEECCHHHHHHHHhc--CCccCC--eEEEEeecCCCCC
Q 030822            8 KAHRGIGFITFASADSVENLMVD--THELGG--STVVVDRATPKED   49 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~--~~~i~g--r~i~v~~a~~~~~   49 (171)
                      ++++|||||+|++.++|++|++.  +..|.|  +.|+|.++.++..
T Consensus        81 k~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak~~~l  126 (164)
T 1sjr_A           81 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSL  126 (164)
T ss_dssp             SSSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECSSSSC
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEecCCcc
Confidence            34789999999999999999994  788855  9999999987643

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.36  E-value=6.5e-07  Score=59.07  Aligned_cols=37  Identities=11%  Similarity=0.222  Sum_probs=32.2

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCcc-----CCeEEEEeecCC
Q 030822           10 HRGIGFITFASADSVENLMVD--THEL-----GGSTVVVDRATP   46 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i-----~gr~i~v~~a~~   46 (171)
                      +||||||+|++.++|++|++.  +.++     .|++|.|.++..
T Consensus        62 ~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l~v~~a~~  105 (114)
T 2cq2_A           62 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEK  105 (114)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEESC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEEEEEeccc
Confidence            489999999999999999994  6776     689999998864

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=98.28  E-value=8.9e-07  Score=59.76  Aligned_cols=40  Identities=10%  Similarity=0.194  Sum_probs=35.1

Q ss_pred             Cccce-EEEEECCHHHHHHHHhc--CCccCC--eEEEEeecCCCC
Q 030822            9 AHRGI-GFITFASADSVENLMVD--THELGG--STVVVDRATPKE   48 (171)
Q Consensus         9 ~srGf-gFV~F~~~~~a~~Al~~--~~~i~g--r~i~v~~a~~~~   48 (171)
                      ++||| |||+|.+.++|++|++.  +..|.|  +.|+|.++.++.
T Consensus        63 ~~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~~~  107 (130)
T 3zzy_A           63 KNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS  107 (130)
T ss_dssp             ETTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSCSS
T ss_pred             CCCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCCCc
Confidence            35788 99999999999999994  888888  999999998764

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A

Probab=98.23  E-value=1.2e-06  Score=57.74  Aligned_cols=36  Identities=14%  Similarity=0.361  Sum_probs=29.9

Q ss_pred             ceEEEEECCHHHHHHHHhc--CCccCCeE-----EEEeecCCC
Q 030822           12 GIGFITFASADSVENLMVD--THELGGST-----VVVDRATPK   47 (171)
Q Consensus        12 GfgFV~F~~~~~a~~Al~~--~~~i~gr~-----i~v~~a~~~   47 (171)
                      |||||+|.+.++|++||+.  +..|+|+.     |.|..+.++
T Consensus        52 g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~~~~~~   94 (115)
T 3beg_B           52 GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKVDGPR   94 (115)
T ss_dssp             SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEECC--
T ss_pred             CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEeccCCCC
Confidence            9999999999999999994  78999998     666665543

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=98.16  E-value=1.3e-06  Score=64.98  Aligned_cols=39  Identities=21%  Similarity=0.344  Sum_probs=33.5

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCcc------------CCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THEL------------GGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i------------~gr~i~v~~a~~~   47 (171)
                      .+||||||+|.+.++|+.|++.  +..|            +|+.|.|+||...
T Consensus       177 ~~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          177 ESKNCGFVKFKYQANAEFAKEAMSNQTLLLPSDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             GGGTEEEEEESSHHHHHHHHHHHTTCCCCCTTSTTGGGGGGSCCCEEEECC--
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHhCCCEEeccccccccccCCCCEEEEEEccCC
Confidence            3799999999999999999984  6777            8999999999765

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=98.13  E-value=3.5e-06  Score=56.38  Aligned_cols=37  Identities=19%  Similarity=0.366  Sum_probs=32.9

Q ss_pred             ce-EEEEECCHHHHHHHHh--cCCccCC--eEEEEeecCCCC
Q 030822           12 GI-GFITFASADSVENLMV--DTHELGG--STVVVDRATPKE   48 (171)
Q Consensus        12 Gf-gFV~F~~~~~a~~Al~--~~~~i~g--r~i~v~~a~~~~   48 (171)
                      || |||+|.+.++|++|++  ++..|.|  +.|.|.++.++.
T Consensus        62 Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           62 GIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             SEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             CCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            86 9999999999999999  4888887  699999998764

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=97.99  E-value=8.9e-06  Score=51.11  Aligned_cols=36  Identities=22%  Similarity=0.342  Sum_probs=32.4

Q ss_pred             eEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCC
Q 030822           13 IGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus        13 fgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~   48 (171)
                      .+||+|.+.++|.+||+ ++..+.||.|+|+.+++..
T Consensus        51 ~~fVtF~d~~sAlaAi~mnG~~v~Gr~LkV~lkt~dW   87 (91)
T 2dnr_A           51 KMWVTFLEGSSALNVLSLNGKELLNRTITIALKSPSG   87 (91)
T ss_dssp             SEEEEESSHHHHHHGGGGTTCEETTEEEEEEECCCSS
T ss_pred             CEEEEECChHHHHHHHhcCCeEeCCeEEEEEeCCCCc
Confidence            38999999999999999 5889999999999988653

>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=97.91  E-value=9.6e-06  Score=59.29  Aligned_cols=49  Identities=14%  Similarity=0.102  Sum_probs=42.8

Q ss_pred             CCCHHHHHHHhhcccceEEEEecCc------------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          112 EATAEDLRRYFSRFGRILDVYVPKR------------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       112 ~~te~~L~~~F~~fG~v~~v~i~~d------------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .-.+++|++.|++||.|.++.|+++            +.||+|.+.++    |.+|++.|||..+
T Consensus       140 ~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~----a~~a~~~l~gr~~  200 (222)
T 3dxb_A          140 DDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASE----THKAIQALNGRWF  200 (222)
T ss_dssp             TTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHH----HHHHHHHHTTCBS
T ss_pred             HHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHH----HHHHHHHhcCceE
Confidence            3457899999999999999999732            57899999999    9999999999764

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.80  E-value=9.2e-05  Score=46.87  Aligned_cols=56  Identities=21%  Similarity=0.252  Sum_probs=45.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHh
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ...+-++| +.|.++...||.++|++||.| .|+.+-| -+||.|.+++.    |..|+..+.
T Consensus        14 ~r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDTsAlvvf~~~~~----a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDTSAFVSLSQPEQ----VQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETTEEEEECSCHHH----HHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCCeEEEEecCHHH----HHHHHHhcc
Confidence            34455666 999999999999999999964 4555544 78999999999    999998875

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=97.66  E-value=7.3e-05  Score=48.39  Aligned_cols=62  Identities=10%  Similarity=0.054  Sum_probs=56.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcc-----cceEEEEecCcce--eEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRF-----GRILDVYVPKRFW--FCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~f-----G~v~~v~i~~d~~--fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|-+.|||.++++..++.+.++|     |.++.+.+..|.+  .|.|.+...    |.+|.-+|+|..+.
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~GAivef~d~~~----AgKasLaL~G~ef~   88 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFNGAIIIFRDSKF----AAKMLMILNGSQFQ   88 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTTEEEEECSCHHH----HHHHHHHHSSEEET
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCCceEEEEccchh----hHHHHhhcCCeeec
Confidence            46899999999999999999999999     9999999999964  699999999    99999999886543

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=97.64  E-value=3.7e-05  Score=48.58  Aligned_cols=32  Identities=22%  Similarity=0.365  Sum_probs=29.3

Q ss_pred             EEEEECCHHHHHHHHh-cCCccCCeEEEEeecC
Q 030822           14 GFITFASADSVENLMV-DTHELGGSTVVVDRAT   45 (171)
Q Consensus        14 gFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~   45 (171)
                      +||+|.+.++|.+||+ ++..++||.|+|++..
T Consensus        61 ~fVtF~d~~sAl~AI~ldG~~v~Gr~L~V~~k~   93 (95)
T 1ufw_A           61 MLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             EEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             EEEEEcChHHHHHHHhcCCeeeCCeEEEEeccC
Confidence            9999999999999999 5899999999998643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.62  E-value=0.00014  Score=46.54  Aligned_cols=56  Identities=20%  Similarity=0.083  Sum_probs=50.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhc-c----cceEEEEecCcceeEEecCCcccHHHHHHHHHH
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSR-F----GRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~-f----G~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ....+|.|.|||+.++++.|.-+|+. -    |+|.++....+.+.|+|.++..    |++.+++
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~~~AvItF~d~~v----a~rVL~k   66 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLGCGGVLTFREPAD----AERVLAQ   66 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEETTEEEEEESSHHH----HHHHHTC
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcCCcEEEEEcChHH----HHHHhcC
Confidence            34789999999999999999999998 2    8999999888888999999999    8888877

>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=97.60  E-value=3.6e-05  Score=56.21  Aligned_cols=27  Identities=11%  Similarity=0.117  Sum_probs=24.5

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD   30 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~   30 (171)
                      |..+|+++||+||+|.+.++|++|++.
T Consensus       168 ~~~~~~~~G~~fv~f~~~~~a~~a~~~  194 (222)
T 3dxb_A          168 EEEDAEIIVKIFVEFSIASETHKAIQA  194 (222)
T ss_dssp             SSTTCCEEEEEEEEESSHHHHHHHHHH
T ss_pred             cccCcCceeEEEEEECCHHHHHHHHHH
Confidence            456789999999999999999999994

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4

Probab=97.38  E-value=0.00049  Score=43.25  Aligned_cols=58  Identities=12%  Similarity=0.027  Sum_probs=47.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ++|.|++||+++||+++.+..++...+.....+..          ++.+.|.+.++    +..-.+.++|..
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~----v~~f~~~~~g~~   69 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQED----IILFRDRFDGYV   69 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHH----HHHHHHHHTTCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHH----HHHHHHHhCCcE
Confidence            58999999999999999999999988776665432          45699999988    777777777653

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*

Probab=97.38  E-value=0.00013  Score=56.98  Aligned_cols=35  Identities=14%  Similarity=0.301  Sum_probs=27.0

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCcc---CCe--EEEEeec
Q 030822           10 HRGIGFITFASADSVENLMVD--THEL---GGS--TVVVDRA   44 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i---~gr--~i~v~~a   44 (171)
                      +||||||+|++.++|++||+.  +.++   .|+  .|.+.++
T Consensus        55 ~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~ly~~~~   96 (345)
T 3tht_A           55 NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFV   96 (345)
T ss_dssp             TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEECEEEEC
T ss_pred             CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceEEEEEEe
Confidence            689999999999999999995  4444   345  4555555

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=97.31  E-value=0.00059  Score=43.30  Aligned_cols=53  Identities=21%  Similarity=0.256  Sum_probs=44.1

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHh
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      +-++| +.|.++...||.++|++||. ..|..+-| -+||.|.+++.    |..|+..+.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDTsAlvvf~~~~~----a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDTSAFVSLSQPEQ----VKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETTEEEEEEEEECH----HHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCCeEEEEecCHHH----HHHHHHhcc
Confidence            44555 99999999999999999995 44555555 68999999999    999998874

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.23  E-value=0.00062  Score=43.55  Aligned_cols=36  Identities=28%  Similarity=0.522  Sum_probs=31.7

Q ss_pred             ceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCC
Q 030822           12 GIGFITFASADSVENLMVD-THELGGSTVVVDRATPK   47 (171)
Q Consensus        12 GfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~   47 (171)
                      +=|+|+|.+.+.|++.|+. .|.|+|-.|.|....++
T Consensus        48 ~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P~~~~   84 (104)
T 2dhx_A           48 CGGVLTFREPADAERVLAQADHELHGAQLSLRPAPPR   84 (104)
T ss_dssp             TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEEECCCC
T ss_pred             CcEEEEEcChHHHHHHhcCCcceecCeEEEEEcCCCC
Confidence            4589999999999999998 89999999999865543

>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=97.17  E-value=0.0002  Score=49.00  Aligned_cols=21  Identities=14%  Similarity=0.438  Sum_probs=19.8

Q ss_pred             ccceEEEEECCHHHHHHHHhc
Q 030822           10 HRGIGFITFASADSVENLMVD   30 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~   30 (171)
                      +||||||+|.+.++|++||..
T Consensus       109 ~~g~afV~f~~~~~a~~A~~~  129 (150)
T 2i2y_A          109 PPGFAFVEFEDPRDAADAVRE  129 (150)
T ss_dssp             SCSEEEEEESSHHHHHHHHHH
T ss_pred             CCcEEEEEECCHHHHHHHHHH
Confidence            699999999999999999984

>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=96.36  E-value=0.0068  Score=39.83  Aligned_cols=56  Identities=16%  Similarity=0.095  Sum_probs=44.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcce--eEEecCCcccHHHHHHHHHH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW--FCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~--fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ....+-|.|.+.|+.. -..+..+|++||.|++........  .|+|.++.+    |++|+..
T Consensus        21 ~~~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~~~NWihI~Y~s~~~----A~rAL~k   78 (119)
T 1wwh_A           21 HLDDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQ----ARKALSK   78 (119)
T ss_dssp             CGGGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECSSSSEEEEEESSHHH----HHHHHTT
T ss_pred             CCCCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCCCCCeEEEEeCCHHH----HHHHHHh
Confidence            3446889999999885 556677899999999999854333  499999999    9999865

>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=96.20  E-value=0.004  Score=39.87  Aligned_cols=61  Identities=7%  Similarity=0.046  Sum_probs=50.0

Q ss_pred             CceEEEeCCCCCC-C----HHHHHHHhhcccceEEEEecCcc--eeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEA-T----AEDLRRYFSRFGRILDVYVPKRF--WFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~-t----e~~L~~~F~~fG~v~~v~i~~d~--~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++|+|.||+..+ .    .+.++++|..|+++......+.+  --|.|.+.++    |.+|-..||+...+
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFRRirv~F~~~~~----A~~AR~~Lh~~~f~   72 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLS----AADARLRLHKTEFL   72 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTH----HHHHHHTSTTSEET
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcceEEEEEeCChHH----HHHHHHHhccceec
Confidence            4789999998754 2    25789999999999998888764  3599999999    99999999887543

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.72  E-value=0.0083  Score=37.96  Aligned_cols=59  Identities=10%  Similarity=-0.017  Sum_probs=41.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC----------cceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK----------RFWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~----------d~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      -+-+|.|+.||+.+||+++.+.+++.=++.....+.          -++.|.|.+.++    ...-.+.++|.
T Consensus         8 ~~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~ed----v~~F~~~f~g~   76 (97)
T 2l08_A            8 HSHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDD----ILLFRDRFDGY   76 (97)
T ss_dssp             CCCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHH----HHHHHHHSTTE
T ss_pred             cceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHH----HHHHHHHcCCc
Confidence            357899999999999999998888764443322221          145699999888    55555555443

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.66  E-value=0.0073  Score=48.84  Aligned_cols=47  Identities=17%  Similarity=0.504  Sum_probs=36.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcce---eEEecCCcc
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFW---FCHLCGRSC  147 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~---fv~f~~~~~  147 (171)
                      ..++|||. .|...++.+|.++|++||+|.++..=++++   -|+|.+.++
T Consensus        52 a~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g~~~~vef~~~~~  101 (464)
T 3pq1_A           52 AQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFGLYAVVEFCQKES  101 (464)
T ss_dssp             HHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSSEEEEEECC---C
T ss_pred             hcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCCeEEEEEeCCHHH
Confidence            35889996 799999999999999999999999887755   499999998

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=94.64  E-value=0.045  Score=36.08  Aligned_cols=32  Identities=22%  Similarity=0.204  Sum_probs=26.4

Q ss_pred             eEEEEECC-HHHHHHHHhc----CCccCCeEEEEeec
Q 030822           13 IGFITFAS-ADSVENLMVD----THELGGSTVVVDRA   44 (171)
Q Consensus        13 fgFV~F~~-~~~a~~Al~~----~~~i~gr~i~v~~a   44 (171)
                      .|||.|.+ +++|..|+..    +..|.|..+.+...
T Consensus        57 tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~evL   93 (121)
T 1owx_A           57 EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   93 (121)
T ss_dssp             EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEEC
Confidence            49999999 7899999884    67888988877654

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=93.59  E-value=0.085  Score=34.11  Aligned_cols=31  Identities=10%  Similarity=0.272  Sum_probs=27.1

Q ss_pred             ceEEEEECCHHHHHHHHh--cCCccCCeEEEEe
Q 030822           12 GIGFITFASADSVENLMV--DTHELGGSTVVVD   42 (171)
Q Consensus        12 GfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~   42 (171)
                      |=|+|+|.+...|-+|.-  +|.+|+||+|+|.
T Consensus        63 ~GAivef~d~~~AgKasLaL~G~ef~gr~Lr~g   95 (117)
T 2l9w_A           63 NGAIIIFRDSKFAAKMLMILNGSQFQGKVIRSG   95 (117)
T ss_dssp             TEEEEECSCHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CceEEEEccchhhHHHHhhcCCeeecCeEEEec
Confidence            349999999999999864  6999999999986

>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=92.52  E-value=0.33  Score=39.70  Aligned_cols=56  Identities=21%  Similarity=0.220  Sum_probs=45.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHhH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....++|+ +|..|...+|.++|+.||.| +|..+-| ..+|.|.+.+.    |..+++.+..
T Consensus       439 R~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt~a~V~~~~~~~----a~~~l~~~~~  495 (507)
T 3d45_A          439 RDHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDTSAFVSLSQPEQ----VQIAVNTSKY  495 (507)
T ss_dssp             GGGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSSEEEEECSCHHH----HHHHHHHHTT
T ss_pred             cCcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCCeEEEEECCHHH----HHHHHHHHHh
Confidence            45566666 99999999999999999964 5555544 57899999999    9989888853

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=90.77  E-value=0.072  Score=35.49  Aligned_cols=52  Identities=19%  Similarity=0.164  Sum_probs=35.4

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEE-EecC-------------------cce--eEEecCCcccHHHHHHHHH
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPK-------------------RFW--FCHLCGRSCSRSCFSKVSR  157 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~-------------------d~~--fv~f~~~~~~~~~a~~Ai~  157 (171)
                      ..-|.|.+.|+..... +-++|++||.|.+- .+.+                   ...  -|+|+++.+    |.+|+.
T Consensus         7 e~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~----A~rAL~   80 (132)
T 3p3d_A            7 ELAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPAS----AVDALL   80 (132)
T ss_dssp             -CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHH----HHHHHT
T ss_pred             ceEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHH----HHHHHH
Confidence            4568888998776655 55679999999872 2211                   111  389999888    887764

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=87.08  E-value=0.78  Score=30.50  Aligned_cols=36  Identities=17%  Similarity=0.143  Sum_probs=31.3

Q ss_pred             cceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCC
Q 030822           11 RGIGFITFASADSVENLMVD-THELGGSTVVVDRATP   46 (171)
Q Consensus        11 rGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~   46 (171)
                      ..|-.|+|.++.+|++||.. +..|+|.-|-|.+..+
T Consensus        62 ~NWikItYds~~~A~rAL~~NG~ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           62 NSWTKITYDNPASAVDALLENGAVFNGVLLGVIPYTK   98 (132)
T ss_dssp             TTEEEEEBSSHHHHHHHHTTTTCEETTEECEEEECCH
T ss_pred             CcEEEEEcCCHHHHHHHHHhCCeEeCcEEEEEEECCH
Confidence            46889999999999999995 8999999888887653

---

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	171
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	7e-09
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	4e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	5e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	2e-04
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-07
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-04
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-07
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-05
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-07
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	7e-07
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	6e-05
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	8e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-07
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-06
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	1e-06
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-06
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	3e-06
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	3e-06
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	4e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	6e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	8e-06
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	2e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	9e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	9e-06
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	1e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	7e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	1e-05
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-05
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-05
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	2e-05
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-05
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	3e-05
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	4e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-05
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	6e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	6e-05
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	7e-05
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	7e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	7e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	1e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	1e-04
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-04
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	1e-04
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-04
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	2e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	4e-04
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-04
d1owxa_	113	d.58.7.1 (A:) Lupus LA protein {Human (Homo sapien	5e-04
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-04
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	5e-04
d1whxa_	111	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	9e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.003
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.001
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.001
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.004
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	0.002
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	0.002
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	0.002
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	0.002
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	0.003
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	0.003
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.003
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.004

>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 = 48.8 bits (116), Expect = 7e-09
 Identities = 9/43 (20%), Positives = 21/43 (48%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
              ++ G +    T + +R+ FS FG+I+++ V     +  + 
Sbjct: 18  NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVR 60

>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 = 46.8 bits (111), Expect = 2e-08
 Identities = 12/45 (26%), Positives = 18/45 (40%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
            ++VG L  + T   L   FS  G IL + V +        G + 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAY 46

>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 = 46.1 bits (109), Expect = 4e-08
 Identities = 9/45 (20%), Positives = 15/45 (33%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           K+ V  L    +  D++  F+ FG +    V        L     
Sbjct: 2   KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADV 46

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.1 bits (109), Expect = 5e-08
 Identities = 10/49 (20%), Positives = 19/49 (38%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED 49
          + KD  +   +G GF+ F   ++   +M   H + G          K+ 
Sbjct: 40 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS 88

>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 = 36.5 bits (84), Expect = 2e-04
 Identities = 17/44 (38%), Positives = 22/44 (50%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCG 144
              + V  LP + T +DL+ YFS FG +L V V K     H  G
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKG 51

>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 = 44.5 bits (105), Expect = 3e-07
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
             ++   KI V  +P +A   ++R  FS FG +  V +PK+ 
Sbjct: 3   PKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKM 44

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (83), Expect = 3e-04
 Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVE---NLMVDTHELGGSTVVVDRATPKE 48
            K  G+ AHRG GF+ F +    +   N +  +  L G  +V++ A  + 
Sbjct: 41 PKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEV 91

>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 = 44.2 bits (104), Expect = 3e-07
 Identities = 10/45 (22%), Positives = 18/45 (40%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
            + V  LPQ+ T  +L   F   G I    + + +   +  G + 
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAF 48

>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 = 46.1 bits (108), Expect = 3e-07
 Identities = 14/44 (31%), Positives = 22/44 (50%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGR 145
           +K+F+G L  E T E LR +F ++G + D  V +        G 
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 50

>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 = 40.4 bits (93), Expect = 2e-05
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED 49
           +  D+GS   RG  F+TF   DSV+ +++   H + G    V +A  K++
Sbjct: 129 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQE 178

>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 = 43.5 bits (102), Expect = 5e-07
 Identities = 12/49 (24%), Positives = 23/49 (46%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCG 144
           S+      ++V  LP+  T ++L + FS++GRI+   +          G
Sbjct: 1   SASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRG 49

>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 = 43.0 bits (101), Expect = 6e-07
 Identities = 15/53 (28%), Positives = 30/53 (56%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRS 146
           GE +     ++FVG LP + T E++R+ F ++G+  +V++ K   F  +   +
Sbjct: 1   GEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLET 53

>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 = 43.1 bits (101), Expect = 7e-07
 Identities = 5/54 (9%), Positives = 19/54 (35%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVS 156
           ++F+G +P+    E++    ++    +   +        +  R  +   +    
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHR 56

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.1 bits (88), Expect = 6e-05
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 4/53 (7%)

Query: 1  MPKDQGSKAHRGIGFITFASADS----VENLMVDTHELGGSTVVVDRATPKED 49
                   +RG  F+ + S  +       LM    +L G  + VD A P+ D
Sbjct: 35 YASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID 87

>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 = 43.0 bits (101), Expect = 8e-07
 Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 2/50 (4%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           GES +     ++V  LP+  T + L   F ++G I+   + +        
Sbjct: 1   GESIK--DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPR 48

>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 = 42.9 bits (101), Expect = 9e-07
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)

Query: 98  QRIGKKIFVGRLPQEATAE-DLRRYFSRFGRILDVYVPKRFWFCH 141
           + +  ++F+G L      + D+   FS++G+I+   V K F F  
Sbjct: 12  RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQ 56

>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 = 42.4 bits (99), Expect = 1e-06
 Identities = 11/41 (26%), Positives = 19/41 (46%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           K+++G L    TA+DLR+ F      L   V  +  +  + 
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVD 43

>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 = 42.8 bits (100), Expect = 1e-06
 Identities = 8/66 (12%), Positives = 16/66 (24%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLW 160
              I+V  L    T +DL  +F + G +       +        +   +           
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 67

Query: 161 TAGCNR 166
                 
Sbjct: 68  PPTAKA 73

>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 = 41.9 bits (98), Expect = 1e-06
 Identities = 13/41 (31%), Positives = 18/41 (43%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           KIFVG L  +   E +R YF  FG +  + +P         
Sbjct: 1   KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRR 41

>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 = 41.9 bits (98), Expect = 2e-06
 Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 4/45 (8%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           K+F+G L  + T E LR YF +FG               L  RS 
Sbjct: 2   KMFIGGLSWQTTQEGLREYFGQFGE----VKECLVMRDPLTKRSR 42

>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 = 41.6 bits (97), Expect = 3e-06
 Identities = 10/44 (22%), Positives = 18/44 (40%)

Query: 98  QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           +R  + +F  +L       DL  +FS  G++ DV +        
Sbjct: 15  ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRR 58

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 12/46 (26%), Positives = 21/46 (45%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           + ++VG L +E   + L   F  FG I D+ +P  +      G + 
Sbjct: 6   RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAF 51

>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 = 40.9 bits (95), Expect = 4e-06
 Identities = 4/45 (8%), Positives = 11/45 (24%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
            +++   P   T  ++R        +          F      + 
Sbjct: 3   TLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAY 47

>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 = 40.4 bits (94), Expect = 6e-06
 Identities = 7/46 (15%), Positives = 16/46 (34%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           K ++V  L    + E + + F+         V K   +  +   + 
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNR 54

>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 = 40.4 bits (94), Expect = 8e-06
 Identities = 15/52 (28%), Positives = 26/52 (50%)

Query: 93  RGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCG 144
           R +  +   +K+F+G L  E T E LR Y+ ++G++ D  V +        G
Sbjct: 12  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRG 63

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.7 bits (92), Expect = 2e-05
 Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 1   MPKDQGSKAHRGIGFITFASADSVENLM-VDTHELGGSTVVVDRATPKED 49
           + +D  SK  RG GF+TF+S   V+  M    H + G  V   RA  +E+
Sbjct: 52  VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE 101

>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 = 40.1 bits (93), Expect = 9e-06
 Identities = 13/38 (34%), Positives = 15/38 (39%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           IF+G L  E   + L   FS FG IL      R     
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTG 38

>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 = 40.0 bits (93), Expect = 9e-06
 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 1/49 (2%)

Query: 96  SSQRIG-KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           S ++ G   IF+  L +    + L   FS FG IL   V          
Sbjct: 2   SLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY 50

>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 = 40.0 bits (93), Expect = 1e-05
 Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 3/51 (5%)

Query: 10 HRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDDFRPVGRMSHG 60
           R   F+TFA     ++L  +   + G +V +  A PK +        S G
Sbjct: 41 FRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNSNSG---PSSG 88

>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 = 37.7 bits (87), Expect = 7e-05
 Identities = 15/42 (35%), Positives = 26/42 (61%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
             +FVGR   + T ++LR +FS++G ++DV++PK F      
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFV 47

>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 = 39.6 bits (92), Expect = 1e-05
 Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 1/54 (1%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILD-VYVPKRFWFCHLCGRSCSRSCFSKVS 156
           +F+  L    T E L+  FS+ G I       K+     L         + K  
Sbjct: 1   LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 54

>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 = 39.6 bits (92), Expect = 1e-05
 Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 6/50 (12%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSC 151
           +K+F+G L  E T E LR +F ++                      SR  
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQW------GTLTDCVVMRDPNTKRSRGF 50

>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 = 39.3 bits (91), Expect = 2e-05
 Identities = 13/47 (27%), Positives = 18/47 (38%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
              + V  L    T  DLR  FS++G I DV +          G + 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 55

>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 = 39.2 bits (91), Expect = 2e-05
 Identities = 11/49 (22%), Positives = 18/49 (36%)

Query: 95  ESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           E   +    ++VG L    T E +   FS+ G I  + +         C
Sbjct: 1   EKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC 49

>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 = 39.0 bits (90), Expect = 2e-05
 Identities = 8/51 (15%), Positives = 19/51 (37%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCF 152
           ++++VG +P   T E +  +F+   R+  +          +         F
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAF 52

>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 = 38.9 bits (90), Expect = 2e-05
 Identities = 14/47 (29%), Positives = 22/47 (46%)

Query: 97  SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           S+   K++ V  +P      DLR+ F +FG+ILDV +          
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 53

>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 = 39.2 bits (91), Expect = 3e-05
 Identities = 9/42 (21%), Positives = 19/42 (45%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           + +++  LP + TAE++   F ++G I  + V          
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTA 49

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 7/42 (16%), Positives = 16/42 (38%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           + ++VG L ++ T   + + FS+ G      +          
Sbjct: 9   RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPY 50

>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 = 38.5 bits (89), Expect = 4e-05
 Identities = 9/48 (18%), Positives = 21/48 (43%)

Query: 96  SSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           S +     ++VG L ++ +   L   F + G +++ ++PK        
Sbjct: 4   SERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQ 51

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.2 bits (88), Expect = 4e-05
 Identities = 14/41 (34%), Positives = 20/41 (48%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           KIFVG L    T ED++ YF +FG++ D  +          
Sbjct: 1   KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHR 41

>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 = 38.1 bits (88), Expect = 6e-05
 Identities = 12/46 (26%), Positives = 18/46 (39%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
             I V  L ++    DL+  F  FG I  +Y+ K        G + 
Sbjct: 9   ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 54

>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 = 38.1 bits (88), Expect = 6e-05
 Identities = 7/45 (15%), Positives = 13/45 (28%)

Query: 99  RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           R  + +    L    T ++L+  F     I  V    +       
Sbjct: 14  RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYI 58

>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 = 37.3 bits (86), Expect = 7e-05
 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%)

Query: 97  SQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           + R G  ++V       T   LR  FS FG I+D+ +        + 
Sbjct: 1   APRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVT 45

>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 = 37.7 bits (87), Expect = 7e-05
 Identities = 11/41 (26%), Positives = 20/41 (48%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           +I+VG LP +   +D+   F ++G I D+ +  R       
Sbjct: 16  RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFA 56

>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 = 37.4 bits (86), Expect = 7e-05
 Identities = 12/42 (28%), Positives = 20/42 (47%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           KKIFVG + ++     LR YF ++G+I  + +          
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKR 44

>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 = 37.5 bits (86), Expect = 1e-04
 Identities = 12/47 (25%), Positives = 19/47 (40%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           GK +F+  L  ++  E L     +FG +  V V       H  G + 
Sbjct: 8   GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAF 54

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 37.4 bits (86), Expect = 1e-04
 Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 4/56 (7%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRS 146
           YG+   +     +++VG L    +   L R F RFG I  +   K   F ++   S
Sbjct: 11  YGKANPT----TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYES 62

>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 = 36.8 bits (84), Expect = 1e-04
 Identities = 9/42 (21%), Positives = 14/42 (33%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCG 144
            + V  LP+      + +YF   G I+ V V           
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFA 43

>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 = 36.9 bits (85), Expect = 1e-04
 Identities = 11/23 (47%), Positives = 17/23 (73%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRF 125
           K+F+G L  + T +DL+ YFS+F
Sbjct: 1   KMFIGGLSWDTTKKDLKDYFSKF 23

>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 = 37.0 bits (85), Expect = 1e-04
 Identities = 9/47 (19%), Positives = 22/47 (46%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           G  +FV  + +EA  ++++  F  +G I ++++          G + 
Sbjct: 7   GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYAL 53

>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 = 36.6 bits (84), Expect = 2e-04
 Identities = 4/50 (8%), Positives = 14/50 (28%), Gaps = 1/50 (2%)

Query: 95  ESSQRIGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           +      + + +      +     L +    FG I +  +  +     + 
Sbjct: 2   KGRVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIE 51

>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 = 36.3 bits (83), Expect = 2e-04
 Identities = 6/46 (13%), Positives = 21/46 (45%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           + +++   P +AT +D++ +    G++L++ + +            
Sbjct: 7   RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFV 52

>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 = 36.6 bits (84), Expect = 2e-04
 Identities = 6/55 (10%), Positives = 18/55 (32%)

Query: 83  LYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRF 137
           +Y +P +     +  +     + +     E   E       ++G + ++ V    
Sbjct: 9   IYRNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL 63

>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 = 36.7 bits (84), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 91  YGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           Y  GE +    K +++  L    T  DL   F+RF       +  R     + G++ 
Sbjct: 12  YNPGEPN----KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAF 64

>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 = 36.2 bits (83), Expect = 4e-04
 Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 4/52 (7%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCF 152
           G  +F+  LPQE   +DL + F  FG ++        +       S      
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAK----VFIDKQTNLSKCFGFV 65

>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 = 35.9 bits (82), Expect = 5e-04
 Identities = 13/46 (28%), Positives = 20/46 (43%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           + +FVG +P EAT E L+  FS  G ++   +          G   
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGF 54

>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 = 35.9 bits (82), Expect = 5e-04
 Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 1/52 (1%)

Query: 93  RGESSQRIG-KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
            G   ++IG    F G L  +   EDL   FS  G I  +   +      + 
Sbjct: 2   HGSLEEKIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIIL 53

>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 = 35.1 bits (80), Expect = 5e-04
 Identities = 11/45 (24%), Positives = 15/45 (33%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
            + V  LPQ  T E+ R  F   G I    + +        G   
Sbjct: 4   NLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGF 48

>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 = 35.5 bits (81), Expect = 5e-04
 Identities = 13/54 (24%), Positives = 24/54 (44%)

Query: 94  GESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           G S      ++FV  L   ++ EDL + FS +G + +++ P         G + 
Sbjct: 1   GSSGSSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAF 54

>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 = 7e-04
 Identities = 17/65 (26%), Positives = 23/65 (35%), Gaps = 2/65 (3%)

Query: 92  GRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSR 149
           G   SS R    I    LP    A +++  FSRFG +  V +P               +R
Sbjct: 1   GSSGSSGRSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEAR 60

Query: 150 SCFSK 154
             F  
Sbjct: 61  KAFRH 65

>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 = 34.7 bits (79), Expect = 9e-04
 Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 2/52 (3%)

Query: 1  MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKEDD 50
          + KD+ ++  RG GF+TF + D  ++ M+  +   + G  + VD+A    D+
Sbjct: 37 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSDN 88

>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 = 33.2 bits (75), Expect = 0.003
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           K+FVG L  +   + L + FS++G+I +V V K        G   
Sbjct: 7   KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGF 51

>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 = 35.3 bits (80), Expect = 0.001
 Identities = 10/46 (21%), Positives = 16/46 (34%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           + + V  +P       LR+ F R+G I  V +          G   
Sbjct: 43  RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGF 88

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.2 bits (78), Expect = 0.001
 Identities = 8/39 (20%), Positives = 16/39 (41%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCH 141
           K+F+G LP     + ++   + FG +    + K      
Sbjct: 3   KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGL 41

>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 = 32.7 bits (74), Expect = 0.004
 Identities = 7/40 (17%), Positives = 18/40 (45%), Gaps = 2/40 (5%)

Query: 10 HRGIGFITFASADSVENLM--VDTHELGGSTVVVDRATPK 47
           +G  F  +   +  +  +  ++  +LG   ++V RA+  
Sbjct: 42 SKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG 81

>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 = 33.6 bits (76), Expect = 0.002
 Identities = 8/52 (15%), Positives = 15/52 (28%), Gaps = 2/52 (3%)

Query: 101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCF 152
           G++I +  L  E   E+L R    F     +              +   +  
Sbjct: 4   GREIMIRNLSTELLDENLLRES--FEGFGSIEKINIPAGQKEHSFNNCCAFM 53

>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 = 33.9 bits (77), Expect = 0.002
 Identities = 5/40 (12%), Positives = 12/40 (30%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
           +  G L    +   L     + G +  + +P    +    
Sbjct: 23  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFAR 62

>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 = 33.8 bits (77), Expect = 0.002
 Identities = 11/58 (18%), Positives = 20/58 (34%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNL 159
            +I V  L    T + L + FS+FG +L +    +        +            +L
Sbjct: 8   LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSL 65

>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 = 33.9 bits (77), Expect = 0.002
 Identities = 17/43 (39%), Positives = 19/43 (44%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCG 144
            KIFVG LP   T   LR+YF  FG I +  V          G
Sbjct: 11  TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRG 53

>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 = 33.6 bits (76), Expect = 0.003
 Identities = 8/42 (19%), Positives = 13/42 (30%)

Query: 102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLC 143
             + V  L +     DL     +FG I  V +        + 
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVE 57

>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 = 33.4 bits (76), Expect = 0.003
 Identities = 6/42 (14%), Positives = 13/42 (30%), Gaps = 2/42 (4%)

Query: 10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED 49
            G+  ++F   +  +  +   D    GG  +         D
Sbjct: 56 PDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD 97

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.2 bits (75), Expect = 0.003
 Identities = 5/48 (10%), Positives = 15/48 (31%)

Query: 103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRS 150
            +++  LP     ++L      FG+++   + +               
Sbjct: 20  NLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARME 67

>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 = 32.4 bits (73), Expect = 0.004
 Identities = 7/44 (15%), Positives = 15/44 (34%)

Query: 104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSC 147
           +++  L    T +DL +    +G+I+              G   
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGF 44

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	171
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.88
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.72
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.72
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.69
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.69
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.68
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.68
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.68
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.67
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.67
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.67
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.67
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.67
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.66
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.66
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.66
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.66
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.66
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.66
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.66
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.66
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.66
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.66
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.66
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.65
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.65
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.65
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.65
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.65
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.64
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.64
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.63
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.63
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.63
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.63
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.62
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.62
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.62
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.61
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.61
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.61
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.61
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.61
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.6
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.6
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.59
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.59
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.59
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.58
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.58
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.57
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.56
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.56
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.56
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.56
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.55
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.55
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.54
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.54
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.53
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.53
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.53
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.53
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.53
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.52
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.51
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.51
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.5
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.5
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.5
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.49
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.49
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.48
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.47
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.45
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.44
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.41
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.4
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.4
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.4
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.4
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.39
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.39
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.39
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.38
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.37
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.36
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.36
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.36
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.35
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.35
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.35
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.34
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.34
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.31
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.3
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.3
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.29
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.29
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.29
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.28
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.27
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.26
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.25
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.25
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.24
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.23
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.22
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.22
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.22
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.21
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.19
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.19
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.18
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.18
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.18
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.16
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.16
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.15
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	99.12
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.11
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.1
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.1
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.07
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.07
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.06
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.04
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.03
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.03
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	99.02
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.02
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.01
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	98.95
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	98.94
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	98.93
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.93
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	98.91
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	98.91
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	98.9
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	98.9
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.89
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	98.89
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	98.86
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	98.85
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.79
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	98.78
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.78
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	98.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	98.74
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	98.74
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	98.72
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	98.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	98.71
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	98.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	98.6
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	98.54
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	98.54
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	98.53
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	98.51
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.46
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	98.45
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.39
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	98.38
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	98.38
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	98.3
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	98.29
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	97.68
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	97.42
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.41
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	97.13
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.61
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	94.99
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	86.09

>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=99.88  E-value=7.9e-23  Score=145.36  Aligned_cols=115  Identities=30%  Similarity=0.513  Sum_probs=95.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCCCCCCCCcCCCCCCCCccccchhhhhhhccC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKEDDFRPVGRMSHGGYGAYNAYISAATRYAALG   79 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g   79 (171)
                      |++|+.+|++||||||+|.+.++|++|+.. +..++++.+.+.+..++.......                         
T Consensus        38 ~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------------------   92 (183)
T d1u1qa_          38 VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG-------------------------   92 (183)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCCTTGGGSTT-------------------------
T ss_pred             eeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhhcccccccc-------------------------
Confidence            367889999999999999999999999996 678889998888765443221100                         


Q ss_pred             CCCccCCCCCCCCCCCCCCCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHH
Q 030822           80 APTLYDHPGSFYGRGESSQRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSC  151 (171)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~  151 (171)
                                       .....++|||+|||+.+|+++|+++|+.||.|..+.|+.|        ++||.|.++++    
T Consensus        93 -----------------~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~----  151 (183)
T d1u1qa_          93 -----------------AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS----  151 (183)
T ss_dssp             -----------------TTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHH----
T ss_pred             -----------------cccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHH----
Confidence                             1345689999999999999999999999999999999865        57999999999    


Q ss_pred             HHHHHHHHhHh
Q 030822          152 FSKVSRNLWTA  162 (171)
Q Consensus       152 a~~Ai~~l~~~  162 (171)
                      |.+|+. +++.
T Consensus       152 A~~Al~-~~~~  161 (183)
T d1u1qa_         152 VDKIVI-QKYH  161 (183)
T ss_dssp             HHHHHT-SSCE
T ss_pred             HHHHHH-hCCC
Confidence            999996 4443

>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=99.72  E-value=3.5e-18  Score=107.20  Aligned_cols=60  Identities=15%  Similarity=0.189  Sum_probs=57.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++|||+|||+++++++|+++|++||+|.++.|++| ++||+|.+.++    |++||..||+..++
T Consensus         1 nrvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~g~afV~f~~~~~----a~~Ai~~l~g~~~~   61 (87)
T d3begb1           1 NRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDGTGVVEFVRKED----MTYAVRKLDNTKFR   61 (87)
T ss_dssp             CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTTSEEEEEESSHHH----HHHHHHHHTTCBCC
T ss_pred             CeEEEECCCCcCCHHHHHHHHhhhcccccccccccceeeEEeCCHHH----HHHHHHHhCCCEEC
Confidence            47999999999999999999999999999999988 89999999999    99999999998865

>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=99.72  E-value=7.7e-18  Score=105.18  Aligned_cols=63  Identities=21%  Similarity=0.304  Sum_probs=57.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+|+++|+++|++||+|++++|++|        ++||+|.++++    |++|++.||+..+.
T Consensus         4 ~k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~----a~~Ai~~lng~~~~   74 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIE----AEEAIKGLNGQKPS   74 (85)
T ss_dssp             GTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCCCT
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHH----HHHHHHHhCCCEeC
Confidence            34688999999999999999999999999999999865        57899999999    99999999998764

>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=99.69  E-value=1.3e-17  Score=103.45  Aligned_cols=61  Identities=18%  Similarity=0.268  Sum_probs=55.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++|||+|||+++++++|+++|++||+|.+|+|++|        ++||+|.++++    |++|++.||+..+.
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~----A~~ai~~lng~~~~   70 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMD----SQRAIKVLNGITVR   70 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHH----HHHHHHHhCCCEEC
Confidence            578999999999999999999999999999999865        57999999999    99999999986543

>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=99.69  E-value=1.9e-17  Score=102.84  Aligned_cols=63  Identities=22%  Similarity=0.159  Sum_probs=57.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+.++|||+|||+.+|+++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|++.||+..+.
T Consensus         7 ~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~----A~~Ai~~l~g~~~~   77 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD----AKEAKERANGMELD   77 (83)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHH----HHHHHHHHTTEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHH----HHHHHHHcCCCEEC
Confidence            35689999999999999999999999999999999865        57899999999    99999999987543

>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=99.68  E-value=2.1e-17  Score=102.38  Aligned_cols=61  Identities=21%  Similarity=0.292  Sum_probs=55.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++|||+|||+++++++|+++|++||+|.+|+|++|        ++||.|.++++    |+.|++.||+..+.
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~----a~~a~~~l~g~~~~   70 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKD----AEKAINTLNGLRLQ   70 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            467999999999999999999999999999999865        57899999999    99999999987553

>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=99.68  E-value=4.7e-17  Score=101.51  Aligned_cols=62  Identities=18%  Similarity=0.268  Sum_probs=57.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+.+++++|+++|++||+|.+++|++|        ++||+|.++++    |.+|++.||+..+
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g~~~   73 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREE----AQEAISALNNVIP   73 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHHTTCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHH----HHHHHHHHCCCEe
Confidence            35678999999999999999999999999999999976        57999999999    9999999999765

>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=99.68  E-value=3.6e-17  Score=104.94  Aligned_cols=63  Identities=21%  Similarity=0.272  Sum_probs=57.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+++++++|+++|++||+|.+|.|++|        ++||+|.+.++    |..||+.||+..+.
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~----a~~A~~~l~g~~~~   76 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEH----AVKAYAEVDGQVFQ   76 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHH----HHHHHHHTTTEESS
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHH----HHHHHHHcCCCEEC
Confidence            34678999999999999999999999999999999876        57999999999    99999999987653

>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=99.67  E-value=5.2e-17  Score=103.95  Aligned_cols=63  Identities=17%  Similarity=0.202  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .....+|||+|||+.+++++|+++|++||+|+++.|.++ ++||+|.+.++    |++||+.||+..+
T Consensus        12 ~~~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~~g~afV~f~~~~~----a~~Ai~~lng~~~   75 (98)
T d1wg4a_          12 RRSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGMGMVEYLRKED----MEYALRKLDDTKF   75 (98)
T ss_dssp             CSCSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEETTTEEEEEESSHHH----HHHHHHHHSSEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhhcccccccccccceEEEEECCHHH----HHHHHHHhCCCEe
Confidence            445678999999999999999999999999999999966 89999999999    9999999998755

>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=99.67  E-value=5.4e-17  Score=102.91  Aligned_cols=63  Identities=14%  Similarity=0.222  Sum_probs=57.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+|+++|+++|++||+|++|+|++|        ++||.|.+.++    |++|++.||+..+.
T Consensus         7 ~~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~----A~~Ai~~l~g~~~~   77 (93)
T d1x5ua1           7 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEED----ADYAIKIMDMIKLY   77 (93)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHH----HHHHHHHSSSCBCS
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHH----HHHHHHHcCCCEEC
Confidence            34679999999999999999999999999999999876        67999999999    99999999987764

>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=99.67  E-value=1.6e-16  Score=101.49  Aligned_cols=63  Identities=19%  Similarity=0.255  Sum_probs=58.5

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++.++|||+|||+++++++|+++|++||+|+.+++.++  ++||+|.+.++    |++|++.||+..+.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~~~~afV~f~~~~~----A~~A~~~l~~~~i~   79 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDA----AQAACAKMRGFPLG   79 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSSSCCEEEEESSHHH----HHHHHHHHTTCBCS
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeeccccEEEeccCCHHH----HHHHHHHhCCCEeC
Confidence            45789999999999999999999999999999999876  68999999999    99999999998764

>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=99.67  E-value=8e-17  Score=102.12  Aligned_cols=64  Identities=25%  Similarity=0.400  Sum_probs=58.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|+.|      ++||.|.++++    |++|++.||+..+.
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~----a~~Ai~~l~~~~~~   77 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSAD----ADRAREKLHGTVVE   77 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHH----HHHHHHHcCCCEEC
Confidence            345688999999999999999999999999999999866      68999999999    99999999987554

>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=99.67  E-value=4e-17  Score=103.51  Aligned_cols=62  Identities=21%  Similarity=0.298  Sum_probs=57.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+++|||+|||+++|+++|+++|++||+|.+|.|++|        ++||+|.+.++    |..|++.||+..+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~----A~~Ai~~l~g~~~   74 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRAD----AENAMRYINGTRL   74 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHHTTTSEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHH----HHHHHHHhCCCEE
Confidence            45789999999999999999999999999999999875        58999999999    9999999998754

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.66  E-value=4.1e-17  Score=106.64  Aligned_cols=63  Identities=24%  Similarity=0.286  Sum_probs=57.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+.+++++|+++|++||+|++|.|.+.  ++||.|.+.++    |.+|++.||+..+.
T Consensus         8 r~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~~kg~afV~f~~~~~----A~~A~~~lng~~~~   72 (111)
T d1whxa_           8 RSKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLE----ARKAFRHLAYSKFH   72 (111)
T ss_dssp             EEEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCSSSSCEEEEESCHHH----HHHHHHHHTTCBSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeeccCceEEEEEcCHHH----HHHHHHHHcCCccC
Confidence            34689999999999999999999999999999999865  78899999999    99999999988764

>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=99.66  E-value=1.1e-16  Score=99.36  Aligned_cols=63  Identities=17%  Similarity=0.194  Sum_probs=57.9

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+++++|||+|||+.+++++|+++|++||+|.+|+++++   ++||.|.+.++    |..|+..||+..+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~~g~afV~f~~~~~----A~~A~~~l~g~~~   70 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNRHDIAFVEFTTELQ----SNAAKEALQGFKI   70 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTTCSCEEEEESSHHH----HHHHHHHHTTCBS
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecccceeEEEecCCHHH----HHHHHHHhCCcEe
Confidence            456789999999999999999999999999999999854   68999999999    9999999998765

>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=99.66  E-value=6.3e-17  Score=106.30  Aligned_cols=62  Identities=16%  Similarity=0.254  Sum_probs=57.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+++|||+|||+.+++++|+++|++||+|++|+|..+     ++||+|.+.++    |..||+.||+..+
T Consensus         5 ~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~~~kG~afV~f~~~~~----A~~Ai~~l~g~~~   71 (114)
T d2f9da1           5 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFD----AKNACDHLSGFNV   71 (114)
T ss_dssp             TCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTTTTTEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccCCcCCeEEEEECCHHH----HHHHHHHhCCCEE
Confidence            34689999999999999999999999999999999865     78999999999    9999999998764

>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=99.66  E-value=6e-17  Score=102.08  Aligned_cols=63  Identities=13%  Similarity=0.178  Sum_probs=57.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+++|+++|+++|++||+|.+|.|++|      ++||+|.+.++    |+.|+..||+..+.
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~----A~~A~~~l~~~~~~   74 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRD----AAAALAAMNGRKIL   74 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHH----HHHHHHHHTTEEET
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHH----HHHHHHHcCCCEEC
Confidence            34679999999999999999999999999999999866      57999999999    99999999987543

>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=99.66  E-value=9.2e-17  Score=100.39  Aligned_cols=61  Identities=28%  Similarity=0.516  Sum_probs=56.5

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .++|||+|||+++++++|+++|++||+|.+|.++++  ++||+|.+.++    |++|++.||+..+.
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~k~~afV~f~~~~~----A~~A~~~l~g~~i~   70 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTL----AEIAKVELDNMPLR   70 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETTTTEEEEECSSSHH----HHHHHHHHTTCCBT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecccceEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            568999999999999999999999999999999976  57899999999    99999999987654

>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=99.66  E-value=9.3e-17  Score=102.02  Aligned_cols=63  Identities=27%  Similarity=0.465  Sum_probs=56.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHH-hHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNL-WTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l-~~~~~  164 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|         ++||.|.+.++    |.+||+.| |+..+
T Consensus         5 ~~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~----A~~Ai~~l~~~~~~   77 (94)
T d2cpha1           5 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQD----AKKAFNALCHSTHL   77 (94)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHH----HHHHHHHHHTCCBS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHH----HHHHHHHccCCcEE
Confidence            345788999999999999999999999999999999865         57999999999    99999998 76543

>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=99.66  E-value=5.1e-17  Score=99.74  Aligned_cols=59  Identities=17%  Similarity=0.190  Sum_probs=54.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +|||+|||+++++++|+++|++||+|.+|+|++|       ++||+|.+.++    |.+|++.||+..++
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~~g~~~g~afV~f~~~~~----A~~Ai~~l~g~~l~   67 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKAD----ALKAMKQYNGVPLD   67 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHH----HHHHHHHHTTCEET
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            6999999999999999999999999999999976       68999999999    99999999987553

>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=99.66  E-value=3.7e-17  Score=104.65  Aligned_cols=63  Identities=19%  Similarity=0.315  Sum_probs=57.3

Q ss_pred             CCCCceEEEeCCC-CCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLP-QEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp-~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .....+|||+||| +.+++++|+++|++||+|++|.|.+.++||+|.+.++    |++||+.||+..+
T Consensus        12 ~~~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~rg~aFV~f~~~~~----A~~Ai~~lng~~~   75 (98)
T d1wf2a_          12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERN----ARAAVAGEDGRMI   75 (98)
T ss_dssp             SSCCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEETEEEEEEESSHHH----HHHHHHTTTTCEE
T ss_pred             CCCCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEeCCeEEEEECCHHH----HHHHHHHcCCCEE
Confidence            3446789999997 5788999999999999999999999999999999999    9999999998754

>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=99.66  E-value=4.6e-17  Score=101.56  Aligned_cols=60  Identities=18%  Similarity=0.395  Sum_probs=55.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .+|||+|||+.+|+++|+++|++||+|++|+|++|        ++||+|.++++    |..|++.||+..+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~----A~~a~~~l~~~~l~   69 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINV----TDQAIAGLNGMQLG   69 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHH----HHHHHHTSSSCCCS
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            57999999999999999999999999999999875        57899999999    99999999987654

>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=99.66  E-value=9e-17  Score=103.57  Aligned_cols=62  Identities=23%  Similarity=0.286  Sum_probs=56.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +++++|||+|||+++++++|+++|++||.|+++.++.|        ++||+|.+.++    |+.||..||+..+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~----A~~Ai~~lng~~~   85 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVS----AQAAIQSMNGFQI   85 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHH----HHHHHHHhCCCEE
Confidence            45688999999999999999999999999999999865        58999999999    9999999998754

>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=99.66  E-value=1.8e-16  Score=100.82  Aligned_cols=64  Identities=20%  Similarity=0.327  Sum_probs=57.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+.++|||+|||+++++++|+++|++||.|..+.+..+     ++||.|.+.++    |+.||+.||+..+.
T Consensus        11 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~~g~afV~f~~~e~----a~~Ai~~l~g~~~~   79 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRD----AEDAVYGRDGYDYD   79 (95)
T ss_dssp             CCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSSSSSCCEEEEESCHHH----HHHHHHHHTTCEET
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccccccceEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            345679999999999999999999999999999998754     68999999999    99999999987653

>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=99.66  E-value=5.1e-17  Score=102.42  Aligned_cols=59  Identities=32%  Similarity=0.433  Sum_probs=53.7

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ....++|||+|||+++|+++|+++|++||+|.+|.|++|        ++||+|.+.++    |++||+++|
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~----a~~al~~~~   71 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYET----QVKVMSQRH   71 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHH----HHHHHHSCE
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHH----HHHHHhcCC
Confidence            345789999999999999999999999999999999976        67899999999    999998765

>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=99.65  E-value=3.4e-17  Score=103.01  Aligned_cols=61  Identities=23%  Similarity=0.331  Sum_probs=56.3

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||+++|+++|+++|++||+|.+|.|++|        ++||.|.+.++    |++|+..||+..+
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~----A~~ai~~l~~~~i   72 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED----AAAAIDNMNESEL   72 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHH----HHHHHHHHTTEEE
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHH----HHHHHHHcCCCEE
Confidence            4689999999999999999999999999999999865        57899999999    9999999998754

>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=99.65  E-value=4.2e-17  Score=99.87  Aligned_cols=59  Identities=29%  Similarity=0.484  Sum_probs=53.3

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++|||+|||+++|+++|+++|++||+|++++|++|        ++||.|.++++    |.+|+. +|+..++
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~----a~~al~-~~~~~i~   67 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAG----VDKVLA-QSRHELD   67 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTH----HHHHHH-TTTCCCS
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHH----HHHHHH-cCCCEEC
Confidence            68999999999999999999999999999999876        57899999999    999996 6776653

>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=99.65  E-value=1.1e-16  Score=100.41  Aligned_cols=62  Identities=16%  Similarity=0.224  Sum_probs=56.3

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+++|||+|||+.+|+++|+++|++||+|.+|+|++|        ++||+|.+.++    |++|+..||+..+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~----A~~A~~~lng~~l   74 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ----ALAAKEALNGAEI   74 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHH----HHHHHHHcCCCEE
Confidence            45789999999999999999999999999999999876        47999999999    9999999998654

>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=99.65  E-value=4.7e-17  Score=100.37  Aligned_cols=59  Identities=19%  Similarity=0.243  Sum_probs=54.6

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +|||+|||+.+|+++|+++|++||+|.+|+|++|        ++||+|.++++    |+.|++.||+..++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~----a~~ai~~l~g~~~~   68 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPAD----AERALDTMNFDVIK   68 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHTTSTTCEET
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHH----HHHHHHHcCCCEEC
Confidence            5999999999999999999999999999999975        67899999999    99999999987654

>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=99.65  E-value=1.4e-16  Score=101.59  Aligned_cols=62  Identities=16%  Similarity=0.291  Sum_probs=56.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +..++|||+|||..+++++|+++|++||+|++|+|++|  ++||+|.++++    |++|+..||+..+
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~kg~afV~f~~~~~----A~~Ai~~l~~~~i   79 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKGYSFVRFSTHES----AAHAIVSVNGTTI   79 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHTTCEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEecceEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            34678999999999999999999999999999999987  57899999999    9999999998654

>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=99.64  E-value=4.1e-16  Score=100.26  Aligned_cols=62  Identities=11%  Similarity=0.236  Sum_probs=57.0

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++++++|+++|++||+|..+.++.+       ++||+|.+.++    |.+||+.||+..+.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~----A~~Ai~~lng~~i~   85 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEK----CEAVIGHFNGKFIK   85 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHH----HHHHHHHHBTCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHH----HHHHHHHhCCCEEC
Confidence            4589999999999999999999999999999998865       68999999999    99999999998754

>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=99.64  E-value=1.6e-16  Score=100.07  Aligned_cols=62  Identities=24%  Similarity=0.349  Sum_probs=56.4

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++++++|+++|++||+|..+.++++        ++||.|.++++    |++|++.||+..+.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~----a~~Ai~~l~~~~~~   73 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDD----AKDAMMAMNGKSVD   73 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHH----HHHHHHHHTTCCTT
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHH----HHHHHHHcCCCEEC
Confidence            3578999999999999999999999999999998864        57999999999    99999999987653

>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=99.63  E-value=2.1e-16  Score=95.41  Aligned_cols=58  Identities=19%  Similarity=0.327  Sum_probs=53.9

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       104 lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      |||+|||+++|+++|+++|++||+|..++++++        ++||+|.++++    |.+|++.||+..++
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~----A~~Ai~~lng~~~~   66 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSA----AQKAVTALKASGVQ   66 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHH----HHHHHHHHHHHTCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHH----HHHHHHHhCCCEEC
Confidence            799999999999999999999999999999865        57899999999    99999999998754

>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=99.63  E-value=7.6e-17  Score=101.40  Aligned_cols=61  Identities=23%  Similarity=0.283  Sum_probs=55.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+|||+|||+++|+++|+++|++||.|.+++|++|      ++||+|.+.++    |++||+.||+..++
T Consensus         8 ~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~----A~~Ai~~l~g~~~~   74 (89)
T d1cvja2           8 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEA----AERAIEKMNGMLLN   74 (89)
T ss_dssp             TTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHH----HHHHTTSSSEEEET
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHH----HHHHHHHcCCCEEC
Confidence            467999999999999999999999999999999975      68999999999    99999999986543

>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=99.63  E-value=1.4e-16  Score=102.81  Aligned_cols=60  Identities=30%  Similarity=0.509  Sum_probs=54.5

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....++|||+|||+.+++++|+++|++||+|.+|.|++|        ++||.|.+.++    |++||+.+|+
T Consensus         7 d~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~----A~~Ai~~~~~   74 (103)
T d2cqda1           7 DTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAA----AERACKDPNP   74 (103)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHH----HHHHHTCSSC
T ss_pred             CCCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHH----HHHHHHHCCC
Confidence            345678999999999999999999999999999999865        57999999999    9999998874

>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=99.63  E-value=1.8e-16  Score=96.50  Aligned_cols=56  Identities=30%  Similarity=0.513  Sum_probs=50.9

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      +|||+|||+++|+++|+++|++||+|.+|.|++|        ++||+|.+.++    |++||+ +++..
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~----a~~Al~-~~~~~   64 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESES----VDKVMD-QKEHK   64 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHH----HHHHHH-TCCCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHH----HHHHHh-cCCCE
Confidence            5999999999999999999999999999999875        67999999999    999996 66554

>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=99.62  E-value=1.2e-16  Score=97.28  Aligned_cols=52  Identities=31%  Similarity=0.601  Sum_probs=48.7

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHH
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      +|||+|||+++|+++|+++|++||+|.+|.|++|        ++||+|.+.++    |++||+.
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~----a~~al~~   60 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEP----VKKIMEK   60 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHH----HHHHTTC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHH----HHHHHhh
Confidence            6999999999999999999999999999999976        67999999999    9999865

>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=99.62  E-value=2.1e-16  Score=99.55  Aligned_cols=62  Identities=24%  Similarity=0.363  Sum_probs=56.6

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+++++++|+++|++||+|.+|.|++|        ++||.|.+.++    |++||+.||+..+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~----A~~Ai~~l~g~~~   75 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRED----AARAIAGVSGFGY   75 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHH----HHHHHHHTTTCEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHH----HHHHHHHhCCCEE
Confidence            34689999999999999999999999999999999876        57999999999    9999999998654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.6e-16  Score=103.35  Aligned_cols=62  Identities=18%  Similarity=0.162  Sum_probs=56.8

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+..+|||+|||+.+|+++|+++|++||.|++|.|+++    ++||+|.+.++    |++|+..||+..+
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~~~g~aFV~f~~~e~----A~~Ai~~ln~~~l   70 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVS----AQHAKLSLDGQNI   70 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEETTEEEEEEEESCHHH----HHHHHHHHHSCCS
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeCCCCeEEEEECCHHH----HHHHHHHHCCCEe
Confidence            35678999999999999999999999999999999754    68999999999    9999999998765

>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=99.62  E-value=2e-16  Score=98.61  Aligned_cols=57  Identities=25%  Similarity=0.330  Sum_probs=52.7

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-----------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-----------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       104 lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-----------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      |||+|||+++|+++|+++|++||+|.+|.|++|           ++||+|.+.++    |++|++.||+..+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~----A~~A~~~~~~~~~   68 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ----AQKALKQLQGHTV   68 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHH----HHHHHHHSTTCEE
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHH----HHHHHHHhCCCEE
Confidence            899999999999999999999999999999864           47899999999    9999999998654

>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=99.61  E-value=6.3e-16  Score=104.88  Aligned_cols=62  Identities=19%  Similarity=0.286  Sum_probs=56.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++|+++|+++|++||+|++|.|++|        ++||+|.+.++    |++||+.||+..+.
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~----A~~Ai~~lng~~~~  110 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSS----AQQAIAGLNGFNIL  110 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHH----HHHHHHHTTTEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHH----HHHHHHHhCCCEEC
Confidence            4578999999999999999999999999999999865        58999999999    99999999987654

>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=99.61  E-value=7.1e-16  Score=99.09  Aligned_cols=59  Identities=19%  Similarity=0.353  Sum_probs=54.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++|||+|||+++++++|+++|++||+|.+|+|++|        ++||.|.+.++    |.+|+ +||+..+
T Consensus        18 ~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~----a~~A~-~l~g~~~   84 (101)
T d2cq4a1          18 ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS----VPLAI-GLTGQRL   84 (101)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGG----HHHHH-HHTTEEE
T ss_pred             CCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHH----HHHHH-HHCCCEE
Confidence            478999999999999999999999999999999976        67999999999    99999 4998654

>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=99.61  E-value=2.4e-16  Score=97.34  Aligned_cols=60  Identities=8%  Similarity=0.102  Sum_probs=54.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++|||+|||+++|+++|+++|++||+|..+.++++        ++||+|.+.++    |.+|++.||+..++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~----A~~Ai~~l~g~~~~   69 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKED----ARYCVEKLNGLKIE   69 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHH----HHHHHHHHTTCEET
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHH----HHHHHHHhCCCEEC
Confidence            78999999999999999999999999998887644        57999999999    99999999987543

>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=99.61  E-value=1.3e-16  Score=100.38  Aligned_cols=62  Identities=16%  Similarity=0.216  Sum_probs=55.4

Q ss_pred             CCCceEEEeCCCCCCCHHHH---HHHhhcccceEEEEecCc-----------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDL---RRYFSRFGRILDVYVPKR-----------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L---~~~F~~fG~v~~v~i~~d-----------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ...++|||+|||+++++++|   +++|++||+|.+|.|++|           ++||+|.+.++    |.+||+.||+..+
T Consensus         6 iq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~----A~~Ai~~lng~~~   81 (89)
T d2cpia1           6 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSED----ALRAIQCVNNVVV   81 (89)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHH----HHHHHHHHTTEEE
T ss_pred             EecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchh----HHHHHHHhCCCEE
Confidence            34678999999999999999   778999999999999876           35899999999    9999999998754

>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=99.61  E-value=5.9e-16  Score=100.72  Aligned_cols=61  Identities=13%  Similarity=0.120  Sum_probs=55.5

Q ss_pred             CceEEEeCCCC-CCCHHHHHHHhhcccceEEEEecCc---ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          101 GKKIFVGRLPQ-EATAEDLRRYFSRFGRILDVYVPKR---FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       101 ~~~lfV~nLp~-~~te~~L~~~F~~fG~v~~v~i~~d---~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +++|||+|||+ .+|+++|+++|++||+|.+|.|++|   ++||+|.+.++    |.+|++.||+..+.
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~kg~afV~f~~~~~----A~~ai~~lng~~l~   66 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGNQ----AQLAMSHLNGHKLH   66 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTSCCEEEEESCHHH----HHHHHHHHTTCBCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecccceEEEEECCHHH----HHHHHHHhCCCEEC
Confidence            47899999965 5999999999999999999999976   69999999999    99999999987654

>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=99.60  E-value=8.7e-16  Score=96.22  Aligned_cols=62  Identities=13%  Similarity=0.182  Sum_probs=56.1

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC----cceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK----RFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~----d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +++++|||+|||+++++++|+++|++||.|..+.+..    .++||+|.+.++    |.+|+..||+..+
T Consensus         8 pPs~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~afV~f~~~~~----A~~A~~~l~~~~i   73 (88)
T d2adca2           8 PPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE----AVQALIDLHNHDL   73 (88)
T ss_dssp             CSCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSSSTTCEEEEESSHHH----HHHHHHHHTTCBS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeecccceeEEEECCHHH----HHHHHHhccCCEe
Confidence            4578999999999999999999999999999887763    378999999999    9999999999765

>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=99.60  E-value=2.7e-16  Score=101.63  Aligned_cols=62  Identities=27%  Similarity=0.436  Sum_probs=56.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..++|||+|||+++++++|+++|++||+|.+|.|++|        ++||+|.+.++    |++|++.||+..+.
T Consensus         7 ~~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~----a~~ai~~l~~~~~~   76 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET----ALSAMRNLNGREFS   76 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHH----HHHHHHHSSSBSCS
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHH----HHHHHHHcCCCEEC
Confidence            3578999999999999999999999999999999865        57999999999    99999999988764

>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=99.60  E-value=4.7e-16  Score=96.67  Aligned_cols=58  Identities=26%  Similarity=0.374  Sum_probs=51.7

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ..++|||+|||+++|+++|+++|++||+|.++.|++|        ++||.|.+.++    |++||.. ++.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~----a~~ai~~-~~~   70 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE----VDAAMNA-RPH   70 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHT-CSC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHH----HHHHHHh-CCC
Confidence            3579999999999999999999999999999999866        67899999999    9999864 443

>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=99.59  E-value=4.1e-16  Score=97.75  Aligned_cols=60  Identities=17%  Similarity=0.221  Sum_probs=53.9

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhccc-ceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFG-RILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG-~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .++|||+|||+++++++|+++|++|| .+..+...+.++||+|.+.++    |++||+.||+..+
T Consensus         5 s~~i~V~nLp~~~t~~~l~~lF~~~G~~~~~~~~~kg~afV~f~~~~~----A~~Ai~~ln~~~~   65 (88)
T d1wg1a_           5 SSGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTAFVTLLNGEQ----AQNAIQMFHQYSF   65 (88)
T ss_dssp             CCCEEEESCCSSCCHHHHHHHTCSSCCCCEEEEGGGTEEEECCSCHHH----HHHHHHHHTTEEE
T ss_pred             CCEEEEeCCCCccChHHHHHHHHhcCceeeeeeccCCceEEEECCHHH----HHHHHHHhCCCEE
Confidence            57899999999999999999999999 566666667899999999999    9999999998754

>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=99.59  E-value=6.3e-16  Score=94.96  Aligned_cols=61  Identities=23%  Similarity=0.248  Sum_probs=55.2

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ..+++|||+||+  +|+++|+++|++||.|.+|.+.++  ++||+|.+.++    |..|+..||+..+.
T Consensus         3 ~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~~~~afV~f~~~~~----A~~Ai~~lng~~~~   65 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPRNCAFVTYEKMES----ADQAVAELNGTQVE   65 (79)
T ss_dssp             CCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETTTTEEEEECSSHHH----HHHHHHHHTTCBCS
T ss_pred             CCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccCCCEEEEEEcccHH----HHHHHHHhCCCEEC
Confidence            457899999986  899999999999999999999765  77899999999    99999999988764

>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=99.59  E-value=1.4e-15  Score=97.09  Aligned_cols=60  Identities=20%  Similarity=0.257  Sum_probs=54.7

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ..+++|||+|||+++|+++|+++|++||+|.++.++.+        ++||+|.++++    |.+||+.||..
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~----a~~ai~~l~~~   73 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEA----AQKCLAAASLE   73 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHH----HHHHHHHHCTT
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHH----HHHHHHHcccc
Confidence            35689999999999999999999999999999999865        68999999999    99999999743

>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=99.58  E-value=2e-15  Score=94.59  Aligned_cols=61  Identities=15%  Similarity=0.202  Sum_probs=55.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      .+++++|||+|||+.+++++|+++|++||.|.++.++++  ++||+|.+.++    |+.|++.|++.
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~~~~afV~f~~~e~----A~~a~~~~~~~   67 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQAFLELATEEA----AITMVNYYSAV   67 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHHHS
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcccccccccccccceEEEEEeCCHHH----HHHHHHHHccC
Confidence            456899999999999999999999999999999999854  78999999999    99999988654

>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=99.58  E-value=2.9e-16  Score=96.75  Aligned_cols=57  Identities=23%  Similarity=0.293  Sum_probs=52.2

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ++|||+|||+++|+++|+++|++||.|.++.++  +.++||+|.++++    |.+|++.||+.
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~rg~aFV~f~~~~~----A~~Ai~~lng~   60 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNW----AIRAIETLSGK   60 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEETTEEEECCSCHHH----HHHHHHHHTTT
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecccceEEEEECCHHH----HHHHHHHhCCC
Confidence            579999999999999999999999999887666  5578999999999    99999999975

>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=99.57  E-value=6.3e-16  Score=94.04  Aligned_cols=57  Identities=18%  Similarity=0.218  Sum_probs=51.5

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ++|||+|||+++++++|+++|++||+|..++|+++      ++||.|.++++    |.+|+. ||+..
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~~~~~~afV~F~~~~~----a~~Al~-~~~~~   63 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDG----ALAAIT-KTHKV   63 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHH----HHHHHT-TTTCE
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHH----hHHHHH-hcCcE
Confidence            47999999999999999999999999999999866      57899999999    999984 77654

>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=99.56  E-value=8e-15  Score=94.55  Aligned_cols=62  Identities=13%  Similarity=0.059  Sum_probs=56.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ..++++|||+|||+.+|+++|+++|++||.|+++.+.++  ++||+|.+.++    |+.|+..|+...
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~k~~AfV~f~~~e~----A~~ai~~~~~~~   75 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDS----AKECVTFAADVP   75 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETTTTEEEEEESSHHH----HHHHHHHHHHSC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEecceeEEEEeCCHHH----HHHHHHHHcCCC
Confidence            446789999999999999999999999999999999865  68999999999    999999987654

>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=99.56  E-value=8.2e-16  Score=93.42  Aligned_cols=57  Identities=32%  Similarity=0.523  Sum_probs=51.3

Q ss_pred             eEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          103 KIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       103 ~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +|||+|||+++|+++|+++|++||.|..+.++.+        ++||+|.+.++    |++|++ ||+..+
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~----a~~al~-~~~~~l   65 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI----VEKVCE-IHFHEI   65 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHH----HHHHHH-CSSCCB
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHH----HHHHHh-cCCCEE
Confidence            5999999999999999999999999999999865        57899999999    999986 887654

>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=99.56  E-value=1.6e-15  Score=93.07  Aligned_cols=58  Identities=26%  Similarity=0.428  Sum_probs=51.0

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      .++|||+|||+++|+++|+++|++||.|..+.++.|        ++||.|.++++    +++|++ ||+..
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~----~~~al~-~~~~~   67 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDS----VDKIVI-QKYHT   67 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHH-CSCCE
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHH----HHHHHH-hCCCE
Confidence            479999999999999999999999999999999865        57899999877    888874 66654

>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=99.56  E-value=2.7e-15  Score=93.55  Aligned_cols=63  Identities=16%  Similarity=0.132  Sum_probs=55.0

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEe--cCcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYV--PKRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i--~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...++|||+|||+++++++|+++|++||.|..+.+  .++++||.|.++++    |..|+..||+..+.
T Consensus         6 ~~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~~rg~afV~f~~~~~----A~~Ai~~l~~~~i~   70 (86)
T d2cpda1           6 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNRED----AVEAMKALNGKVLD   70 (86)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEECSSEEEEEESSHHH----HHHHHHHHSSEEET
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEccccEEEEEEeCCHHH----HHHHHHHcCCCEEC
Confidence            34578999999999999999999999988776665  46788999999999    99999999987543

>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=99.55  E-value=3.4e-15  Score=94.04  Aligned_cols=62  Identities=24%  Similarity=0.402  Sum_probs=54.8

Q ss_pred             CCceEEEeCCCCCCCHHHHHH----HhhcccceEEEEecC-----cceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRR----YFSRFGRILDVYVPK-----RFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~----~F~~fG~v~~v~i~~-----d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++++|||+|||+.+++++|++    +|++||+|.+|.+.+     .++||+|.+.++    |.+|++.||+..++
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~~~~~g~afV~F~~~~~----A~~A~~~~~~~~~~   72 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSS----ATNALRSMQGFPFY   72 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHHHHHTTCEEEEESSHHH----HHHHHHHHTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeeeccCCCceEEEECCHHH----HHHHHHHhCCCEEC
Confidence            368999999999999998864    689999999999974     589999999999    99999999987543

>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=99.55  E-value=1.7e-15  Score=94.86  Aligned_cols=55  Identities=29%  Similarity=0.650  Sum_probs=50.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecC---cceeEEecCCcccHHHHHHHHHH
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPK---RFWFCHLCGRSCSRSCFSKVSRN  158 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~---d~~fv~f~~~~~~~~~a~~Ai~~  158 (171)
                      ..++|||+|||+++|+++|+++|++||.|.+|+++.   .++||+|.+.++    |++|+.+
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~~~gfafV~f~~~~~----a~~a~~~   61 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQI----AQSLCGE   61 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSSCCSCCEEECSCHHH----HHHTTTC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeeccCceEEEEECCHHH----HHHHHhC
Confidence            468999999999999999999999999999999874   478999999988    9998864

>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=99.54  E-value=2.8e-15  Score=95.38  Aligned_cols=59  Identities=20%  Similarity=0.362  Sum_probs=53.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccc-eEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGR-ILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~-v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ++|||+|||..+++++|+++|++||+ |.++.|++|         ++||+|.++++    |..|++.|++..+
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~----A~~Ai~~l~~~~~   70 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRA----AAMARRKLMPGRI   70 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHH----HHHHHTTTTTCCS
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHH----HHHHHHHHcCCCe
Confidence            68999999999999999999999996 999999865         57999999999    9999999986554

>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=99.54  E-value=1.1e-15  Score=94.73  Aligned_cols=57  Identities=23%  Similarity=0.303  Sum_probs=51.1

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcccceEEE-EecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          104 IFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       104 lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      |||+|||+++|+++|+++|++||.|.++ .|++|        ++||+|.+.++    |++|++.||+..+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~----a~~Ai~~~~g~~~   66 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA----SDAAIEAMNGQYL   66 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHH----HHHHHHTTTTCEE
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHH----HHHHHHhCCCcEE
Confidence            7999999999999999999999999765 67754        57899999999    9999999998654

>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=99.53  E-value=8.5e-16  Score=96.89  Aligned_cols=63  Identities=16%  Similarity=0.142  Sum_probs=55.6

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .....+|||+|||+.+++++|+++|++||.|.++.|+.+       ++||.|.+.++    |.+||+ ||+..+.
T Consensus        10 ~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~----a~~Al~-~~g~~~~   79 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAED----LEKALE-LTGLKVF   79 (91)
T ss_dssp             CSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHH----HHHHHH-GGGEEET
T ss_pred             CCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHH----HHHHHh-cCCcEEC
Confidence            345679999999999999999999999999999988643       78999999999    999995 9987654

>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=99.53  E-value=1.5e-15  Score=94.73  Aligned_cols=60  Identities=20%  Similarity=0.304  Sum_probs=52.0

Q ss_pred             CCceEEEeCCCCCCC-HHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEAT-AEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~t-e~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|||+|||++++ +++|+++|++||+|++|+|+.+         ++||+|.+.++    |++|++ ||+..+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~----a~~Al~-~n~~~~   72 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDS----AERALQ-MNRSLL   72 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHH----HHHHGG-GTTEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHH----HHHHHh-cCCCEE
Confidence            368999999999976 5669999999999999999753         57899999999    999995 988654

>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=99.53  E-value=2.7e-15  Score=95.44  Aligned_cols=63  Identities=16%  Similarity=0.097  Sum_probs=55.8

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEec---CcceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP---KRFWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~---~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....++|||+|||+++|+++|+++|++||.|..+...   +.++||.|.+.++    |+.|+..||+..+
T Consensus        13 ~~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~~~~~~~~afV~f~~~~~----A~~A~~~l~~~~~   78 (96)
T d1fjca_          13 VRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEAD----AEKNLEEKQGAEI   78 (96)
T ss_dssp             TTGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEETTEEEEEEEEEESSHHH----HHHHHHHTTEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeeecCccccEEEEEeCCHHH----HHHHHHHcCCCEE
Confidence            3457899999999999999999999999999888755   4578999999999    9999999998654

>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=99.53  E-value=3.6e-15  Score=93.74  Aligned_cols=49  Identities=20%  Similarity=0.390  Sum_probs=45.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~   49 (171)
                      ||+|+.||+|||||||+|.++++|++||++++.|+||.|.|+++.+++.
T Consensus        40 i~~d~~tg~srG~aFV~f~~~~~a~~al~~~~~l~Gr~i~v~~a~~k~~   88 (90)
T d2cqga1          40 VKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQS   88 (90)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHSCEEETTEEEEEECCCTTCC
T ss_pred             eccCCCCcccCCEEEEEECCHHHHHHHHhcCCccCCEEeEEEeCCCCCC
Confidence            5789999999999999999999999999998999999999999987654

>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=99.53  E-value=3.5e-15  Score=96.11  Aligned_cols=57  Identities=26%  Similarity=0.470  Sum_probs=51.2

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      .++|||+|||+++++++|+++|++||.|..+.|++|        ++||.|.+.++    |.+|++ |++.
T Consensus        20 ~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~----a~~al~-~~~~   84 (103)
T d1x4ba1          20 FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAE----VDAAMA-ARPH   84 (103)
T ss_dssp             HTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHH----HHHHHT-SCSE
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHH----HHHHHH-hCCC
Confidence            478999999999999999999999999999999865        67999999999    999985 4443

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.52  E-value=5.6e-15  Score=94.79  Aligned_cols=62  Identities=11%  Similarity=0.143  Sum_probs=55.9

Q ss_pred             CCCceEEEeC--CCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGR--LPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~n--Lp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+..+|||.|  ||+.+|+++|+++|++||.|+++.++++  ++||+|.+.++    |++|++.||+..+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~k~~aFV~f~~~e~----A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEE----SKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTTCSCEEEEESSHHH----HHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccCccEEEEEECCHHH----HHHHHHHhCCCCC
Confidence            4567899955  9999999999999999999999999976  78999999999    9999999998754

>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=99.51  E-value=5.2e-15  Score=92.04  Aligned_cols=58  Identities=14%  Similarity=0.316  Sum_probs=51.6

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ..++|||+|||+++|+++|+++|+.||+|.+|.|+++       ++||.|.++++    |.+|++ +++.
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~----a~~al~-~~~~   69 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIES----AKKFVE-TPGQ   69 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHH----HHHHHT-CCCC
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHH----HHHHHH-HCCC
Confidence            3689999999999999999999999999999999855       67999999999    999985 4543

>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=99.51  E-value=1.1e-14  Score=93.02  Aligned_cols=59  Identities=15%  Similarity=0.250  Sum_probs=52.3

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      ...+++|||+|||+. +|+++|.++|++||.|.++.++++  ++||.|.+.++    |..|++.++
T Consensus        15 ~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~k~~afV~f~~~~~----A~~Ai~~~~   76 (99)
T d1x4fa1          15 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQAFIEMETRED----AMAMVDHCL   76 (99)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETTTTEEEEECSSHHH----HHHHHHHHH
T ss_pred             CCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeecCCcEEEEecchHH----HHHHHHHHh
Confidence            345789999999985 899999999999999999999865  68999999999    999998544

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.4e-14  Score=94.79  Aligned_cols=59  Identities=17%  Similarity=0.101  Sum_probs=52.4

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCC-cccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGR-SCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~-~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..+||+|||+.+|+++|+++|++||+|.+|.|+++  ++||.|.++ ++    |..|+..||+..+
T Consensus        12 ~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~kg~gfV~F~~~~~~----A~~a~~~~~~~~l   73 (113)
T d1owxa_          12 LLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAKEGIILFKEKAKE----ALGKAKDANNGNL   73 (113)
T ss_dssp             EEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCSEEEEEESSCHHH----HHHHHHHTTTSCB
T ss_pred             eEEEECCCCCCCCHHHHHHHHHhcCChheEEEecCCceEEEEecCcHHH----HHHHHHHhcCCce
Confidence            45699999999999999999999999999999966  678999997 56    8899999987644

>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=99.50  E-value=2e-14  Score=92.61  Aligned_cols=59  Identities=20%  Similarity=0.383  Sum_probs=49.9

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc---------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR---------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d---------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      +.++|||+|||+++|+++|+++|++|| |+++.++.+         ++||+|.+.++    |++|+ .||+..+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~----a~~~~-~~~~~~~   81 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDS----LLSAL-SLNEESL   81 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHH----HHHHH-GGGTCEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHH----HHHHH-HcCCCEE
Confidence            468999999999999999999999999 778877643         67999999988    87555 6887654

>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=99.50  E-value=1e-14  Score=93.48  Aligned_cols=64  Identities=13%  Similarity=0.064  Sum_probs=54.2

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceE--------EEEecCc--------ceeEEecCCcccHHHHHHHHHHHhH
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRIL--------DVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWT  161 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~--------~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~  161 (171)
                      ....++|||+|||+.+|+++|+++|++||+|.        .+.+.+|        ++||+|.++++    |.+||+.||+
T Consensus         5 ~~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~----a~~Ai~~l~g   80 (101)
T d2cpea1           5 DSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPT----AKAAVEWFDG   80 (101)
T ss_dssp             CCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHH----HHHHHHHHTT
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHH----HHHHHHHhCC
Confidence            34578999999999999999999999999985        3444443        58999999999    9999999998


Q ss_pred             hCCC
Q 030822          162 AGCN  165 (171)
Q Consensus       162 ~~~~  165 (171)
                      ..++
T Consensus        81 ~~~~   84 (101)
T d2cpea1          81 KDFQ   84 (101)
T ss_dssp             CEET
T ss_pred             CEEC
Confidence            6543

>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=99.50  E-value=1.9e-14  Score=90.13  Aligned_cols=61  Identities=10%  Similarity=0.068  Sum_probs=54.6

Q ss_pred             CCCCceEEEeCCCCC-CCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRLPQE-ATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~-~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ..++++|||+|||.. +|+++|.++|++||.|.+|.++++  ++||+|.+.++    |..|++.|+..
T Consensus         5 ~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k~~afV~f~~~~~----A~~A~~~l~~~   68 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKINEAFIEMATTED----AQAAVDYYTTT   68 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSSSCEEEEESSHHH----HHHHHHHHHHS
T ss_pred             CCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccceEEEEEEcchhh----HHHHHHHHhhC
Confidence            345789999999986 889999999999999999999865  78999999999    99999988654

>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=99.49  E-value=1.8e-14  Score=87.43  Aligned_cols=57  Identities=16%  Similarity=0.251  Sum_probs=50.2

Q ss_pred             EEEeCCCCCCCHHHHHHHhhcccceEEEEec--CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          104 IFVGRLPQEATAEDLRRYFSRFGRILDVYVP--KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       104 lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~--~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      |||+|||+++++++|+++|++|| +..+.+.  +.++||.|.+.++    |++|+..||+..++
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~~~~g~afv~f~~~~~----A~~Ai~~ln~~~~~   59 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYKGTAFVTLLNGEQ----AEAAINTFHQSRLR   59 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTTTEEEEEESSHHH----HHHHHHHHTTEESS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeecccceeEEEEECCHHH----HHHHHHHhCCccCC
Confidence            79999999999999999999999 5555554  5678999999999    99999999987654

>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=99.49  E-value=2.5e-15  Score=96.56  Aligned_cols=62  Identities=16%  Similarity=0.108  Sum_probs=56.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++++|||+|||+.+++++|+++|++||.|..+.++.+        ++||.|.+.++    |..|++.||+..+.
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~----A~~Ai~~l~g~~~~   86 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEI----AWQALHLVNGYKLY   86 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHH----HHHHHHHSTTCBCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHH----HHHHHHHhCCCEEC
Confidence            4689999999999999999999999999999988753        67899999999    99999999987653

>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=99.48  E-value=2.7e-14  Score=91.70  Aligned_cols=62  Identities=16%  Similarity=0.130  Sum_probs=52.4

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      .....+|||+|||+++|+++|+++|+.||. +.+.++++       ++||.|.+.++    |++|++ ||+..+.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~----a~~Al~-~~~~~i~   80 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHED----AVAAMA-KDKANMQ   80 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHH----HHHHHT-TSSCCSS
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHH----HHHHHH-cCCCEEC
Confidence            445789999999999999999999999984 56777655       57999999999    999985 8876553

>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=99.47  E-value=7.4e-14  Score=89.90  Aligned_cols=62  Identities=11%  Similarity=0.100  Sum_probs=52.3

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ......|||+|||+++|+++|+++|++||.|..+.++.+        ++||.|.++++    |++|++ ||+..+
T Consensus        12 ~~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~----a~~a~~-~~~~~i   81 (104)
T d1wg5a_          12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEI----AEKALK-KHKERI   81 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHH----HHHHHT-TTTCCS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHH----HHHHHh-hCCCEE
Confidence            345668999999999999999999999999988666543        68999999999    998885 877654

>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=99.45  E-value=1.1e-14  Score=90.71  Aligned_cols=63  Identities=11%  Similarity=0.054  Sum_probs=53.9

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEE-EecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      +..+.|||+|||+++++++|+++|+.||.|... .+..+       ++||.|.+.++    |.+|++.||+..+.
T Consensus         7 p~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~----a~~Ai~~l~~~~l~   77 (86)
T d2cqpa1           7 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDE----ATAAVIDLNDRPIG   77 (86)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHH----HHHHHHHTTTCEET
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHH----HHHHHHHcCCCEEC
Confidence            446789999999999999999999999999764 44422       67999999999    99999999987653

>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=99.44  E-value=9.2e-14  Score=85.78  Aligned_cols=49  Identities=24%  Similarity=0.371  Sum_probs=44.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..++|++|.|.++.++..
T Consensus        31 i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~~   81 (83)
T d1x5ta1          31 IMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDS   81 (83)
T ss_dssp             ECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCCC
T ss_pred             EEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCCc
Confidence            478999999999999999999999999984  7899999999999987643

>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=99.41  E-value=6.6e-15  Score=92.49  Aligned_cols=59  Identities=17%  Similarity=0.241  Sum_probs=51.7

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEec-------------CcceeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVP-------------KRFWFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~-------------~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ++|||+|||+.+|+++|+++|++||.|..+.+.             +.++||+|.+.++    |+.|++ ||+..+.
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~----a~~a~~-l~g~~~~   73 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE----TTQAMA-FDGIIFQ   73 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTT----TTTGGG-GSSCCSS
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHH----HHHHHh-hCCcEEC
Confidence            689999999999999999999999998877764             2368999999999    999985 9887764

>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=99.40  E-value=9.5e-14  Score=84.13  Aligned_cols=44  Identities=32%  Similarity=0.561  Sum_probs=40.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      |++|+.||++||||||+|.+.++|++||+. .+.|+|+.|.|+.|
T Consensus        31 i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1          31 LPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             ccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            689999999999999999999999999985 78999999999865

>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=99.40  E-value=4.5e-14  Score=86.05  Aligned_cols=44  Identities=32%  Similarity=0.549  Sum_probs=41.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      |++|+.||+|||||||+|.++++|++||+. ++.++||.|.|+.|
T Consensus        32 i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_          32 VMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             EECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             eecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            578999999999999999999999999984 89999999999976

>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=99.40  E-value=2.1e-13  Score=85.94  Aligned_cols=49  Identities=31%  Similarity=0.585  Sum_probs=44.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+  ++..|+|++|.|++|.++..
T Consensus        41 ~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~~~~~   91 (93)
T d1x5ua1          41 MPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASAHNK   91 (93)
T ss_dssp             CCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETTTTSC
T ss_pred             eeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            57899999999999999999999999998  47899999999999987643

>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=99.40  E-value=1.6e-13  Score=83.14  Aligned_cols=44  Identities=32%  Similarity=0.572  Sum_probs=40.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      |++|+.||++||||||+|.++++|++||+. ++.|+|+.|.|++|
T Consensus        31 i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_          31 LKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             cccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            688999999999999999999999999995 78999999999864

>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=99.39  E-value=2.6e-13  Score=84.87  Aligned_cols=47  Identities=32%  Similarity=0.543  Sum_probs=43.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+.  ++.|+|+.|.|++|.|+
T Consensus        37 i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p~   85 (89)
T d2cqba1          37 IPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKPM   85 (89)
T ss_dssp             CCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             cccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCCC
Confidence            578999999999999999999999999984  88999999999999875

>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=99.39  E-value=1.4e-13  Score=86.22  Aligned_cols=48  Identities=19%  Similarity=0.372  Sum_probs=44.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..++|+.|.|.+|.|+.
T Consensus        40 i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~akp~~   89 (90)
T d2cq0a1          40 LAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPST   89 (90)
T ss_dssp             EEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEESSCCC
T ss_pred             ccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEeeeCCC
Confidence            468999999999999999999999999994  789999999999998864

>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=99.39  E-value=5.8e-14  Score=90.40  Aligned_cols=62  Identities=6%  Similarity=0.024  Sum_probs=54.3

Q ss_pred             CCceEEEeCCCCCC-CH----HHHHHHhhcccceEEEEecCcc--eeEEecCCcccHHHHHHHHHHHhHhCCC
Q 030822          100 IGKKIFVGRLPQEA-TA----EDLRRYFSRFGRILDVYVPKRF--WFCHLCGRSCSRSCFSKVSRNLWTAGCN  165 (171)
Q Consensus       100 ~~~~lfV~nLp~~~-te----~~L~~~F~~fG~v~~v~i~~d~--~fv~f~~~~~~~~~a~~Ai~~l~~~~~~  165 (171)
                      ...+|||+||+..+ ++    ++|+++|++||.|+++++++.+  +||+|.+.++    |.+|+..||+..+.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~~~~afV~f~~~~~----A~~Ai~~lng~~~~   72 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFKRVRINFSNPLS----AADARLRLHKTEFL   72 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTTEEEEECSSTTH----HHHHHHTSTTSEET
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecCCCEEEEEECCHHH----HHHHHHHhcccccC
Confidence            46889999999876 33    5699999999999999999765  8999999999    99999999986543

>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=99.38  E-value=2.7e-13  Score=87.07  Aligned_cols=49  Identities=37%  Similarity=0.636  Sum_probs=45.1

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.|+++||||||+|.+.++|++||+. ++.|+|+.|.|++|.++++
T Consensus        52 i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~ke~  101 (103)
T d1x4ba1          52 VMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREE  101 (103)
T ss_dssp             EECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSSCCC
T ss_pred             ecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcccCC
Confidence            478999999999999999999999999984 7899999999999998865

>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=99.37  E-value=9.5e-13  Score=83.82  Aligned_cols=49  Identities=22%  Similarity=0.345  Sum_probs=44.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..|+||.|.|.++.++.+
T Consensus        40 i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~~~~~   90 (99)
T d1whwa_          40 YPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPSTIKKE   90 (99)
T ss_dssp             CCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECCCCST
T ss_pred             ecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCc
Confidence            578999999999999999999999999984  7899999999999987644

>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=99.36  E-value=2.5e-13  Score=84.03  Aligned_cols=45  Identities=33%  Similarity=0.619  Sum_probs=41.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~   45 (171)
                      |++|+.||++||||||+|.++++|++||+. ++.|+||.|.|+.|.
T Consensus        38 i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1          38 VMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             ecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            478999999999999999999999999984 789999999999875

>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=99.36  E-value=1.9e-13  Score=85.34  Aligned_cols=47  Identities=17%  Similarity=0.259  Sum_probs=43.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++|+.  ++..++|+.|.|.||.++
T Consensus        39 i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~~k   87 (88)
T d1rk8a_          39 LNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVK   87 (88)
T ss_dssp             EEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEEC
T ss_pred             ccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEecCC
Confidence            46899999999999999999999999998  478999999999999865

>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=99.36  E-value=9e-13  Score=84.54  Aligned_cols=48  Identities=25%  Similarity=0.335  Sum_probs=43.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.||++||||||+|.+.++|++||+. ...|+||+|.|+++.++.
T Consensus        42 i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~Gr~l~V~~a~~~~   90 (103)
T d2cqda1          42 VITDRQTGKSRGYGFVTMADRAAAERACKDPNPIIDGRKANVNLAYLGA   90 (103)
T ss_dssp             ESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSCEETTEECEEEESTTTC
T ss_pred             ccccccccccCCeEEEEECCHHHHHHHHHHCCCcCCCEEEEEEEcCCCC
Confidence            578999999999999999999999999996 457999999999987653

>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=99.35  E-value=3.6e-13  Score=82.82  Aligned_cols=46  Identities=17%  Similarity=0.271  Sum_probs=42.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.+|++||||||+|.++++|++||+  ++..++|++|.|++|.|
T Consensus        34 i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1          34 IMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            57889999999999999999999999998  48899999999999875

>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=99.35  E-value=3.8e-13  Score=83.37  Aligned_cols=47  Identities=19%  Similarity=0.415  Sum_probs=43.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.++++|++|++.  +..|+|++|.|.+|.+.
T Consensus        33 i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_          33 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             EECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             eeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            478999999999999999999999999995  78999999999999764

>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=99.35  E-value=1e-13  Score=89.02  Aligned_cols=59  Identities=12%  Similarity=0.026  Sum_probs=50.1

Q ss_pred             CCceEEEeCCCCCCCHHHHHHHhhcccceEEE-EecC-------cceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          100 IGKKIFVGRLPQEATAEDLRRYFSRFGRILDV-YVPK-------RFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       100 ~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v-~i~~-------d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ...+|||+|||+++|+++|+++|+.||.|..+ .++.       .++||.|.+.++    |++||+ ||+..
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~----a~~Al~-~n~~~   73 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDD----ARKSER-LHRKK   73 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHH----HHHHGG-GCSEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHH----HHHHHh-cCCCe
Confidence            45789999999999999999999999999874 4443       267999999999    999995 87654

>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=99.34  E-value=3.8e-13  Score=82.39  Aligned_cols=45  Identities=13%  Similarity=0.244  Sum_probs=41.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      |++|+.||++||||||+|.++++|++||+.  +..++||+|+|.++.
T Consensus        32 i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1          32 VCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            578999999999999999999999999984  889999999999884

>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=99.34  E-value=2.9e-13  Score=88.17  Aligned_cols=61  Identities=13%  Similarity=0.143  Sum_probs=51.4

Q ss_pred             CCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822           99 RIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ....+|||+|||+++|+++|+++|+.||.|..+.++.+        ++||.|.+.++    |.+|++ ||+..+
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~----a~~al~-~~~~~i   84 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEAD----YKAALC-RHKQYM   84 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHH----HHHHHT-SCSBCS
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHH----HHHHHH-cCCCcC
Confidence            35679999999999999999999999999977554422        68999999999    998885 887754

>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=99.31  E-value=6.7e-13  Score=85.03  Aligned_cols=49  Identities=16%  Similarity=0.314  Sum_probs=44.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..|+|+.|.|+++.++.+
T Consensus        50 ~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~~k~~  100 (102)
T d2cpza1          50 VFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKRSKND  100 (102)
T ss_dssp             EEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCCCSCC
T ss_pred             eeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeCCCCC
Confidence            367899999999999999999999999984  8899999999999988754

>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=99.30  E-value=3.5e-13  Score=86.19  Aligned_cols=46  Identities=22%  Similarity=0.419  Sum_probs=42.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.||+|||||||+|.+.++|++||+ ++..|+|+.|.|+++.+
T Consensus        50 i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~~   96 (101)
T d2cq4a1          50 IISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA   96 (101)
T ss_dssp             ECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             eeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECCC
Confidence            57899999999999999999999999998 58899999999998754

>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=99.30  E-value=5.8e-13  Score=81.69  Aligned_cols=58  Identities=16%  Similarity=0.091  Sum_probs=50.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      .+.|+|+|||++++++.| ++|++||+|+++++.++  ++||+|.++++    |++|++ ||+..+
T Consensus         4 ~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~~~~~~~fV~f~~~~~----A~~Al~-~nG~~~   63 (81)
T d1wwha1           4 DTWVTVFGFPQASASYIL-LQFAQYGNILKHVMSNTGNWMHIRYQSKLQ----ARKALS-KDGRIF   63 (81)
T ss_dssp             GGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEECSSSSEEEEEESSHHH----HHHHHT-TTTCEE
T ss_pred             ccEEEEECCChHHHHHHH-HHHHhhhhhheEEecCCCCEEEEEEcccHH----HHHHHh-cCCCeE
Confidence            577999999999997766 57999999999999864  67899999999    999995 888765

>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=99.29  E-value=1.7e-12  Score=87.53  Aligned_cols=49  Identities=20%  Similarity=0.381  Sum_probs=44.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+.||++||||||+|.+.++|++||+  +++.|+||.|.|+++.++..
T Consensus        74 i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~~~~~  124 (139)
T d1u6fa1          74 IVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAASGHQ  124 (139)
T ss_dssp             EEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESSCCCC
T ss_pred             cccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCCCC
Confidence            46789999999999999999999999998  47999999999999976543

>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=99.29  E-value=3.1e-12  Score=81.53  Aligned_cols=48  Identities=15%  Similarity=0.205  Sum_probs=43.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      +++|+.||+++|||||+|.+.++|++||+.  +..|+||.|.|+++.++.
T Consensus        48 ~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~a~~~~   97 (101)
T d2cpea1          48 IYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP   97 (101)
T ss_dssp             CCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETTEECEEECSSCCC
T ss_pred             EeeccccccccceeeEEecCHHHHHHHHHHhCCCEECCEEEEEEEcCCCC
Confidence            367899999999999999999999999984  899999999999998753

>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=99.29  E-value=3.1e-12  Score=80.60  Aligned_cols=49  Identities=29%  Similarity=0.578  Sum_probs=42.5

Q ss_pred             CCCCC-CCCCccceEEEEECCHHHHHHHHh---cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQ-GSKAHRGIGFITFASADSVENLMV---DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~-~tg~srGfgFV~F~~~~~a~~Al~---~~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+ .||++||||||+|.+.++|++||+   ++..|+||+|.|.+|.++..
T Consensus        40 i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~A~~~~~   92 (94)
T d2cpha1          40 LPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEWADSEVT   92 (94)
T ss_dssp             CCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEECCCCCC
T ss_pred             EEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEEcCCCCC
Confidence            46775 489999999999999999999998   36789999999999976643

>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=99.28  E-value=1.6e-12  Score=79.78  Aligned_cols=46  Identities=22%  Similarity=0.388  Sum_probs=42.4

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      |++|+.+|++||||||+|.++++|++|++  +++.++|+.|.|.+|.|
T Consensus        34 i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1          34 LVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            46789999999999999999999999998  48999999999999875

>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=99.27  E-value=2.3e-12  Score=81.12  Aligned_cols=47  Identities=23%  Similarity=0.266  Sum_probs=42.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.+|++||||||+|.+.++|++||+  ++..++|++|.|.|+.+.
T Consensus        39 i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~~~   87 (93)
T d1h2vz_          39 MGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGF   87 (93)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEESCC
T ss_pred             cccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            46899999999999999999999999998  478999999999998654

>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=99.26  E-value=2.3e-12  Score=90.39  Aligned_cols=56  Identities=27%  Similarity=0.369  Sum_probs=50.8

Q ss_pred             CceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc--------ceeEEecCCcccHHHHHHHHHHHh
Q 030822          101 GKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR--------FWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus       101 ~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d--------~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      .++|||+|||+.+|+++|+++|++||.|.++.|+++        ++||.|.+.++    |..|+..++
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~----a~~a~~~~~   69 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE----VDAAMNARP   69 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHH----HHHHHHTCS
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHH----HHHHHHhcC
Confidence            479999999999999999999999999999999865        56899999999    999987654

>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=99.25  E-value=3.3e-12  Score=79.76  Aligned_cols=49  Identities=31%  Similarity=0.607  Sum_probs=44.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +++++.+|++||||||+|.+.++|++||+  +++.|+|+.|.|+++.++.+
T Consensus        37 ~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~~~~~   87 (90)
T d1x5sa1          37 VVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAGKSSD   87 (90)
T ss_dssp             ECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEECCCC
T ss_pred             eccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCCC
Confidence            36788999999999999999999999998  48899999999999977654

>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=99.25  E-value=5.3e-12  Score=78.22  Aligned_cols=45  Identities=22%  Similarity=0.324  Sum_probs=38.4

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      .|+.+|++||||||+|.+.++|++||+ +++.++||.|.|+++.++
T Consensus        40 ~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a~~k   85 (86)
T d2ghpa3          40 GQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK   85 (86)
T ss_dssp             CCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECCCC
T ss_pred             ccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEcCCC
Confidence            357899999999999999999999998 588999999999999765

>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=99.24  E-value=3e-12  Score=78.42  Aligned_cols=45  Identities=16%  Similarity=0.248  Sum_probs=35.3

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      ++|..+|++||||||+|.+.++|++|++  ++..++|++|.|+++.|
T Consensus        34 ~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1          34 LPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5677899999999999999999999998  48999999999999876

>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=99.23  E-value=2e-12  Score=83.00  Aligned_cols=47  Identities=21%  Similarity=0.430  Sum_probs=42.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      |++|+.||++||||||+|.+.++|++||+.  ++.|+|+.|.|+++.++
T Consensus        40 i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~~   88 (104)
T d1p1ta_          40 LVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAASE   88 (104)
T ss_dssp             EEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTCT
T ss_pred             cccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            467899999999999999999999999984  78999999999998764

>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=99.22  E-value=4.1e-12  Score=77.38  Aligned_cols=44  Identities=34%  Similarity=0.662  Sum_probs=40.3

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a   44 (171)
                      ++.|+.+++++|||||+|.+++++++|++ +++.|+||.|.|+.|
T Consensus        34 ~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2          34 IMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             cccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            35788999999999999999999999998 488999999999976

>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=99.22  E-value=3.2e-12  Score=79.01  Aligned_cols=44  Identities=16%  Similarity=0.318  Sum_probs=39.0

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCC--eEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGG--STVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~g--r~i~v~~a   44 (171)
                      |++|+.+|++||||||+|.+.++|++||+.  +..+.|  ++|.|++|
T Consensus        38 ~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~A   85 (85)
T d1b7fa2          38 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA   85 (85)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             eecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEEC
Confidence            468999999999999999999999999994  667765  88999986

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.22  E-value=6.7e-12  Score=75.61  Aligned_cols=44  Identities=36%  Similarity=0.594  Sum_probs=40.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a   44 (171)
                      +++|+.+|+++|||||+|.+.++|++||+ +++.|+||+|.|++|
T Consensus        31 ~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_          31 LMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             eeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            46788999999999999999999999998 489999999999875

>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=99.21  E-value=8.6e-12  Score=75.83  Aligned_cols=44  Identities=18%  Similarity=0.203  Sum_probs=39.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~   45 (171)
                      |++|+ +|++||||||+|.+.++|++|++  ++..++|++|.|+++.
T Consensus        32 i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_          32 VHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             ESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            46775 89999999999999999999998  4889999999999875

>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=99.19  E-value=2e-11  Score=77.24  Aligned_cols=49  Identities=16%  Similarity=0.375  Sum_probs=43.2

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--------CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--------THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--------~~~i~gr~i~v~~a~~~~~   49 (171)
                      +++|+.++++||||||+|.+.++|++||+.        +..++||.|.|.++.++.+
T Consensus        40 ~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          40 VVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             CCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCEEEEECCCCCCC
T ss_pred             eccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEEEEEEECCCCCc
Confidence            467889999999999999999999999983        4678999999999987643

>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=99.19  E-value=2.2e-11  Score=76.90  Aligned_cols=49  Identities=22%  Similarity=0.342  Sum_probs=41.7

Q ss_pred             CCCCC-CCCCccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQ-GSKAHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~-~tg~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|. .+|++||||||+|.+.++|.+||+.    +..++|+.|.|.||.|+.+
T Consensus        34 ~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~A~p~~~   87 (96)
T d2disa1          34 VYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDWAEPEID   87 (96)
T ss_dssp             CCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEESCSSCS
T ss_pred             EeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEEcCCCCC
Confidence            46774 5799999999999999999999984    3567899999999987644

>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=99.18  E-value=6e-12  Score=77.74  Aligned_cols=46  Identities=15%  Similarity=0.376  Sum_probs=39.2

Q ss_pred             CCCCCCC---CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            2 PKDQGSK---AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         2 ~~D~~tg---~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ++|+.++   +|||||||+|.+.++|++||+.  ++.++|+.|.|+++.+.
T Consensus        31 ~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~~   81 (85)
T d2cpfa1          31 SKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISERA   81 (85)
T ss_dssp             EEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSCS
T ss_pred             ecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            4565555   6899999999999999999984  78999999999998543

>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=99.18  E-value=5.5e-12  Score=78.98  Aligned_cols=45  Identities=18%  Similarity=0.409  Sum_probs=40.1

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      .|..+|++||||||+|.+.++|++||+ +++.++|++|.|.++..|
T Consensus        46 ~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak~k   91 (91)
T d1fjeb1          46 VDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPKGR   91 (91)
T ss_dssp             CEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCCCS
T ss_pred             eecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecCCC
Confidence            355799999999999999999999998 488999999999988653

>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=99.18  E-value=7.5e-12  Score=77.33  Aligned_cols=44  Identities=27%  Similarity=0.427  Sum_probs=38.8

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCC--eEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGG--STVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~g--r~i~v~~a   44 (171)
                      |++|+.+|++||||||+|.++++|++|++  ++..++|  ++|.|+||
T Consensus        38 i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~A   85 (85)
T d1fxla2          38 ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA   85 (85)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             cccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEeC
Confidence            46899999999999999999999999998  4788887  55888875

>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=99.16  E-value=1e-11  Score=76.34  Aligned_cols=41  Identities=29%  Similarity=0.462  Sum_probs=37.7

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEE
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVV   41 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v   41 (171)
                      |++|+.||++||||||+|.+.++|++||+.  +..|+||+|+|
T Consensus        41 i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1          41 IVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             EEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             ccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            468999999999999999999999999984  88999999986

>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=99.16  E-value=1.1e-11  Score=79.14  Aligned_cols=48  Identities=21%  Similarity=0.218  Sum_probs=43.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      +.|+.+|+++|||||+|.+.++|++||+.  +..|.|+.|.|.++.++.+
T Consensus        51 ~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak~k~~  100 (102)
T d2cpxa1          51 QFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKNKKQ  100 (102)
T ss_dssp             EEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECCCCSC
T ss_pred             ecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCCCccc
Confidence            46678999999999999999999999984  7899999999999987654

>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=99.15  E-value=5e-11  Score=76.22  Aligned_cols=46  Identities=24%  Similarity=0.456  Sum_probs=40.5

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +..+|++||||||+|.+.++|++|++ +++.|+||.|.|+++.++..
T Consensus        50 ~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~~~~~   96 (104)
T d1wi8a_          50 PSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVADQAQD   96 (104)
T ss_dssp             SSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECCCCCC
T ss_pred             eccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            45689999999999999999998887 48999999999999987644

>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=99.12  E-value=2.3e-13  Score=87.56  Aligned_cols=59  Identities=10%  Similarity=0.034  Sum_probs=54.0

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc-------ceeEEecCCcccHHHHHHHHHHHhHhCC
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR-------FWFCHLCGRSCSRSCFSKVSRNLWTAGC  164 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d-------~~fv~f~~~~~~~~~a~~Ai~~l~~~~~  164 (171)
                      ..++|++++..++|++|+++|++||+|++|.|+++       ++||+|.+.++    |.+|+..||+..+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~----A~~Ai~~lng~~~   93 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREED----AEKAVIDLNNRWF   93 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHH----HHHHHHHHTTCEE
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhH----HHHHHHHHCCCEE
Confidence            56999999999999999999999999999999865       57999999999    9999999998654

>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=99.11  E-value=6.2e-11  Score=75.82  Aligned_cols=48  Identities=17%  Similarity=0.216  Sum_probs=42.3

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~~   49 (171)
                      +++..+|+++|||||+|.++++|++|++ +++.|+||.|.|.++.+++.
T Consensus        48 ~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~~~~~   96 (104)
T d1wg5a_          48 LPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSSRAEV   96 (104)
T ss_dssp             CCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEECTTTS
T ss_pred             EEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECCHHHh
Confidence            4566789999999999999999999998 48899999999999877643

>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=99.10  E-value=3.4e-11  Score=74.94  Aligned_cols=47  Identities=21%  Similarity=0.435  Sum_probs=39.9

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      |++|+  +.+||||||+|.+.++|++||+.  +..|+|+.|.|.++.++.+
T Consensus        40 i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~~~~   88 (89)
T d1cvja2          40 VVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKE   88 (89)
T ss_dssp             ECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCCTTT
T ss_pred             EEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            35665  34899999999999999999985  7899999999999987643

>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=99.10  E-value=2.7e-11  Score=75.22  Aligned_cols=45  Identities=27%  Similarity=0.426  Sum_probs=40.4

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhcCCccCCeEEEEeecCCCCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMVDTHELGGSTVVVDRATPKEDD   50 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~~~~i~gr~i~v~~a~~~~~~   50 (171)
                      .++.++|||||+|++.++|++||.+++.|+|++|.|+++.++...
T Consensus        37 ~~~~~~gfafV~f~~~~~a~~a~~~~~~i~g~~l~v~~a~~k~~~   81 (88)
T d1wf0a_          37 IPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISNAEPKHNS   81 (88)
T ss_dssp             CCSSCCSCCEEECSCHHHHHHTTTCEEEETTEEEEEECCCCCCCC
T ss_pred             EeeccCceEEEEECCHHHHHHHHhCCCEECCEEeEEEeCCCCCCC
Confidence            456789999999999999999999889999999999999877543

>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=99.07  E-value=5e-11  Score=73.52  Aligned_cols=42  Identities=17%  Similarity=0.260  Sum_probs=37.7

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc-CCccCCeEEEEeec
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD-THELGGSTVVVDRA   44 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~-~~~i~gr~i~v~~a   44 (171)
                      ++| .+|++||||||+|.++++|++||+. +..+.|+.|.|++.
T Consensus        39 ~~~-~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~   81 (85)
T d1zh5a2          39 RRT-LHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   81 (85)
T ss_dssp             EEC-TTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEG
T ss_pred             eee-ccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEc
Confidence            345 4899999999999999999999984 88999999999975

>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=99.07  E-value=1.1e-10  Score=72.61  Aligned_cols=46  Identities=20%  Similarity=0.271  Sum_probs=39.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      |++|+.++  +|||||+|.+.++|++|++  +++.|.|+.|.|.+|.++.
T Consensus        40 i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~~~~   87 (90)
T d2cqia1          40 MITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWATTPS   87 (90)
T ss_dssp             EECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCCTT
T ss_pred             eecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            35676654  8999999999999999998  4889999999999997653

>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=99.06  E-value=5.3e-11  Score=73.51  Aligned_cols=42  Identities=19%  Similarity=0.296  Sum_probs=37.6

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      .+..+|+++|||||+|.++++|++||+.  +..|+||+|.|+++
T Consensus        43 ~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1          43 KYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             EECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             EeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4557899999999999999999999984  78999999999864

>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=99.04  E-value=1.4e-10  Score=72.70  Aligned_cols=45  Identities=20%  Similarity=0.414  Sum_probs=39.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      ++|+  +.+||||||+|.+.++|++||+  ++..|+|+.|.|.+|.++.
T Consensus        44 ~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~~r~   90 (93)
T d2cq3a1          44 IFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATARV   90 (93)
T ss_dssp             ECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCSSC
T ss_pred             cccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecCcCC
Confidence            4554  4489999999999999999998  4899999999999998763

>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=99.03  E-value=8.2e-11  Score=74.99  Aligned_cols=46  Identities=13%  Similarity=0.073  Sum_probs=40.4

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~~   48 (171)
                      ++| .+|+++|||||+|.++++|++||+ +++.|+||.|.|.++.++.
T Consensus        47 ~~~-~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~~~~   93 (102)
T d1weza_          47 EIG-PDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNSTAG   93 (102)
T ss_dssp             EES-SSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEECCCC
T ss_pred             EEe-cCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcCCCC
Confidence            445 478999999999999999999998 5889999999999987654

>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=99.03  E-value=7.4e-11  Score=74.37  Aligned_cols=46  Identities=22%  Similarity=0.332  Sum_probs=41.1

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      ++.+|+++|||||+|.+.++|++|++.  +..|+||+|.|.++.++..
T Consensus        46 ~~~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~k~~   93 (96)
T d1fjca_          46 VSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGEKGG   93 (96)
T ss_dssp             EEETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSSSCC
T ss_pred             eeecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCCCCC
Confidence            456899999999999999999999984  7899999999999987743

>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=99.02  E-value=1.1e-10  Score=74.64  Aligned_cols=43  Identities=12%  Similarity=0.256  Sum_probs=38.5

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeec
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRA   44 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a   44 (171)
                      |++| .+|++||||||+|.+.++|.+|++.  +.+++||+|.|.++
T Consensus        59 I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          59 VCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             ECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             eecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4566 6999999999999999999999994  89999999999864

>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=99.02  E-value=1.2e-10  Score=70.94  Aligned_cols=48  Identities=19%  Similarity=0.260  Sum_probs=40.8

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHhc--CC-ccCCeEEEEeecCCCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMVD--TH-ELGGSTVVVDRATPKED   49 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~-~i~gr~i~v~~a~~~~~   49 (171)
                      +.+...+++||||||+|.+.++|++||+.  +. .++|+.|.|.++.|+..
T Consensus        28 i~~~~~~~~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k~~   78 (80)
T d2cqha1          28 PLAGQVLLKSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSKKL   78 (80)
T ss_dssp             CCSSCEEEETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCCCC
T ss_pred             EEEeEEecccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCcCc
Confidence            34556778999999999999999999984  54 69999999999988643

>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=99.01  E-value=1.1e-10  Score=74.38  Aligned_cols=45  Identities=16%  Similarity=0.178  Sum_probs=39.8

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATP   46 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~   46 (171)
                      +.+..+|+++|||||+|.+.++|++||+ +++.|+||.|.|.++..
T Consensus        41 ~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1          41 VLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             ECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEECH
T ss_pred             EEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECCH
Confidence            3456799999999999999999999998 47899999999998754

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.95  E-value=2.2e-10  Score=70.63  Aligned_cols=44  Identities=25%  Similarity=0.376  Sum_probs=39.2

Q ss_pred             CCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      .++++||||||+|.+.++|.+||..  +..|+|+.|.|.++.|+..
T Consensus        39 ~~~~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~~~   84 (86)
T d2cpda1          39 RVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVDK   84 (86)
T ss_dssp             EEEECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCCCC
T ss_pred             EEccccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCCCC
Confidence            4578999999999999999999984  7899999999999987643

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.94  E-value=1.3e-10  Score=72.51  Aligned_cols=44  Identities=18%  Similarity=0.246  Sum_probs=39.4

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCC
Q 030822            5 QGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKE   48 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~   48 (171)
                      ..+++++|||||+|.+.++|++|++.  +..++|+.|.|.+|.++.
T Consensus        40 ~~~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~ak~~~   85 (91)
T d1nu4a_          40 SRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDS   85 (91)
T ss_dssp             CHHHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSSCC
T ss_pred             eeeccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeCCCc
Confidence            45678999999999999999999984  789999999999998764

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.93  E-value=4.9e-10  Score=69.54  Aligned_cols=42  Identities=7%  Similarity=0.230  Sum_probs=36.2

Q ss_pred             CCCCCCCCCcc---ceEEEEECCHHHHHHHHh--cCCccCCeEEEEe
Q 030822            1 MPKDQGSKAHR---GIGFITFASADSVENLMV--DTHELGGSTVVVD   42 (171)
Q Consensus         1 i~~D~~tg~sr---GfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~   42 (171)
                      |++|+.++.++   |||||+|+++++|++||+  ++..++||.|+|.
T Consensus        43 i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lkvS   89 (89)
T d2cpia1          43 INNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKAS   89 (89)
T ss_dssp             EECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             EeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEEEC
Confidence            46787777665   999999999999999998  4889999999873

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.93  E-value=3.6e-10  Score=71.57  Aligned_cols=63  Identities=19%  Similarity=0.183  Sum_probs=53.2

Q ss_pred             CCCCceEEEeCC--CCCCC---------HHHHHHHhhcccceEEEEecCc----ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822           98 QRIGKKIFVGRL--PQEAT---------AEDLRRYFSRFGRILDVYVPKR----FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus        98 ~~~~~~lfV~nL--p~~~t---------e~~L~~~F~~fG~v~~v~i~~d----~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ...+++|+|.||  |.++.         +++|++.|++||.|..|.++.+    ++||+|.+.++    |.+|+..||+.
T Consensus         5 ~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~~~G~~fV~f~~~e~----A~~A~~~lng~   80 (99)
T d2dita1           5 MRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEE----ADYCIQTLDGR   80 (99)
T ss_dssp             CCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTCTTCEEEEECSCHHH----HHHHHHHSTTC
T ss_pred             CCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCCCccEEEEEECCHHH----HHHHHHHhCCc
Confidence            446799999999  55432         3789999999999999999865    67999999999    99999999986


Q ss_pred             CC
Q 030822          163 GC  164 (171)
Q Consensus       163 ~~  164 (171)
                      .+
T Consensus        81 ~~   82 (99)
T d2dita1          81 WF   82 (99)
T ss_dssp             EE
T ss_pred             EE
Confidence            54

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=5.5e-10  Score=69.14  Aligned_cols=44  Identities=11%  Similarity=0.197  Sum_probs=38.7

Q ss_pred             CCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            4 DQGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         4 D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      +..++++||||||+|.+.++|++||+.  +..++|+.|.|.++..+
T Consensus        33 ~~~~~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_          33 YCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CEEEEGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             eeeeeccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            345678999999999999999999984  88999999999998554

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.91  E-value=1.5e-10  Score=69.00  Aligned_cols=39  Identities=15%  Similarity=0.341  Sum_probs=34.6

Q ss_pred             CCCCCCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEE
Q 030822            1 MPKDQGSKAHRGIGFITFASADSVENLMVD--THELGGSTV   39 (171)
Q Consensus         1 i~~D~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i   39 (171)
                      +++|+.+++++|||||+|.+.++|++|++.  +..|+||.|
T Consensus        30 ~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~   70 (72)
T d1x4ea1          30 AILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMA   70 (72)
T ss_dssp             EECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESC
T ss_pred             cccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEC
Confidence            357889999999999999999999999984  778888876

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=1.9e-10  Score=74.52  Aligned_cols=46  Identities=17%  Similarity=0.252  Sum_probs=40.7

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeecCCC
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a~~~   47 (171)
                      +.+..+|+++|||||+|.+.++|++||+ +++.|+||.|.|.++.++
T Consensus        51 ~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~~~   97 (112)
T d1wela1          51 IAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPITKK   97 (112)
T ss_dssp             EEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEECHH
T ss_pred             eecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcChH
Confidence            4566799999999999999999999998 588999999999987643

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.90  E-value=3.7e-10  Score=67.88  Aligned_cols=42  Identities=14%  Similarity=0.190  Sum_probs=37.6

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCC
Q 030822            5 QGSKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATP   46 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~   46 (171)
                      ..++++||||||+|.+.++|++|++.  +..++|++|.|.++..
T Consensus        27 ~~~~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1          27 CFVDKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             eeecccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            34678999999999999999999984  7899999999999854

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=3.9e-10  Score=72.05  Aligned_cols=61  Identities=18%  Similarity=0.252  Sum_probs=51.5

Q ss_pred             CCceEEEeCC--CCCCC--------HHHHHHHhhcccceEEEEecCc----------ceeEEecCCcccHHHHHHHHHHH
Q 030822          100 IGKKIFVGRL--PQEAT--------AEDLRRYFSRFGRILDVYVPKR----------FWFCHLCGRSCSRSCFSKVSRNL  159 (171)
Q Consensus       100 ~~~~lfV~nL--p~~~t--------e~~L~~~F~~fG~v~~v~i~~d----------~~fv~f~~~~~~~~~a~~Ai~~l  159 (171)
                      +++.|.+.||  |..+.        .+||++.|++||.|++|.|+++          +.||+|.+.++    |.+|+..|
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~----A~~A~~~l   78 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFD----CQKAMQGL   78 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHH----HHHHHHHH
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHH----HHHHHHHH
Confidence            4688999999  54433        3679999999999999999863          57899999999    99999999


Q ss_pred             hHhCC
Q 030822          160 WTAGC  164 (171)
Q Consensus       160 ~~~~~  164 (171)
                      ||-.+
T Consensus        79 ~Gr~f   83 (104)
T d1o0pa_          79 TGRKF   83 (104)
T ss_dssp             SSCCS
T ss_pred             CCCEE
Confidence            98654

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.89  E-value=1.5e-09  Score=68.42  Aligned_cols=38  Identities=13%  Similarity=0.404  Sum_probs=35.0

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      +||||||+|++.++|++||+.  +..|+|+.|.|.++.++
T Consensus        49 ~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   88 (98)
T d1wf2a_          49 HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAEP   88 (98)
T ss_dssp             ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTSC
T ss_pred             eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            689999999999999999994  78999999999998754

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.86  E-value=7.3e-10  Score=71.77  Aligned_cols=42  Identities=12%  Similarity=0.161  Sum_probs=37.7

Q ss_pred             CCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            5 QGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         5 ~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      ..++++||||||+|.+.++|+.||+  +++.|+|+.|.|.++.+
T Consensus        40 ~~~~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1          40 GNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             ECSTTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             cccCCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            3577899999999999999999998  48899999999998854

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=4.1e-10  Score=71.50  Aligned_cols=43  Identities=23%  Similarity=0.410  Sum_probs=37.4

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      .| .+|+++|||||+|.+.++|++||+  ++..|.||++.|.++.|
T Consensus        52 ~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~P   96 (101)
T d1x5oa1          52 RD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTEP   96 (101)
T ss_dssp             EC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSSC
T ss_pred             cc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCCC
Confidence            44 589999999999999999999998  58899999988876654

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.79  E-value=4.2e-09  Score=65.91  Aligned_cols=41  Identities=15%  Similarity=0.295  Sum_probs=36.9

Q ss_pred             CCCCccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATP   46 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~   46 (171)
                      .++.+||||||+|++.++|++||+  +++.|+|++|.|.++.+
T Consensus        48 ~~~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          48 NRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CSSSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             ccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            456789999999999999999998  48999999999999864

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=1.9e-09  Score=65.22  Aligned_cols=41  Identities=15%  Similarity=0.315  Sum_probs=36.7

Q ss_pred             CCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            7 SKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ..+++|||||+|.+.++|++|++.  +..++|+.|.|.++.++
T Consensus        35 ~~~~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~~   77 (79)
T d2bz2a1          35 MDPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ   77 (79)
T ss_dssp             EETTTTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECCSS
T ss_pred             eccCCCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEecCC
Confidence            356889999999999999999984  88999999999999754

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.78  E-value=1.7e-10  Score=71.74  Aligned_cols=42  Identities=19%  Similarity=0.334  Sum_probs=37.4

Q ss_pred             CCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeec
Q 030822            3 KDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (171)
Q Consensus         3 ~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a   44 (171)
                      .|..++++||||||+|.++++|++|++ ++..++|+.|.|+++
T Consensus        40 ~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r~   82 (90)
T d1u2fa_          40 LAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRP   82 (90)
T ss_dssp             EECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBCT
T ss_pred             eecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECCC
Confidence            466789999999999999999999997 589999999999743

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.75  E-value=1e-08  Score=65.25  Aligned_cols=42  Identities=14%  Similarity=-0.028  Sum_probs=37.5

Q ss_pred             CCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            8 KAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      .+++|||||+|.+.++|.+|++.  +..|+|+.|.|.++.++..
T Consensus        43 ~k~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~a~~~~~   86 (104)
T d1weya_          43 FKSFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLYFAQTLHI   86 (104)
T ss_dssp             ETTTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEECCCCSSC
T ss_pred             ecCCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEeecccCCC
Confidence            46899999999999999999995  7899999999999976543

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.74  E-value=5.7e-09  Score=64.34  Aligned_cols=41  Identities=17%  Similarity=0.338  Sum_probs=35.4

Q ss_pred             CCCccceEEEEECCHHHHHHHHhc--CCcc-CCeEEEEeecCCC
Q 030822            7 SKAHRGIGFITFASADSVENLMVD--THEL-GGSTVVVDRATPK   47 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~~--~~~i-~gr~i~v~~a~~~   47 (171)
                      ++++||||||+|++.++|.+|+..  +..+ +|++|+|.++.++
T Consensus        44 ~~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~~   87 (88)
T d2adca2          44 FQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST   87 (88)
T ss_dssp             CSSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             eecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCCC
Confidence            567899999999999999999985  6666 6999999998653

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.74  E-value=9.1e-09  Score=64.89  Aligned_cols=43  Identities=12%  Similarity=0.290  Sum_probs=37.8

Q ss_pred             CCCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCCCC
Q 030822            7 SKAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPKED   49 (171)
Q Consensus         7 tg~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~~~   49 (171)
                      ++.++|||||+|+++++|++|+..  +..++||+|.|.++.++.+
T Consensus        53 ~~~~~G~~fV~f~~~e~A~~A~~~lng~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          53 DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             TTCTTCEEEEECSCHHHHHHHHHHSTTCEETTEECEEEECCSCCC
T ss_pred             CCCCccEEEEEECCHHHHHHHHHHhCCcEECCEEEEEEEeCCcCC
Confidence            346789999999999999999994  8999999999999876643

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=8.6e-09  Score=64.61  Aligned_cols=38  Identities=18%  Similarity=0.401  Sum_probs=34.5

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      .||||||+|.+.++|++|+.  ++..|+|+.|+|.|+.++
T Consensus        53 ~kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~~   92 (96)
T d1x4ga1          53 EKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES   92 (96)
T ss_dssp             TTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCCC
T ss_pred             cceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            48999999999999999998  488999999999998654

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.72  E-value=1.2e-08  Score=65.29  Aligned_cols=38  Identities=13%  Similarity=0.292  Sum_probs=34.3

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822           10 HRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      +||||||+|++.++|++||+.  +..|.|+.|.|.++..+
T Consensus        39 ~kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1          39 KKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             TSCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             ccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            489999999999999999994  88999999999998644

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.71  E-value=7e-09  Score=63.70  Aligned_cols=39  Identities=26%  Similarity=0.359  Sum_probs=35.6

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      ++||||||+|.+.++|++|++.  +..|+|+.|.|++|.+.
T Consensus        42 ~~k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1          42 KDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TTTTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            5689999999999999999994  88999999999999765

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.71  E-value=7e-09  Score=62.06  Aligned_cols=41  Identities=15%  Similarity=0.200  Sum_probs=34.2

Q ss_pred             CCCCCCCCccceEEEEECCHHHHHHHHh-cCCccCCeEEEEeec
Q 030822            2 PKDQGSKAHRGIGFITFASADSVENLMV-DTHELGGSTVVVDRA   44 (171)
Q Consensus         2 ~~D~~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~a   44 (171)
                      ++|+.+  ++|||||+|+++++|++||. +++.|+|+.|.|..+
T Consensus        33 ~~~~~~--~~~~afV~F~~~~~a~~Al~~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2          33 ADSLKK--NFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             EECTTS--SSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             Eeeccc--cceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            455543  45799999999999999998 478999999999865

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.60  E-value=3e-08  Score=63.50  Aligned_cols=40  Identities=5%  Similarity=-0.007  Sum_probs=35.5

Q ss_pred             CCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecCCC
Q 030822            8 KAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRATPK   47 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~~~   47 (171)
                      .++||||||+|.+.++|++||+.  +..|.|+.|.|.++...
T Consensus        43 ~~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_          43 PEGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             CSSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             eccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            35799999999999999999984  88999999999998543

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.54  E-value=1.5e-08  Score=61.46  Aligned_cols=42  Identities=17%  Similarity=0.109  Sum_probs=35.4

Q ss_pred             CCCCccceEEEEECCHHHHHHHHh-cCCccCCeE-EEEeecCCC
Q 030822            6 GSKAHRGIGFITFASADSVENLMV-DTHELGGST-VVVDRATPK   47 (171)
Q Consensus         6 ~tg~srGfgFV~F~~~~~a~~Al~-~~~~i~gr~-i~v~~a~~~   47 (171)
                      ..+++||||||+|.++++|++||+ ++..|+|+. |.|+++..+
T Consensus        34 ~~~~~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~~k   77 (81)
T d1wwha1          34 VMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDK   77 (81)
T ss_dssp             EECSSSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECCCH
T ss_pred             EecCCCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCCCh
Confidence            457889999999999999999998 588999985 568876543

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=6.5e-08  Score=59.38  Aligned_cols=40  Identities=15%  Similarity=0.282  Sum_probs=35.0

Q ss_pred             CccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPKE   48 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~~   48 (171)
                      +++|||||+|.+.++|++|++.    +..++|++|.|.++..++
T Consensus        42 ~~~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~sk~~~   85 (88)
T d2cq1a1          42 KGKNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYSNHKE   85 (88)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEECSCSS
T ss_pred             ccceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEECCCCC
Confidence            5789999999999999999983    578999999999987553

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.53  E-value=1.2e-07  Score=60.11  Aligned_cols=39  Identities=15%  Similarity=0.264  Sum_probs=34.5

Q ss_pred             CccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~   47 (171)
                      ++||||||+|.+.++|++||..    +..++|++|.|.++..+
T Consensus        49 ~~k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~s~~~   91 (104)
T d1wexa_          49 PFKRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYSTSK   91 (104)
T ss_dssp             TTTTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEECSSS
T ss_pred             ecceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEEcCCC
Confidence            5789999999999999999973    56789999999999654

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.51  E-value=2.6e-08  Score=61.19  Aligned_cols=38  Identities=13%  Similarity=0.217  Sum_probs=33.3

Q ss_pred             ccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCC
Q 030822           10 HRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPK   47 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~   47 (171)
                      ++|||||+|.+.++|++||+  ++..|+|+.|.|.++.++
T Consensus        34 ~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1          34 RDGTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             TTSEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             ccceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            45999999999999999998  488999999998877544

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.46  E-value=8.6e-08  Score=60.22  Aligned_cols=40  Identities=15%  Similarity=0.185  Sum_probs=34.9

Q ss_pred             CCccceEEEEECCHHHHHHHHh----cCCccCCeEEEEeecCCC
Q 030822            8 KAHRGIGFITFASADSVENLMV----DTHELGGSTVVVDRATPK   47 (171)
Q Consensus         8 g~srGfgFV~F~~~~~a~~Al~----~~~~i~gr~i~v~~a~~~   47 (171)
                      .++||||||+|.+.++|.+||+    ++..++|+.|.|.++..+
T Consensus        52 ~~~k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V~~s~~~   95 (99)
T d1x4fa1          52 MRMKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVDLSEKY   95 (99)
T ss_dssp             ETTTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEEEECSC
T ss_pred             eecCCcEEEEecchHHHHHHHHHHhcCCceECCEEEEEEEcCCc
Confidence            3578999999999999999997    267899999999998654

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.45  E-value=1.3e-07  Score=60.30  Aligned_cols=40  Identities=10%  Similarity=0.164  Sum_probs=33.8

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCcc--CCeEEEEeecCCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THEL--GGSTVVVDRATPKE   48 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i--~gr~i~v~~a~~~~   48 (171)
                      ++||||||+|+++++|++||..  +..|  .|++|.|.++.++.
T Consensus        43 ~~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~~~~   86 (108)
T d2adba1          43 NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTS   86 (108)
T ss_dssp             TTEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECSSCS
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecCCcc
Confidence            5799999999999999999984  6666  68899999887653

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.39  E-value=2.2e-07  Score=58.80  Aligned_cols=45  Identities=18%  Similarity=0.265  Sum_probs=37.5

Q ss_pred             CCCCCCC--CCccceEEEEECCHHHHHHHHhc--CCccCCeEEEEeecC
Q 030822            1 MPKDQGS--KAHRGIGFITFASADSVENLMVD--THELGGSTVVVDRAT   45 (171)
Q Consensus         1 i~~D~~t--g~srGfgFV~F~~~~~a~~Al~~--~~~i~gr~i~v~~a~   45 (171)
                      |+++..+  ..++|++||+|.+.++|.+|+..  +..++||.|.+.+..
T Consensus        46 I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~f~gR~v~v~f~~   94 (104)
T d1o0pa_          46 IPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCD   94 (104)
T ss_dssp             CCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCCSSSSCCEEEEEC
T ss_pred             EeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCEECCeEEEEEEcC
Confidence            4555544  44579999999999999999994  899999999999864

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=98.38  E-value=1.8e-07  Score=56.73  Aligned_cols=36  Identities=11%  Similarity=0.175  Sum_probs=31.3

Q ss_pred             ccceEEEEECCHHHHHHHHhc--CCcc-CCeEEEEeecC
Q 030822           10 HRGIGFITFASADSVENLMVD--THEL-GGSTVVVDRAT   45 (171)
Q Consensus        10 srGfgFV~F~~~~~a~~Al~~--~~~i-~gr~i~v~~a~   45 (171)
                      +||||||+|.+.++|.+|++.  +..| +|+.|.|.||.
T Consensus        44 ~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~ak   82 (83)
T d2b0ga1          44 RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFAK   82 (83)
T ss_dssp             TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEECC
T ss_pred             cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEec
Confidence            579999999999999999984  6666 57999999874

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.38  E-value=6.6e-08  Score=60.65  Aligned_cols=40  Identities=10%  Similarity=0.211  Sum_probs=34.8

Q ss_pred             CccceEEEEECCHHHHHHHHh--cCCccCCeEEEEeecCCCC
Q 030822            9 AHRGIGFITFASADSVENLMV--DTHELGGSTVVVDRATPKE   48 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~--~~~~i~gr~i~v~~a~~~~   48 (171)
                      .++|||||+|.+.++|++||+  ++..++|+.|.|.++.++.
T Consensus        48 ~~~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~~~   89 (98)
T d1wg4a_          48 QKDGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRVYP   89 (98)
T ss_dssp             ETTTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEEEC
T ss_pred             cccceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEecCC
Confidence            357999999999999999998  4789999999999876543

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.30  E-value=3.8e-07  Score=56.87  Aligned_cols=39  Identities=23%  Similarity=0.364  Sum_probs=32.9

Q ss_pred             CccceEEEEECCHHHHHHHHhc--CCccCC--eEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD--THELGG--STVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~--~~~i~g--r~i~v~~a~~~   47 (171)
                      ++||||||+|.+.++|++|++.  +..|+|  ++|.|.++.+.
T Consensus        51 ~~~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak~~   93 (97)
T d1whya_          51 KGDSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSG   93 (97)
T ss_dssp             SSSCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECCCC
T ss_pred             ccccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCCCC
Confidence            4689999999999999999994  677876  58999998653

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.29  E-value=6.2e-07  Score=55.04  Aligned_cols=39  Identities=15%  Similarity=0.120  Sum_probs=33.8

Q ss_pred             CccceEEEEECCHHHHHHHHhc----CCccCCeEEEEeecCCC
Q 030822            9 AHRGIGFITFASADSVENLMVD----THELGGSTVVVDRATPK   47 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~----~~~i~gr~i~v~~a~~~   47 (171)
                      ++++||||+|++.++|..|++.    +..++|++|.|.++.+.
T Consensus        43 ~~k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V~~s~~~   85 (89)
T d1x4da1          43 NKINEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHLSQKY   85 (89)
T ss_dssp             SSSSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEECCC
T ss_pred             ccceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEEEECCCc
Confidence            4678999999999999999982    56899999999998643

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.68  E-value=1.7e-05  Score=49.51  Aligned_cols=22  Identities=9%  Similarity=0.309  Sum_probs=20.4

Q ss_pred             CccceEEEEECCHHHHHHHHhc
Q 030822            9 AHRGIGFITFASADSVENLMVD   30 (171)
Q Consensus         9 ~srGfgFV~F~~~~~a~~Al~~   30 (171)
                      ++||||||+|.+.++|++|++.
T Consensus        54 ~~k~~aFV~f~~~e~A~~A~~~   75 (101)
T d2cq2a1          54 PNKPYSFARYRTTEESKRAYVT   75 (101)
T ss_dssp             TTCSCEEEEESSHHHHHHHHHH
T ss_pred             cCccEEEEEECCHHHHHHHHHH
Confidence            5689999999999999999986

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.42  E-value=3.3e-05  Score=49.10  Aligned_cols=38  Identities=16%  Similarity=0.035  Sum_probs=27.5

Q ss_pred             CccceEEEEECCH-HHHHHHHhc--CCccCCeEEEEeecCC
Q 030822            9 AHRGIGFITFASA-DSVENLMVD--THELGGSTVVVDRATP   46 (171)
Q Consensus         9 ~srGfgFV~F~~~-~~a~~Al~~--~~~i~gr~i~v~~a~~   46 (171)
                      +.+|||||.|+++ ++|..|+..  +..+.++.+.|.++..
T Consensus        45 ~~kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          45 RGAKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             TTCSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             cCCceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            4589999999996 678888884  4556666666665543

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Smg-4/UPF3
domain: RNA processing protein UPF3x, RRM domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.41  E-value=0.00021  Score=43.37  Aligned_cols=57  Identities=12%  Similarity=0.046  Sum_probs=46.9

Q ss_pred             ceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCc----------ceeEEecCCcccHHHHHHHHHHHhHh
Q 030822          102 KKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKR----------FWFCHLCGRSCSRSCFSKVSRNLWTA  162 (171)
Q Consensus       102 ~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d----------~~fv~f~~~~~~~~~a~~Ai~~l~~~  162 (171)
                      ++|.|+.||+++||+++.+.++..|.+....-...          ++.+.|.+.++    ...-.+.++|.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~----v~~F~~~f~g~   68 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQED----IILFRDRFDGY   68 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHH----HHHHHHHHTTC
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHH----HHHHHHHcCCc
Confidence            68999999999999999999999999888776543          45699999999    66666666554

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.13  E-value=0.00099  Score=40.56  Aligned_cols=59  Identities=20%  Similarity=0.226  Sum_probs=48.1

Q ss_pred             CCCCceEEEeCCCCCCCHHHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHh
Q 030822           98 QRIGKKIFVGRLPQEATAEDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLW  160 (171)
Q Consensus        98 ~~~~~~lfV~nLp~~~te~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~  160 (171)
                      .+.-..||.-..|..|...||.++|++||.|.--.|----+||...+++.    +..+++.+.
T Consensus        12 ~p~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~VswIddTSa~V~L~~~e~----~~~v~~~~~   70 (100)
T d1whva_          12 QPKRDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQ----VQIAVNTSK   70 (100)
T ss_dssp             CCCCCSEEEEECCTTCCHHHHHHHHTTTCSCCCEEEETTEEEEECSCHHH----HHHHHHHHH
T ss_pred             CCCcceeEEEeCCcccchhHHHHHhcCCCceEEEEecCceEEEEecCHHH----HHHHHHHhc
Confidence            44566788889999999999999999999987666644467899999888    877777654

>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=96.61  E-value=0.0011  Score=39.69  Aligned_cols=60  Identities=10%  Similarity=0.107  Sum_probs=45.6

Q ss_pred             CCCceEEEeCCCCCCCH---------HHHHHHhhcccceEEEEecCcceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822           99 RIGKKIFVGRLPQEATA---------EDLRRYFSRFGRILDVYVPKRFWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus        99 ~~~~~lfV~nLp~~~te---------~~L~~~F~~fG~v~~v~i~~d~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      ++..+|.|.=+.++..+         .+|.+.|+.||+|+-++++.|.-.|+|.+-..    |.+|+. |++..
T Consensus        13 PpDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d~mwVTF~dG~S----AL~al~-l~g~~   81 (95)
T d1ufwa_          13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQMLVTFADSHS----ALSVLD-VDGMK   81 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTEEEEECSCSHH----HHHHHH-GGGSE
T ss_pred             CCCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCCeEEEEECCcHH----HHHHhc-cCCeE
Confidence            34577888555444433         47889999999999999999999999999988    776653 44443

>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=94.99  E-value=0.016  Score=32.84  Aligned_cols=44  Identities=14%  Similarity=0.093  Sum_probs=36.4

Q ss_pred             HHHHHHhhcccceEEEEecCc-----ceeEEecCCcccHHHHHHHHHHHhHhC
Q 030822          116 EDLRRYFSRFGRILDVYVPKR-----FWFCHLCGRSCSRSCFSKVSRNLWTAG  163 (171)
Q Consensus       116 ~~L~~~F~~fG~v~~v~i~~d-----~~fv~f~~~~~~~~~a~~Ai~~l~~~~  163 (171)
                      +.|.+.|+++|+|.++.|...     .+-|...+..+    |.-|+.+||...
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~dg~~~A~V~v~~~q~----A~~~v~~LhR~K   59 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHTDYQLKAVVQMENLQD----AIGAVNSLHRYK   59 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCCSTTCCEEEEESSHHH----HHHHHHHHTTEE
T ss_pred             HHHHHHHHhheeEEEEEEEeccCCcEEEEEEcCCHHH----HHHHHHHHHHHh
Confidence            456678999999999999754     23599999999    999999998754

>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=86.09  E-value=0.41  Score=28.20  Aligned_cols=30  Identities=23%  Similarity=0.369  Sum_probs=27.0

Q ss_pred             EEEEECCHHHHHHHHh-cCCccCCeEEEEee
Q 030822           14 GFITFASADSVENLMV-DTHELGGSTVVVDR   43 (171)
Q Consensus        14 gFV~F~~~~~a~~Al~-~~~~i~gr~i~v~~   43 (171)
                      -.|+|.+-++|-+|++ ++.++.|+.|.|..
T Consensus        61 mwVTF~dG~SAL~al~l~g~~v~G~~l~It~   91 (95)
T d1ufwa_          61 MLVTFADSHSALSVLDVDGMKVKGRAVKISG   91 (95)
T ss_dssp             EEEECSCSHHHHHHHHGGGSEETTEEEEEEC
T ss_pred             EEEEECCcHHHHHHhccCCeEEcceEEEEec
Confidence            4799999999999999 58999999998874