Citrus Sinensis ID: 036791

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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-------
Protein Sequence
MAAQSLIQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHccccccccEEEEcccccccccccccccccccccHHHHHccccccEEEccccccccHHHHHHHHHccccEEEEEEcccccccccccEEEEEcccHHHHHHHHHHHccccccccEEEEEccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHEEcccccccccHHHHccccEEEEcccHcHHHHHccccccccccHHHHHHHHccccccEEEccccccHHHHHHHHHHcccEEEEEEEEEcccccccccEEEEcccHHHHHHHHHHcccccccccEEEEcccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MAAQSLIQTRKIqqfnsyftedsllsfsskpyqvvNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIgknrskgygyvtsSTEEEAQKALVDMNgklldgrvifvdnvrpsrryntdaslarqpaqspeen
Flexible Loop (DISEMBL)
maaqsliqtrkiqqfnSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFvdnvrpsrryntdaslarqpaqspeen
Low Complexity Region (SEG)
MAAQSLIQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN
Disordered region (IsUnstruct)
**********KIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVT*********ALVDMNGKLLDGRVIFVDNV***********************
Disordered Region (DISOPRED)
*************QFNSYFTEDSL***********************************WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF***************************
Disordered Region (DISEMBL)
********TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYN****************
Disordered Region (DISPRO)
******IQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV***********************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAQSLIQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN
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	157	2.2.26 [Sep-21-2011]
Q28IQ9	166	Cold-inducible RNA-bindin	yes	no	0.471	0.445	0.432	8e-11
Q99070	168	Glycine-rich RNA-binding	N/A	no	0.464	0.434	0.426	3e-10
Q9LIS2	136	Glycine-rich RNA-binding	no	no	0.433	0.5	0.455	5e-10
Q9DED4	166	Cold-inducible RNA-bindin	N/A	no	0.471	0.445	0.391	6e-10
Q03251	169	Glycine-rich RNA-binding	no	no	0.464	0.431	0.44	8e-10
Q9PTX2	164	Cold-inducible RNA-bindin	N/A	no	0.471	0.451	0.405	1e-09
Q03878	157	Glycine-rich RNA-binding	N/A	no	0.464	0.464	0.426	1e-09
Q99069	142	Glycine-rich RNA-binding	N/A	no	0.375	0.415	0.525	1e-09
O89086	153	Putative RNA-binding prot	yes	no	0.471	0.483	0.391	1e-09
P98179	157	Putative RNA-binding prot	yes	no	0.484	0.484	0.394	2e-09

>sp|Q28IQ9|CIRBP_XENTR Cold-inducible RNA-binding protein OS=Xenopus tropicalis GN=cirbp PE=2 SV=1

 Score = 66.2 bits (160), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 47/74 (63%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            ++F TT+E L   FS++GQV E  ++ D    RS+G+G+VT    E+A+ A++ MNGK 
Sbjct: 12  GLNFETTEESLEQVFSKYGQVAEVVVVKDRESKRSRGFGFVTFENPEDAKDAMMAMNGKS 71

Query: 124 LDGRVIFVDNVRPS 137
           +DGR I VD    S
Sbjct: 72  VDGRQIRVDQAGKS 85

Cold-inducible mRNA binding protein. Acts cooperatively with elavl1/elrA to stabilize AU-rich element (ARE)-containing mRNAs by binding to themm and inhibiting their deadenylation. Essential for embryonic gastrulation and neural development, acting to maintain the expression of a set of adhesion molecules, and cell movement during embryogenesis. Required for pronephros development.
Xenopus tropicalis (taxid: 8364)

>sp|Q99070|GRP2_SORBI Glycine-rich RNA-binding protein 2 OS=Sorghum bicolor GN=GRP2 PE=2 SV=1

 Score = 64.3 bits (155), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 49/75 (65%), Gaps = 2/75 (2%)

Query: 60  WRCI--SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
           +RC    ++++T  E L  AF+ FGQV ++ +I D    RS+G+G+VT S+E+    A+ 
Sbjct: 8   YRCFVGGLAWATNNETLEQAFANFGQVIDSKVITDRETGRSRGFGFVTFSSEQSMLDAIE 67

Query: 118 DMNGKLLDGRVIFVD 132
           +MNGK LDGR I V+
Sbjct: 68  NMNGKELDGRNITVN 82

Possibly has a role in RNA transcription or processing during stress.

Sorghum bicolor (taxid: 4558)

>sp|Q9LIS2|RBG4_ARATH Glycine-rich RNA-binding protein 4, mitochondrial OS=Arabidopsis thaliana GN=RBG4 PE=2 SV=1

 Score = 63.5 bits (153), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/68 (45%), Positives = 46/68 (67%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ T    L  AF+ FG+VTEAT+I D    RS+G+G+V+ S E+ A  A+ +M+GK L
Sbjct: 42  LSWGTDDSSLKQAFTSFGEVTEATVIADRETGRSRGFGFVSFSCEDSANNAIKEMDGKEL 101

Query: 125 DGRVIFVD 132
           +GR I V+
Sbjct: 102 NGRQIRVN 109

Possibly has a role in RNA transcription or processing during stress. Binds sequence non-specifically to RNAs and DNAs.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9DED4|CIRBB_XENLA Cold-inducible RNA-binding protein B OS=Xenopus laevis GN=cirbp-b PE=1 SV=1

 Score = 63.2 bits (152), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 47/74 (63%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            ++F T +E L   FS++GQ++E  ++ D    RS+G+G+VT    ++A+ A++ MNGK 
Sbjct: 11  GLNFDTNEESLEQVFSKYGQISEVVVVKDRETKRSRGFGFVTFENPDDAKDAMMAMNGKA 70

Query: 124 LDGRVIFVDNVRPS 137
           +DGR I VD    S
Sbjct: 71  VDGRQIRVDQAGKS 84

Cold-inducible mRNA binding protein. Acts cooperatively with elavl1/elrA to stabilize AU-rich element (ARE)-containing mRNAs by binding to them and inhibiting their deadenylation. Essential for embryonic gastrulation and neural development, acting to maintain the expression of a set of adhesion molecules, and cell movement during embryogenesis. Required for pronephros development.

Xenopus laevis (taxid: 8355)

>sp|Q03251|RBG8_ARATH Glycine-rich RNA-binding protein 8 OS=Arabidopsis thaliana GN=RBG8 PE=1 SV=1

 Score = 62.8 bits (151), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 33/75 (44%), Positives = 48/75 (64%), Gaps = 2/75 (2%)

Query: 60  WRCI--SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
           +RC    ++++T  E L   FSQFG V ++ II D    RS+G+G+VT   E+  + A+ 
Sbjct: 6   YRCFVGGLAWATNDEDLQRTFSQFGDVIDSKIINDRESGRSRGFGFVTFKDEKAMRDAIE 65

Query: 118 DMNGKLLDGRVIFVD 132
           +MNGK LDGRVI V+
Sbjct: 66  EMNGKELDGRVITVN 80

Possibly has a role in RNA transcription or processing during stress.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9PTX2|CIRBP_LITCT Cold-inducible RNA-binding protein OS=Lithobates catesbeiana GN=cirbp PE=2 SV=1

 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 45/74 (60%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF T ++ L   FS++GQ+ E  ++ D    RS+G+G+VT    E+A+ A+  MNGK 
Sbjct: 12  GLSFDTDEQCLETVFSKYGQIQEVVVVKDRETKRSRGFGFVTFENCEDAKDAMAGMNGKT 71

Query: 124 LDGRVIFVDNVRPS 137
           +DGR I VD    S
Sbjct: 72  VDGRQIRVDQAGKS 85

Cold-inducible mRNA binding protein. Acts cooperatively with elavl1/elrA to stabilize AU-rich element (ARE)-containing mRNAs by binding to them and inhibiting their deadenylation. Essential for embryonic gastrulation and neural development, acting to maintain the expression of a set of adhesion molecules, and cell movement during embryogenesis. Required for pronephros development (By similarity). May play a role in hibernation.

Lithobates catesbeiana (taxid: 8400)

>sp|Q03878|GRP1_DAUCA Glycine-rich RNA-binding protein OS=Daucus carota PE=2 SV=1

 Score = 62.4 bits (150), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 32/75 (42%), Positives = 48/75 (64%), Gaps = 2/75 (2%)

Query: 60  WRCI--SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
           +RC    ++++T  E L  AFSQFG +T++ II D    RS+G+G+VT   E+  + A+ 
Sbjct: 6   YRCFVGGLAWATNDESLEQAFSQFGDITDSKIINDRETGRSRGFGFVTFKDEKSMRDAIE 65

Query: 118 DMNGKLLDGRVIFVD 132
            MNG+ LDGR I V+
Sbjct: 66  GMNGQELDGRNITVN 80

May play a role in the biosynthesis and processing of heterogeneous nuclear RNA and in the maturation of specific mRNAs in response to wounding.

Daucus carota (taxid: 4039)

>sp|Q99069|GRP1_SORBI Glycine-rich RNA-binding protein 1 (Fragment) OS=Sorghum bicolor GN=GRP1 PE=2 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 41/59 (69%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD 132
           L  AFS +G+V E+ II+D    RS+G+G+VT STEE  + A+  MNGK LDGR I V+
Sbjct: 3   LHSAFSTYGEVLESKIILDRETQRSRGFGFVTFSTEEAMRSAIEGMNGKELDGRNITVN 61

Possibly has a role in RNA transcription or processing during stress.

Sorghum bicolor (taxid: 4558)

>sp|O89086|RBM3_MOUSE Putative RNA-binding protein 3 OS=Mus musculus GN=Rbm3 PE=1 SV=1

 Score = 62.0 bits (149), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            ++F+T ++ L D FS FG ++E  ++ D    RS+G+G++T +  E A  A+  MNG+ 
Sbjct: 12  GLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNGES 71

Query: 124 LDGRVIFVDNVRPS 137
           LDGR I VD+   S
Sbjct: 72  LDGRQIRVDHAGKS 85

Cold-inducible mRNA binding protein that enhances global protein synthesis at both physiological and mild hypothermic temperatures. Reduces the relative abundance of microRNAs, when overexpressed. Enhances phosphoryaltion of translation initiation factors and active polysome formation.

Mus musculus (taxid: 10090)

>sp|P98179|RBM3_HUMAN Putative RNA-binding protein 3 OS=Homo sapiens GN=RBM3 PE=1 SV=1

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 47/76 (61%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            ++F+T ++ L D FS FG ++E  ++ D    RS+G+G++T +  E A  A+  MNG+ 
Sbjct: 12  GLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASVAMRAMNGES 71

Query: 124 LDGRVIFVDNVRPSRR 139
           LDGR I VD+   S R
Sbjct: 72  LDGRQIRVDHAGKSAR 87

Cold-inducible mRNA binding protein that enhances global protein synthesis at both physiological and mild hypothermic temperatures. Reduces the relative abundance of microRNAs, when overexpressed. Enhances phosphoryaltion of translation initiation factors and active polysome formation.

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	157
351724633	113	uncharacterized protein LOC100527061 [Gl	0.477	0.663	0.586	2e-17
359482021	133	PREDICTED: glycine-rich RNA-binding prot	0.566	0.669	0.494	2e-17
224091949	139	predicted protein [Populus trichocarpa]	0.713	0.805	0.419	4e-17
255565709	121	Cold-inducible RNA-binding protein, puta	0.573	0.743	0.489	5e-17
388502672	140	unknown [Medicago truncatula]	0.611	0.685	0.427	9e-17
255579369	127	RNA binding protein, putative [Ricinus c	0.566	0.700	0.494	9e-17
359479548	111	PREDICTED: cold-inducible RNA-binding pr	0.630	0.891	0.482	1e-16
357457753	134	Cold-inducible RNA-binding protein [Medi	0.496	0.582	0.525	2e-16
351725383	130	uncharacterized protein LOC100527079 [Gl	0.726	0.876	0.388	6e-16
449500867	134	PREDICTED: glycine-rich RNA-binding prot	0.579	0.679	0.468	8e-16

>gi|351724633|ref|NP_001238088.1| uncharacterized protein LOC100527061 [Glycine max] gi|255631468|gb|ACU16101.1| unknown [Glycine max]

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/75 (58%), Positives = 58/75 (77%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            ++FSTT+E LA AFSQ+G V +A II++  KNRSKG+GYV  + EEEA KA +DMNGK+
Sbjct: 39  GLAFSTTEEELAKAFSQYGSVLKANIILNKAKNRSKGFGYVIFAKEEEACKAQIDMNGKI 98

Query: 124 LDGRVIFVDNVRPSR 138
           L GRVI+VD   P++
Sbjct: 99  LHGRVIYVDVQLPNK 113

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482021|ref|XP_002276063.2| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Vitis vinifera] gi|297740158|emb|CBI30340.3| unnamed protein product [Vitis vinifera]

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/89 (49%), Positives = 63/89 (70%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT++ L++ FSQ+GQV EA I+MD   +RSKG+G+VT ++EEEAQKA  +M+GK 
Sbjct: 40  GLSFYTTEKGLSEHFSQYGQVVEAKIVMDRVSDRSKGFGFVTFASEEEAQKARTEMDGKE 99

Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQ 152
           L+GR IFVD  +P   +     +AR P +
Sbjct: 100 LNGRTIFVDYAKPRADFGGGMPIARGPPE 128

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224091949|ref|XP_002309412.1| predicted protein [Populus trichocarpa] gi|222855388|gb|EEE92935.1| predicted protein [Populus trichocarpa]

 Score = 92.8 bits (229), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 47/112 (41%), Positives = 70/112 (62%)

Query: 41  HCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKG 100
             +  P++  I Q    +      +S  TT+  L++AFSQ+GQV EA I+MD   +RSKG
Sbjct: 22  KLVAAPTALFIWQRGITTKLFVGGLSIYTTENGLSEAFSQYGQVVEAKIVMDRALDRSKG 81

Query: 101 YGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQ 152
           +G+VT ++E+EAQKAL +MNGK L+GRVI+VD  +    +     +AR P +
Sbjct: 82  FGFVTYASEDEAQKALDEMNGKALNGRVIYVDYAKLKTNFGGGIPIARGPPE 133

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255565709|ref|XP_002523844.1| Cold-inducible RNA-binding protein, putative [Ricinus communis] gi|223536932|gb|EEF38570.1| Cold-inducible RNA-binding protein, putative [Ricinus communis]

 Score = 92.4 bits (228), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 45/92 (48%), Positives = 62/92 (67%), Gaps = 2/92 (2%)

Query: 45  RPSSDLIMQLVNVSFWRCI--SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYG 102
           +P++ L     + S  R     +SFS+T E L +AFS+FG++ E  II D   +R KGY 
Sbjct: 19  KPNTPLFFSTNSASSSRLFVKGISFSSTTESLTEAFSKFGEIVEVNIIKDKAMDRPKGYA 78

Query: 103 YVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV 134
           YVT +TE EA+KAL +MNGK++DGR +FVDNV
Sbjct: 79  YVTFATENEAKKALTEMNGKVIDGRPVFVDNV 110

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388502672|gb|AFK39402.1| unknown [Medicago truncatula]

 Score = 91.7 bits (226), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 44/103 (42%), Positives = 69/103 (66%), Gaps = 7/103 (6%)

Query: 57  VSFWRCIS-------VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTE 109
           ++F R I+       +SF TT++ L+DAFS +GQV EA +I D    +SKGYG+VT +++
Sbjct: 24  LTFRRAIAFKLFVGGLSFHTTEKTLSDAFSNYGQVVEAKVITDRISEKSKGYGFVTFASQ 83

Query: 110 EEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQ 152
           +EA+KA+ +MN K L+GRV+FVD  +P  + +    +AR P +
Sbjct: 84  DEAEKAITEMNEKALNGRVVFVDYAKPDTKRSMGMPIARGPPE 126

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255579369|ref|XP_002530529.1| RNA binding protein, putative [Ricinus communis] gi|223529933|gb|EEF31861.1| RNA binding protein, putative [Ricinus communis]

 Score = 91.7 bits (226), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 44/89 (49%), Positives = 62/89 (69%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT + L +AFSQ+GQV EATI+ D   +RSKG+G+VT ++E+EA  AL +MNGK 
Sbjct: 37  GLSFYTTDKGLTEAFSQYGQVVEATIVSDRVLDRSKGFGFVTFASEDEAHNALSEMNGKT 96

Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQ 152
           L+GRVI+VD  +P      +  +AR P +
Sbjct: 97  LNGRVIYVDYAKPRTDSRNEVPIARGPPE 125

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359479548|ref|XP_003632289.1| PREDICTED: cold-inducible RNA-binding protein-like [Vitis vinifera] gi|296084877|emb|CBI28286.3| unnamed protein product [Vitis vinifera]

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 54/112 (48%), Positives = 69/112 (61%), Gaps = 13/112 (11%)

Query: 22  DSLLSFSS-KPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQ 80
           D+ L FSS  PY +            SS LI      S      +SFSTT++ LA+AFSQ
Sbjct: 9   DTFLRFSSLNPYLL------------SSQLIFCRGIASTLFVKGISFSTTEKTLAEAFSQ 56

Query: 81  FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD 132
           FG+V EA IIMD  K R KG+ YVT + E+EA+KAL +MNGK++DGR + VD
Sbjct: 57  FGEVVEAKIIMDKRKLRPKGFAYVTFTREDEAEKALTEMNGKVVDGRTVLVD 108

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357457753|ref|XP_003599157.1| Cold-inducible RNA-binding protein [Medicago truncatula] gi|355488205|gb|AES69408.1| Cold-inducible RNA-binding protein [Medicago truncatula]

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 41/78 (52%), Positives = 59/78 (75%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            ++FSTT+E LA+AFSQ+G V +A I+++  K R KG+GYVT + EEEA+KA + MNGK+
Sbjct: 38  GLAFSTTEEKLAEAFSQYGNVVKADIVLNKAKKRCKGFGYVTFAEEEEARKAQIGMNGKI 97

Query: 124 LDGRVIFVDNVRPSRRYN 141
           L GRV++VD   P+ + N
Sbjct: 98  LHGRVLYVDMDPPNEQKN 115

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725383|ref|NP_001238370.1| uncharacterized protein LOC100527079 [Glycine max] gi|255631508|gb|ACU16121.1| unknown [Glycine max]

 Score = 89.0 bits (219), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 47/121 (38%), Positives = 76/121 (62%), Gaps = 7/121 (5%)

Query: 39  SLHCIVRPSSDLIMQLVNVSFWRCIS-------VSFSTTKEMLADAFSQFGQVTEATIIM 91
           ++  I+  + + I+    +SF R I+       +SF TT+  L++AFS +GQV EA I+ 
Sbjct: 3   AVRKIIEVNRNKILSPSLLSFRRGIAYKLFVGGLSFYTTENALSEAFSNYGQVIEAKIVT 62

Query: 92  DIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPA 151
           D   +RSKG+G+VT ++++EA+ A+ DM GK L+GRVIFVD  +P+     +  +AR P 
Sbjct: 63  DRVSDRSKGFGFVTFASQDEAENAIEDMKGKTLNGRVIFVDYAKPNINTRGEIPIARGPP 122

Query: 152 Q 152
           +
Sbjct: 123 E 123

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449500867|ref|XP_004161215.1| PREDICTED: glycine-rich RNA-binding protein 2, mitochondrial-like [Cucumis sativus]

 Score = 88.6 bits (218), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 44/94 (46%), Positives = 65/94 (69%), Gaps = 3/94 (3%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +S+ TT + L++AFSQ+GQV EAT++MD   ++SKG+G+VT ++ +EA  AL +MNGK 
Sbjct: 41  GLSYYTTDKGLSEAFSQYGQVIEATVVMDRVSDKSKGFGFVTFASLDEAHTALSEMNGKP 100

Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN 157
           L+GRVIFV+  +P+        +AR P   PEE 
Sbjct: 101 LNGRVIFVNYAKPTTSSRGAIPIARGP---PEEK 131

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	157
TAIR|locus:2039590	116	AT2G27330 [Arabidopsis thalian	0.503	0.681	0.468	7.7e-16
TAIR|locus:2160752	146	AT5G06210 [Arabidopsis thalian	0.433	0.465	0.558	1.6e-15
TAIR|locus:2049816	142	AT2G37510 [Arabidopsis thalian	0.433	0.478	0.558	3.3e-15
TAIR|locus:2206850	181	AT1G73530 [Arabidopsis thalian	0.452	0.392	0.478	1e-13
TAIR|locus:2172144	156	AT5G54580 [Arabidopsis thalian	0.547	0.551	0.404	1.5e-12
UNIPROTKB|Q28IQ9	166	cirbp "Cold-inducible RNA-bind	0.464	0.439	0.438	2.4e-12
TAIR|locus:2077137	102	AT3G46020 [Arabidopsis thalian	0.433	0.666	0.455	2.4e-12
UNIPROTKB|K7ENX8	89	CIRBP "Cold-inducible RNA-bind	0.464	0.820	0.418	6.4e-12
ZFIN|ZDB-GENE-030131-5841	224	cirbp "cold inducible RNA bind	0.605	0.424	0.343	8.2e-12
ZFIN|ZDB-GENE-050417-329	185	zgc:112425 "zgc:112425" [Danio	0.433	0.367	0.455	1e-11

TAIR|locus:2039590 AT2G27330 [Arabidopsis thaliana (taxid:3702)]

 Score = 198 (74.8 bits), Expect = 7.7e-16, P = 7.7e-16
 Identities = 37/79 (46%), Positives = 58/79 (73%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +SFS+T+E L  AFSQ+GQV +  +IMD  + R KG+ YVT S++EEA+KAL+++N +L+
Sbjct:    28 ISFSSTEETLTQAFSQYGQVLKVDVIMDKIRCRPKGFAYVTFSSKEEAEKALLELNAQLV 87

Query:   125 DGRVIFVDNVRPSRRYNTD 143
             DGRV+ +D  + ++    D
Sbjct:    88 DGRVVILDTTKAAKHNPPD 106

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2160752 AT5G06210 [Arabidopsis thaliana (taxid:3702)]

 Score = 195 (73.7 bits), Expect = 1.6e-15, P = 1.6e-15
 Identities = 38/68 (55%), Positives = 55/68 (80%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +SF TT++ L++AFS+ GQV EA I+MD   +RSKG+G+VT ++ +EAQKAL++ NG+ L
Sbjct:    41 LSFCTTEQGLSEAFSKCGQVVEAQIVMDRVSDRSKGFGFVTFASADEAQKALMEFNGQQL 100

Query:   125 DGRVIFVD 132
             +GR IFVD
Sbjct:   101 NGRTIFVD 108

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

TAIR|locus:2049816 AT2G37510 [Arabidopsis thaliana (taxid:3702)]

 Score = 192 (72.6 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 38/68 (55%), Positives = 48/68 (70%)

Query:    69 TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
             TT E L DAF+ FGQ+ +A +I D    RSKG+G+VT +T E+A+KA  +MN K LDG V
Sbjct:    45 TTNEKLQDAFASFGQLVDARVITDRDSGRSKGFGFVTYATIEDAEKAKAEMNAKFLDGWV 104

Query:   129 IFVDNVRP 136
             IFVD  RP
Sbjct:   105 IFVDPARP 112

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

TAIR|locus:2206850 AT1G73530 [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 1.0e-13, P = 1.0e-13
 Identities = 34/71 (47%), Positives = 47/71 (66%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +SF TT++ L D F QFG +    ++MD   NR KG+ ++   TEEEA KA+  M+GK L
Sbjct:    84 LSFRTTEDTLRDTFEQFGNLIHMNMVMDKVANRPKGFAFLRYETEEEAMKAIQGMHGKFL 143

Query:   125 DGRVIFVDNVR 135
             DGRVIFV+  +
Sbjct:   144 DGRVIFVEEAK 154

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

TAIR|locus:2172144 AT5G54580 [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 1.5e-12, P = 1.5e-12
 Identities = 36/89 (40%), Positives = 54/89 (60%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +S  TT E L  AF+QFG+V +A ++ D     SKG+G+V  +T E++ K +  M+GK L
Sbjct:    63 LSKRTTSEGLRTAFAQFGEVADAKVVTDRVSGYSKGFGFVRYATLEDSAKGIAGMDGKFL 122

Query:   125 DGRVIFVDNVRP---SRRYNTDASLARQP 150
             DG VIF +  RP   S+ Y    +++R P
Sbjct:   123 DGWVIFAEYARPREQSQSYQPQNNMSRPP 151

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

UNIPROTKB|Q28IQ9 cirbp "Cold-inducible RNA-binding protein" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 32/73 (43%), Positives = 47/73 (64%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             ++F TT+E L   FS++GQV E  ++ D    RS+G+G+VT    E+A+ A++ MNGK +
Sbjct:    13 LNFETTEESLEQVFSKYGQVAEVVVVKDRESKRSRGFGFVTFENPEDAKDAMMAMNGKSV 72

Query:   125 DGRVIFVDNVRPS 137
             DGR I VD    S
Sbjct:    73 DGRQIRVDQAGKS 85

GO:0003729 "mRNA binding" evidence=ISS

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

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0007369 "gastrulation" evidence=ISS

GO:0009409 "response to cold" evidence=ISS

GO:0009790 "embryo development" evidence=ISS

GO:0016477 "cell migration" evidence=ISS

GO:0019899 "enzyme binding" evidence=ISS

GO:0022008 "neurogenesis" evidence=ISS

GO:0045727 "positive regulation of translation" evidence=ISS

GO:0048255 "mRNA stabilization" evidence=ISS

GO:0048793 "pronephros development" evidence=ISS

GO:0060212 "negative regulation of nuclear-transcribed mRNA poly(A) tail shortening" evidence=ISS

GO:0005840 "ribosome" evidence=ISS

TAIR|locus:2077137 AT3G46020 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.4e-12, P = 2.4e-12
 Identities = 31/68 (45%), Positives = 48/68 (70%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +S  TT + L   FS FGQ+ EA +I D    R KG+G++T  +E++A+KAL  ++GK++
Sbjct:    14 LSAYTTDQSLRQLFSPFGQIKEARLIRDSETQRPKGFGFITFDSEDDARKALKSLDGKIV 73

Query:   125 DGRVIFVD 132
             DGR+IFV+
Sbjct:    74 DGRLIFVE 81

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|K7ENX8 CIRBP "Cold-inducible RNA-binding protein" [Homo sapiens (taxid:9606)]

 Score = 161 (61.7 bits), Expect = 6.4e-12, P = 6.4e-12
 Identities = 31/74 (41%), Positives = 50/74 (67%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +SF T ++ L   FS++GQ++E  ++ D    RS+G+G+VT    ++A+ A++ MNGK +
Sbjct:    13 LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV 72

Query:   125 DGRVIFVDN-VRPS 137
             DGR I VD  +RPS
Sbjct:    73 DGRQIRVDQPLRPS 86

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

ZFIN|ZDB-GENE-030131-5841 cirbp "cold inducible RNA binding protein" [Danio rerio (taxid:7955)]

 Score = 160 (61.4 bits), Expect = 8.2e-12, P = 8.2e-12
 Identities = 33/96 (34%), Positives = 58/96 (60%)

Query:    42 CIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGY 101
             C+   +S++I+       +    +S+ TT++ L +AFS++G + +  +I D   +RS+G+
Sbjct:     8 CVFNRNSEVIIMSDEGKLF-IGGLSYDTTEQSLEEAFSKYGTIAKVDVIRDRETDRSRGF 66

Query:   102 GYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS 137
             G+VT    E+A+ A+  MNGK +DGR+I VD    S
Sbjct:    67 GFVTFENPEDAKDAMAAMNGKQVDGRMIRVDEAGKS 102

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0009409 "response to cold" evidence=IDA

ZFIN|ZDB-GENE-050417-329 zgc:112425 "zgc:112425" [Danio rerio (taxid:7955)]

 Score = 159 (61.0 bits), Expect = 1.0e-11, P = 1.0e-11
 Identities = 31/68 (45%), Positives = 46/68 (67%)

Query:    65 VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             +SF TT++ L DAFS++G +T   +  +   NRS+G+G+VT    ++A+ AL  MNGK +
Sbjct:    12 LSFDTTEQSLEDAFSKYGVITNVHVARNRETNRSRGFGFVTFENPDDAKDALEGMNGKSV 71

Query:   125 DGRVIFVD 132
             DGR I VD
Sbjct:    72 DGRTIRVD 79

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid 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

Your Input:
	estExt_fgenesh4_pg.C_LG_VI1354	hypothetical protein (140 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0049021701	hypothetical protein (272 aa)			•						0.501
	gw1.232.53.1	hypothetical protein (203 aa)			•						0.494
	gw1.XV.2574.1	hypothetical protein (203 aa)			•						0.490
	eugene3.00050125	hypothetical protein (218 aa)			•						0.488
	estExt_fgenesh4_pg.C_LG_VII0461	hypothetical protein (218 aa)			•						0.485
	gw1.VIII.2127.1	hypothetical protein (133 aa)			•						0.476
	gw1.X.2172.1	hypothetical protein (232 aa)			•						0.459
	estExt_fgenesh4_kg.C_LG_X0007	SubName- Full=Putative uncharacterized protein; (252 aa)			•						0.458
	gw1.XVI.1974.1	hypothetical protein (131 aa)			•						0.438
	eugene3.00170125	hypothetical protein (199 aa)			•						0.409

---

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	157
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	6e-21
smart00360	73	smart00360, RRM, RNA recognition motif	7e-20
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	2e-18
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	3e-18
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	7e-17
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	7e-17
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	8e-16
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	1e-15
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	2e-15
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	4e-15
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-15
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	5e-15
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-14
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-14
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	6e-14
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-13
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	1e-13
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-13
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	3e-13
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	4e-13
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	9e-13
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	1e-12
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	1e-12
cd12365	73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	8e-12
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-11
cd12377	78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	1e-11
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-11
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-11
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	3e-11
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-11
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	5e-11
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	7e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	9e-11
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	1e-10
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	1e-10
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	2e-10
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	3e-10
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	4e-10
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	4e-10
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	5e-10
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	5e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-10
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	7e-10
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	8e-10
cd12407	76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-09
cd12370	76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	1e-09
cd12355	80	cd12355, RRM_RBM18, RNA recognition motif in eukar	1e-09
cd12345	80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	1e-09
cd12617	80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	2e-09
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	2e-09
cd12618	80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	3e-09
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	4e-09
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-09
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	4e-09
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	6e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	6e-09
cd12319	84	cd12319, RRM4_MRD1, RNA recognition motif 4 in yea	9e-09
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	9e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-08
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	1e-08
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	1e-08
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	1e-08
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-08
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-08
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	2e-08
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	2e-08
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-08
cd12393	78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-08
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-08
cd12567	79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	4e-08
cd12417	74	cd12417, RRM_SAFB_like, RNA recognition motif in t	4e-08
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	4e-08
cd12236	91	cd12236, RRM_snRNP70, RNA recognition motif in U1	5e-08
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-08
cd12654	86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	5e-08
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	6e-08
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	6e-08
cd12653	84	cd12653, RRM3_HuR, RNA recognition motif 3 in vert	7e-08
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	8e-08
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	9e-08
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	9e-08
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	9e-08
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	9e-08
cd12661	77	cd12661, RRM3_hnRNPM, RNA recognition motif 3 in v	1e-07
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	1e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-07
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	2e-07
cd12278	84	cd12278, RRM_eIF3B, RNA recognition motif in eukar	2e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	2e-07
cd12655	85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	2e-07
cd12612	82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	2e-07
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-07
cd12389	77	cd12389, RRM2_RAVER, RNA recognition motif 2 in ri	2e-07
cd12656	86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	2e-07
cd12621	74	cd12621, RRM3_TIA1, RNA recognition motif 3 in nuc	3e-07
cd12675	83	cd12675, RRM2_Nop4p, RNA recognition motif 2 in ye	3e-07
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	4e-07
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	5e-07
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	5e-07
cd12305	75	cd12305, RRM_NELFE, RNA recognition motif in negat	5e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	6e-07
cd12662	77	cd12662, RRM3_MYEF2, RNA recognition motif 3 in ve	8e-07
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	8e-07
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	8e-07
cd12243	71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	1e-06
cd12642	79	cd12642, RRM_TRA2A, RNA recognition motif in trans	1e-06
cd12333	80	cd12333, RRM2_p54nrb_like, RNA recognition motif 2	1e-06
cd12620	73	cd12620, RRM3_TIAR, RNA recognition motif 3 in nuc	1e-06
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	1e-06
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	1e-06
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	2e-06
cd12679	76	cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in	2e-06
cd12613	80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	3e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	3e-06
cd12418	75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	4e-06
cd12400	74	cd12400, RRM_Nop6, RNA recognition motif in Saccha	4e-06
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-06
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	5e-06
cd12254	73	cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognit	5e-06
cd12404	77	cd12404, RRM2_NCL, RNA recognition motif 2 in vert	6e-06
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	7e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	1e-05
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	1e-05
cd12394	91	cd12394, RRM1_RBM34, RNA recognition motif 1 in RN	1e-05
cd12589	80	cd12589, RRM2_PSP1, RNA recognition motif 2 in ver	1e-05
cd12324	88	cd12324, RRM_RBM8, RNA recognition motif in RNA-bi	1e-05
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	1e-05
cd12495	72	cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in v	2e-05
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	2e-05
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	2e-05
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-05
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	3e-05
cd12332	71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-05
cd12591	80	cd12591, RRM2_p54nrb, RNA recognition motif 2 in v	4e-05
cd12406	78	cd12406, RRM4_NCL, RNA recognition motif 4 in vert	4e-05
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	4e-05
cd12233	70	cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition m	5e-05
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	5e-05
cd12411	89	cd12411, RRM_ist3_like, RNA recognition motif in i	8e-05
cd12639	79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	8e-05
cd12590	80	cd12590, RRM2_PSF, RNA recognition motif 2 in vert	8e-05
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	8e-05
TIGR01648	578	TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonu	1e-04
cd12453	86	cd12453, RRM1_RIM4_like, RNA recognition motif 1 i	1e-04
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	1e-04
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	1e-04
cd12640	79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	1e-04
cd12416	98	cd12416, RRM4_RBM28_like, RNA recognition motif 4	1e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	1e-04
cd12770	83	cd12770, RRM1_HuD, RNA recognition motif 1 in vert	1e-04
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	2e-04
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	2e-04
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-04
cd12369	68	cd12369, RRM4_RBM45, RNA recognition motif 4 in RN	2e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	2e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-04
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	2e-04
cd12560	84	cd12560, RRM_SRSF12, RNA recognition motif in seri	3e-04
cd12232	89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	3e-04
cd12431	80	cd12431, RRM_ALKBH8, RNA recognition motif in alky	3e-04
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	3e-04
cd12606	67	cd12606, RRM1_RBM4, RNA recognition motif 1 in ver	3e-04
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	3e-04
cd12341	68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	3e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	4e-04
cd12494	72	cd12494, RRM3_hnRNPR, RNA recognition motif 3 in v	4e-04
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	4e-04
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	4e-04
smart00361	70	smart00361, RRM_1, RNA recognition motif	5e-04
cd12386	74	cd12386, RRM2_hnRNPM_like, RNA recognition motif 2	6e-04
cd12610	84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	6e-04
cd12486	78	cd12486, RRM1_ACF, RNA recognition motif 1 found i	7e-04
cd12310	72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	7e-04
cd12665	77	cd12665, RRM2_RAVER1, RNA recognition motif 2 foun	8e-04
cd12409	84	cd12409, RRM1_RRT5, RNA recognition motif 1 in yea	8e-04
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	8e-04
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	9e-04
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	0.001
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.001
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	0.001
cd12680	75	cd12680, RRM_THOC4, RNA recognition motif in THO c	0.001
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	0.001
cd12351	77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	0.001
cd12282	91	cd12282, RRM2_TatSF1_like, RNA recognition motif 2	0.001
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	0.001
cd12285	85	cd12285, RRM3_RBM39_like, RNA recognition motif 3	0.001
cd12244	79	cd12244, RRM2_MSSP, RNA recognition motif 2 in the	0.002
cd12637	80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	0.002
cd12622	74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	0.002
cd12594	74	cd12594, RRM1_SRSF4, RNA recognition motif 1 in ve	0.002
cd12397	73	cd12397, RRM2_Nop13p_fungi, RNA recognition motif	0.002
cd12666	77	cd12666, RRM2_RAVER2, RNA recognition motif 2 in v	0.002
cd12593	75	cd12593, RRM_RBM11, RNA recognition motif in verte	0.003
cd12774	81	cd12774, RRM2_HuD, RNA recognition motif 2 in vert	0.003
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.003
cd12485	78	cd12485, RRM1_RBM47, RNA recognition motif 1 found	0.003
cd12231	77	cd12231, RRM2_U2AF65, RNA recognition motif 2 foun	0.003
cd12385	76	cd12385, RRM1_hnRNPM_like, RNA recognition motif 1	0.004
cd12372	76	cd12372, RRM_CFIm68_CFIm59, RNA recognition motif	0.004
cd12292	75	cd12292, RRM2_La_like, RNA recognition motif 2 in	0.004
cd12438	98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	0.004
cd12775	90	cd12775, RRM2_HuB, RNA recognition motif 2 in vert	0.004

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

 Score = 80.7 bits (200), Expect = 6e-21
 Identities = 30/71 (42%), Positives = 42/71 (59%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            ++ T+E L D F QFG+VT A +I D    RS+G+G+V   T EEA  A+  +NG    
Sbjct: 8   PYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFG 67

Query: 126 GRVIFVDNVRP 136
           GR + V+  RP
Sbjct: 68  GRTLTVNEARP 78

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

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

 Score = 77.6 bits (192), Expect = 7e-20
 Identities = 28/67 (41%), Positives = 43/67 (64%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   TT+E L + FS+FG+V    ++ D    +SKG+ +V   +EE+A+KAL  +NGK L
Sbjct: 7   LPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKEL 66

Query: 125 DGRVIFV 131
           DGR + V
Sbjct: 67  DGRPLKV 73

Length = 73

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

 Score = 74.5 bits (183), Expect = 2e-18
 Identities = 29/73 (39%), Positives = 47/73 (64%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF T ++ L   FS++GQ++E  ++ D    RS+G+G+VT    ++A+ A++ MNGK +
Sbjct: 8   LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSV 67

Query: 125 DGRVIFVDNVRPS 137
           DGR I VD    S
Sbjct: 68  DGRQIRVDQAGKS 80

This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. . Length = 80

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

 Score = 73.6 bits (181), Expect = 3e-18
 Identities = 31/69 (44%), Positives = 43/69 (62%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++S+S   E L   F +FG V  A +I D    RS+G+GYV   + E+A+KA+  M+GK 
Sbjct: 6   NLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKE 65

Query: 124 LDGRVIFVD 132
           LDGR I VD
Sbjct: 66  LDGRPINVD 74

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

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

 Score = 70.0 bits (172), Expect = 7e-17
 Identities = 27/68 (39%), Positives = 42/68 (61%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   TT+E L + FS+FG++    I+ D    +SKG+ +V   + E+A+KAL  +NGK L
Sbjct: 6   LPPDTTEEDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEALNGKEL 64

Query: 125 DGRVIFVD 132
           DGR + V 
Sbjct: 65  DGRKLKVS 72

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

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

 Score = 69.9 bits (172), Expect = 7e-17
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   TT+E L D FS+FG +    I+ D    RSKG+ +V    EE+A+KAL  +NGK L
Sbjct: 6   LPPDTTEEDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALNGKEL 64

Query: 125 DGRVI 129
            GR +
Sbjct: 65  GGREL 69

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

>gnl|CDD|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 = 67.6 bits (166), Expect = 8e-16
 Identities = 29/68 (42%), Positives = 45/68 (66%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  TT++ L   FS+FG+V E  ++ D     S+G+G+VT  + E+A  A+ D+NGK L
Sbjct: 9   LSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRDLNGKEL 68

Query: 125 DGRVIFVD 132
           +GRVI V+
Sbjct: 69  EGRVIKVE 76

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

 Score = 67.3 bits (165), Expect = 1e-15
 Identities = 23/69 (33%), Positives = 40/69 (57%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ + TT E L + FS+ G +    ++ D G  + +G+GYVT + EE+A++AL +     
Sbjct: 6   NLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTK 65

Query: 124 LDGRVIFVD 132
             GR I V+
Sbjct: 66  FGGRKIHVE 74

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

 Score = 66.9 bits (164), Expect = 2e-15
 Identities = 28/64 (43%), Positives = 43/64 (67%), Gaps = 1/64 (1%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   E L + FS FG +T A ++ D  K RSKG+G+V  S+ EEA KA+ +MNG+++ G+
Sbjct: 12  SIDDERLREEFSPFGTITSAKVMTD-EKGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGK 70

Query: 128 VIFV 131
            ++V
Sbjct: 71  PLYV 74

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

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

 Score = 67.8 bits (165), Expect = 4e-15
 Identities = 32/75 (42%), Positives = 47/75 (62%), Gaps = 2/75 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ T    L DAF+ FG V +A +I+D    RS+G+G+V  + E  A  A+ +M+GK L
Sbjct: 42  LSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKEL 101

Query: 125 DGRVIFVD--NVRPS 137
           +GR I V+  N RPS
Sbjct: 102 NGRHIRVNPANDRPS 116

Length = 144

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

 Score = 65.5 bits (160), Expect = 4e-15
 Identities = 24/60 (40%), Positives = 40/60 (66%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
             E L  AF+ FG++++A ++ D+   +SKGYG+V+   +E+A+ A+  MNG+ L GR I
Sbjct: 12  DTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSMNGQWLGGRAI 71

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

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

 Score = 65.7 bits (161), Expect = 5e-15
 Identities = 22/63 (34%), Positives = 41/63 (65%), Gaps = 1/63 (1%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
              E L + F ++G++T A ++ D  + +SKG+G+V     E AQKA+ ++NGK ++G+ 
Sbjct: 13  MDDEKLKELFGKYGKITSAKVMKD-DEGKSKGFGFVNFENHEAAQKAVEELNGKEVNGKK 71

Query: 129 IFV 131
           ++V
Sbjct: 72  LYV 74

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

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

 Score = 63.8 bits (156), Expect = 2e-14
 Identities = 26/64 (40%), Positives = 40/64 (62%), Gaps = 1/64 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + + TT + L   FSQFG++ EA +I D    +S+GYG+VT   +E A++A  D N  ++
Sbjct: 8   LPYHTTDDSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAERACKDPN-PII 66

Query: 125 DGRV 128
           DGR 
Sbjct: 67  DGRK 70

This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 76

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

 Score = 62.7 bits (153), Expect = 5e-14
 Identities = 25/68 (36%), Positives = 39/68 (57%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ F+ T++ L   F  FG++    +  D    RSKGYG++  +  E+A+KAL  +NG  
Sbjct: 5   NLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFE 64

Query: 124 LDGRVIFV 131
           L GR I V
Sbjct: 65  LAGRPIKV 72

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

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

 Score = 62.9 bits (153), Expect = 6e-14
 Identities = 26/69 (37%), Positives = 42/69 (60%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +++FS T+E L D FS    +  A ++ D     S+GYG+VT +  E+AQ+AL  +  K 
Sbjct: 6   NLAFSVTQEDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKK 65

Query: 124 LDGRVIFVD 132
           L GR++ +D
Sbjct: 66  LHGRILRLD 74

This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 61.9 bits (151), Expect = 1e-13
 Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F  T+  L   FS FG V E TI       + KG+ +V  +++ +A+KA+  +NGK + 
Sbjct: 8   PFKCTEADLKKLFSPFGFVWEVTIPRKP-DGKKKGFAFVQFTSKADAEKAIKGVNGKKIK 66

Query: 126 GRVIFVD 132
           GR + VD
Sbjct: 67  GRPVAVD 73

This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 76

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

 Score = 61.9 bits (151), Expect = 1e-13
 Identities = 26/65 (40%), Positives = 36/65 (55%), Gaps = 1/65 (1%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           FS T + L D F + G V  A +  D    RSKG+G V   + E+AQ+A+   NG  L+G
Sbjct: 8   FSVTWQDLKDLFRECGNVLRADVKTD-NDGRSKGFGTVLFESPEDAQRAIEMFNGYDLEG 66

Query: 127 RVIFV 131
           R + V
Sbjct: 67  RELEV 71

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

>gnl|CDD|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins

 Score = 61.0 bits (149), Expect = 3e-13
 Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   + L D FS FG +    +  D     SKGYG+V   TEE A +A+  +NG LL+ +
Sbjct: 13  SIDNKALYDTFSAFGNILSCKVATD-ENGGSKGYGFVHFETEEAAVRAIEKVNGMLLNDK 71

Query: 128 VIFV 131
            +FV
Sbjct: 72  KVFV 75

This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. . Length = 77

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

 Score = 60.8 bits (148), Expect = 3e-13
 Identities = 29/67 (43%), Positives = 42/67 (62%), Gaps = 2/67 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+S  ++ L + F + G+V +  I  D    RSKG+G+V  +TEE AQKAL + +G+ L 
Sbjct: 8   SWSAEQDDLEEFFKECGEVVDVRIAQD-DDGRSKGFGHVEFATEEGAQKAL-EKSGEELL 65

Query: 126 GRVIFVD 132
           GR I VD
Sbjct: 66  GREIRVD 72

This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 77

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

 Score = 60.3 bits (147), Expect = 4e-13
 Identities = 26/74 (35%), Positives = 44/74 (59%), Gaps = 3/74 (4%)

Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           C+ V   S  TT+  L + FS++G + +  ++ D    RS+G+G+V   + E+A++A   
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFESVEDAKEAKER 60

Query: 119 MNGKLLDGRVIFVD 132
           +NG  +DGR I VD
Sbjct: 61  LNGMEIDGRRIRVD 74

This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 78

>gnl|CDD|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 = 59.6 bits (145), Expect = 9e-13
 Identities = 23/66 (34%), Positives = 40/66 (60%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F+TT+E L + F  FG+++E  + +D    RSKG+ +V+    E A KA  +++G +  
Sbjct: 8   PFTTTEEELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAVKAYSELDGSIFQ 67

Query: 126 GRVIFV 131
           GR++ V
Sbjct: 68  GRLLHV 73

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

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

 Score = 59.1 bits (144), Expect = 1e-12
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ TT+E L + FS++G+V +  I+ D    RS+G+G+VT +      K L      +L
Sbjct: 6   LSWDTTEESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKP-HVL 64

Query: 125 DGRVI 129
           DGR I
Sbjct: 65  DGREI 69

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

 Score = 59.2 bits (144), Expect = 1e-12
 Identities = 21/68 (30%), Positives = 38/68 (55%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +++ TT + L   F ++G+V +  I  D     S+G+ +V    + +A+ A+  M+GK L
Sbjct: 6   LTYRTTPDDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAMDGKEL 65

Query: 125 DGRVIFVD 132
           DGR + V 
Sbjct: 66  DGRELRVQ 73

This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. . Length = 73

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

 Score = 57.2 bits (139), Expect = 8e-12
 Identities = 21/62 (33%), Positives = 36/62 (58%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
            K+ L + FS +G V +  + +D   N  +GY YV   + E+A+KA+  M+G  +DG+ +
Sbjct: 11  NKDHLKEIFSNYGTVKDVDLPIDREVNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQEV 70

Query: 130 FV 131
            V
Sbjct: 71  TV 72

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

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

 Score = 61.4 bits (149), Expect = 1e-11
 Identities = 24/64 (37%), Positives = 44/64 (68%), Gaps = 1/64 (1%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           + T E L + FS+ G++T A +++D  K  S+G+G+V  S  EEA +A+ +M+G++L G+
Sbjct: 296 TVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354

Query: 128 VIFV 131
            ++V
Sbjct: 355 PLYV 358

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

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

 Score = 56.6 bits (137), Expect = 1e-11
 Identities = 30/73 (41%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           CI V        + +L   FS FG VT   +I D+  N+ KGYG+VT +  EEA  A+  
Sbjct: 3   CIFVYNLPPDADESLLWQLFSPFGAVTNVKVIRDLTTNKCKGYGFVTMTNYEEAYSAIAS 62

Query: 119 MNGKLLDGRVIFV 131
           +NG  L GRV+ V
Sbjct: 63  LNGYRLGGRVLQV 75

This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 56.4 bits (137), Expect = 1e-11
 Identities = 22/59 (37%), Positives = 35/59 (59%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
            +  + T+E +   F ++G + E TII D    +SKG  +V  S+ EEAQKA+  ++GK
Sbjct: 6   QLPKTATEEDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGK 64

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

 Score = 55.8 bits (135), Expect = 2e-11
 Identities = 23/67 (34%), Positives = 39/67 (58%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF   ++ + +AF ++G+++   +  D    R KG+GYV  S++E AQ AL  + G  L 
Sbjct: 7   SFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDALGGTDLL 66

Query: 126 GRVIFVD 132
           GR + +D
Sbjct: 67  GRPVRLD 73

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

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

 Score = 55.7 bits (135), Expect = 3e-11
 Identities = 23/68 (33%), Positives = 41/68 (60%), Gaps = 2/68 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +S  ++ L   FS+ G++T+  ++ +  K +SKGY YV    EE  Q+AL  ++ +L+
Sbjct: 7   LDYSVPEDELRKLFSKCGEITDVRLVKN-YKGKSKGYAYVEFENEESVQEALK-LDRELI 64

Query: 125 DGRVIFVD 132
            GR +FV 
Sbjct: 65  KGRPMFVS 72

This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 72

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

 Score = 56.0 bits (135), Expect = 3e-11
 Identities = 24/65 (36%), Positives = 40/65 (61%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S   T   L  AFS F   ++A ++ D+   RS+GYG+V+  ++++A+ A+ +MNGK L
Sbjct: 7   LSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGKWL 66

Query: 125 DGRVI 129
             R I
Sbjct: 67  GSRPI 71

This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 75

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

 Score = 54.9 bits (133), Expect = 5e-11
 Identities = 22/65 (33%), Positives = 41/65 (63%), Gaps = 2/65 (3%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S T+E L + FS +G+V    ++ +  K+R +G+ +V  ++ E+A+ AL  +NG +L
Sbjct: 6   LPPSVTEEDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALKKLNGLVL 63

Query: 125 DGRVI 129
           DGR +
Sbjct: 64  DGRTL 68

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

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

 Score = 55.0 bits (133), Expect = 7e-11
 Identities = 25/67 (37%), Positives = 38/67 (56%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S  TT+E L + FS++G +    ++ DI    SKGY +V    E +A +A  D +  ++D
Sbjct: 12  SLQTTEETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFVEYEHERDALRAYRDAHKLVID 71

Query: 126 GRVIFVD 132
           G  IFVD
Sbjct: 72  GSEIFVD 78

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

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

 Score = 58.0 bits (139), Expect = 9e-11
 Identities = 28/116 (24%), Positives = 57/116 (49%), Gaps = 3/116 (2%)

Query: 45  RPSSDLIMQLVNVSFWRCISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGY 101
           R S     +  +      + V    +  T+E L + F +FG V    ++ D    +S+G+
Sbjct: 100 RSSESPKSRQKSKEENNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGF 159

Query: 102 GYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN 157
            +V   +EE A+KA+ ++NGK L+GR + V   +P+ +  ++ S     + + + +
Sbjct: 160 AFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLS 215

Length = 306

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

 Score = 54.2 bits (131), Expect = 1e-10
 Identities = 30/76 (39%), Positives = 42/76 (55%), Gaps = 7/76 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +   TT+E L D FS+FG V +  II D  G   SKGYG+VT  T+E+A+K L   N   
Sbjct: 10  IPPDTTEEELRDFFSRFGSVKDVKIITDRAGV--SKGYGFVTFETQEDAEKILAMGNLNF 67

Query: 124 LDGRVIFVDNVRPSRR 139
              ++    N+ P+ R
Sbjct: 68  RGKKL----NIGPAIR 79

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

 Score = 53.8 bits (130), Expect = 1e-10
 Identities = 19/64 (29%), Positives = 32/64 (50%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
              +++L  AF  FG + +  I +D    + +G+ +V     E+A  A+ +MN   L GR
Sbjct: 9   EVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNMNESELFGR 68

Query: 128 VIFV 131
            I V
Sbjct: 69  TIRV 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|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

 Score = 53.8 bits (130), Expect = 2e-10
 Identities = 24/61 (39%), Positives = 37/61 (60%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
            T E+LA AFS++    +A ++ D    +SKGYG+V+ S   +  KA+ +MNGK +  R 
Sbjct: 18  VTDEVLARAFSKYPSFQKAKVVRDKRTGKSKGYGFVSFSDPNDYLKAMKEMNGKYVGNRP 77

Query: 129 I 129
           I
Sbjct: 78  I 78

This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 83

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

 Score = 53.4 bits (129), Expect = 3e-10
 Identities = 29/73 (39%), Positives = 39/73 (53%), Gaps = 5/73 (6%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL-----VDM 119
           + F  T+E L + FSQFG+V  A I+ D     SKG  +V   T+E AQK L      + 
Sbjct: 8   LPFDATEEELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAED 67

Query: 120 NGKLLDGRVIFVD 132
           +G  LDGR + V 
Sbjct: 68  SGLSLDGRRLIVT 80

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

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

 Score = 53.1 bits (128), Expect = 4e-10
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 73  MLADAFSQFGQVTEATIIM-DIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           +L D FS FG + +   IM D     SKG+ +++  + E +  A+  MNG+ L  R I V
Sbjct: 17  LLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLCNRPITV 76

Query: 132 D 132
            
Sbjct: 77  S 77

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

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

 Score = 53.0 bits (128), Expect = 4e-10
 Identities = 22/64 (34%), Positives = 34/64 (53%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
           TT E L   FS+FG++    +I D     S  Y ++   T+E+ ++A   M+  L+D R 
Sbjct: 15  TTDEDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKEDCEEAYFKMDNVLIDDRR 74

Query: 129 IFVD 132
           I VD
Sbjct: 75  IHVD 78

This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. Length = 83

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

 Score = 52.7 bits (126), Expect = 5e-10
 Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ T+K+ L D F++FG+VT+ TI MD    RS+G+G++        +K L +     L
Sbjct: 7   LSWDTSKKDLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVL-EQKEHRL 65

Query: 125 DGRVI 129
           DGR+I
Sbjct: 66  DGRLI 70

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

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

 Score = 52.6 bits (127), Expect = 5e-10
 Identities = 27/70 (38%), Positives = 37/70 (52%), Gaps = 5/70 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATII-----MDIGKNRSKGYGYVTSSTEEEAQKALVDM 119
           ++F TT+E L   F + G V   TI         GK  S GYG+V   ++E AQKAL  +
Sbjct: 8   LNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAAQKALKRL 67

Query: 120 NGKLLDGRVI 129
            G +LDG  +
Sbjct: 68  QGTVLDGHAL 77

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

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

 Score = 52.4 bits (126), Expect = 6e-10
 Identities = 22/64 (34%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+ TT + L + FSQ+G++T+  ++ D    RS+G+G+VT ++  E   A+     K +D
Sbjct: 8   SYETTDDSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHK-VD 66

Query: 126 GRVI 129
           GR +
Sbjct: 67  GREV 70

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

 Score = 51.9 bits (125), Expect = 7e-10
 Identities = 21/69 (30%), Positives = 36/69 (52%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ +  T+E L + FS+ G V    ++ D    + KGYG+      E A  A+ ++NG  
Sbjct: 5   NIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNLNGYE 64

Query: 124 LDGRVIFVD 132
            +GR + VD
Sbjct: 65  FNGRALRVD 73

This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. Length = 75

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

 Score = 51.9 bits (125), Expect = 8e-10
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSK---GYGYVTSSTEEEAQKALVDMNGK 122
            F   ++ L   FS+FG+V    I     + + +   G+ +VT      A+ AL  +NG 
Sbjct: 9   DFKLDEDDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENAL-QLNGT 67

Query: 123 LLDGRVIFV 131
            L GR I V
Sbjct: 68  ELGGRKISV 76

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

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

 Score = 51.6 bits (124), Expect = 1e-09
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN 133
           L   F QFG + +  II +  +  SKG+G+VT +   +A +A   ++G +++GR I V+N
Sbjct: 17  LRQMFGQFGPILDVEIIFN--ERGSKGFGFVTFANSADADRAREKLHGTVVEGRKIEVNN 74

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

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

 Score = 51.3 bits (123), Expect = 1e-09
 Identities = 25/68 (36%), Positives = 35/68 (51%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+SF   ++ +  AFS FG +    +  D    + KG+ +V     E AQ AL  MNG +
Sbjct: 7   SISFELGEDTIRQAFSPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQLALEQMNGVM 66

Query: 124 LDGRVIFV 131
           L GR I V
Sbjct: 67  LGGRNIKV 74

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

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 3/66 (4%)

Query: 70  TKEMLADAFSQFGQVTEATIIM-DIGKNR--SKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           T+  L   FS++G++ +   +    G  +   +GY +VT  T+EEA+KAL  +NGK   G
Sbjct: 12  TEFHLLKLFSKYGKIKKFDFLFHKSGPLKGQPRGYCFVTFETKEEAEKALKSLNGKTALG 71

Query: 127 RVIFVD 132
           + + V 
Sbjct: 72  KKLVVR 77

This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. . Length = 80

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 23/61 (37%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 70  TKEMLADAFSQ-FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
           T  ML + F   +  V  A ++MD    RSKGYG+V    E+E  +AL +MNG     R 
Sbjct: 14  TDYMLQETFRARYPSVRGAKVVMDPVTGRSKGYGFVRFGDEDERDRALTEMNGVYCSSRP 73

Query: 129 I 129
           +
Sbjct: 74  M 74

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

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

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 23/61 (37%), Positives = 43/61 (70%), Gaps = 1/61 (1%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
           TT+++ + AF+ FG++++A ++ D+   +SKGYG+V+   + +A+ A+V M G+ L GR 
Sbjct: 14  TTEDIKS-AFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQ 72

Query: 129 I 129
           I
Sbjct: 73  I 73

This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 50.8 bits (122), Expect = 2e-09
 Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +    T+E   + FSQFG+V +A ++ D    RS+G+G+VT    E A + +       L
Sbjct: 7   LPPDVTEEEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFD-SESAVERVFSAGMLEL 65

Query: 125 DGRVIFV 131
            G+ + V
Sbjct: 66  GGKQVEV 72

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

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

 Score = 50.9 bits (121), Expect = 3e-09
 Identities = 22/65 (33%), Positives = 41/65 (63%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S   T + +  AF+ FG++++A ++ D+   +SKGYG+V+   + +A+ A+  M G+ L
Sbjct: 9   LSPEITTDDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 68

Query: 125 DGRVI 129
            GR I
Sbjct: 69  GGRQI 73

This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 80

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

 Score = 50.1 bits (120), Expect = 4e-09
 Identities = 22/67 (32%), Positives = 41/67 (61%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +S  ++ L   FS+FG+++E  + +D    +SKG+ YV     E+A KA  +++GK+ 
Sbjct: 10  LPYSCKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAVKAYKELDGKVF 69

Query: 125 DGRVIFV 131
            GR+I +
Sbjct: 70  QGRLIHI 76

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

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

 Score = 49.9 bits (120), Expect = 4e-09
 Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 8/64 (12%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           STT+E L + FS++G+V     I D        Y +V     ++A KA+ +MNGK L+G 
Sbjct: 12  STTEEQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVKAMEEMNGKELEGS 63

Query: 128 VIFV 131
            I V
Sbjct: 64  PIEV 67

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

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

 Score = 49.9 bits (119), Expect = 4e-09
 Identities = 27/65 (41%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ TTK+ L + FS+FG+V + TI +D    RS+G+G+V        +K L D     L
Sbjct: 6   LSWDTTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVL-DQKEHKL 64

Query: 125 DGRVI 129
           DGRVI
Sbjct: 65  DGRVI 69

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

>gnl|CDD|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 = 6e-09
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 8/67 (11%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  +TT E L   F ++G VTE     D+ KN    YG+V    EE+A+ A+  +NG   
Sbjct: 7   LPDATTSEELRALFEKYGTVTEC----DVVKN----YGFVHMEEEEDAEDAIKALNGYEF 58

Query: 125 DGRVIFV 131
            G+ I V
Sbjct: 59  MGKRINV 65

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

 Score = 53.4 bits (128), Expect = 6e-09
 Identities = 25/68 (36%), Positives = 38/68 (55%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ F+ T++ L   F  FG + +  +  D    RSKG+G++     EEA++AL  MNG  
Sbjct: 193 NLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFE 252

Query: 124 LDGRVIFV 131
           L GR I V
Sbjct: 253 LAGRPIKV 260

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

>gnl|CDD|240765 cd12319, RRM4_MRD1, RNA recognition motif 4 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 49.5 bits (118), Expect = 9e-09
 Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 8/80 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDI-----GKNRSKGYGYVTSSTEEEAQKALVDM 119
           ++FSTT + L DAF        A +         G+  S G+G+V   T+E+AQ AL  M
Sbjct: 8   LNFSTTNQHLTDAFKHLDGFVFARVKTKPDPKRPGQTLSMGFGFVGFKTKEQAQAALKAM 67

Query: 120 NGKLLDGRVIFVDNVRPSRR 139
           +G +LDG  +    V+ S R
Sbjct: 68  DGFVLDGHTL---VVKFSHR 84

This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 84

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

 Score = 49.3 bits (117), Expect = 9e-09
 Identities = 25/65 (38%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT S+ EE   A+ +     +
Sbjct: 10  LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAM-NARPHKV 68

Query: 125 DGRVI 129
           DGRV+
Sbjct: 69  DGRVV 73

This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. . Length = 81

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

 Score = 52.5 bits (126), Expect = 1e-08
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   + L D FS+FG +    +  D    +S+GYG+V    EE A+ A+  +NG LL+ +
Sbjct: 99  SVDNKALFDTFSKFGNILSCKVATDE-NGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDK 157

Query: 128 VIFVDN-VRPSRRYNT 142
            ++V   ++   R   
Sbjct: 158 EVYVGRFIKKHEREAA 173

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

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

 Score = 48.7 bits (117), Expect = 1e-08
 Identities = 18/65 (27%), Positives = 35/65 (53%)

Query: 61  RCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           R  ++S    ++ L + F  FG ++   +  D    +S+G+ +VT  T E+A++A+  +N
Sbjct: 3   RVTNLSEDADEDDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKLN 62

Query: 121 GKLLD 125
           G   D
Sbjct: 63  GFGYD 67

This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. . Length = 77

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

 Score = 48.8 bits (116), Expect = 1e-08
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 4/65 (6%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD----MN 120
           +S+ TTK+ L D FS+FG+V + T+ +D    RS+G+G+V     E   K +      +N
Sbjct: 6   LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLN 65

Query: 121 GKLLD 125
           GK++D
Sbjct: 66  GKVID 70

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

>gnl|CDD|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins

 Score = 48.8 bits (117), Expect = 1e-08
 Identities = 19/54 (35%), Positives = 29/54 (53%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           L   F+ FG V  A + +D    +SK +G+V+    E AQ A+  MNG  + G+
Sbjct: 15  LYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPESAQAAIKAMNGFQVGGK 68

This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. . Length = 73

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

 Score = 48.6 bits (116), Expect = 1e-08
 Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 4/70 (5%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DMN 120
           +S+ TT E L + FS+FG++ E  ++ D    RS+G+G+VT S      K L     +++
Sbjct: 6   LSWQTTAEGLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTFSDPASVDKVLAQGPHELD 65

Query: 121 GKLLDGRVIF 130
           GK +D +V F
Sbjct: 66  GKKIDPKVAF 75

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

 Score = 51.7 bits (124), Expect = 2e-08
 Identities = 28/95 (29%), Positives = 52/95 (54%), Gaps = 9/95 (9%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-- 125
           S  ++ L + F++FG++T A  +M  G  RS+G+ +V     E+A KA+ +MNGK +   
Sbjct: 189 SVNEDKLRELFAKFGEITSA-AVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLA 247

Query: 126 --GRVIFVDNVRP-SRRYNTDASLARQPAQSPEEN 157
             G+ ++V   +  + R   +A L R+  +  +E 
Sbjct: 248 KEGKKLYVGRAQKRAER---EAELRRKFEELQQER 279

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

>gnl|CDD|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 = 48.4 bits (116), Expect = 2e-08
 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
             T+E L   FS FG + E  +  D      KGY +V   T E A  A+V +NG  ++G+
Sbjct: 11  GLTEEELQRTFSPFGAIEEVRVFKD------KGYAFVRFDTHEAAATAIVAVNGTSINGQ 64

Query: 128 VI 129
            +
Sbjct: 65  TV 66

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

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

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 4/65 (6%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA----LVDMN 120
           +S +TT++ +   FSQFG+V +A ++ D   NR +G+G+VT  +E+   K       ++N
Sbjct: 7   LSANTTEDDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDKVCEIHFHEIN 66

Query: 121 GKLLD 125
            K+++
Sbjct: 67  NKMVE 71

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

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 7/68 (10%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRS---KGYGYVTSSTEEEAQKALVDMNGKL 123
           FS TKE L   F + G V    ++     NRS   KG  YV    E  A +A++ M+G  
Sbjct: 12  FSVTKEELEKLFKKHGVVKSVRLVT----NRSGKPKGLAYVEYENESSASQAVLKMDGTE 67

Query: 124 LDGRVIFV 131
           +  + I V
Sbjct: 68  IKEKTISV 75

This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 81

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

 Score = 47.9 bits (115), Expect = 3e-08
 Identities = 20/62 (32%), Positives = 31/62 (50%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
             T+ ML + FS  G V    +  D+   RS GY YV      +A++AL  +N  ++ G+
Sbjct: 10  DVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLNFDVIKGK 69

Query: 128 VI 129
            I
Sbjct: 70  PI 71

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

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

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 22/63 (34%), Positives = 34/63 (53%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           FS T   L   FS++G+V + TI+ D    +SKG  ++     E+A K +  +N K L G
Sbjct: 11  FSLTNNDLHKIFSKYGKVVKVTIVKDKETRKSKGVAFILFLDREDAHKCVKALNNKELFG 70

Query: 127 RVI 129
           R +
Sbjct: 71  RTL 73

This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. . Length = 78

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

 Score = 48.1 bits (114), Expect = 4e-08
 Identities = 24/68 (35%), Positives = 40/68 (58%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A    NG  L
Sbjct: 17  LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 76

Query: 125 DGRVIFVD 132
           DGR I VD
Sbjct: 77  DGRRIRVD 84

This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. . Length = 89

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

 Score = 47.8 bits (114), Expect = 4e-08
 Identities = 19/66 (28%), Positives = 39/66 (59%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +++ T+E L   FS++G ++E  + +D    + KG+ +VT    E A KA  +++G +  
Sbjct: 11  AYTCTEEDLEKLFSKYGPLSEVHLPIDKLTKKPKGFAFVTYMIPEHAVKAFAELDGTVFQ 70

Query: 126 GRVIFV 131
           GR++ +
Sbjct: 71  GRLLHL 76

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

>gnl|CDD|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family

 Score = 47.3 bits (113), Expect = 4e-08
 Identities = 26/76 (34%), Positives = 43/76 (56%), Gaps = 3/76 (3%)

Query: 58  SFWRCISVSFSTTKEM-LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           + W  +S   STTK   L   FS++G+V  A I+ +     ++ +G+VT ++ EEA K +
Sbjct: 1   NLW--VSGLSSTTKAADLKQLFSKYGKVVGAKIVTNARSPGARCFGFVTMASVEEAAKCI 58

Query: 117 VDMNGKLLDGRVIFVD 132
             ++   L GRVI V+
Sbjct: 59  QHLHRTELHGRVISVE 74

This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. . Length = 74

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

 Score = 47.3 bits (113), Expect = 4e-08
 Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +V + TT E L + F   G +   TI+ D    + KG+ Y+    +   + AL+ +N   
Sbjct: 6   NVDYGTTPEELQEHFKSCGTINRITILCDKFTGQPKGFAYIEFLDKSSVENALL-LNESE 64

Query: 124 LDGRVIFV 131
             GR I V
Sbjct: 65  FRGRQIKV 72

This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. . Length = 73

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

 Score = 47.6 bits (114), Expect = 5e-08
 Identities = 17/68 (25%), Positives = 35/68 (51%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +++ TT+  L   F ++G +    ++ D    + +GY ++    E + + A    +GK +
Sbjct: 9   LNYDTTESKLRREFEEYGPIKRIRLVRDKKTGKPRGYAFIEFEHERDMKAAYKYADGKKI 68

Query: 125 DGRVIFVD 132
           DGR + VD
Sbjct: 69  DGRRVLVD 76

This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. Length = 91

>gnl|CDD|241115 cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins

 Score = 47.1 bits (112), Expect = 5e-08
 Identities = 24/70 (34%), Positives = 39/70 (55%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ +  T+E L D FS+ G V    ++ D    + KGYG+     +E A  A+ ++NG  
Sbjct: 5   NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYKDQETALSAMRNLNGYE 64

Query: 124 LDGRVIFVDN 133
           L+GR + VDN
Sbjct: 65  LNGRQLRVDN 74

This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. . Length = 75

>gnl|CDD|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)

 Score = 47.4 bits (112), Expect = 5e-08
 Identities = 23/61 (37%), Positives = 34/61 (55%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           + +L   F  FG VT   +I D   N+ KG+G+VT +  +EA  A+  +NG  L  RV+ 
Sbjct: 17  ESILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQ 76

Query: 131 V 131
           V
Sbjct: 77  V 77

This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

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

 Score = 47.1 bits (112), Expect = 6e-08
 Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +  T+   L   F+++G++TE  +++D    RS+G+G++T S+ +EA +A+       +D
Sbjct: 11  NLKTSDSGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQ-PHSID 69

Query: 126 GRVI 129
           G  I
Sbjct: 70  GNQI 73

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

 Score = 47.0 bits (112), Expect = 6e-08
 Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 4/59 (6%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL----VDMNGK 122
           + T+  L   FSQFG VTE  ++ D  K R +G+G++T  +E+   + +     D+NGK
Sbjct: 13  NVTETDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEHFHDINGK 71

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|241097 cd12653, RRM3_HuR, RNA recognition motif 3 in vertebrate Hu-antigen R (HuR)

 Score = 47.0 bits (111), Expect = 7e-08
 Identities = 22/59 (37%), Positives = 33/59 (55%)

Query: 73  MLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           +L   F  FG VT   +I D   N+ KG+G+VT +  EEA  A+  +NG  L  +++ V
Sbjct: 17  ILWQMFGPFGAVTNVKVIRDFNTNKCKGFGFVTMTNYEEAAMAIASLNGYRLGDKILQV 75

This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 84

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

 Score = 47.0 bits (111), Expect = 8e-08
 Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF TT + L + F ++G +T+  ++ D    RS+G+G+VT S  EE   A+     K +
Sbjct: 10  LSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHK-V 68

Query: 125 DGRVI 129
           DGRV+
Sbjct: 69  DGRVV 73

This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

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

 Score = 49.9 bits (119), Expect = 9e-08
 Identities = 28/73 (38%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           CI V   S  T + +L   F  FG V    II D+  N+ KGYG+V+ +  +EA  A++ 
Sbjct: 271 CIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILS 330

Query: 119 MNGKLLDGRVIFV 131
           +NG  L  RV+ V
Sbjct: 331 LNGYTLGNRVLQV 343

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 47.0 bits (111), Expect = 9e-08
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF TT+E L + + Q+G++T+  ++ D    RS+G+G+VT S   E   A+       +
Sbjct: 10  LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA-ARPHTI 68

Query: 125 DGRVI 129
           DGRV+
Sbjct: 69  DGRVV 73

This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 81

>gnl|CDD|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE

 Score = 46.7 bits (111), Expect = 9e-08
 Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           + F T +  L   FSQ+G V E  I+ D     SKGYG+VT  T+E+AQK L + N
Sbjct: 10  IDFKTNENDLRKFFSQYGTVKEVKIVND-RAGVSKGYGFVTFETQEDAQKILQEAN 64

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

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

 Score = 46.4 bits (111), Expect = 9e-08
 Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 8/73 (10%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSK----GYGYVTSSTEEEAQKALVDM 119
           ++SF TT+E + + FS+ G +    IIM  G +R      G+ +V   T E+A+ A+  +
Sbjct: 5   NLSFYTTEEQIYELFSRCGDIKR--IIM--GLDRFTKTPCGFCFVEYYTREDAENAVKYL 60

Query: 120 NGKLLDGRVIFVD 132
           NG  LD R+I VD
Sbjct: 61  NGTKLDDRIIRVD 73

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

>gnl|CDD|241105 cd12661, RRM3_hnRNPM, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M)

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 31/75 (41%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ F  T +ML D F++ G V  A I M+ GK  SKG G V   + E A++A   MNG  
Sbjct: 6   NLPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVRFESPEVAERACRMMNGYK 63

Query: 124 LDGRVIFVDNVRPSR 138
           L+GR I   +VR  R
Sbjct: 64  LNGREI---DVRIDR 75

This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). . Length = 77

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

 Score = 46.5 bits (110), Expect = 1e-07
 Identities = 24/70 (34%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DMN 120
           +S+ TT+E L + F QFG+V E  ++ D    RS+G+G+VT   +    K L     +++
Sbjct: 8   LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELD 67

Query: 121 GKLLDGRVIF 130
            K +D +V F
Sbjct: 68  SKTIDPKVAF 77

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

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

 Score = 49.0 bits (117), Expect = 2e-07
 Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
             T+  L D F  FG V    +  D    RS GYGYV      +A++AL  MN K L G+
Sbjct: 11  DVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGK 70

Query: 128 VIFV--DNVRPSRRYN 141
            I +      PS R +
Sbjct: 71  PIRIMWSQRDPSLRRS 86

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

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

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 2/65 (3%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +++ TT + L + F QFG+VT+ T++ D    RS+G+G++T    +   + +   +  +L
Sbjct: 6   LNWETTDDSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEH--IL 63

Query: 125 DGRVI 129
           DG++I
Sbjct: 64  DGKII 68

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|240724 cd12278, RRM_eIF3B, RNA recognition motif in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKN-RSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           K++L   FS+FG      I M + +  ++KGY +V  +T EEA++A+  +NG  LD +  
Sbjct: 21  KKVLRKIFSKFGVGKIVGIYMPVDETGKTKGYAFVEFATPEEAKEAVKALNGYKLDKKHT 80

Query: 130 FVDN 133
           F  N
Sbjct: 81  FAVN 84

This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. . Length = 84

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

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + ++   + L + FSQFG+V    +  D     SKGYG+V+ S+ +  + AL      +L
Sbjct: 7   LPWTVGSKELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENAL-QKQKHIL 65

Query: 125 DGRVIFV 131
           +G  + V
Sbjct: 66  EGNKLQV 72

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|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)

 Score = 45.9 bits (108), Expect = 2e-07
 Identities = 24/68 (35%), Positives = 37/68 (54%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++S    + +L   F  FG VT   +I D   N+ KG+G+VT +  +EA  A+  +NG  
Sbjct: 8   NLSPEADESVLWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYR 67

Query: 124 LDGRVIFV 131
           L  RV+ V
Sbjct: 68  LGDRVLQV 75

This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 85

>gnl|CDD|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 18/50 (36%), Positives = 29/50 (58%), Gaps = 2/50 (4%)

Query: 73  MLADAFSQ-FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
            L + FS+ +     A +++D   N S+GYG+V  S E E ++AL +M G
Sbjct: 17  QLYEFFSKRYPSCKGAKVVLDQNGN-SRGYGFVRFSDESEQKRALTEMQG 65

This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 82

>gnl|CDD|206064 pfam13893, RRM_5, RNA recognition motif

 Score = 44.8 bits (107), Expect = 2e-07
 Identities = 24/59 (40%), Positives = 32/59 (54%), Gaps = 5/59 (8%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD 132
           L   FS FG V +  I +   K    G+ +V  STEE A+KA+  +NG L  GR + VD
Sbjct: 1   LYKLFSPFGNVEK--IKLLKKK---PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVD 54

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

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

 Score = 45.7 bits (109), Expect = 2e-07
 Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)

Query: 62  CIS-VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           C+  +    T E   +  S FG V    ++       SKGYG+V  +++  A KA   ++
Sbjct: 3   CVGNLPLEFTDEQFRELVSPFGAVERCFLVYSESTGESKGYGFVEYASKASALKAKNQLD 62

Query: 121 GKLLDGRVIFVD 132
           GK + GR + VD
Sbjct: 63  GKQIGGRKLQVD 74

This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 77

>gnl|CDD|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)

 Score = 45.9 bits (108), Expect = 2e-07
 Identities = 23/68 (33%), Positives = 37/68 (54%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++S  + + +L   F  FG V    +I D   N+ KG+G+VT +  +EA  A+  +NG  
Sbjct: 10  NLSPDSDESVLWQLFGPFGAVNNVKVIRDFNTNKCKGFGFVTMTNYDEAAMAIASLNGYR 69

Query: 124 LDGRVIFV 131
           L  RV+ V
Sbjct: 70  LGDRVLQV 77

This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 86

>gnl|CDD|241065 cd12621, RRM3_TIA1, RNA recognition motif 3 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins

 Score = 45.4 bits (107), Expect = 3e-07
 Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 62  CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           C  V+   T++++   FS FGQ+ E  +  D      KGY +V  ++ E A  A+V +NG
Sbjct: 5   CGGVTSGLTEQLMRQTFSPFGQIMEVRVFPD------KGYSFVRFNSHESAAHAIVSVNG 58

Query: 122 KLLDGRVI 129
             ++G V+
Sbjct: 59  TTIEGHVV 66

This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|241119 cd12675, RRM2_Nop4p, RNA recognition motif 2 in yeast nucleolar protein 4 (Nop4p) and similar proteins

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 72  EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
             L   F ++G+V EATI       +  G+ +VT    + A+ AL + NG  +DGR + V
Sbjct: 16  VKLKKIFGRYGKVREATIPRK-RGGKLCGFAFVTMKKRKNAEIALENTNGLEIDGRPVAV 74

Query: 132 D 132
           D
Sbjct: 75  D 75

This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 83

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

 Score = 45.0 bits (107), Expect = 4e-07
 Identities = 22/65 (33%), Positives = 35/65 (53%)

Query: 63  ISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           I    S T++ L +AF+ FG++ +  ++ D     SKG  YV  +    A +A+ +MNGK
Sbjct: 8   IVCGKSVTEDDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSAARAMEEMNGK 67

Query: 123 LLDGR 127
            L G 
Sbjct: 68  CLGGD 72

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

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

 Score = 44.6 bits (106), Expect = 5e-07
 Identities = 14/49 (28%), Positives = 25/49 (51%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
            T+E L + FSQ+G V    I+ D    + +G+ +VT    +   K ++
Sbjct: 11  VTEEDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVL 59

This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 73

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

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ TT+E L   FSQ+G+V +  I+ D   NRS+G+G+V           L       L
Sbjct: 7   LSWETTQETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVL-AGGPHTL 65

Query: 125 DGRVI 129
           DGR I
Sbjct: 66  DGRTI 70

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

>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins

 Score = 44.6 bits (106), Expect = 5e-07
 Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 6/69 (8%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           +  T+E+L  AFS FG +    I M+  KN     G+VT    E A +A+ ++NG  + G
Sbjct: 12  YGLTEEILKKAFSPFGNIIN--ISMEKEKNC----GFVTFEKMESADRAIAELNGTTVQG 65

Query: 127 RVIFVDNVR 135
             + V   R
Sbjct: 66  VQLKVSLAR 74

This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. . Length = 75

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

 Score = 44.1 bits (105), Expect = 6e-07
 Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 1/70 (1%)

Query: 62  CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
            + +S    +  L + FS+ G+V +  II D    RSKG  YV    EE    AL  + G
Sbjct: 4   VMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESVPLAL-GLTG 62

Query: 122 KLLDGRVIFV 131
           + L G+ I V
Sbjct: 63  QRLLGQPIMV 72

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

>gnl|CDD|241106 cd12662, RRM3_MYEF2, RNA recognition motif 3 in vertebrate myelin expression factor 2 (MEF-2)

 Score = 44.3 bits (104), Expect = 8e-07
 Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 2/68 (2%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ F  T + L + FSQ G V  A I M+ GK  SKG G V   + E A+KA   MNG  
Sbjct: 6   NLPFDLTWQKLKEKFSQCGHVMFAEIKMENGK--SKGCGTVRFDSPESAEKACRLMNGIK 63

Query: 124 LDGRVIFV 131
           ++GR I V
Sbjct: 64  INGREIDV 71

This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. . Length = 77

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

 Score = 44.2 bits (105), Expect = 8e-07
 Identities = 20/60 (33%), Positives = 33/60 (55%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
            +  +  AF++ G+VT   II +    +S GYG+V  +T E A++AL  +NGK +     
Sbjct: 12  DEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQSLNGKPIPNTQQ 71

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

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

 Score = 44.9 bits (106), Expect = 8e-07
 Identities = 17/53 (32%), Positives = 27/53 (50%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           ++ +  T+E LA  FS+FG V  A  ++D    R+KG G+V    +      L
Sbjct: 8   NLPYDATEESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACL 60

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

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

 Score = 43.4 bits (103), Expect = 1e-06
 Identities = 20/55 (36%), Positives = 30/55 (54%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           +TT E L      FG++     I+D   N+ KGYG+V   + E A KA+  +NG+
Sbjct: 11  NTTDEDLEKLCQPFGKIISTKAILDKKTNKCKGYGFVDFDSPEAALKAIEGLNGR 65

This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 71

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

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 24/74 (32%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           C+ V   S  TT+  L + FS++G +    ++ D    RS+G+ +V     +++++A+  
Sbjct: 1   CLGVFGLSLYTTERDLREVFSRYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAMEH 60

Query: 119 MNGKLLDGRVIFVD 132
            NG  LDGR I VD
Sbjct: 61  ANGMELDGRRIRVD 74

This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. . Length = 79

>gnl|CDD|240779 cd12333, RRM2_p54nrb_like, RNA recognition motif 2 in the p54nrb/PSF/PSP1 family

 Score = 43.8 bits (104), Expect = 1e-06
 Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
            + E+L  AFSQFG+V  A +I+D  + RS G G V  S +  AQ A+
Sbjct: 11  VSNELLEQAFSQFGEVERAVVIVDD-RGRSTGEGIVEFSRKPGAQAAI 57

This subfamily corresponds to the RRM2 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. The family 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 contains 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 = 80

>gnl|CDD|241064 cd12620, RRM3_TIAR, RNA recognition motif 3 in nucleolysin TIAR and similar proteins

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 6/68 (8%)

Query: 62  CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           C  ++   T++++   FS FGQ+ E  +  +      KGY ++  ST E A  A+V +NG
Sbjct: 5   CGGIASGLTEQLMRQTFSPFGQIMEIRVFPE------KGYSFIRFSTHESAAHAIVSVNG 58

Query: 122 KLLDGRVI 129
             ++G V+
Sbjct: 59  TTIEGHVV 66

This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 73

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

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 22/70 (31%), Positives = 40/70 (57%), Gaps = 4/70 (5%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL----VDMN 120
           +S+ T+ + L D FS+FG++ E  ++ D    RS+G+G+VT +      K L     +++
Sbjct: 7   LSWQTSPDSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQPHHELD 66

Query: 121 GKLLDGRVIF 130
            K +D +V F
Sbjct: 67  SKTIDPKVAF 76

This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 76

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

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ T+K+ L +  S+FG+V + TI  D    RS+G+G+V         K L ++    L
Sbjct: 7   LSWDTSKKDLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKVL-ELKEHKL 65

Query: 125 DGRVI 129
           DG++I
Sbjct: 66  DGKLI 70

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

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

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 24/68 (35%), Positives = 36/68 (52%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++ L   FS  G+V  A +I D     S GYG+V     ++A++A+  +NG  L  + I
Sbjct: 14  TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTLNGLRLQSKTI 73

Query: 130 FVDNVRPS 137
            V   RPS
Sbjct: 74  KVSYARPS 81

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

>gnl|CDD|241123 cd12679, RRM_SAFB1_SAFB2, RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 3/76 (3%)

Query: 58  SFWRCISVSFSTTKEM-LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           + W  +S   STT+   L + FS++G+V  A ++ +     ++ YG+VT ST EEA K +
Sbjct: 3   NLW--VSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSEEATKCI 60

Query: 117 VDMNGKLLDGRVIFVD 132
             ++   L GR+I V+
Sbjct: 61  NHLHRTELHGRMISVE 76

This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. Length = 76

>gnl|CDD|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 19/53 (35%), Positives = 29/53 (54%)

Query: 79  SQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           S+F     A I+ D     S+GYG+V  S E + Q+AL++M G    GR + +
Sbjct: 24  SRFPSCKSAKIMTDPVTGVSRGYGFVRFSDENDQQRALIEMQGVYCGGRPMRI 76

This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 80

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

 Score = 42.7 bits (100), Expect = 3e-06
 Identities = 19/50 (38%), Positives = 32/50 (64%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQK 114
           +S +TT E +   F QFG+V +A ++ D   NR +G+G+VT  +E+  +K
Sbjct: 7   LSVNTTVEDVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK 56

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

 Score = 45.4 bits (107), Expect = 3e-06
 Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 2/74 (2%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+SF   ++ +  AF  FG +    +  D    + KG+ +V     E AQ AL  MNG++
Sbjct: 114 SISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQM 173

Query: 124 LDGRVIFVDNVRPS 137
           L GR I V   RPS
Sbjct: 174 LGGRNIKVG--RPS 185

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

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

 Score = 42.2 bits (100), Expect = 4e-06
 Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           +  T+E L + F + G+V +  I  D    RS+G   V     E+A++A+   NG LLDG
Sbjct: 10  YDVTEEDLEELFGRVGEVKKVKINYDR-SGRSEGTADVVFEKREDAERAIKQFNGVLLDG 68

Query: 127 RVI 129
           + +
Sbjct: 69  QPM 71

This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. . Length = 75

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

 Score = 42.3 bits (100), Expect = 4e-06
 Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 1/69 (1%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ + TT E L   F   G      ++ D    +SKG  +V   T E   KAL  ++  L
Sbjct: 7   NLPYDTTAEDLLAHFKNAGAPPSVRLLTDKKTGKSKGCAFVEFDTAEAMTKAL-KLHHTL 65

Query: 124 LDGRVIFVD 132
           L GR I V+
Sbjct: 66  LKGRKINVE 74

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

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

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 20/65 (30%), Positives = 34/65 (52%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           + T++ +   FS  G++    +I D    +S GYG+V     E+A+KA+  +NG  L  +
Sbjct: 12  NMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRLQNK 71

Query: 128 VIFVD 132
            I V 
Sbjct: 72  TIKVS 76

This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 78

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

 Score = 45.0 bits (106), Expect = 5e-06
 Identities = 30/110 (27%), Positives = 51/110 (46%), Gaps = 17/110 (15%)

Query: 51  IMQLVNVSFWRCISVSFSTTKEMLADAFSQF--GQVTEATIIMDIGKNRSKGYGYVTSST 108
           +M  V + + R  ++  +TT+E++  +FS+F  G+V     I D        Y +V    
Sbjct: 229 VMAKVKILYVR--NLMTTTTEEIIEKSFSEFKPGKVERVKKIRD--------YAFVHFED 278

Query: 109 EEEAQKALVDMNGKLLDGRVIFVDNVRP-----SRRYNTDASLARQPAQS 153
            E+A KA+ ++NGK L+G  I V   +P       RY        +  Q+
Sbjct: 279 REDAVKAMDELNGKELEGSEIEVTLAKPVDKKSYVRYTRGTGGRGKERQA 328

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

>gnl|CDD|240700 cd12254, RRM_hnRNPH_ESRPs_RBM12_like, RNA recognition motif found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins

 Score = 41.8 bits (99), Expect = 5e-06
 Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 3/66 (4%)

Query: 67  FSTTKEMLADAFSQFGQVTEA-TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           FS T+E + D FS      +   I+ D    R  G  YV  ++ E+A++AL   N K + 
Sbjct: 9   FSATEEDIRDFFSGLDIPPDGIHIVYD-DDGRPTGEAYVEFASPEDARRALRKHNNK-MG 66

Query: 126 GRVIFV 131
           GR I V
Sbjct: 67  GRYIEV 72

The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|240850 cd12404, RRM2_NCL, RNA recognition motif 2 in vertebrate nucleolin

 Score = 41.8 bits (98), Expect = 6e-06
 Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 4/68 (5%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + ++ T + L + F       +  +        SKG  Y+   TE EA+KAL +  G  +
Sbjct: 11  LPYNITVDELKEVFED---AVDIRLPSGKD-GSSKGIAYIEFKTEAEAEKALEEKQGAEV 66

Query: 125 DGRVIFVD 132
           DGR I VD
Sbjct: 67  DGRSIVVD 74

This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. . Length = 77

>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 44.5 bits (105), Expect = 7e-06
 Identities = 22/54 (40%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 78  FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           FS+ G+V +   I D    RSKG  YV     E   KAL  + G++L GR I V
Sbjct: 110 FSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIV 162

This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. Length = 457

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

 Score = 43.4 bits (102), Expect = 1e-05
 Identities = 24/77 (31%), Positives = 39/77 (50%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T+E +   F+  G++    ++ D    +S GYG+V     E+A+KA+  +NG  L  + I
Sbjct: 16  TQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTI 75

Query: 130 FVDNVRPSRRYNTDASL 146
            V   RPS      A+L
Sbjct: 76  KVSYARPSSDSIKGANL 92

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 20/59 (33%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           TT++ L D FS FG++    +  D    +SKG+G+V  +  E+  K L      ++DGR
Sbjct: 11  TTEQDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLS--QRHMIDGR 67

This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. . Length = 77

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

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 23/85 (27%), Positives = 31/85 (36%), Gaps = 18/85 (21%)

Query: 65  VSFSTTKEMLADAFSQFGQV-----------------TEATIIMDIGKNRSKGYGYVTSS 107
           +  +T K+ L   F QFG +                   A I       +     YV   
Sbjct: 8   LPLTTKKKDLKKLFKQFGPIESVRFRSVPVKEKKLPKKVAAIKKKFHDKKDNVNAYVVFK 67

Query: 108 TEEEAQKALVDMNGKLLDGRVIFVD 132
            EE A+KAL  +NG   +G  I VD
Sbjct: 68  EEESAEKALK-LNGTEFEGHHIRVD 91

This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. . Length = 91

>gnl|CDD|241033 cd12589, RRM2_PSP1, RNA recognition motif 2 in vertebrate paraspeckle protein 1 (PSP1 or PSPC1)

 Score = 40.8 bits (95), Expect = 1e-05
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 5/67 (7%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           + E+L  AFSQFG V  A +I+D  + R  G G+V  + +  A+KAL     +  DG  +
Sbjct: 12  SNELLEQAFSQFGPVERAVVIVD-DRGRPTGKGFVEFAAKPAARKAL----ERCADGAFL 66

Query: 130 FVDNVRP 136
                RP
Sbjct: 67  LTTTPRP 73

This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. . Length = 80

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

 Score = 41.0 bits (97), Expect = 1e-05
 Identities = 22/64 (34%), Positives = 36/64 (56%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
             +E + D F++FG++    + +D      KGY  +   T++EAQ A+  +NGK L G+ 
Sbjct: 18  AQEEDVHDKFAEFGEIKNLHLNLDRRTGFVKGYALIEYETKKEAQAAIEGLNGKELLGQT 77

Query: 129 IFVD 132
           I VD
Sbjct: 78  ISVD 81

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

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

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 16/59 (27%), Positives = 32/59 (54%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           + T++ L   FS +G++  + I+ D     S+G G++      EA++A+  +NG +  G
Sbjct: 11  TMTQQELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKALNGTIPPG 69

This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 79

>gnl|CDD|240939 cd12495, RRM3_hnRNPQ, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q)

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 10/82 (12%)

Query: 55  VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQK 114
           V V F R  +++ + T+E+L  AF QFG++            + K Y ++     + A K
Sbjct: 1   VKVLFVR--NLANTVTEEILEKAFGQFGKLERV--------KKLKDYAFIHFDERDGAVK 50

Query: 115 ALVDMNGKLLDGRVIFVDNVRP 136
           A+ +MNGK L+G  I +   +P
Sbjct: 51  AMEEMNGKELEGENIEIVFAKP 72

This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. . Length = 72

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

 Score = 40.2 bits (94), Expect = 2e-05
 Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +VS + T + L   F +FG+V E   +        K Y +V    EEEA  A+  +NGK 
Sbjct: 7   NVSATCTSDELRGLFEEFGRVVECDKV--------KDYAFVHMEREEEALAAIEALNGKE 58

Query: 124 LDGRVIFVD 132
           + GR I V+
Sbjct: 59  VKGRRINVE 67

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

 Score = 40.4 bits (95), Expect = 2e-05
 Identities = 18/75 (24%), Positives = 35/75 (46%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V+ +T  + L   F ++G + +  I +D    R +G+ YV      +A+ AL  ++    
Sbjct: 8   VADATRPDDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRF 67

Query: 125 DGRVIFVDNVRPSRR 139
            GR I +   +  R+
Sbjct: 68  LGREIEIQFAQGDRK 82

This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. . Length = 84

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

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 21/69 (30%), Positives = 35/69 (50%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           + T+E L   F   G++    ++ D    +S GYG+V     ++A+KA+  +NG  L  +
Sbjct: 15  NMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTK 74

Query: 128 VIFVDNVRP 136
            I V   RP
Sbjct: 75  TIKVSYARP 83

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

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

 Score = 39.8 bits (94), Expect = 3e-05
 Identities = 23/65 (35%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           F   +E L   F   G V    I+ D      KG+GYV   T++    AL  +NG  L G
Sbjct: 9   FDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALAL-KLNGIKLKG 67

Query: 127 RVIFV 131
           R I V
Sbjct: 68  RKIRV 72

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

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

 Score = 39.6 bits (93), Expect = 3e-05
 Identities = 19/64 (29%), Positives = 36/64 (56%), Gaps = 6/64 (9%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
             T+E   + FS++G+V+E  +      N+ KG+G++   T   A+KA  +++G +  GR
Sbjct: 12  DITEEEFKELFSKYGEVSEVFL------NKEKGFGFIRLDTRTNAEKAKAELDGIMRKGR 65

Query: 128 VIFV 131
            + V
Sbjct: 66  QLRV 69

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

>gnl|CDD|241035 cd12591, RRM2_p54nrb, RNA recognition motif 2 in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb)

 Score = 40.0 bits (93), Expect = 4e-05
 Identities = 20/47 (42%), Positives = 29/47 (61%), Gaps = 1/47 (2%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           + E+L +AFS FGQV  A +I+D  + R  G G V  + +  A+KAL
Sbjct: 12  SNELLEEAFSMFGQVERAVVIVD-DRGRPTGKGIVEFAGKPSARKAL 57

This subgroup corresponds to the RRM2 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. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer 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 = 80

>gnl|CDD|240852 cd12406, RRM4_NCL, RNA recognition motif 4 in vertebrate nucleolin

 Score = 39.6 bits (92), Expect = 4e-05
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  TT+E L ++F   G +  A I+ D     SKG+G+V  S+EE+A+ A   M    +
Sbjct: 8   LSEDTTEETLKESFD--GSIA-ARIVTDRDTGSSKGFGFVDFSSEEDAKAAKEAMEDGEI 64

Query: 125 DGRVIFVDNVRP 136
           DG  + +D  +P
Sbjct: 65  DGNKVTLDFAKP 76

This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. . Length = 78

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

 Score = 39.3 bits (92), Expect = 4e-05
 Identities = 16/48 (33%), Positives = 29/48 (60%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           TT+E + + F +FG + E  + MD   N+ +G+ ++T  +EE  +K L
Sbjct: 11  TTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKIL 58

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|240679 cd12233, RRM_Srp1p_AtRSp31_like, RNA recognition motif found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 8/67 (11%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
           T +E +   F  FG +       DI K     + +V     E+A KAL  ++G  +DG V
Sbjct: 12  TREEDIEKLFEPFGPLVR----CDIRKT----FAFVEFEDSEDATKALEALHGSRIDGSV 63

Query: 129 IFVDNVR 135
           + V+ V+
Sbjct: 64  LTVEFVK 70

This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. Length = 70

>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 = 39.1 bits (92), Expect = 5e-05
 Identities = 19/52 (36%), Positives = 26/52 (50%)

Query: 78  FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           FSQFG VT   +       +SKGY +V   + E A+     MN  LL  R++
Sbjct: 20  FSQFGTVTRLRLSRSKKTGKSKGYAFVEFESPEVAKIVAETMNNYLLFERLL 71

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

 Score = 39.2 bits (92), Expect = 8e-05
 Identities = 20/62 (32%), Positives = 36/62 (58%), Gaps = 8/62 (12%)

Query: 78  FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DMNGKLLDGRVIFVDN 133
           FSQ+G++ +  ++ D    +SKG+ ++      E Q++ +    ++NG  L GR I VD+
Sbjct: 30  FSQYGEIVDINLVRDKKTGKSKGFAFL----AYEDQRSTILAVDNLNGIKLLGRTIRVDH 85

Query: 134 VR 135
           VR
Sbjct: 86  VR 87

This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. . Length = 89

>gnl|CDD|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins

 Score = 38.7 bits (90), Expect = 8e-05
 Identities = 18/48 (37%), Positives = 25/48 (52%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           L   F  FG V  A + +D   N+SK +G+V+      AQ A+  MNG
Sbjct: 21  LMQMFLPFGNVISAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNG 68

This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. . Length = 79

>gnl|CDD|241034 cd12590, RRM2_PSF, RNA recognition motif 2 in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF)

 Score = 38.9 bits (90), Expect = 8e-05
 Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           + E+L +AFSQFG V  A +I+D  + RS G G V  +++  A+KA 
Sbjct: 12  SNELLEEAFSQFGPVERAVVIVD-DRGRSTGKGIVEFASKPAARKAF 57

This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. . Length = 80

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

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 17/59 (28%), Positives = 34/59 (57%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           + T++ L   FSQ+G++  + I+ D     S+G G++      EA++A+  +NG+  +G
Sbjct: 11  TMTQKELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEG 69

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

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

 Score = 40.8 bits (95), Expect = 1e-04
 Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 10/69 (14%)

Query: 74  LADAFSQFGQVTEATIIMDI-GKNRSKGYGYVTSSTEEEAQKALVDMN------GKLLDG 126
           L   F + G + E  ++MD  G+NR  GY +VT   +EEA++A+  +N      G+LL G
Sbjct: 75  LVPLFEKAGPIYELRLMMDFSGQNR--GYAFVTFCGKEEAKEAVKLLNNYEIRPGRLL-G 131

Query: 127 RVIFVDNVR 135
             I VDN R
Sbjct: 132 VCISVDNCR 140

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

>gnl|CDD|240899 cd12453, RRM1_RIM4_like, RNA recognition motif 1 in yeast meiotic activator RIM4 and similar proteins

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 76  DAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR 135
           + FS++G +    ++ D    R + Y +V  + +++A+ AL    G +LDGR I  +  +
Sbjct: 25  EHFSKYGTLVFVKVLRD---WRQRPYAFVQFTNDDDAKNALAKGQGTILDGRHIRCERAK 81

Query: 136 PSR 138
            +R
Sbjct: 82  VNR 84

This subfamily corresponds to the RRM1 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 = 86

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

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 18/49 (36%), Positives = 26/49 (53%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           S T+E L + F +FG +   +I+ D     SKG+GYV      +A  AL
Sbjct: 11  SYTEEDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKFHKPSQAAVAL 59

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

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 38.0 bits (89), Expect = 1e-04
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 7/66 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGK---NRSKGYGYVTSSTEEEAQKALVDMNG 121
           V F  TK+ L + FS FGQV      + + K      +G+ +V   T++EAQ A+  +  
Sbjct: 8   VPFEATKKELRELFSPFGQVKS----VRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKS 63

Query: 122 KLLDGR 127
             L GR
Sbjct: 64  THLYGR 69

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|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           LA  F  FG V  A + +D   N SK +G+V+    + AQ A+  MNG
Sbjct: 21  LAQTFLPFGNVISAKVFIDKQTNLSKCFGFVSYDNPDSAQAAIQAMNG 68

This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. . Length = 79

>gnl|CDD|240862 cd12416, RRM4_RBM28_like, RNA recognition motif 4 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 38.7 bits (91), Expect = 1e-04
 Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 11/61 (18%)

Query: 71  KEMLADAFSQF-----GQVTEATIIMD------IGKNRSKGYGYVTSSTEEEAQKALVDM 119
           KE+   A S+       ++ +  I+ D       GK +SKGYG+V  +  E A KAL  +
Sbjct: 18  KELFLKAVSERAGKKKPKIKQVKIMRDLKRVDPNGKGKSKGYGFVEFTNHEHALKALRAL 77

Query: 120 N 120
           N
Sbjct: 78  N 78

This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. . Length = 98

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

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 22/68 (32%), Positives = 31/68 (45%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T E     F   G V    I+ D     S G+G+V   + E+AQ+A+  +NG  L  + I
Sbjct: 13  TDEEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRI 72

Query: 130 FVDNVRPS 137
            V   RP 
Sbjct: 73  KVAYARPG 80

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

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

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 21/68 (30%), Positives = 34/68 (50%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T+E     F   G++    ++ D    +S GYG+V     ++A+KA+  +NG  L  + I
Sbjct: 15  TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74

Query: 130 FVDNVRPS 137
            V   RPS
Sbjct: 75  KVSYARPS 82

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

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

 Score = 40.3 bits (94), Expect = 2e-04
 Identities = 26/80 (32%), Positives = 39/80 (48%), Gaps = 6/80 (7%)

Query: 43  IVRPSSDLIMQL-VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGY 101
             RPSSD I    + VS      +  + T+  L   FS FGQ+  + I+ D     SKG 
Sbjct: 79  YARPSSDSIKGANLYVS-----GLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGV 133

Query: 102 GYVTSSTEEEAQKALVDMNG 121
           G++     +EA +A+  +NG
Sbjct: 134 GFIRFDKRDEADRAIKTLNG 153

This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). Length = 352

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

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQK 114
           +S +T  E +   F QFG+V +A ++ D   NR +G+G+VT   E+  +K
Sbjct: 11  LSANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEK 60

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

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 3/64 (4%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           + T+++LA+ FSQ G +    +I +   N    Y +V       A  AL  MNG+L+ G+
Sbjct: 9   TVTEDLLAELFSQIGPIKSCKLIRE-HGNDP--YAFVEYYDHRSAAAALQTMNGRLILGQ 65

Query: 128 VIFV 131
            I V
Sbjct: 66  EIKV 69

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

>gnl|CDD|240815 cd12369, RRM4_RBM45, RNA recognition motif 4 in RNA-binding protein 45 (RBM45) and similar proteins

 Score = 37.3 bits (87), Expect = 2e-04
 Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 72  EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
            +L D F +FG + +  ++        K YGY   +  E A++A+  ++GK ++G
Sbjct: 14  YILEDVFCRFGGLIDVYLV------PGKNYGYAKYADRESAERAITTLHGKEVNG 62

This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 68

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

 Score = 37.6 bits (88), Expect = 2e-04
 Identities = 23/62 (37%), Positives = 32/62 (51%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T+E+L + F Q G V    I  D      +GYG+V   +EE+A  A+  MN   L G+ I
Sbjct: 11  TEELLWELFIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPI 70

Query: 130 FV 131
            V
Sbjct: 71  RV 72

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

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

 Score = 37.7 bits (88), Expect = 2e-04
 Identities = 16/67 (23%), Positives = 32/67 (47%), Gaps = 2/67 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S   TKE L + FS+ G++ E  +I       +  + ++    E+ A +A+   N  +L
Sbjct: 11  LSPDVTKEELNERFSRHGKILEVNLIKRANHTNA--FAFIKFEREQAAARAVESENHSML 68

Query: 125 DGRVIFV 131
             + + V
Sbjct: 69  KNKTMHV 75

This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. . Length = 80

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

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 17/44 (38%), Positives = 25/44 (56%)

Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
           L + FSQFG V +A +I D    + +G+G+V     + A KA V
Sbjct: 16  LTEHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAV 59

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

 Score = 37.7 bits (87), Expect = 3e-04
 Identities = 19/76 (25%), Positives = 39/76 (51%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +V+ +T  E L   F ++G + +  + +D    R +G+ Y+      +A+ AL ++N K 
Sbjct: 7   NVADATRPEDLRREFGRYGPIVDVYVPLDFYTRRPRGFAYIQFEDVRDAEDALYNLNRKW 66

Query: 124 LDGRVIFVDNVRPSRR 139
           + GR I +   +  R+
Sbjct: 67  VCGRQIEIQFAQGDRK 82

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|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 37.5 bits (88), Expect = 3e-04
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 78  FSQFGQVTEATIIMDIGKNRSK-GYG--YVTSSTEEEAQKALVDMNGKLLDGRVI 129
             ++G+V    I     +     G G  +V  +  E+AQKA + + G+  DGR +
Sbjct: 32  CGKYGKVLSVVIPRPEAEGVDVPGVGKVFVEFADVEDAQKAQLALAGRKFDGRTV 86

This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 89

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

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 13/63 (20%)

Query: 78  FSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP 136
           F + G + E  ++MD  G NR  GY +VT + +E AQ+A+     K L    I     RP
Sbjct: 22  FEKAGPIYELRLMMDFSGLNR--GYAFVTYTNKEAAQRAV-----KQLHNYEI-----RP 69

Query: 137 SRR 139
            +R
Sbjct: 70  GKR 72

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

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

 Score = 37.4 bits (86), Expect = 3e-04
 Identities = 21/68 (30%), Positives = 32/68 (47%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T+E     F   G++    ++ D    +S GYG+V      +A KA+  +NG  L  + I
Sbjct: 16  TQEEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTI 75

Query: 130 FVDNVRPS 137
            V   RPS
Sbjct: 76  KVSYARPS 83

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

>gnl|CDD|240877 cd12431, RRM_ALKBH8, RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 6/56 (10%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           ++E L   F ++G V    ++M  GK     Y +V+ S+ E+A  A   +NGK L+
Sbjct: 16  SREELLRVFEKYGTVE--DLVMPPGKP----YCFVSYSSIEDAAAAYDALNGKELE 65

This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. . Length = 80

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

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++ L + F   G+VT+  + M     +S+ +G+V   +EE+AQ+A+   N   +D   I
Sbjct: 13  TEDRLREHFESKGEVTDVKV-MRTRDGKSRRFGFVGFKSEEDAQQAVKYFNKTFIDTSKI 71

Query: 130 FVD 132
            V+
Sbjct: 72  SVE 74

This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 36.8 bits (85), Expect = 3e-04
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
            T++ +   F Q+G+V E  II        K YG+V    +  A +A+ +++   L G  
Sbjct: 12  ATEQEIRSLFEQYGKVLECDII--------KNYGFVHMDDKTAADEAIRNLHHYKLHGVA 63

Query: 129 IFVD 132
           I V+
Sbjct: 64  INVE 67

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

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

 Score = 36.9 bits (85), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           +S  TT+E + + F  FG++    + MD   N  +G+ +VT + EE  QK L
Sbjct: 7   LSPDTTEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL 58

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

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

 Score = 36.8 bits (86), Expect = 3e-04
 Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 8/61 (13%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
            +KE L + FS++G++   ++         KGYG+V    EE+A+ A+   NG+ + G+ 
Sbjct: 13  VSKEDLEEIFSKYGKILGISL--------HKGYGFVQFDNEEDARAAVAGENGREIAGQK 64

Query: 129 I 129
           +
Sbjct: 65  L 65

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

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 22/67 (32%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V +  T E L   F   G V   TI+ D      KG+ Y+  S +E  + AL  ++  L 
Sbjct: 7   VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTAL-ALDESLF 65

Query: 125 DGRVIFV 131
            GR I V
Sbjct: 66  RGRQIKV 72

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

>gnl|CDD|240938 cd12494, RRM3_hnRNPR, RNA recognition motif 3 in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R)

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 23/82 (28%), Positives = 43/82 (52%), Gaps = 10/82 (12%)

Query: 55  VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQK 114
           V V F R  +++ + T+E+L  +FS+FG++            + K Y +V     + A +
Sbjct: 1   VKVLFVR--NLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEERDAAVR 50

Query: 115 ALVDMNGKLLDGRVIFVDNVRP 136
           A+ +MNGK ++G  I +   +P
Sbjct: 51  AMDEMNGKEIEGEEIEIVLAKP 72

This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. . Length = 72

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

 Score = 36.8 bits (85), Expect = 4e-04
 Identities = 15/58 (25%), Positives = 27/58 (46%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           T++ L   F  +G + +  ++ D      +G  +V     EEAQ A+  +NG +  G 
Sbjct: 13  TEDELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYDKREEAQAAISSLNGTIPPGS 70

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

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

 Score = 36.7 bits (85), Expect = 4e-04
 Identities = 22/61 (36%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           KE+    FSQFG V    +        SK YG++     E A  A   MN  LL G+V+ 
Sbjct: 14  KELKK-YFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

Query: 131 V 131
           V
Sbjct: 73  V 73

This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 77

>gnl|CDD|214637 smart00361, RRM_1, RNA recognition motif

 Score = 36.6 bits (85), Expect = 5e-04
 Identities = 19/52 (36%), Positives = 32/52 (61%), Gaps = 3/52 (5%)

Query: 81  FGQVTEA-TIIMDI--GKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           FG+V +   I +D    +N  +G  Y+T    E+A +A+VD+NG+  DGR++
Sbjct: 16  FGEVGKINKIYIDDVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLV 67

Length = 70

>gnl|CDD|240832 cd12386, RRM2_hnRNPM_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 36.2 bits (84), Expect = 6e-04
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           +    + L + F   G+V  A I  D     S+G G V      EA +A+   NG++L  
Sbjct: 8   YKVGWKKLKEVFKLAGKVVRADIKEDKEGK-SRGMGVVQFEHPIEAVQAISMFNGQMLFD 66

Query: 127 RVIFV 131
           R + V
Sbjct: 67  RPMRV 71

This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 74

>gnl|CDD|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)

 Score = 36.5 bits (85), Expect = 6e-04
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 7/61 (11%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNR----SKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            +  +  AF+  G+   +  I+   +N+      GY +V  + E  A++ L  +NGK + 
Sbjct: 12  DENFIKRAFASMGETVLSVKII---RNKLTGGPAGYCFVEFADEATAERCLHKLNGKPIP 68

Query: 126 G 126
           G
Sbjct: 69  G 69

This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. . Length = 84

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

 Score = 36.5 bits (84), Expect = 7e-04
 Identities = 17/53 (32%), Positives = 35/53 (66%), Gaps = 2/53 (3%)

Query: 80  QFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG-KLLDGRVIFV 131
           + G++ E  ++MD   N ++GY +VT S ++EA+ A+  +N  ++ +GR++ V
Sbjct: 24  KIGKIYEMRMMMDFNGN-NRGYAFVTFSNKQEAKNAIKQLNNYEIRNGRLLGV 75

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

>gnl|CDD|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family

 Score = 36.0 bits (84), Expect = 7e-04
 Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 11/69 (15%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG-- 126
           T+   L   F +FG +        I  +  + Y Y+   + E AQ A   + G  L G  
Sbjct: 10  TSLAELEREFDRFGAIR------RIDYDPGRNYAYIEYESIEAAQAAKEALRGFPLGGPG 63

Query: 127 ---RVIFVD 132
              RV F D
Sbjct: 64  RRLRVDFAD 72

This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 72

>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1)

 Score = 36.1 bits (83), Expect = 8e-04
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 62  CIS-VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           CI+ +  + T++   +    FG +    ++       SKGYG+V    ++ A +A  D+ 
Sbjct: 3   CIANLPPTYTQQQFEELVRPFGNLERCFLVYSETTGHSKGYGFVEYMKKDSAARAKSDLL 62

Query: 121 GKLLDGRVIFV 131
           GK L  R ++V
Sbjct: 63  GKQLGSRTLYV 73

This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. . Length = 77

>gnl|CDD|240855 cd12409, RRM1_RRT5, RNA recognition motif 1 in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins

 Score = 36.2 bits (84), Expect = 8e-04
 Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 65  VSFSTTKEMLADAFSQFGQV-----TEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM 119
           +S+S+++E L +    F  V     ++        + R  G  Y   S+ E+A+K + D+
Sbjct: 7   LSYSSSEEDLEEFLKDFEPVSVLIPSQTVRGFRSRRVRPLGIAYAEFSSPEQAEKVVKDL 66

Query: 120 NGKLLDGRVIFV 131
           NGK+   R +FV
Sbjct: 67  NGKVFKNRKLFV 78

This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 84

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

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
           T++E L   F  +G V    ++        + + +V    E  A +A+ ++NG+ L GR 
Sbjct: 12  TSQEELRALFEAYGAVLSCAVM--------RQFAFVHLRGEAAADRAIEELNGRELHGRK 63

Query: 129 IFVD 132
           + V+
Sbjct: 64  LVVE 67

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

 Score = 36.2 bits (84), Expect = 9e-04
 Identities = 16/51 (31%), Positives = 23/51 (45%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM 119
            T++ L + F +FG V E  I    G  R   +G+V     E  QK L + 
Sbjct: 15  ITEDELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILANK 65

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|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 36.0 bits (83), Expect = 0.001
 Identities = 24/75 (32%), Positives = 35/75 (46%), Gaps = 4/75 (5%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +V + +T E L   FS  G +   TI+ D      KGY Y+  +T +  + A V ++   
Sbjct: 6   NVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKGYAYIEFATRDSVEAA-VALDESS 64

Query: 124 LDGRVIFVDNVRPSR 138
             GRVI    V P R
Sbjct: 65  FRGRVI---KVLPKR 76

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 6/64 (9%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
            T+E L + F ++G++    +I        +G  YV   T ++A +AL  +    L G+ 
Sbjct: 14  VTEEDLKNLFEEYGEIQSIDMIP------PRGCAYVCMETRQDAHRALQKLRNVKLAGKK 67

Query: 129 IFVD 132
           I V 
Sbjct: 68  IKVA 71

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 19/54 (35%), Positives = 27/54 (50%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
             T+E L   F   G +    I+ D    +S GYG+V    E +AQKA+  +NG
Sbjct: 11  DMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNG 64

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

>gnl|CDD|241124 cd12680, RRM_THOC4, RNA recognition motif in THO complex subunit 4 (THOC4) and similar proteins

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 22/63 (34%), Positives = 30/63 (47%), Gaps = 5/63 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           VS    KE+    F++FG + +A +  D    RS G   V      +A KA+   NG  L
Sbjct: 12  VSDDDIKEL----FAEFGALKKAAVHYD-RSGRSLGTADVVFERRADALKAMKQYNGVPL 66

Query: 125 DGR 127
           DGR
Sbjct: 67  DGR 69

This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. . Length = 75

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

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 17/64 (26%), Positives = 31/64 (48%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           SV    +++ +   F  FG++   ++  D    + KGYG++     + AQ A+  MN   
Sbjct: 7   SVHPDLSEDDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFD 66

Query: 124 LDGR 127
           L G+
Sbjct: 67  LGGQ 70

This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. . Length = 77

>gnl|CDD|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins

 Score = 35.3 bits (82), Expect = 0.001
 Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 6/68 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S T++ L   FS++G V    I      +R +G   V     E AQ A+ +M G+ L
Sbjct: 15  LDESVTEQYLTRHFSRYGPVVHVVI------DRQRGQALVFFDKVEAAQAAVNEMKGRKL 68

Query: 125 DGRVIFVD 132
            GR + VD
Sbjct: 69  GGRKLQVD 76

This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is 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 = 77

>gnl|CDD|240728 cd12282, RRM2_TatSF1_like, RNA recognition motif 2 in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 4/59 (6%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           ++ L +   +FGQV +  +          G   V     EEA + +  +NG+   GR +
Sbjct: 26  RDDLREECEKFGQVKKVVVF----DRHPDGVASVKFKEPEEADRCIEALNGRWFAGRQL 80

This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. . Length = 91

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

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 13/76 (17%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDI--GKNR----SKGYGYVTSSTEEEAQKALVDM 119
              TT+E +  A S    V     I D+   +++    S+G+ +V   + E+A + +  +
Sbjct: 11  DLLTTEEDILQALSAIASVP----IKDVRLIRDKLTGTSRGFAFVEFPSLEDATQWMDAL 66

Query: 120 NGKL---LDGRVIFVD 132
           N      +DGRV+ V 
Sbjct: 67  NNLDPFVIDGRVVRVS 82

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

>gnl|CDD|240731 cd12285, RRM3_RBM39_like, RNA recognition motif 3 in vertebrate RNA-binding protein 39 (RBM39) and similar proteins

 Score = 35.6 bits (83), Expect = 0.001
 Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 79  SQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           S+FG V    +     KN  +G  YV   T E AQK +  +NG+  DGR I
Sbjct: 33  SKFGPVEHIKVD----KNSPEGVVYVKFKTVEAAQKCIQALNGRWFDGRQI 79

This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

>gnl|CDD|240690 cd12244, RRM2_MSSP, RNA recognition motif 2 in the c-myc gene single-strand binding proteins (MSSP) family

 Score = 35.4 bits (82), Expect = 0.002
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
            ++ L      +GQV    I+ D  K +S+G G+    + E+ +  +   NGK L G
Sbjct: 13  DEQDLETMLKPYGQVISTRILRD-SKGQSRGVGFARMESREKCEDIISKFNGKYLKG 68

This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. . Length = 79

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 17/53 (32%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
            T++ + + FS +G+V +  ++ D  K +S+G  +V  S++E AQ A+  +NG
Sbjct: 11  ATEKEVEEVFSPYGRVEDIYMMRDEMK-QSRGCAFVKYSSKEMAQAAIKALNG 62

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|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           TT+  L   F  FG + E     D      +G+ +V   T E+A  A+V + G  + GR
Sbjct: 12  TTQADLIPLFQNFGYILEFRHQPD------RGFAFVKLDTHEQAAMAIVQLQGFPVHGR 64

This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

>gnl|CDD|241038 cd12594, RRM1_SRSF4, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 4 (SRSF4)

 Score = 35.0 bits (80), Expect = 0.002
 Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 8/62 (12%)

Query: 78  FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS 137
           F  +G++ E  +     KN   GYG+V      +A  A+ ++NGK L G  + V++ R  
Sbjct: 20  FKGYGKILEVDL-----KN---GYGFVEFDDLRDADDAVYELNGKDLCGERVIVEHARGP 71

Query: 138 RR 139
           RR
Sbjct: 72  RR 73

This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. . Length = 74

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 7/64 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIM--DIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           SF TT++ L   F + G++    ++   D GK   KG+ +V     E A  AL    GK 
Sbjct: 7   SFETTEDELRAHFGRVGRIRRVRMMTFEDSGK--CKGFAFVDFEEIEFATNALK---GKH 61

Query: 124 LDGR 127
           L+GR
Sbjct: 62  LNGR 65

This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 73

>gnl|CDD|241110 cd12666, RRM2_RAVER2, RNA recognition motif 2 in vertebrate ribonucleoprotein PTB-binding 2 (raver-2)

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 1/71 (1%)

Query: 62  CIS-VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           C++ +  S T E   +    +G +    ++       SKGYG+V    ++ A KA +++ 
Sbjct: 3   CVTNLPISFTLEEFEELVRAYGNIERCFLVYSEVTGHSKGYGFVEYMKKDSASKARLELL 62

Query: 121 GKLLDGRVIFV 131
           GK L    +F 
Sbjct: 63  GKQLGESTLFA 73

This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. . Length = 77

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

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           +E+L + F Q G +T+ TI  D  + + K +G+V     E    A+  +NG  L GR I 
Sbjct: 15  EEILYELFLQAGPLTKVTICKD-KEGKPKSFGFVCFKHSESVPYAIALLNGIRLYGRPIK 73

Query: 131 V 131
           V
Sbjct: 74  V 74

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

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

 Score = 34.7 bits (79), Expect = 0.003
 Identities = 16/55 (29%), Positives = 33/55 (60%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           + T++ L   FSQ+G++  + I++D     S+G G++      EA++A+  +NG+
Sbjct: 13  TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 67

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

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           TT+  L   F  FG++ E T+     ++    YG+VT     +A +A+
Sbjct: 14  TTRSELRQRFQPFGEIEEITLHF---RDDGDNYGFVTYRYACDAFRAI 58

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

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 4/63 (6%)

Query: 71  KEMLADAFSQFGQVTEATIIMDI-GKNRSKGYGYVTSSTEEEAQKALVDMNG-KLLDGRV 128
           ++ L   F   G++ E  ++MD  GKNR  GY +V  + + EA++A+ ++N  ++  GR+
Sbjct: 15  EDELVPVFESVGRIYEMRLMMDFDGKNR--GYAFVMYTQKHEAKRAVRELNNYEIRPGRL 72

Query: 129 IFV 131
           + V
Sbjct: 73  LGV 75

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

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

 Score = 34.1 bits (79), Expect = 0.003
 Identities = 12/63 (19%), Positives = 27/63 (42%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
            +++ + +    FG++    ++ D     SKGY +          +A+  +NG  L  + 
Sbjct: 12  LSEDQVKELLESFGKLKAFNLVKDSATGLSKGYAFCEYLDPSVTDQAIAGLNGMQLGDKK 71

Query: 129 IFV 131
           + V
Sbjct: 72  LTV 74

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

>gnl|CDD|240831 cd12385, RRM1_hnRNPM_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins

 Score = 34.3 bits (79), Expect = 0.004
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 74  LADAF-SQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           L D F  + G+VT   +  D  + +S+G G V    +E  QKAL  MN   L GR + V
Sbjct: 16  LKDLFREKVGEVTYVELFKD-EEGKSRGCGVVEFKDKESVQKALETMNRYELKGRKLVV 73

This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. . Length = 76

>gnl|CDD|240818 cd12372, RRM_CFIm68_CFIm59, RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins

 Score = 34.2 bits (79), Expect = 0.004
 Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 69  TTKEMLADAFSQFGQVTEATI-IMDIGKN-RSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           TT E L  A ++ G V   +I   +   N +SKG+ YV  ++E  A      + G+  +G
Sbjct: 10  TTDEDLEGALAEAGVVDVKSIKFFEHKANGKSKGFAYVEFASEAAAAAVKEKLEGREFNG 69

Query: 127 R 127
           +
Sbjct: 70  K 70

This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. . Length = 76

>gnl|CDD|240738 cd12292, RRM2_La_like, RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins

 Score = 34.2 bits (79), Expect = 0.004
 Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 6/67 (8%)

Query: 63  ISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
            S+    T+E +   F+QFG+V      +D  +      GY+   T E AQKA      K
Sbjct: 7   TSIGPGVTREDIKAVFAQFGEV----KYVDFTEGADT--GYIRFKTPEAAQKAREAFVEK 60

Query: 123 LLDGRVI 129
                  
Sbjct: 61  GEGLLGK 67

This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), 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. LARP7 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. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 75

>gnl|CDD|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins

 Score = 34.4 bits (80), Expect = 0.004
 Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 15/61 (24%)

Query: 78  FSQFGQVTEATIIMDIGKNRSKGYG---------YVTSSTEEEAQKALVDMNGKLLDGRV 128
           F Q+G+      I  I  NR+  Y          YVT S +E+A + +  ++G  LDGR+
Sbjct: 29  FGQYGK------IKKIVINRNTSYNGSQGPSASAYVTYSRKEDALRCIQAVDGFYLDGRL 82

Query: 129 I 129
           +
Sbjct: 83  L 83

This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T. Length = 98

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

 Score = 34.4 bits (78), Expect = 0.004
 Identities = 16/55 (29%), Positives = 33/55 (60%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           + T++ L   FSQ+G++  + I++D     S+G G++      EA++A+  +NG+
Sbjct: 16  TMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQ 70

This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. . Length = 90

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	157
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.87
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.81
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.8
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.8
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.78
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.78
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.78
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.76
KOG0122	270	consensus Translation initiation factor 3, subunit	99.75
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.71
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.7
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.7
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.69
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.68
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.68
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.68
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.67
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.67
PLN03120	260	nucleic acid binding protein; Provisional	99.67
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.67
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.67
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.66
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.66
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.65
PLN03213	759	repressor of silencing 3; Provisional	99.65
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.64
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.64
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.61
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.6
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.6
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.6
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.6
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.6
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.6
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.59
smart00362	72	RRM_2 RNA recognition motif.	99.59
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
PLN03121	243	nucleic acid binding protein; Provisional	99.57
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.57
smart00360	71	RRM RNA recognition motif.	99.57
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.56
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.55
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.54
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.53
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.51
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.5
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.5
smart00361	70	RRM_1 RNA recognition motif.	99.45
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.44
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.44
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.42
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.41
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.41
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.39
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.37
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.35
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.34
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.33
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.32
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.31
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.28
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.27
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.26
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.25
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.24
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.24
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.18
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.14
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.12
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.12
KOG0226	290	consensus RNA-binding proteins [General function p	99.11
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.1
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.09
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.08
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.08
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.02
KOG0151	877	consensus Predicted splicing regulator, contains R	99.01
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.99
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.94
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.91
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.9
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.79
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.71
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.64
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.54
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.44
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.41
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.33
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.3
KOG4210	285	consensus Nuclear localization sequence binding pr	98.28
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.25
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.24
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	98.15
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.13
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.05
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.98
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	97.88
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.84
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.83
KOG3152	278	consensus TBP-binding protein, activator of basal	97.81
KOG2314	698	consensus Translation initiation factor 3, subunit	97.69
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.66
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	97.61
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.55
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.49
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.47
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	97.43
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.43
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.41
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.38
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	97.17
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	97.11
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.06
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.05
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.03
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.98
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.91
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	96.86
KOG1996	378	consensus mRNA splicing factor [RNA processing and	96.84
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.7
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.69
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	96.62
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.61
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.61
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.36
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.01
KOG2068	327	consensus MOT2 transcription factor [Transcription	95.92
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	95.91
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	95.44
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	95.31
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.09
KOG4660	549	consensus Protein Mei2, essential for commitment t	94.81
KOG2135	526	consensus Proteins containing the RNA recognition	94.81
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.54
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	94.1
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	93.81
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.25
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	92.76
KOG4210	285	consensus Nuclear localization sequence binding pr	91.92
KOG2591	684	consensus c-Mpl binding protein, contains La domai	91.81
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	91.35
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	91.14
COG0724	306	RNA-binding proteins (RRM domain) [General functio	86.84
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	86.48
KOG4410	396	consensus 5-formyltetrahydrofolate cyclo-ligase [C	86.47

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

Probab=99.87  E-value=2.7e-21  Score=132.77  Aligned_cols=84  Identities=33%  Similarity=0.512  Sum_probs=79.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+.+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.|++..|+|+.|+|.++.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      ++..
T Consensus       113 ~~~~  116 (144)
T PLN03134        113 DRPS  116 (144)
T ss_pred             cCCC
Confidence            6654

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.81  E-value=3.6e-19  Score=138.36  Aligned_cols=82  Identities=30%  Similarity=0.435  Sum_probs=78.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      .+|||+|||+.+++++|+++|++||.|..++++.++.++.++|||||.|.+.++|.+|+..|||..|+|+.|+|.|..++
T Consensus       270 ~~lfV~NL~~~~~e~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       270 YCIFVYNLSPDTDETVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence            36999999999999999999999999999999999999999999999999999999999999999999999999999887


Q ss_pred             CC
Q 036791          138 RR  139 (157)
Q Consensus       138 ~~  139 (157)
                      ..
T Consensus       350 ~~  351 (352)
T TIGR01661       350 AY  351 (352)
T ss_pred             CC
Confidence            64

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.80  E-value=2.2e-18  Score=133.55  Aligned_cols=82  Identities=21%  Similarity=0.335  Sum_probs=76.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~  133 (157)
                      ..++|||+|||+.+++++|+++|++||.|..+.|+.++.+++.+|||||+|.+.++|++||+.||+..+.+  ++|+|.+
T Consensus       192 ~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l~V~~  271 (346)
T TIGR01659       192 KDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPLTVRL  271 (346)
T ss_pred             ccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeEEEEE
Confidence            34679999999999999999999999999999999999899999999999999999999999999999866  7899999


Q ss_pred             ecCC
Q 036791          134 VRPS  137 (157)
Q Consensus       134 ~~~~  137 (157)
                      +...
T Consensus       272 a~~~  275 (346)
T TIGR01659       272 AEEH  275 (346)
T ss_pred             CCcc
Confidence            8753

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=99.80  E-value=1.8e-18  Score=141.16  Aligned_cols=122  Identities=16%  Similarity=0.205  Sum_probs=96.3

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCC-cchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPS-SDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEA   87 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~   87 (157)
                      ++|++++|+..+.++.+++....    +.    ....+. ...........+|||+||++++++++|+++|+.||.|..+
T Consensus       163 ~~Ai~~lnG~~i~GR~IkV~rp~----~~----p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~sv  234 (612)
T TIGR01645       163 QLALEQMNGQMLGGRNIKVGRPS----NM----PQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKC  234 (612)
T ss_pred             HHHHHhcCCeEEecceeeecccc----cc----cccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEE
Confidence            66777888888888877654200    00    000000 0011111234689999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           88 TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        88 ~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      .+..++.+++++|||||+|.+.++|.+|++.||+..|+|+.|+|.++.++.
T Consensus       235 rl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~kAi~pP  285 (612)
T TIGR01645       235 QLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVTPP  285 (612)
T ss_pred             EEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEecCCCc
Confidence            999999999999999999999999999999999999999999999998654

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.

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

Probab=99.78  E-value=9e-19  Score=114.81  Aligned_cols=86  Identities=26%  Similarity=0.305  Sum_probs=80.1

Q ss_pred             hhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           51 IMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        51 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      .......++||||||+..++|+.|.++|+++|+|..|.+-.|+.+...+|||||+|.+.++|+.|++.++|..++.++|+
T Consensus        30 ~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir  109 (153)
T KOG0121|consen   30 LEALRKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIR  109 (153)
T ss_pred             HHHHhhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccccccee
Confidence            33445678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecC
Q 036791          131 VDNVRP  136 (157)
Q Consensus       131 v~~~~~  136 (157)
                      ++|.-.
T Consensus       110 ~D~D~G  115 (153)
T KOG0121|consen  110 IDWDAG  115 (153)
T ss_pred             eecccc
Confidence            999764

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

Probab=99.78  E-value=3.2e-18  Score=124.92  Aligned_cols=126  Identities=17%  Similarity=0.215  Sum_probs=99.2

Q ss_pred             hhHHHHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCe
Q 036791            5 SLIQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQV   84 (157)
Q Consensus         5 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i   84 (157)
                      +..-|+||++||+.++.++.++.....-.+.+.....  ..=.+-......+.++||||||+.-++|++|++.|+.||+|
T Consensus       114 k~dAEnAI~~MnGqWlG~R~IRTNWATRKp~e~n~~~--ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I  191 (321)
T KOG0148|consen  114 KEDAENAIQQMNGQWLGRRTIRTNWATRKPSEMNGKP--LTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPI  191 (321)
T ss_pred             hHHHHHHHHHhCCeeeccceeeccccccCccccCCCC--ccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcc
Confidence            4456999999999999999998776322221110000  00011123333556899999999999999999999999999


Q ss_pred             eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           85 TEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        85 ~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      .+|++.++      +||+||.|.++|.|.+||..+|+.+|.|..+++.|.+...
T Consensus       192 ~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  192 QEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             eEEEEecc------cceEEEEecchhhHHHHHHHhcCceeCceEEEEeccccCC
Confidence            99999887      5899999999999999999999999999999999987643

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.78  E-value=2.2e-18  Score=134.03  Aligned_cols=83  Identities=27%  Similarity=0.405  Sum_probs=79.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||+|||..+++++|+++|+.||.|..|.|+.++.+|+++|||||+|.+.++|++||+.|+|..|.|++|+|.++++
T Consensus         3 ~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~~   82 (352)
T TIGR01661         3 KTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYARP   82 (352)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeecc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 036791          137 SRR  139 (157)
Q Consensus       137 ~~~  139 (157)
                      ...
T Consensus        83 ~~~   85 (352)
T TIGR01661        83 SSD   85 (352)
T ss_pred             ccc
Confidence            653

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

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=4.1e-18  Score=132.02  Aligned_cols=84  Identities=21%  Similarity=0.310  Sum_probs=79.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+++++++|+++|+.||.|..|.|+.|+.+++++|||||+|.++++|++|++.|++..|.+++|+|.++
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~~a  184 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVSYA  184 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeeecc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      ++..
T Consensus       185 ~p~~  188 (346)
T TIGR01659       185 RPGG  188 (346)
T ss_pred             cccc
Confidence            7643

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).

>PF00076 RRM_1: RNA recognition motif

Probab=99.76  E-value=1.1e-17  Score=100.81  Aligned_cols=70  Identities=37%  Similarity=0.595  Sum_probs=67.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      |||+|||.++++++|+++|+.||.+..+.+..+ .++..+|+|||+|.+.++|++|++.|+|..+.|++|+
T Consensus         1 l~v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~-~~~~~~~~a~V~F~~~~~a~~a~~~l~g~~~~~~~ir   70 (70)
T PF00076_consen    1 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            799999999999999999999999999999988 6789999999999999999999999999999999885

(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 ....

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

Probab=99.75  E-value=1.4e-17  Score=119.98  Aligned_cols=82  Identities=27%  Similarity=0.436  Sum_probs=79.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +..+|-|.||+.++++.+|+++|.+||.|.++.+.+|+.||.++|||||.|.+.++|.+||..|||.=+++-.|+|+|++
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEwsk  267 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEWSK  267 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEecC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      |+
T Consensus       268 P~  269 (270)
T KOG0122|consen  268 PS  269 (270)
T ss_pred             CC
Confidence            86

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

Probab=99.71  E-value=2.2e-17  Score=118.45  Aligned_cols=81  Identities=33%  Similarity=0.468  Sum_probs=74.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++||||+|+|.+..+.|++.|++||+|.+..++.|+.+|+++||+||+|.+.+.|.+|++- ..-.|+||+..+.++
T Consensus        10 T~~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   10 TTFTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKANCNLA   88 (247)
T ss_pred             ceEEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCcccccccccchh
Confidence            4457899999999999999999999999999999999999999999999999999999999985 456789999988887


Q ss_pred             cC
Q 036791          135 RP  136 (157)
Q Consensus       135 ~~  136 (157)
                      .-
T Consensus        89 ~l   90 (247)
T KOG0149|consen   89 SL   90 (247)
T ss_pred             hh
Confidence            43

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

Probab=99.70  E-value=1.3e-16  Score=117.83  Aligned_cols=92  Identities=24%  Similarity=0.390  Sum_probs=84.0

Q ss_pred             CCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 036791           45 RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL  124 (157)
Q Consensus        45 ~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~  124 (157)
                      .|..+......+-+||||+-|+..++|..|+..|+.||.|..|.|+.++.||+++|||||+|..+.+...|-+..+|..|
T Consensus        89 dP~~dp~a~gDPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~I  168 (335)
T KOG0113|consen   89 DPNNDPNAIGDPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKI  168 (335)
T ss_pred             CCCCCCcccCCccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCcee
Confidence            34555555556678999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcEEEEEeecC
Q 036791          125 DGRVIFVDNVRP  136 (157)
Q Consensus       125 ~g~~l~v~~~~~  136 (157)
                      +|+.|.|++-+.
T Consensus       169 dgrri~VDvERg  180 (335)
T KOG0113|consen  169 DGRRILVDVERG  180 (335)
T ss_pred             cCcEEEEEeccc
Confidence            999999998754

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

Probab=99.70  E-value=9e-17  Score=132.11  Aligned_cols=82  Identities=29%  Similarity=0.523  Sum_probs=77.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+||++.+++++|+++|+.||.|..+.++.+ .+|+++|||||.|.+.++|.+|+..|||..+.|++|.|.++.
T Consensus       284 ~~~~l~V~nl~~~~~~~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~  362 (562)
T TIGR01628       284 QGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQ  362 (562)
T ss_pred             CCCEEEEeCCCCccCHHHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEecc
Confidence            4567999999999999999999999999999999999 789999999999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      .+.
T Consensus       363 ~k~  365 (562)
T TIGR01628       363 RKE  365 (562)
T ss_pred             CcH
Confidence            654

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

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

Probab=99.69  E-value=5.8e-16  Score=125.83  Aligned_cols=81  Identities=17%  Similarity=0.264  Sum_probs=77.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||+|||..+++++|+++|..||.|..+.++.++.+|.++|||||+|.+.++|..|+..|+|..|+|+.|.|.++..
T Consensus       295 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~  374 (509)
T TIGR01642       295 KDRIYIGNLPLYLGEDQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACV  374 (509)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECcc
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      .
T Consensus       375 ~  375 (509)
T TIGR01642       375 G  375 (509)
T ss_pred             C
Confidence            4

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

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.68  E-value=5e-16  Score=93.86  Aligned_cols=70  Identities=37%  Similarity=0.544  Sum_probs=64.7

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      |||+|||+++++++|.++|+.||.|..+.+..++. +..+|+|||+|.+.++|.+|+..+++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            79999999999999999999999999999999876 89999999999999999999999999999999874

k.a. RRM, RBD, or RNP domain); PDB: 2DNN_A 1WI6_A 2EVZ_A 2ADC_A 1QM9_A 2KG1_A 2HGN_A 1U2F_A 2G4B_A 2HZC_A ....

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

Probab=99.68  E-value=2e-16  Score=129.24  Aligned_cols=80  Identities=30%  Similarity=0.439  Sum_probs=76.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+||++.+++++|+++|.+||.|.++.++.|+.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999998654

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.

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

Probab=99.68  E-value=9.6e-16  Score=123.11  Aligned_cols=79  Identities=32%  Similarity=0.449  Sum_probs=76.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..+|||+|||..+++++|+++|..||.|..+.++.++.+|+++|||||+|.+.++|.+|+..|+|..|.|++|+|.++.
T Consensus       186 ~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~  264 (457)
T TIGR01622       186 FLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVGYAQ  264 (457)
T ss_pred             CCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEEEcc
Confidence            5789999999999999999999999999999999999889999999999999999999999999999999999999975

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.

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

Probab=99.67  E-value=4e-16  Score=107.48  Aligned_cols=79  Identities=22%  Similarity=0.279  Sum_probs=71.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      -.++||||||+..+++.+|+..|..||.+..|-|-..     ..|||||+|++..+|+.|+..|+|..|+|..|+|+++.
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArn-----PPGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~   83 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARN-----PPGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELST   83 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeec-----CCCceEEeccCcccHHHHHhhcCCccccCceEEEEeec
Confidence            3578999999999999999999999999988866543     46999999999999999999999999999999999998


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      ....
T Consensus        84 G~~r   87 (195)
T KOG0107|consen   84 GRPR   87 (195)
T ss_pred             CCcc
Confidence            6544

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

Probab=99.67  E-value=5.4e-17  Score=115.63  Aligned_cols=86  Identities=26%  Similarity=0.402  Sum_probs=80.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++||||+|...+++.-|...|-.||+|..+.++.|-.++++|||+||+|.-.++|.+||..||+.+|.|+.|+|.+++
T Consensus         9 ~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~Ak   88 (298)
T KOG0111|consen    9 QKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLAK   88 (298)
T ss_pred             cceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeecC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 036791          136 PSRRYN  141 (157)
Q Consensus       136 ~~~~~~  141 (157)
                      |..-..
T Consensus        89 P~kike   94 (298)
T KOG0111|consen   89 PEKIKE   94 (298)
T ss_pred             CccccC
Confidence            864443

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.67  E-value=1.3e-15  Score=112.30  Aligned_cols=76  Identities=18%  Similarity=0.251  Sum_probs=70.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+||++.+++++|+++|+.||.|.++.|+.++.   .+|||||+|.+.++|+.|+. |+|..|.|+.|+|.++..
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt~a~~   79 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTITPAED   79 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEEeccC
Confidence            46899999999999999999999999999999998853   57999999999999999996 999999999999999864

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

Probab=99.67  E-value=1.1e-16  Score=123.36  Aligned_cols=123  Identities=20%  Similarity=0.199  Sum_probs=99.2

Q ss_pred             cccCcccccccCCceeceeccccccc---------------------CCCcchhhccccccEEEEcCCCCCCCHHHHHHH
Q 036791           19 FTEDSLLSFSSKPYQVVNYFSLHCIV---------------------RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADA   77 (157)
Q Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~   77 (157)
                      .+..|..+..+++++++.|.....+.                     ++-+....+.....+||||.|+..++|.+++++
T Consensus        65 nl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~i  144 (510)
T KOG0144|consen   65 NLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREI  144 (510)
T ss_pred             EeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHH
Confidence            34556666778899999988775521                     122222333344678999999999999999999


Q ss_pred             HhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-c--CCcEEEEEeecCCCCCCC
Q 036791           78 FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL-L--DGRVIFVDNVRPSRRYNT  142 (157)
Q Consensus        78 f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~-~--~g~~l~v~~~~~~~~~~~  142 (157)
                      |++||.|++|.|++| ..+.+||||||.|.+.+.|..||++|||.. +  +..+|.|+|+.+++++..
T Consensus       145 Fs~fG~Ied~~ilrd-~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFADtqkdk~~  211 (510)
T KOG0144|consen  145 FSRFGHIEDCYILRD-PDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFADTQKDKDG  211 (510)
T ss_pred             HHhhCccchhhheec-ccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEecccCCCchH
Confidence            999999999999999 569999999999999999999999999987 3  358999999998766543

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

Probab=99.67  E-value=9.2e-16  Score=125.09  Aligned_cols=118  Identities=17%  Similarity=0.085  Sum_probs=90.0

Q ss_pred             hhhHHHHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCC
Q 036791            4 QSLIQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQ   83 (157)
Q Consensus         4 ~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~   83 (157)
                      +.....+|+.++++|.+.........        ..++.    ..+ .......++|||+|||+++++++|+++|++||.
T Consensus        18 ~~~~a~~a~~~~~gy~~~~~~g~r~~--------g~Pp~----~~~-~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~   84 (578)
T TIGR01648        18 PDEAALKALLERTGYTLVQENGQRKY--------GGPPP----GWS-GVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGP   84 (578)
T ss_pred             ccHHHHHHHHHhhCccccccCCcccC--------CCCCC----ccc-CCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCC
Confidence            34455678888888887655442221        11111    111 111234578999999999999999999999999


Q ss_pred             eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEeec
Q 036791           84 VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-GRVIFVDNVR  135 (157)
Q Consensus        84 i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~v~~~~  135 (157)
                      |..++|++| .+|+++|||||+|.+.++|++||+.||+..+. |+.|.|..+.
T Consensus        85 I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~  136 (578)
T TIGR01648        85 IYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV  136 (578)
T ss_pred             EEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc
Confidence            999999999 88999999999999999999999999999884 7777776553

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=99.66  E-value=7.3e-16  Score=126.78  Aligned_cols=79  Identities=30%  Similarity=0.347  Sum_probs=75.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      +|||+|||.++++++|+++|++||.|..|++.+|+.+++++|||||+|.+.++|++|++.+++..+.|++|+|.|+...
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F~~~~~A~~Al~~ln~~~i~gk~i~i~~s~~~   80 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQRD   80 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccccc
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999998643

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

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

Probab=99.66  E-value=1.7e-16  Score=112.07  Aligned_cols=80  Identities=26%  Similarity=0.471  Sum_probs=76.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|-|-||...++.++|+.+|++||.|-+|.|+.|+.|+..+|||||.|....+|+.|+++|+|.+|+|+.|+|+.++
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999998875

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

Probab=99.65  E-value=5.7e-16  Score=115.87  Aligned_cols=80  Identities=28%  Similarity=0.510  Sum_probs=74.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..+.|+|.|||+...+-||+.+|.+||.|.+|.|+.+ + .-+||||||+|++.++|++|-..|||..+.||+|.|..+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfN-E-RGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFN-E-RGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEec-c-CCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            3467999999999999999999999999999999886 2 3479999999999999999999999999999999999998


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      .+
T Consensus       173 ar  174 (376)
T KOG0125|consen  173 AR  174 (376)
T ss_pred             hh
Confidence            65

>PLN03213 repressor of silencing 3; Provisional

Probab=99.65  E-value=7.4e-16  Score=120.90  Aligned_cols=77  Identities=17%  Similarity=0.258  Sum_probs=71.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCH--HHHHHHHHHhCCCccCCcEEEEEee
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTE--EEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~--~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ..+||||||++.+++++|+.+|..||.|..+.|+  +.+|  ||||||+|.+.  .++.+||..|||..++|+.|+|..+
T Consensus        10 gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKA   85 (759)
T PLN03213         10 GVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKA   85 (759)
T ss_pred             ceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeec
Confidence            4579999999999999999999999999999998  5667  99999999987  7899999999999999999999999


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      ++.
T Consensus        86 KP~   88 (759)
T PLN03213         86 KEH   88 (759)
T ss_pred             cHH
Confidence            873

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

Probab=99.64  E-value=9.1e-16  Score=112.23  Aligned_cols=82  Identities=32%  Similarity=0.483  Sum_probs=78.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ...+||+.|...++-++|++.|.+||+|.++++++|..|+|++||+||.|.+.++|++||..|||.=|++|.|+-.|+..
T Consensus        62 hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWATR  141 (321)
T KOG0148|consen   62 HFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWATR  141 (321)
T ss_pred             ceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeecccccc
Confidence            34699999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 036791          137 SR  138 (157)
Q Consensus       137 ~~  138 (157)
                      |.
T Consensus       142 Kp  143 (321)
T KOG0148|consen  142 KP  143 (321)
T ss_pred             Cc
Confidence            76

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

Probab=99.64  E-value=9.4e-16  Score=101.59  Aligned_cols=84  Identities=27%  Similarity=0.303  Sum_probs=79.0

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ....-.|||.++....+++++...|..||.|..+.+.+|+.||..+||+.|+|.+.+.|++|+..+||..|+|..|.|+|
T Consensus        69 SVEGwIi~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw  148 (170)
T KOG0130|consen   69 SVEGWIIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDW  148 (170)
T ss_pred             ceeeEEEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEE
Confidence            34456799999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 036791          134 VRPS  137 (157)
Q Consensus       134 ~~~~  137 (157)
                      +..+
T Consensus       149 ~Fv~  152 (170)
T KOG0130|consen  149 CFVK  152 (170)
T ss_pred             EEec
Confidence            8643

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

Probab=99.61  E-value=1.7e-15  Score=110.45  Aligned_cols=116  Identities=25%  Similarity=0.317  Sum_probs=98.0

Q ss_pred             ccccCcccccccCCceeceeccccccc---------------------CCCcchhhccccccEEEEcCCCCCCCHHHHHH
Q 036791           18 YFTEDSLLSFSSKPYQVVNYFSLHCIV---------------------RPSSDLIMQLVNVSFWRCISVSFSTTKEMLAD   76 (157)
Q Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~   76 (157)
                      +.+-++.++..+-+|++|+|..+..+.                     +|+++.    ....+|||.+||..++..+|++
T Consensus        71 cKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyARPSs~~----Ik~aNLYvSGlPktMtqkelE~  146 (360)
T KOG0145|consen   71 CKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYARPSSDS----IKDANLYVSGLPKTMTQKELEQ  146 (360)
T ss_pred             eeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEeccCChhh----hcccceEEecCCccchHHHHHH
Confidence            445566677788889999998876632                     334433    3467899999999999999999


Q ss_pred             HHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEeecCC
Q 036791           77 AFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDNVRPS  137 (157)
Q Consensus        77 ~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~~~~~  137 (157)
                      +|+.||.|...+|+.|..+|.++|.+||.|....+|+.||+.|||..-.|  .+|.|.++...
T Consensus       147 iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AIk~lNG~~P~g~tepItVKFannP  209 (360)
T KOG0145|consen  147 IFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAIKGLNGQKPSGCTEPITVKFANNP  209 (360)
T ss_pred             HHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHHHhccCCCCCCCCCCeEEEecCCc
Confidence            99999999999999999999999999999999999999999999998655  78999998644

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

Probab=99.60  E-value=5.7e-15  Score=114.39  Aligned_cols=82  Identities=23%  Similarity=0.287  Sum_probs=76.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc-CCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL-DGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~-~g~~l~v~~  133 (157)
                      ...+.||||.||.++.|++|.-+|.+.|.|-++++++|+.+|.+||||||.|.+.++|+.||+.||+.+| .|+.|.|+.
T Consensus        81 ~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~igvc~  160 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLGVCV  160 (506)
T ss_pred             CCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeEEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999999999998 588888887


Q ss_pred             ecC
Q 036791          134 VRP  136 (157)
Q Consensus       134 ~~~  136 (157)
                      +..
T Consensus       161 Sva  163 (506)
T KOG0117|consen  161 SVA  163 (506)
T ss_pred             eee
Confidence            654

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

Probab=99.60  E-value=1.1e-14  Score=116.91  Aligned_cols=81  Identities=28%  Similarity=0.400  Sum_probs=76.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||..+++++|+++|.+||.|..|.++.++.+++++|||||+|.+.++|.+||. |+|..+.|++|.|.++.
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~v~~~~  166 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPIIVQSSQ  166 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeEEeecc
Confidence            45789999999999999999999999999999999999999999999999999999999997 89999999999999876


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ..
T Consensus       167 ~~  168 (457)
T TIGR01622       167 AE  168 (457)
T ss_pred             hh
Confidence            54

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.

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

Probab=99.60  E-value=1.8e-15  Score=104.85  Aligned_cols=80  Identities=28%  Similarity=0.308  Sum_probs=77.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+||+..+++..|.++|-+.|.|..+.+++|+.++.++||||++|.++++|+-|++.||...|.|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999987

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

Probab=99.60  E-value=8.6e-16  Score=106.45  Aligned_cols=87  Identities=23%  Similarity=0.299  Sum_probs=79.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEA-TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ....++||+||.+.+++..|...|+.||.+... .++++..||..+||+||.|.+.+.+.+|+.+++|..+.+++++|.+
T Consensus        94 ~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~itv~y  173 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPITVSY  173 (203)
T ss_pred             cccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceEEEE
Confidence            344789999999999999999999999988764 8888989999999999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 036791          134 VRPSRRYN  141 (157)
Q Consensus       134 ~~~~~~~~  141 (157)
                      +..+...+
T Consensus       174 a~k~~~kg  181 (203)
T KOG0131|consen  174 AFKKDTKG  181 (203)
T ss_pred             EEecCCCc
Confidence            98765444

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

Probab=99.60  E-value=9.1e-15  Score=106.69  Aligned_cols=85  Identities=25%  Similarity=0.374  Sum_probs=80.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|.|.-||..+++++++.+|...|+|+.|++++|+.+|.+-||+||.|-.+++|++|+..|||..+..+.|+|.|++
T Consensus        40 skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSyAR  119 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSYAR  119 (360)
T ss_pred             ccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEecc
Confidence            34578899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      |....
T Consensus       120 PSs~~  124 (360)
T KOG0145|consen  120 PSSDS  124 (360)
T ss_pred             CChhh
Confidence            87553

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

Probab=99.60  E-value=3.3e-15  Score=115.32  Aligned_cols=86  Identities=21%  Similarity=0.257  Sum_probs=78.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-c--CCcEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL-L--DGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~-~--~g~~l~v  131 (157)
                      ...-++|||-||..|+|++|+++|++||.|.+|.|++|+.++.++|||||.|.+.++|.+|+.+||... |  +..+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            445579999999999999999999999999999999999999999999999999999999999999887 3  4489999


Q ss_pred             EeecCCCCC
Q 036791          132 DNVRPSRRY  140 (157)
Q Consensus       132 ~~~~~~~~~  140 (157)
                      +++....++
T Consensus       112 k~Ad~E~er  120 (510)
T KOG0144|consen  112 KYADGERER  120 (510)
T ss_pred             cccchhhhc
Confidence            999876555

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

Probab=99.59  E-value=1.3e-16  Score=110.50  Aligned_cols=80  Identities=24%  Similarity=0.422  Sum_probs=75.7

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +..-|||||||+..+|.+|-.+|++||.|..|.+++|+.||+++||||+.|++-...--|+..|||..|.||.|+|+...
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            44579999999999999999999999999999999999999999999999999999999999999999999999998753

>smart00362 RRM_2 RNA recognition motif

Probab=99.59  E-value=1.5e-14  Score=86.48  Aligned_cols=72  Identities=33%  Similarity=0.505  Sum_probs=67.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      +|||+|||..+++++|+++|..||.+..+.+..++  +.++|+|||+|.+.++|+.|+..+++..+.|++|.|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999999999888775  7788999999999999999999999999999998873

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

Probab=99.57  E-value=1.8e-14  Score=106.69  Aligned_cols=80  Identities=30%  Similarity=0.540  Sum_probs=76.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||+|||..+++++|.++|..||.+..+.+..++.+++.+|||||.|.+.++|..|+..+++..+.|++|.|.+..+
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58899999999999999999999999999999999988999999999999999999999999999999999999999653

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.57  E-value=2.6e-14  Score=104.00  Aligned_cols=76  Identities=17%  Similarity=0.183  Sum_probs=69.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+||++.+++++|+++|+.||.|..|.|+.+   +..+++|||+|.++++++.|+. |+|..|.+++|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D---~et~gfAfVtF~d~~aaetAll-LnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRS---GEYACTAYVTFKDAYALETAVL-LSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecC---CCcceEEEEEECCHHHHHHHHh-cCCCeeCCceEEEEeCc
Confidence            3578999999999999999999999999999999988   4456899999999999999995 89999999999998754

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

Probab=99.57  E-value=2.5e-14  Score=90.72  Aligned_cols=78  Identities=22%  Similarity=0.308  Sum_probs=71.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ...|||.|||+.++.+++.++|.+||.|..+++-..+.   .+|-|||.|++..+|.+|++.|+|..++++.|.|-+..+
T Consensus        18 nriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~---TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE---TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcccceEEEEecCccC---cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            46799999999999999999999999999999976644   489999999999999999999999999999999998765


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      .
T Consensus        95 ~   95 (124)
T KOG0114|consen   95 E   95 (124)
T ss_pred             H
Confidence            3

>smart00360 RRM RNA recognition motif

Probab=99.57  E-value=2.5e-14  Score=85.18  Aligned_cols=71  Identities=37%  Similarity=0.592  Sum_probs=66.7

Q ss_pred             EcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           62 CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        62 V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      |+|||..+++++|+++|..||.|..+.+..++.++.++|+|||+|.+.++|.+|+..+++..+.|+.|+|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999999999999887788999999999999999999999999999999998873

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

Probab=99.56  E-value=1.6e-14  Score=111.95  Aligned_cols=77  Identities=34%  Similarity=0.454  Sum_probs=71.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...+-|||.||+.++|++.|+++|..||.|.+|..++|        ||||.|.+.++|.+|++.+||.+|+|..|.|.++
T Consensus       257 s~VKvLYVRNL~~~tTeE~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLA  328 (506)
T KOG0117|consen  257 SKVKVLYVRNLMESTTEETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLA  328 (506)
T ss_pred             hheeeeeeeccchhhhHHHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEEec
Confidence            34578999999999999999999999999999988766        8999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      +|..+
T Consensus       329 KP~~k  333 (506)
T KOG0117|consen  329 KPVDK  333 (506)
T ss_pred             CChhh
Confidence            98543

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

Probab=99.55  E-value=1.3e-14  Score=114.61  Aligned_cols=82  Identities=24%  Similarity=0.427  Sum_probs=78.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      ..+||||+|+++++++|..+|+..|.|..++++.|+.+|+.+||||++|.+.+++..|++.|||.++.|++|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            67999999999999999999999999999999999999999999999999999999999999999999999999998765


Q ss_pred             CC
Q 036791          138 RR  139 (157)
Q Consensus       138 ~~  139 (157)
                      ..
T Consensus        99 ~~  100 (435)
T KOG0108|consen   99 KN  100 (435)
T ss_pred             ch
Confidence            44

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

Probab=99.54  E-value=4e-14  Score=98.61  Aligned_cols=80  Identities=16%  Similarity=0.205  Sum_probs=71.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+...|||+|||.++.+.+++.+|.+||.|..|.+...   -....||||+|++..+|+.||..-+|..++|..|+|+++
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfp   80 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFP   80 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEec
Confidence            35678999999999999999999999999999987443   234689999999999999999999999999999999998


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      +..
T Consensus        81 rgg   83 (241)
T KOG0105|consen   81 RGG   83 (241)
T ss_pred             cCC
Confidence            754

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

Probab=99.53  E-value=1.1e-13  Score=113.13  Aligned_cols=75  Identities=32%  Similarity=0.507  Sum_probs=69.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQF--GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .++|||+||++.+++++|+++|++|  |.|.+|.+++        +||||+|.+.++|++|++.||+..|+|+.|+|.|+
T Consensus       233 ~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~r--------gfAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~A  304 (578)
T TIGR01648       233 VKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIR--------DYAFVHFEDREDAVKAMDELNGKELEGSEIEVTLA  304 (578)
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeec--------CeEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4689999999999999999999999  9999987653        59999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      ++...
T Consensus       305 kp~~~  309 (578)
T TIGR01648       305 KPVDK  309 (578)
T ss_pred             cCCCc
Confidence            87543

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.

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.53  E-value=2.1e-13  Score=81.85  Aligned_cols=74  Identities=36%  Similarity=0.510  Sum_probs=68.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      +|+|+|||..+++++|+++|..+|.|..+.+..++.+ ..+|+|||+|.+.++|..|++.+++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999887554 7789999999999999999999999999999999864

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).

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

Probab=99.51  E-value=1.6e-13  Score=111.15  Aligned_cols=77  Identities=19%  Similarity=0.209  Sum_probs=70.8

Q ss_pred             cccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +..+|||+||++ .+++++|+++|+.||.|..+.++.++     +|+|||+|.+.++|..|+..|||..|.|++|+|.++
T Consensus       274 ~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s  348 (481)
T TIGR01649       274 PGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPS  348 (481)
T ss_pred             CCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            456899999998 69999999999999999999998863     589999999999999999999999999999999998


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      +..
T Consensus       349 ~~~  351 (481)
T TIGR01649       349 KQQ  351 (481)
T ss_pred             ccc
Confidence            653

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

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

Probab=99.50  E-value=2.2e-13  Score=108.07  Aligned_cols=85  Identities=28%  Similarity=0.388  Sum_probs=77.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .-.|.|.|||+.+...+|+.+|+.||.+..+.|+.. ..|+.+|||||.|....+|..|++.+|+..|+||+|.|+||-+
T Consensus       117 k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~k-~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~  195 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPRK-KDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVD  195 (678)
T ss_pred             cceEEeecCCcccCcHHHHHHHhhcceEEEEEcccC-CCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecc
Confidence            346889999999999999999999999999999966 4477779999999999999999999999999999999999988


Q ss_pred             CCCCCC
Q 036791          137 SRRYNT  142 (157)
Q Consensus       137 ~~~~~~  142 (157)
                      +..+..
T Consensus       196 Kd~ye~  201 (678)
T KOG0127|consen  196 KDTYED  201 (678)
T ss_pred             cccccc
Confidence            766544

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

Probab=99.50  E-value=6.7e-13  Score=107.51  Aligned_cols=77  Identities=17%  Similarity=0.183  Sum_probs=68.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~  133 (157)
                      ...+|||+||++.+++++|+++|+.||.|.++.+..+.    .+|+|||+|.+.++|.+|++.|||..|.|  ..|+|.|
T Consensus        95 ~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~----~~~~afVef~~~~~A~~A~~~Lng~~i~~~~~~l~v~~  170 (481)
T TIGR01649        95 KVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKN----NVFQALVEFESVNSAQHAKAALNGADIYNGCCTLKIEY  170 (481)
T ss_pred             ceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecC----CceEEEEEECCHHHHHHHHHHhcCCcccCCceEEEEEE
Confidence            34579999999999999999999999999999887653    24789999999999999999999999975  4899999


Q ss_pred             ecC
Q 036791          134 VRP  136 (157)
Q Consensus       134 ~~~  136 (157)
                      +++
T Consensus       171 sk~  173 (481)
T TIGR01649       171 AKP  173 (481)
T ss_pred             ecC
Confidence            875

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).

>smart00361 RRM_1 RNA recognition motif

Probab=99.45  E-value=6.6e-13  Score=80.33  Aligned_cols=61  Identities=36%  Similarity=0.603  Sum_probs=55.0

Q ss_pred             HHHHHHHHh----cCCCeeEEE-EeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           71 KEMLADAFS----QFGQVTEAT-IIMDIGK--NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        71 ~~~l~~~f~----~~G~i~~~~-~~~~~~~--~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      +++|+++|+    +||.|.++. ++.++.+  +.++|++||.|.+.++|.+|++.|||..+.|+.|++
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            467888888    999999995 7777666  889999999999999999999999999999999976

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

Probab=99.44  E-value=8.9e-14  Score=105.80  Aligned_cols=75  Identities=32%  Similarity=0.480  Sum_probs=73.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      +.||||.|.+.+.|+.|+..|..||.|..+.+.+|+.|++++||+||+|+-++.|+-|++.|||..++||.|+|.
T Consensus       114 cRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVg  188 (544)
T KOG0124|consen  114 CRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVG  188 (544)
T ss_pred             HheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCcccccc
Confidence            569999999999999999999999999999999999999999999999999999999999999999999999987

>PF13893 RRM_5: RNA recognition motif

Probab=99.44  E-value=1e-12  Score=76.00  Aligned_cols=56  Identities=34%  Similarity=0.615  Sum_probs=50.5

Q ss_pred             HHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           74 LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        74 l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      |.++|++||.|..+.+....     +++|||+|.+.++|.+|++.|||..+.|++|+|.|+
T Consensus         1 L~~~f~~fG~V~~i~~~~~~-----~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKFGEVKKIKIFKKK-----RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTTS-EEEEEEETTS-----TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCcccEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            67899999999999887652     689999999999999999999999999999999986

(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 ....

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

Probab=99.42  E-value=4.8e-13  Score=101.86  Aligned_cols=120  Identities=14%  Similarity=0.160  Sum_probs=93.7

Q ss_pred             HHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEE
Q 036791           10 RKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATI   89 (157)
Q Consensus        10 ~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~   89 (157)
                      =|+++||+.++.++.+++..    +   ...+.+...-+...........|||..+.++.+++||+.+|+.||.|..|.+
T Consensus       170 LAlEqMNg~mlGGRNiKVgr----P---sNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~L  242 (544)
T KOG0124|consen  170 LALEQMNGQMLGGRNIKVGR----P---SNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQL  242 (544)
T ss_pred             HHHHHhccccccCccccccC----C---CCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEe
Confidence            46788999999999887651    0   0000000000111122223457999999999999999999999999999999


Q ss_pred             eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           90 IMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        90 ~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      -+++..+.++||+|++|.+......|+..||-..++|..|+|..+-.
T Consensus       243 Ar~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyLRVGk~vT  289 (544)
T KOG0124|consen  243 ARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVGKCVT  289 (544)
T ss_pred             eccCCCCCccceeeEEeccccchHHHhhhcchhhcccceEecccccC
Confidence            99988889999999999999999999999999999999999987753

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

Probab=99.41  E-value=2.6e-12  Score=100.50  Aligned_cols=79  Identities=32%  Similarity=0.501  Sum_probs=73.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCC
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRR  139 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~  139 (157)
                      +||.||++.++.++|.++|+.||.|..|++..+ .+| ++|| ||.|.+++.|.+|++.+||..+.|++|.|.....+..
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~-~~g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~~~~~e  155 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATD-ENG-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLFERKEE  155 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEc-CCC-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeeccchhh
Confidence            999999999999999999999999999999998 446 8999 9999999999999999999999999999999887666


Q ss_pred             CC
Q 036791          140 YN  141 (157)
Q Consensus       140 ~~  141 (157)
                      +.
T Consensus       156 r~  157 (369)
T KOG0123|consen  156 RE  157 (369)
T ss_pred             hc
Confidence            54

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

Probab=99.41  E-value=5.3e-13  Score=98.76  Aligned_cols=82  Identities=21%  Similarity=0.314  Sum_probs=74.2

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ....++|+||||.+.++..+|+..|.+||.+.++.|+++        |+||.|.-.++|..|++.|++.++.|++++|+.
T Consensus        75 sk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m~vq~  146 (346)
T KOG0109|consen   75 SKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRMHVQL  146 (346)
T ss_pred             CCCccccccCCCCccccCHHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhcccccccccceeeeee
Confidence            345678999999999999999999999999999999876        899999999999999999999999999999999


Q ss_pred             ecCCCCCCCC
Q 036791          134 VRPSRRYNTD  143 (157)
Q Consensus       134 ~~~~~~~~~~  143 (157)
                      +.++..-..+
T Consensus       147 stsrlrtapg  156 (346)
T KOG0109|consen  147 STSRLRTAPG  156 (346)
T ss_pred             eccccccCCC
Confidence            9887554433

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

Probab=99.39  E-value=1.6e-12  Score=103.27  Aligned_cols=80  Identities=34%  Similarity=0.446  Sum_probs=74.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-----CC-CccCCcEEEE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM-----NG-KLLDGRVIFV  131 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l-----~g-~~~~g~~l~v  131 (157)
                      .+|||.|||++++++.|.+.|++||.|..+.++.++.|+.++|.|||.|.+..+|.+||+..     .| ..|.||.|.|
T Consensus       293 ~tVFvRNL~fD~tEEel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv  372 (678)
T KOG0127|consen  293 KTVFVRNLPFDTTEEELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKV  372 (678)
T ss_pred             ceEEEecCCccccHHHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEee
Confidence            68999999999999999999999999999999999999999999999999999999999976     23 4578999999


Q ss_pred             EeecCC
Q 036791          132 DNVRPS  137 (157)
Q Consensus       132 ~~~~~~  137 (157)
                      ..+-++
T Consensus       373 ~~Av~R  378 (678)
T KOG0127|consen  373 TLAVTR  378 (678)
T ss_pred             eeccch
Confidence            998654

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

Probab=99.37  E-value=9.8e-13  Score=96.51  Aligned_cols=85  Identities=24%  Similarity=0.300  Sum_probs=81.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||-.||.+..+.+|.++|..||.|...++..|+.|..+++|+||.|.+...++.||.+|||..|+-++|+|.+.
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      +|+..
T Consensus       363 RPkda  367 (371)
T KOG0146|consen  363 RPKDA  367 (371)
T ss_pred             Ccccc
Confidence            98754

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

Probab=99.35  E-value=1.5e-12  Score=103.24  Aligned_cols=77  Identities=35%  Similarity=0.566  Sum_probs=73.8

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ||||||.+++++++|+.+|..||.|..|.+.+|..||.++||+|++|.+.++|.+|++.|||.+|-|+.|+|....-
T Consensus       281 l~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~  357 (549)
T KOG0147|consen  281 LYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            89999999999999999999999999999999988999999999999999999999999999999999999987643

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

Probab=99.34  E-value=5e-12  Score=90.62  Aligned_cols=80  Identities=19%  Similarity=0.278  Sum_probs=72.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHH----HHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           57 VSFWRCISVSFSTTKEMLAD----AFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ..||||.||+..+..++|+.    +|+.||.|..|....   +.+.+|-|||.|.+.+.|-.|+..|+|..+.|++++|.
T Consensus         9 n~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriq   85 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQ   85 (221)
T ss_pred             CceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchhhee
Confidence            34899999999999998888    999999999887654   47899999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      ||+.+..
T Consensus        86 yA~s~sd   92 (221)
T KOG4206|consen   86 YAKSDSD   92 (221)
T ss_pred             cccCccc
Confidence            9987644

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

Probab=99.33  E-value=2.4e-12  Score=94.47  Aligned_cols=89  Identities=19%  Similarity=0.237  Sum_probs=78.0

Q ss_pred             hccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-C--cE
Q 036791           52 MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-G--RV  128 (157)
Q Consensus        52 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g--~~  128 (157)
                      .+...+++||||.|...-.|+|++.+|..||.|.+|.+++.. .|.++||+||.|.+..+|+.||..|||...+ |  ..
T Consensus        14 srg~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSS   92 (371)
T KOG0146|consen   14 SRGGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSS   92 (371)
T ss_pred             cCCccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCccc
Confidence            333467889999999999999999999999999999999984 5899999999999999999999999998753 3  67


Q ss_pred             EEEEeecCCCCCC
Q 036791          129 IFVDNVRPSRRYN  141 (157)
Q Consensus       129 l~v~~~~~~~~~~  141 (157)
                      |.|+++...++|.
T Consensus        93 LVVK~ADTdkER~  105 (371)
T KOG0146|consen   93 LVVKFADTDKERT  105 (371)
T ss_pred             eEEEeccchHHHH
Confidence            9999998766553

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

Probab=99.32  E-value=6.8e-12  Score=97.52  Aligned_cols=79  Identities=20%  Similarity=0.276  Sum_probs=73.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSFSTTKEMLADAFS-QFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      .+.+||.|||+++.|.+|+.+|. +-|+|..|.++.| .+||.+|||.|+|+++|.+++|++.||...+.|++|.|+...
T Consensus        44 ~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D-~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFD-ESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             cceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecc-cCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            35699999999999999999997 6799999999999 679999999999999999999999999999999999998765


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      -
T Consensus       123 d  123 (608)
T KOG4212|consen  123 D  123 (608)
T ss_pred             c
Confidence            3

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

Probab=99.31  E-value=3.5e-12  Score=94.47  Aligned_cols=71  Identities=25%  Similarity=0.406  Sum_probs=68.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      +|||||||..+++.+|+.+|++||.|.+|.|+++        ||||..++...++.||..|||..|.|..|.|+-++++
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK   74 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK   74 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEecccc
Confidence            6999999999999999999999999999999876        8999999999999999999999999999999999887

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

Probab=99.28  E-value=5.3e-11  Score=96.89  Aligned_cols=129  Identities=16%  Similarity=0.121  Sum_probs=86.2

Q ss_pred             HHHHHHHhccccccCcccccccCCceecee--cccc---cccCCCcc-----hhhccccccEEEEcCCCCCC--------
Q 036791            8 QTRKIQQFNSYFTEDSLLSFSSKPYQVVNY--FSLH---CIVRPSSD-----LIMQLVNVSFWRCISVSFST--------   69 (157)
Q Consensus         8 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~---~~~~~~~~-----~~~~~~~~~~l~V~nl~~~~--------   69 (157)
                      -+.|++.+|+..+.+..+.+.........-  ....   ........     ..........|+|.|+...-        
T Consensus       350 a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~  429 (509)
T TIGR01642       350 TDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLAKALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEY  429 (509)
T ss_pred             HHHHHHHcCCCEECCeEEEEEECccCCCCCCccccccccccccccccchhhhccccCCCceEEEeccCCchhHhcCcchH
Confidence            357888899999888877654311100000  0000   00000000     00111234678999986321        


Q ss_pred             --CHHHHHHHHhcCCCeeEEEEeecC---CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           70 --TKEMLADAFSQFGQVTEATIIMDI---GKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        70 --~~~~l~~~f~~~G~i~~~~~~~~~---~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                        ..++|+++|.+||.|..|.|+.+.   .++.++|++||+|.+.++|++|+..|||..|+|+.|.|.|...
T Consensus       430 ~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       430 EEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             HHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence              125789999999999999998652   3356789999999999999999999999999999999999764

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

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

Probab=99.27  E-value=1e-11  Score=101.17  Aligned_cols=81  Identities=25%  Similarity=0.416  Sum_probs=75.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|.|.|||+..+-.+++.+|..||.+..|+|+.-...+.++|||||+|-++.+|.+|+.+|..+-++||.|.++|+..
T Consensus       613 ~tKIlVRNipFeAt~rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLEwA~~  692 (725)
T KOG0110|consen  613 GTKILVRNIPFEATKREVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLEWAKS  692 (725)
T ss_pred             cceeeeeccchHHHHHHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhheehhcc
Confidence            56899999999999999999999999999999988755677899999999999999999999998889999999999976


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      .
T Consensus       693 d  693 (725)
T KOG0110|consen  693 D  693 (725)
T ss_pred             c
Confidence            4

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

Probab=99.26  E-value=2.6e-11  Score=85.82  Aligned_cols=82  Identities=24%  Similarity=0.271  Sum_probs=75.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQF-GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~-G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...-+||..+|.-+.+..+..+|.++ |.+...++.+++.||.++|||||+|.+.+.|.-|-+.||+..++++.|.+.+-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            34568999999999999999999988 78888899899999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      .|.
T Consensus       128 ppe  130 (214)
T KOG4208|consen  128 PPE  130 (214)
T ss_pred             Cch
Confidence            775

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

Probab=99.25  E-value=1.9e-10  Score=82.61  Aligned_cols=89  Identities=13%  Similarity=0.187  Sum_probs=71.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC---CcEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD---GRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~---g~~l~  130 (157)
                      ...+||||.+||.++...+|..+|..|-.-+.+.+-.. +.....+-+||++|.+..+|.+|+++|||..++   +..|+
T Consensus        32 ~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stLh  111 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTLH  111 (284)
T ss_pred             cccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCceeE
Confidence            44789999999999999999999999855555544332 222234589999999999999999999999985   78999


Q ss_pred             EEeecCCCCCCCC
Q 036791          131 VDNVRPSRRYNTD  143 (157)
Q Consensus       131 v~~~~~~~~~~~~  143 (157)
                      |+++++...+.+.
T Consensus       112 iElAKSNtK~kr~  124 (284)
T KOG1457|consen  112 IELAKSNTKRKRR  124 (284)
T ss_pred             eeehhcCcccccC
Confidence            9999987666554

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

Probab=99.24  E-value=4.3e-11  Score=90.52  Aligned_cols=80  Identities=21%  Similarity=0.256  Sum_probs=69.0

Q ss_pred             hhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-CccCCcEE
Q 036791           51 IMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG-KLLDGRVI  129 (157)
Q Consensus        51 ~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g-~~~~g~~l  129 (157)
                      +..+...++|||++|...+++.+|+.+|.+||+|..+.+...      +++|||+|.+.+.|+.|.+.+-. ..|+|.+|
T Consensus       222 pPeD~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl  295 (377)
T KOG0153|consen  222 PPEDTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGFRL  295 (377)
T ss_pred             CCcccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecceEE
Confidence            344456789999999999999999999999999999988765      46899999999999988765444 44799999


Q ss_pred             EEEeecC
Q 036791          130 FVDNVRP  136 (157)
Q Consensus       130 ~v~~~~~  136 (157)
                      .|.|.++
T Consensus       296 ~i~Wg~~  302 (377)
T KOG0153|consen  296 KIKWGRP  302 (377)
T ss_pred             EEEeCCC
Confidence            9999998

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

Probab=99.24  E-value=1.8e-11  Score=93.03  Aligned_cols=80  Identities=26%  Similarity=0.369  Sum_probs=76.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..-|||-.|.+-+++++|+-+|+.||.|..|.+++|+.||.+..||||+|.+.+++++|.-.|++..|+.++|+|.++.+
T Consensus       239 eNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQS  318 (479)
T KOG0415|consen  239 ENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQS  318 (479)
T ss_pred             cceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhhh
Confidence            34599999999999999999999999999999999999999999999999999999999999999999999999999754

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

Probab=99.18  E-value=1.1e-10  Score=88.90  Aligned_cols=84  Identities=25%  Similarity=0.391  Sum_probs=77.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||++||.++++.++++.|.+||.|..+.++.|..+.+.+||+||.|.+++.+++++.. .-+.|+|+.+.|..|.|
T Consensus        97 tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~-~f~~~~gk~vevkrA~p  175 (311)
T KOG4205|consen   97 TKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ-KFHDFNGKKVEVKRAIP  175 (311)
T ss_pred             eeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc-ceeeecCceeeEeeccc
Confidence            45899999999999999999999999999999999999999999999999999999999874 77889999999999998


Q ss_pred             CCCCC
Q 036791          137 SRRYN  141 (157)
Q Consensus       137 ~~~~~  141 (157)
                      +....
T Consensus       176 k~~~~  180 (311)
T KOG4205|consen  176 KEVMQ  180 (311)
T ss_pred             hhhcc
Confidence            76543

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

Probab=99.14  E-value=1.5e-10  Score=95.21  Aligned_cols=77  Identities=17%  Similarity=0.268  Sum_probs=71.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      +|||||+|+.++++.+|..+|+.||+|.+|.++..      +|||||.+....+|++|+..|....+.++.|+|.|+..+
T Consensus       422 rTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  422 RTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeccccchhhHHHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            68999999999999999999999999999988664      689999999999999999999999999999999999865


Q ss_pred             CCC
Q 036791          138 RRY  140 (157)
Q Consensus       138 ~~~  140 (157)
                      .-+
T Consensus       496 G~k  498 (894)
T KOG0132|consen  496 GPK  498 (894)
T ss_pred             Ccc
Confidence            433

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

Probab=99.12  E-value=1.6e-10  Score=90.00  Aligned_cols=75  Identities=35%  Similarity=0.402  Sum_probs=68.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|+|.|||.++||..|++-|..||.+..+.|+.   +|+.+|  .|.|.++++|+.|+..|+|..++|+.|.|+|+
T Consensus       534 rKa~qIiirNlP~dfTWqmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~V~y~  608 (608)
T KOG4212|consen  534 RKACQIIIRNLPFDFTWQMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIKVTYF  608 (608)
T ss_pred             ccccEEEEecCCccccHHHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceeeeeeC
Confidence            4567899999999999999999999999999998843   488887  99999999999999999999999999999874

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

Probab=99.12  E-value=8.3e-11  Score=89.62  Aligned_cols=86  Identities=30%  Similarity=0.418  Sum_probs=77.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...++||++|+|.++++.|++.|.+||++..+.+++|+.+++.+||+||+|.+.+...+++.. ....|+|+.|.+..+.
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k~av   83 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPKRAV   83 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccceecc
Confidence            457899999999999999999999999999999999999999999999999999998888875 4677999999999998


Q ss_pred             CCCCCCC
Q 036791          136 PSRRYNT  142 (157)
Q Consensus       136 ~~~~~~~  142 (157)
                      ++.....
T Consensus        84 ~r~~~~~   90 (311)
T KOG4205|consen   84 SREDQTK   90 (311)
T ss_pred             Ccccccc
Confidence            8765543

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

Probab=99.11  E-value=1.6e-10  Score=84.23  Aligned_cols=83  Identities=27%  Similarity=0.388  Sum_probs=76.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .++..||+|.|.-+++++.|-..|.+|-.-....+++++.||+++||+||.|.+..++..|++.|+|..++.++|+++.+
T Consensus       188 ~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  188 EDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             cccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccchhHhhhh
Confidence            45678999999999999999999999988888899999999999999999999999999999999999999999998766


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      .-+
T Consensus       268 ~wk  270 (290)
T KOG0226|consen  268 EWK  270 (290)
T ss_pred             hHH
Confidence            543

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

Probab=99.10  E-value=3.9e-10  Score=88.33  Aligned_cols=74  Identities=30%  Similarity=0.316  Sum_probs=69.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      .||||   +++++.+|.++|+.+|.+..+++.+|. |  +.|||||.|.++.+|++||..||...+.|++++|-|+....
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-t--slgy~yvnf~~~~da~~A~~~~n~~~~~~~~~rim~s~rd~   76 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-T--SLGYAYVNFQQPADAERALDTMNFDVLKGKPIRIMWSQRDP   76 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-C--ccceEEEecCCHHHHHHHHHHcCCcccCCcEEEeehhccCC
Confidence            48999   999999999999999999999999996 5  99999999999999999999999999999999999987644

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

Probab=99.09  E-value=4.5e-10  Score=90.12  Aligned_cols=80  Identities=28%  Similarity=0.411  Sum_probs=75.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||.+|...+...+|+.+|++||.|....++.+-.+--.++|+||++.+.++|.++|+.||...|.|+.|.|..++.
T Consensus       405 gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaKN  484 (940)
T KOG4661|consen  405 GRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAKN  484 (940)
T ss_pred             ccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeeccc
Confidence            46899999999999999999999999999999998877777899999999999999999999999999999999998864

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

Probab=99.08  E-value=6.6e-10  Score=87.72  Aligned_cols=80  Identities=21%  Similarity=0.287  Sum_probs=69.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      .+|||+|||.+++..+|+++|..||.|....|..-...++..+||||+|.+.++++.||.+ +-..|++++|.|+..++.
T Consensus       289 ~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek~~~  367 (419)
T KOG0116|consen  289 LGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEKRPG  367 (419)
T ss_pred             cceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEecccc
Confidence            4699999999999999999999999999987765433355559999999999999999997 577899999999998774


Q ss_pred             C
Q 036791          138 R  138 (157)
Q Consensus       138 ~  138 (157)
                      .
T Consensus       368 ~  368 (419)
T KOG0116|consen  368 F  368 (419)
T ss_pred             c
Confidence            3

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

Probab=99.08  E-value=8.5e-10  Score=81.23  Aligned_cols=80  Identities=21%  Similarity=0.390  Sum_probs=74.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|+|.|||..+.+++|+++|..||.+..+.+.++ .+|.+.|.|-|.|...++|.+|++.+++..++|++|++....+
T Consensus        83 ~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~-~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   83 STKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYD-RAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             cceeeeecCCcCcchHHHHHHHHHhccceEEeeccC-CCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            367999999999999999999999999999999998 5699999999999999999999999999999999999988654


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      .
T Consensus       162 ~  162 (243)
T KOG0533|consen  162 P  162 (243)
T ss_pred             c
Confidence            3

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

Probab=99.02  E-value=1.3e-09  Score=89.09  Aligned_cols=77  Identities=31%  Similarity=0.380  Sum_probs=69.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKN---RSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +|||.||+++++.++|..+|.+.|.|..+.|...+...   .+.|||||+|.+.++|++|++.|+|..|+|+.|.|+++.
T Consensus       517 ~lfvkNlnf~Tt~e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  517 KLFVKNLNFDTTLEDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             hhhhhcCCcccchhHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence            49999999999999999999999999999887654321   245999999999999999999999999999999999998

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

Probab=99.01  E-value=3.7e-09  Score=86.62  Aligned_cols=82  Identities=16%  Similarity=0.270  Sum_probs=73.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGK---NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ...+++||+||++.++++.|-..|..||.|..++|++.+.-   ...+-|+||.|-+..+|++|++.|+|..+++..+++
T Consensus       172 P~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~  251 (877)
T KOG0151|consen  172 PQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKL  251 (877)
T ss_pred             CcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeee
Confidence            45678999999999999999999999999999999987533   345678999999999999999999999999999999


Q ss_pred             EeecC
Q 036791          132 DNVRP  136 (157)
Q Consensus       132 ~~~~~  136 (157)
                      .|+++
T Consensus       252 gWgk~  256 (877)
T KOG0151|consen  252 GWGKA  256 (877)
T ss_pred             ccccc
Confidence            99954

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.99  E-value=1.5e-09  Score=79.81  Aligned_cols=84  Identities=24%  Similarity=0.279  Sum_probs=77.8

Q ss_pred             ccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           53 QLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        53 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ...+...+||+|+...++.++++..|+.||.+..+.++.++.++..+||+||+|.+.+.++.++. |+|..|.|+.+.|.
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPAIEVT  175 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCcccccccceee
Confidence            33566889999999999999999999999999999999999999999999999999999999999 99999999999998


Q ss_pred             eecCC
Q 036791          133 NVRPS  137 (157)
Q Consensus       133 ~~~~~  137 (157)
                      +.+-+
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87654

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

Probab=98.94  E-value=1.7e-09  Score=78.09  Aligned_cols=71  Identities=21%  Similarity=0.421  Sum_probs=65.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      .+|||+||+.+.+.+|+.+|..||.+..+.+.        .||+||+|.+..+|..|+..||+..|.|..+.|.+++..
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~   73 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGK   73 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeeccccc
Confidence            58999999999999999999999999988664        368899999999999999999999999998999999864

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.91  E-value=2.2e-08  Score=63.93  Aligned_cols=79  Identities=19%  Similarity=0.220  Sum_probs=70.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhc--CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC----CcEEEE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQ--FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD----GRVIFV  131 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~----g~~l~v  131 (157)
                      +||.|.|||-..+.++|.+++..  .|....+.++.|..++.+.|||||.|.+++.|.+-.+.++|..+.    .+.+.|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            57999999999999999998864  377788899999999999999999999999999999999999874    567888


Q ss_pred             EeecC
Q 036791          132 DNVRP  136 (157)
Q Consensus       132 ~~~~~  136 (157)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.90  E-value=1e-08  Score=77.79  Aligned_cols=81  Identities=15%  Similarity=0.191  Sum_probs=72.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVT--------EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      ...+.|||.|||.++|.+++.++|+++|-|.        .|.+-.+ ..|+.+|=|.+.|...++++-|+..|++..+.|
T Consensus       132 ~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd-~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRD-NQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             ccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEec-CCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            4456799999999999999999999999775        3677777 459999999999999999999999999999999


Q ss_pred             cEEEEEeecC
Q 036791          127 RVIFVDNVRP  136 (157)
Q Consensus       127 ~~l~v~~~~~  136 (157)
                      +.|+|..|+=
T Consensus       211 ~~~rVerAkf  220 (382)
T KOG1548|consen  211 KKLRVERAKF  220 (382)
T ss_pred             cEEEEehhhh
Confidence            9999998863

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

Probab=98.79  E-value=6e-09  Score=83.28  Aligned_cols=72  Identities=19%  Similarity=0.302  Sum_probs=65.1

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      ..+..+|+|-|||..+++++|.++|+.||+|..++.     +-..+|..||+|.+..+|++|+++|++..+.|++|.
T Consensus        72 ~~~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~-----t~~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   72 DMNQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRE-----TPNKRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             cCccceEEEEecCCcCCHHHHHHHHHhhcchhhhhc-----ccccCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            456689999999999999999999999999999654     344578999999999999999999999999999888

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

Probab=98.71  E-value=2.8e-08  Score=79.72  Aligned_cols=84  Identities=14%  Similarity=0.266  Sum_probs=78.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...++||++||..+++..+.++...||.+....++.+..+|-++||||.+|.+......|+..|||..+++..|.|..+.
T Consensus       288 ~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~  367 (500)
T KOG0120|consen  288 SPNKIFVGGLPLYLTEDQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAI  367 (500)
T ss_pred             ccchhhhccCcCccCHHHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhh
Confidence            34679999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      ....
T Consensus       368 ~g~~  371 (500)
T KOG0120|consen  368 VGAS  371 (500)
T ss_pred             ccch
Confidence            6543

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

Probab=98.64  E-value=1.2e-08  Score=73.13  Aligned_cols=78  Identities=21%  Similarity=0.102  Sum_probs=70.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||+|+...++++-|.++|-..|.|.++.|..++. ++.+ ||||.|.++-...-|++.+||..+.+..+.+.+...
T Consensus         9 drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r~G   86 (267)
T KOG4454|consen    9 DRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLRCG   86 (267)
T ss_pred             hhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhhcccccC
Confidence            46799999999999999999999999999999988744 6666 999999999999999999999999999888877543

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes

Probab=98.54  E-value=9.3e-07  Score=54.38  Aligned_cols=71  Identities=20%  Similarity=0.187  Sum_probs=47.7

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           58 SFWRCISVSFSTTKEM----LADAFSQFG-QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~----l~~~f~~~G-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      +.|||.|||.+.....    |++++..+| .+..+.          .+.|++.|.+.+.|.+|++.|+|..+.|.+|.|.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~----------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~   72 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS----------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVS   72 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE------------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEE
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe----------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEE
Confidence            3589999999988765    566666775 554441          2569999999999999999999999999999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      +.....
T Consensus        73 ~~~~~r   78 (90)
T PF11608_consen   73 FSPKNR   78 (90)
T ss_dssp             SS--S-
T ss_pred             EcCCcc
Confidence            986543

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=98.44  E-value=1.3e-06  Score=69.34  Aligned_cols=78  Identities=26%  Similarity=0.308  Sum_probs=66.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ...|-+.+|||++|+++|.++|+.++ |..+.+  .+.+|+..|-|||+|.+.+++++|++. +...+..+-|.|-.+.+
T Consensus        10 ~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~--~r~~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen   10 AFEVRLRGLPWSATEKEILDFFSNCG-IENLEI--PRRNGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYIEVFTAGG   85 (510)
T ss_pred             ceEEEecCCCccccHHHHHHHHhcCc-eeEEEE--eccCCCcCcceEEEeechHHHHHHHHh-hHHHhCCceEEEEccCC
Confidence            34577899999999999999999995 677444  456899999999999999999999994 77788889999988865


Q ss_pred             CC
Q 036791          137 SR  138 (157)
Q Consensus       137 ~~  138 (157)
                      .+
T Consensus        86 ~e   87 (510)
T KOG4211|consen   86 AE   87 (510)
T ss_pred             cc
Confidence            43

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.41  E-value=7.2e-07  Score=68.26  Aligned_cols=85  Identities=21%  Similarity=0.122  Sum_probs=76.5

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVT--------EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      .....+|||.+||..++++++..+|.++|.|.        .+.|-++++|++.+|-|-|.|.+...|++|+..+++..+.
T Consensus        63 ~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            45566899999999999999999999999775        3567788899999999999999999999999999999999


Q ss_pred             CcEEEEEeecCCC
Q 036791          126 GRVIFVDNVRPSR  138 (157)
Q Consensus       126 g~~l~v~~~~~~~  138 (157)
                      |..|+|..+..+.
T Consensus       143 gn~ikvs~a~~r~  155 (351)
T KOG1995|consen  143 GNTIKVSLAERRT  155 (351)
T ss_pred             CCCchhhhhhhcc
Confidence            9999999887654

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

Probab=98.33  E-value=2.5e-07  Score=74.07  Aligned_cols=80  Identities=26%  Similarity=0.366  Sum_probs=73.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...++|+.-|...++..+|.++|+..|.|..|.++.|+.++..+|.+||+|.+.+....|| +|.|+.++|.+|.|....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~ai-aLsGqrllg~pv~vq~sE  256 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAI-ALSGQRLLGVPVIVQLSE  256 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHh-hhcCCcccCceeEecccH
Confidence            4468889889999999999999999999999999999999999999999999999999999 589999999999998865


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      .
T Consensus       257 a  257 (549)
T KOG0147|consen  257 A  257 (549)
T ss_pred             H
Confidence            4

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

Probab=98.30  E-value=4.8e-06  Score=64.90  Aligned_cols=74  Identities=19%  Similarity=0.275  Sum_probs=65.4

Q ss_pred             cEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           58 SFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        58 ~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..|-|.||.. .+|.+.|..+|.-||+|.+|.|...+.     --|.|.|.+...|+-|++.|+|..+.|++|+|.+++-
T Consensus       298 ~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH  372 (492)
T KOG1190|consen  298 VVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKH  372 (492)
T ss_pred             eEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEeeccC
Confidence            4577777755 589999999999999999999988743     3599999999999999999999999999999999863

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.28  E-value=7e-07  Score=67.83  Aligned_cols=83  Identities=24%  Similarity=0.361  Sum_probs=75.8

Q ss_pred             cEEE-EcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           58 SFWR-CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        58 ~~l~-V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++| |++++..+++++|+..|..+|.|..+++..++.++..+|+++|.|.....+..++.. +...+.++++.+.+..+
T Consensus       185 ~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  185 DTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             ccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccCCC
Confidence            4566 999999999999999999999999999999999999999999999999999999887 78889999999999988


Q ss_pred             CCCCC
Q 036791          137 SRRYN  141 (157)
Q Consensus       137 ~~~~~  141 (157)
                      .....
T Consensus       264 ~~~~~  268 (285)
T KOG4210|consen  264 RPKSD  268 (285)
T ss_pred             Ccccc
Confidence            75543

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

Probab=98.25  E-value=1.5e-05  Score=57.65  Aligned_cols=76  Identities=18%  Similarity=0.248  Sum_probs=66.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-GRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~v~~  133 (157)
                      .+...+|+.|||..++.+.+..+|..|.....++++..+     .+.|||+|.+...+..|...+++..|- ...+.|.+
T Consensus       144 ppn~ilf~~niP~es~~e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~  218 (221)
T KOG4206|consen  144 PPNNILFLTNIPSESESEMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITF  218 (221)
T ss_pred             CCceEEEEecCCcchhHHHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceEEecc
Confidence            345679999999999999999999999988999887753     578999999999999999999998875 77888877


Q ss_pred             ec
Q 036791          134 VR  135 (157)
Q Consensus       134 ~~  135 (157)
                      ++
T Consensus       219 a~  220 (221)
T KOG4206|consen  219 AK  220 (221)
T ss_pred             cC
Confidence            64

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

Probab=98.24  E-value=1.2e-06  Score=63.24  Aligned_cols=64  Identities=17%  Similarity=0.174  Sum_probs=53.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL  124 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~  124 (157)
                      +.+|||.||..+++|++|+.+|+.|.....++|..    ...-..+|++|+..+.|..|+..|+|..|
T Consensus       210 cstlfianl~~~~~ed~l~~~~~~~~gf~~l~~~~----~~g~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTEDELKQLLSRYPGFHILKIRA----RGGMPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhHhhhccCCCCCHHHHHHHHHhCCCceEEEEec----CCCcceEeecHHHHHHHHHHHHHhhccee
Confidence            46899999999999999999999997666555532    12345799999999999999999998776

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=98.15  E-value=1.8e-06  Score=66.14  Aligned_cols=74  Identities=18%  Similarity=0.235  Sum_probs=64.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ..+|||||-|++++++|.+.....|  ++.++++..++.+|.++|||.|...+.....+.++.|....|.|..-.|
T Consensus        81 ~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V  156 (498)
T KOG4849|consen   81 YCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTV  156 (498)
T ss_pred             EEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCee
Confidence            4699999999999999988887766  7778888899999999999999999999999999999999888854333

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

Probab=98.13  E-value=7.3e-06  Score=65.17  Aligned_cols=78  Identities=26%  Similarity=0.297  Sum_probs=64.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTE-ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +...|-+.+||+.+++++|.++|+..--+.. +.++.+ ..++..|-|||.|++.+.|++|+.. |...|..+-|.|..+
T Consensus       102 ~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d-~rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEvF~S  179 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMD-QRGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEVFRS  179 (510)
T ss_pred             CCceEEecCCCccCcHHHHHHHhcCCcccccceeeecc-CCCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEeehh
Confidence            5567889999999999999999997643333 456666 4588999999999999999999985 777788888998776


Q ss_pred             c
Q 036791          135 R  135 (157)
Q Consensus       135 ~  135 (157)
                      .
T Consensus       180 s  180 (510)
T KOG4211|consen  180 S  180 (510)
T ss_pred             H
Confidence            4

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.05  E-value=1.4e-05  Score=61.05  Aligned_cols=78  Identities=24%  Similarity=0.400  Sum_probs=61.2

Q ss_pred             EEEEcCCCCCCCHHH------HHHHHhcCCCeeEEEEeecCCC-CCcce--EEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q 036791           59 FWRCISVSFSTTKEM------LADAFSQFGQVTEATIIMDIGK-NRSKG--YGYVTSSTEEEAQKALVDMNGKLLDGRVI  129 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~------l~~~f~~~G~i~~~~~~~~~~~-~~~~g--~afv~f~~~~~a~~ai~~l~g~~~~g~~l  129 (157)
                      -+||-+|++.+..++      -.++|.+||.|..+.+.+.... .-..+  ..||+|.+.++|.++|...+|..++|+-|
T Consensus       116 LvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~l  195 (480)
T COG5175         116 LVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVL  195 (480)
T ss_pred             eeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceE
Confidence            489999999887665      3688999999999877543211 11112  24999999999999999999999999999


Q ss_pred             EEEeecC
Q 036791          130 FVDNVRP  136 (157)
Q Consensus       130 ~v~~~~~  136 (157)
                      +..|...
T Consensus       196 katYGTT  202 (480)
T COG5175         196 KATYGTT  202 (480)
T ss_pred             eeecCch
Confidence            9988754

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

Probab=97.98  E-value=2e-05  Score=51.22  Aligned_cols=69  Identities=29%  Similarity=0.392  Sum_probs=42.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-----ccCCcEEEEEe
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK-----LLDGRVIFVDN  133 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~-----~~~g~~l~v~~  133 (157)
                      .|.|.+++..++.++|++.|+.||.|..|.+...-      .-|+|.|.+.+.|+.|+..+...     .+.+..+.++.
T Consensus         3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~------~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~v   76 (105)
T PF08777_consen    3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGD------TEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEV   76 (105)
T ss_dssp             EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-------SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE-
T ss_pred             EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCC------CEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEE
Confidence            47788899999999999999999999998876542      35899999999999998876544     35555555543

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

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

Probab=97.88  E-value=1.7e-05  Score=57.51  Aligned_cols=72  Identities=28%  Similarity=0.378  Sum_probs=61.6

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ...+.|.+++..+.+.+|...|..+|.+....+        ..+++||.|...+++.+|+..|++..+.++.|++.....
T Consensus        99 ~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~--------~~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~~~~  170 (216)
T KOG0106|consen   99 HFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA--------RRNFAFVEFSEQEDAKRALEKLDGKKLNGRRISVEKNSR  170 (216)
T ss_pred             cceeeeccchhhhhHHHHhhhhcccCCCchhhh--------hccccceeehhhhhhhhcchhccchhhcCceeeecccCc
Confidence            356888999999999999999999998844322        356899999999999999999999999999999955543

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

Probab=97.84  E-value=0.00015  Score=55.60  Aligned_cols=125  Identities=20%  Similarity=0.245  Sum_probs=82.7

Q ss_pred             HHHHhccccccCcccccccCCceeceecccccc--------------------cCCCcchhhccccccEEEEcCCC----
Q 036791           11 KIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCI--------------------VRPSSDLIMQLVNVSFWRCISVS----   66 (157)
Q Consensus        11 a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~l~V~nl~----   66 (157)
                      |+.-|++..+.+..+++.-..+..-.-...+.-                    -+|..+........++|.+.|+=    
T Consensus       199 A~~ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~  278 (382)
T KOG1548|consen  199 AIKILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPED  278 (382)
T ss_pred             HHHHhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHH
Confidence            555577777777777765433322111111110                    01222233344455778888762    


Q ss_pred             CCCC-------HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCC
Q 036791           67 FSTT-------KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRR  139 (157)
Q Consensus        67 ~~~~-------~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~  139 (157)
                      ...+       .++|++-..+||.+..|.+. +   ..+.|.+-|.|.+.++|..+|..|+|..+.|+.|.......+..
T Consensus       279 ~~~~~~l~~dlkedl~eec~K~G~v~~vvv~-d---~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~t~  354 (382)
T KOG1548|consen  279 FEKNPDLLNDLKEDLTEECEKFGQVRKVVVY-D---RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGKTK  354 (382)
T ss_pred             hccCHHHHHHHHHHHHHHHHHhCCcceEEEe-c---cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCcce
Confidence            1222       35677888999999998663 2   34568899999999999999999999999999999988765543

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

Probab=97.83  E-value=0.00015  Score=56.23  Aligned_cols=97  Identities=20%  Similarity=0.309  Sum_probs=70.8

Q ss_pred             eeceecccccccCCCcchhhccccccE--EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHH
Q 036791           33 QVVNYFSLHCIVRPSSDLIMQLVNVSF--WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEE  110 (157)
Q Consensus        33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~  110 (157)
                      ++.+++...+..++..+..   ...+-  +-|-|--..++.+.|..+.-..|.+.+|.|.+.  +   --.|.|+|.+.+
T Consensus        99 Al~NyStsq~i~R~g~es~---~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkk--n---gVQAmVEFdsv~  170 (494)
T KOG1456|consen   99 ALFNYSTSQCIERPGDESA---TPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKK--N---GVQAMVEFDSVE  170 (494)
T ss_pred             hhcccchhhhhccCCCCCC---CCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEec--c---ceeeEEeechhH
Confidence            4455555555666653322   22222  234465667888999999999999999977653  3   346999999999


Q ss_pred             HHHHHHHHhCCCccCC--cEEEEEeecCC
Q 036791          111 EAQKALVDMNGKLLDG--RVIFVDNVRPS  137 (157)
Q Consensus       111 ~a~~ai~~l~g~~~~g--~~l~v~~~~~~  137 (157)
                      .|++|..+|||..|+.  -+|+|+|++|.
T Consensus       171 ~AqrAk~alNGADIYsGCCTLKIeyAkP~  199 (494)
T KOG1456|consen  171 VAQRAKAALNGADIYSGCCTLKIEYAKPT  199 (494)
T ss_pred             HHHHHHhhcccccccccceeEEEEecCcc
Confidence            9999999999999864  56888888774

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.81  E-value=2.6e-05  Score=57.46  Aligned_cols=73  Identities=14%  Similarity=0.149  Sum_probs=61.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC--------CCcc----eEEEEEeCCHHHHHHHHHHhCCCc
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGK--------NRSK----GYGYVTSSTEEEAQKALVDMNGKL  123 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~--------~~~~----g~afv~f~~~~~a~~ai~~l~g~~  123 (157)
                      +..-||+++||+.+...-|+++|+.||.|-+|.+-....+        |.++    .-|+|+|.+...|......||+..
T Consensus        73 k~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~  152 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTP  152 (278)
T ss_pred             cceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCc
Confidence            5567999999999999999999999999999988654433        2222    346799999999999999999999


Q ss_pred             cCCcE
Q 036791          124 LDGRV  128 (157)
Q Consensus       124 ~~g~~  128 (157)
                      |+|++
T Consensus       153 Iggkk  157 (278)
T KOG3152|consen  153 IGGKK  157 (278)
T ss_pred             cCCCC
Confidence            98863

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.69  E-value=0.00011  Score=59.75  Aligned_cols=76  Identities=26%  Similarity=0.375  Sum_probs=62.6

Q ss_pred             cEEEEcCCCCCCCH------HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEE
Q 036791           58 SFWRCISVSFSTTK------EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-GRVIF  130 (157)
Q Consensus        58 ~~l~V~nl~~~~~~------~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~  130 (157)
                      .-|+|.|+|---..      .-|..+|+++|.+....++.+.. |..+||.|++|.+..+|+.|++.|||..|+ +++..
T Consensus        59 ~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~-ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHtf~  137 (698)
T KOG2314|consen   59 SVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEE-GGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHTFF  137 (698)
T ss_pred             eEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCcc-CCeeeEEEEEecChhhHHHHHHhcccceecccceEE
Confidence            45788888764332      35788999999999999998855 559999999999999999999999999975 67787


Q ss_pred             EEee
Q 036791          131 VDNV  134 (157)
Q Consensus       131 v~~~  134 (157)
                      |...
T Consensus       138 v~~f  141 (698)
T KOG2314|consen  138 VRLF  141 (698)
T ss_pred             eehh
Confidence            7654

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

Probab=97.66  E-value=0.00019  Score=58.10  Aligned_cols=66  Identities=18%  Similarity=0.304  Sum_probs=54.7

Q ss_pred             HHHHHHHhcCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           72 EMLADAFSQFGQVTEATIIMDIGK---NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        72 ~~l~~~f~~~G~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      ++++.-+++||.|..|.++.+-..   .-+.|--||+|.+.+++++|+.+|+|..+.|+.+...|..+.
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDED  492 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCHH
Confidence            356777888999999998876222   234577899999999999999999999999999999987653

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=97.61  E-value=0.00027  Score=58.79  Aligned_cols=75  Identities=21%  Similarity=0.355  Sum_probs=64.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCee-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVT-EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~-~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      +-|-|.|+|++++-+|+-++|..|-.+- +|.+-++ +.|+..|-|-|.|++.++|.+|...|++..|.++.+.+.+
T Consensus       868 ~V~~~~n~Pf~v~l~dI~~FF~dY~~~p~sI~~r~n-d~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  868 RVLSCNNFPFDVTLEDIVEFFNDYEPDPNSIRIRRN-DDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             eEEEecCCCccccHHHHHHHhcccccCCCceeEeec-CCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3577899999999999999999996443 3444443 6699999999999999999999999999999999998864

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

Probab=97.55  E-value=0.0018  Score=45.88  Aligned_cols=63  Identities=19%  Similarity=0.164  Sum_probs=56.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      ....+.|.+||++-+|.+|+.+..+-|+++...+.+|       |++.|+|...++.+-|+..|+...+.
T Consensus       114 Se~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cceeEEEecCCCCCchHHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhcccccc
Confidence            3456889999999999999999999999999988877       47999999999999999999888753

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

Probab=97.49  E-value=0.0004  Score=55.86  Aligned_cols=64  Identities=27%  Similarity=0.106  Sum_probs=58.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFS-QFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD  118 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~  118 (157)
                      ...+|||||+||.-++..+|-.+|. -||.|..+.|-.|++-+..+|-|-|+|.+....-+||.+
T Consensus       368 DprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsa  432 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISA  432 (520)
T ss_pred             CccceEEecCCCCcchHHHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhh
Confidence            4557999999999999999999998 799999999999987788999999999999999999975

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

Probab=97.47  E-value=0.00028  Score=55.31  Aligned_cols=74  Identities=15%  Similarity=0.091  Sum_probs=58.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      -.+.|+++-.-++-+.|+.+|++||.+.++.-.. +.+   .--|.|.|.+.+.|+.|..+|+|..|.+-.+.++..-
T Consensus       151 Lr~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~-Knn---~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~  224 (492)
T KOG1190|consen  151 LRTIIENMFYPVSLDVLHQVFSKFGFVLKIITFT-KNN---GFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDF  224 (492)
T ss_pred             EEEEeccceeeeEHHHHHHHHhhcceeEEEEEEe-ccc---chhhhhhccchhhHHHHHHhccCCcccCceeEEEeeh
Confidence            3577899999999999999999999998874322 122   2247899999999999999999999987665555543

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=97.43  E-value=0.00035  Score=59.50  Aligned_cols=80  Identities=23%  Similarity=0.297  Sum_probs=68.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~  132 (157)
                      ...+.+++++|..++....|...|..||.|..|.+      .+..-|++|.|++...++.|++.|-|..|+|  ++++|.
T Consensus       453 t~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy------~hgq~yayi~yes~~~aq~a~~~~rgap~G~P~~r~rvd  526 (975)
T KOG0112|consen  453 TPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDY------RHGQPYAYIQYESPPAAQAATHDMRGAPLGGPPRRLRVD  526 (975)
T ss_pred             ccceeeccCCCCCCChHHHHHHHhhccCcceeeec------ccCCcceeeecccCccchhhHHHHhcCcCCCCCcccccc
Confidence            34467999999999999999999999999998765      3345799999999999999999999999976  779999


Q ss_pred             eecCCCCC
Q 036791          133 NVRPSRRY  140 (157)
Q Consensus       133 ~~~~~~~~  140 (157)
                      ++.+....
T Consensus       527 la~~~~~~  534 (975)
T KOG0112|consen  527 LASPPGAT  534 (975)
T ss_pred             cccCCCCC
Confidence            98765443

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

Probab=97.43  E-value=0.00051  Score=38.92  Aligned_cols=51  Identities=20%  Similarity=0.391  Sum_probs=40.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHH
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL  116 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai  116 (157)
                      .|-|.+.+....+.. ...|..||+|....+..      ...+.++.|.+..+|++|+
T Consensus         3 wI~V~Gf~~~~~~~v-l~~F~~fGeI~~~~~~~------~~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    3 WISVSGFPPDLAEEV-LEHFASFGEIVDIYVPE------STNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             EEEEEeECchHHHHH-HHHHHhcCCEEEEEcCC------CCcEEEEEECCHHHHHhhC
Confidence            466888887776554 45888999999987752      2457999999999999985

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.41  E-value=0.00013  Score=61.61  Aligned_cols=79  Identities=22%  Similarity=0.148  Sum_probs=66.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ...++|.|.|+..|.+.++.++.++|.+..+.++.. ..|+.+|.++|.|.+..++.++....+...+.-..+.|..+.|
T Consensus       736 K~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~-r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  736 KISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTV-RAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhheeCCCCCCchHHHHhhccccCCccccchhhh-hccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCC
Confidence            456999999999999999999999999999988777 4599999999999999999999887777666655566666443

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.38  E-value=0.0012  Score=45.06  Aligned_cols=59  Identities=25%  Similarity=0.355  Sum_probs=45.4

Q ss_pred             HHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCCC
Q 036791           73 MLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRY  140 (157)
Q Consensus        73 ~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~~  140 (157)
                      +|-+.|..||.+.-++++-+        .-+|+|.+-+.|.+|+. ++|..++|+.|+|+...|.+-.
T Consensus        52 ~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals-~dg~~v~g~~l~i~LKtpdW~~  110 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALS-LDGIQVNGRTLKIRLKTPDWLK  110 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHH-GCCSEETTEEEEEEE-------
T ss_pred             HHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHc-cCCcEECCEEEEEEeCCccHHH
Confidence            67788889999888887765        27999999999999998 7999999999999999886543

; PDB: 1UFW_A 2DNR_A.

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=97.17  E-value=0.0029  Score=39.08  Aligned_cols=54  Identities=17%  Similarity=0.257  Sum_probs=41.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG  121 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g  121 (157)
                      -.||. +|..|...||.++|+.||.| .|.++.|.       -|||...+.+.+..++..+..
T Consensus        11 VFhlt-FPkeWK~~DI~qlFspfG~I-~VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen   11 VFHLT-FPKEWKTSDIYQLFSPFGQI-YVSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             EEEEE---TT--HHHHHHHCCCCCCE-EEEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             EEEEe-CchHhhhhhHHHHhccCCcE-EEEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            35555 99999999999999999986 67777762       499999999999999998863

; GO: 0003723 RNA binding, 0004535 poly(A)-specific ribonuclease activity, 0046872 metal ion binding, 0006402 mRNA catabolic process, 0005634 nucleus, 0005737 cytoplasm; PDB: 3CTR_A 2ROK_A 3D45_B 1WHV_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=97.11  E-value=0.00035  Score=55.09  Aligned_cols=77  Identities=21%  Similarity=0.292  Sum_probs=61.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-cCCcEEEEEeecC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQ-VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL-LDGRVIFVDNVRP  136 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~-~~g~~l~v~~~~~  136 (157)
                      ++|++||.+.++..+|+.+|...-- ...-.++       ..||+||.+.+..-|.+|++.++|.. +.|.++.+...-+
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~-------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~   75 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV-------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVP   75 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee-------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhh
Confidence            5899999999999999999975411 1111111       24899999999999999999999986 8999999999887


Q ss_pred             CCCCCC
Q 036791          137 SRRYNT  142 (157)
Q Consensus       137 ~~~~~~  142 (157)
                      +..+.+
T Consensus        76 kkqrsr   81 (584)
T KOG2193|consen   76 KKQRSR   81 (584)
T ss_pred             HHHHhh
Confidence            765443

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

Probab=97.06  E-value=0.0055  Score=47.85  Aligned_cols=75  Identities=15%  Similarity=0.168  Sum_probs=65.0

Q ss_pred             ccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSFS-TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..-+.|-+|... ++.+.|..+|-.||.|.+|.+++.+     .|-|.|++-+..+.++|+..||+..+-|.+|.|..++
T Consensus       287 g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~Sk  361 (494)
T KOG1456|consen  287 GCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSK  361 (494)
T ss_pred             CcEEEEEeccccccchhhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEEeecc
Confidence            356778888765 5568899999999999999998874     3679999999999999999999999999999998875


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      -
T Consensus       362 Q  362 (494)
T KOG1456|consen  362 Q  362 (494)
T ss_pred             c
Confidence            4

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []

Probab=97.05  E-value=0.0043  Score=39.87  Aligned_cols=76  Identities=20%  Similarity=0.274  Sum_probs=49.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-------CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc-EE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDI-------GKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR-VI  129 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-------~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~-~l  129 (157)
                      .-|.|-+.|+... ..+-+.|++||.|.+..-....       .......+-.|.|.++.+|.+||.. ||..+.|. .+
T Consensus         7 ~wVtVFGfp~~~~-~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~g~~mv   84 (100)
T PF05172_consen    7 TWVTVFGFPPSAS-NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFSGSLMV   84 (100)
T ss_dssp             CEEEEE---GGGH-HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEETTCEEE
T ss_pred             eEEEEEccCHHHH-HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEcCcEEE
Confidence            4477888998854 6677789999999776411000       0012356889999999999999995 99999885 44


Q ss_pred             EEEeec
Q 036791          130 FVDNVR  135 (157)
Q Consensus       130 ~v~~~~  135 (157)
                      -|.+.+
T Consensus        85 GV~~~~   90 (100)
T PF05172_consen   85 GVKPCD   90 (100)
T ss_dssp             EEEE-H
T ss_pred             EEEEcH
Confidence            566664

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=97.03  E-value=0.0037  Score=50.46  Aligned_cols=61  Identities=20%  Similarity=0.264  Sum_probs=47.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC-CC--Ccce---EEEEEeCCHHHHHHHHHHh
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIG-KN--RSKG---YGYVTSSTEEEAQKALVDM  119 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-~~--~~~g---~afv~f~~~~~a~~ai~~l  119 (157)
                      .+||||+||++++|+.|...|..||.+ .+.++.... .+  -.+|   |.|+.|+++..+..-+.+.
T Consensus       260 ~KVFvGGlp~dise~~i~~~F~~FGs~-~VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  260 RKVFVGGLPWDITEAQINASFGQFGSV-KVDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cceeecCCCccccHHHHHhhcccccce-EeecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            579999999999999999999999974 555653111 11  2456   9999999998888776653

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.98  E-value=0.0014  Score=51.77  Aligned_cols=68  Identities=19%  Similarity=0.170  Sum_probs=56.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeec---CCCCC----------cceEEEEEeCCHHHHHHHHHHhCC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMD---IGKNR----------SKGYGYVTSSTEEEAQKALVDMNG  121 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~---~~~~~----------~~g~afv~f~~~~~a~~ai~~l~g  121 (157)
                      .+.++|.+-|||.+-.-+.|.++|..+|.|..|+|...   +.+.+          .+-+|+|+|...+.|.+|.+.|+.
T Consensus       229 l~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~~~~  308 (484)
T KOG1855|consen  229 LPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKARELLNP  308 (484)
T ss_pred             cccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHhhch
Confidence            46688999999999988999999999999999999776   33322          256899999999999999998754


Q ss_pred             C
Q 036791          122 K  122 (157)
Q Consensus       122 ~  122 (157)
                      .
T Consensus       309 e  309 (484)
T KOG1855|consen  309 E  309 (484)
T ss_pred             h
Confidence            3

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

Probab=96.91  E-value=0.0018  Score=50.61  Aligned_cols=77  Identities=21%  Similarity=0.336  Sum_probs=64.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC-CeeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFG-QVTE--ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~--~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ..|.+++||+..+.++|-.+|..|. .|..  +.++.+ ..|+..|-|||.|.+.+.|.+|...-+......+.|.|--+
T Consensus       281 dcvRLRGLPy~AtvEdIL~FlgdFa~~i~f~gVHmv~N-~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp~  359 (508)
T KOG1365|consen  281 DCVRLRGLPYEATVEDILDFLGDFATDIRFQGVHMVLN-GQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFPC  359 (508)
T ss_pred             CeeEecCCChhhhHHHHHHHHHHHhhhcccceeEEEEc-CCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEeec
Confidence            3588899999999999999999885 3443  677776 55889999999999999999999887777777898988776


Q ss_pred             c
Q 036791          135 R  135 (157)
Q Consensus       135 ~  135 (157)
                      .
T Consensus       360 S  360 (508)
T KOG1365|consen  360 S  360 (508)
T ss_pred             c
Confidence            4

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=96.86  E-value=0.0097  Score=34.74  Aligned_cols=53  Identities=23%  Similarity=0.175  Sum_probs=43.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcC---CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 036791           59 FWRCISVSFSTTKEMLADAFSQF---GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM  119 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~---G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l  119 (157)
                      .|+|.++.. ++.++++.+|..|   ....++.++-|..       |-|.|.+.+.|.+|+.+|
T Consensus         7 avhirGvd~-lsT~dI~~y~~~y~~~~~~~~IEWIdDtS-------cNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    7 AVHIRGVDE-LSTDDIKAYFSEYFDEEGPFRIEWIDDTS-------CNVVFKDEETAARALVAL   62 (62)
T ss_pred             eEEEEcCCC-CCHHHHHHHHHHhcccCCCceEEEecCCc-------EEEEECCHHHHHHHHHcC
Confidence            588999854 6668899999988   2457899998832       899999999999999764

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=96.84  E-value=0.0052  Score=46.53  Aligned_cols=65  Identities=23%  Similarity=0.297  Sum_probs=53.0

Q ss_pred             HHHHHHHHhcCCCeeEEEEeecCCCCCc-ceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           71 KEMLADAFSQFGQVTEATIIMDIGKNRS-KGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        71 ~~~l~~~f~~~G~i~~~~~~~~~~~~~~-~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ++++++.+.+||.+..|.|...+..-.. .---||+|...+.|-+|+-.|||..++|+.++..+..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            3567888999999999988776544332 2447999999999999999999999999998887653

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.70  E-value=0.0025  Score=47.21  Aligned_cols=62  Identities=19%  Similarity=0.328  Sum_probs=55.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN  120 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~  120 (157)
                      ..|||.||+..++.+.+.+-|+.||+|....+..| ..++..+-++|.|.+.-.+.+|+....
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~   93 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCR   93 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhc
Confidence            56999999999999999999999999988766666 668888999999999999999998764

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.69  E-value=0.00097  Score=49.30  Aligned_cols=62  Identities=24%  Similarity=0.423  Sum_probs=49.1

Q ss_pred             HHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           73 MLADAFS-QFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        73 ~l~~~f~-~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ++...|. +||+|..+.+-.+. .-...|-.+|.|...++|++|+..||+.-+.|++|...+..
T Consensus        84 d~f~E~~~kygEiee~~Vc~Nl-~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   84 DVFTELEDKYGEIEELNVCDNL-GDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHhhhhhhhhhhccc-chhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            3444444 89999988554432 23456889999999999999999999999999999998864

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

Probab=96.62  E-value=0.0026  Score=49.73  Aligned_cols=75  Identities=21%  Similarity=0.227  Sum_probs=57.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhc----CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQ----FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~----~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .-.|..++||+++++.++.++|..    -|....+.++.. -+|+..|=|||.|..+++|+.|+.. |...++.|.|.+.
T Consensus       161 qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIElF  238 (508)
T KOG1365|consen  161 QVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIELF  238 (508)
T ss_pred             ceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHHHH
Confidence            345777899999999999999963    134455655554 4589999999999999999999986 6666666666553


Q ss_pred             e
Q 036791          133 N  133 (157)
Q Consensus       133 ~  133 (157)
                      .
T Consensus       239 R  239 (508)
T KOG1365|consen  239 R  239 (508)
T ss_pred             H
Confidence            3

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.61  E-value=0.00011  Score=62.04  Aligned_cols=76  Identities=18%  Similarity=0.204  Sum_probs=62.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      .++||.||+..+.+.+|...|..+|.+..+++.-...+++.+|+|++.|...+.+.+|+....+..+....+.|+-
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~gK~~v~i~g  743 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFGKISVAISG  743 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhhhhhhheeC
Confidence            4789999999999999999999999888877766667789999999999999999999987665555544444433

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.61  E-value=0.0022  Score=52.63  Aligned_cols=74  Identities=22%  Similarity=0.200  Sum_probs=60.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhc-CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc---CCcEEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQ-FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL---DGRVIFV  131 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~---~g~~l~v  131 (157)
                      ....|||.||-.-.|..+|+.++.+ .|.|... |+ |    +-+..|||.|.+.++|.+...+|||..+   +++.|.+
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-D----kIKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~a  516 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-D----KIKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIA  516 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-HH-H----HhhcceeEecccHHHHHHHHHHHhccccCCCCCceeEe
Confidence            3456999999999999999999985 5555554 32 2    3456799999999999999999999985   5688988


Q ss_pred             Eeec
Q 036791          132 DNVR  135 (157)
Q Consensus       132 ~~~~  135 (157)
                      .|..
T Consensus       517 df~~  520 (718)
T KOG2416|consen  517 DFVR  520 (718)
T ss_pred             eecc
Confidence            8874

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.36  E-value=0.0011  Score=56.49  Aligned_cols=79  Identities=16%  Similarity=0.171  Sum_probs=67.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+||+|||+..+++.+|+..|..+|.+..|.|-..+- +...-|+||.|.+...+..|+-.+.+..|....+++.+..+
T Consensus       372 trTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~  450 (975)
T KOG0112|consen  372 TRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP  450 (975)
T ss_pred             hhhhhhcCcccchhhhhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCccccccccc
Confidence            46899999999999999999999999999998855422 34456899999999999999999999998777777777754

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.01  E-value=0.0043  Score=51.94  Aligned_cols=76  Identities=12%  Similarity=0.020  Sum_probs=62.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTE-ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .-|||..||..+++.++..+|.....|++ |.|.+. -+++.++.|||.|..++++..|...-+...++.+.|+|+-.
T Consensus       435 ~~lyv~~lP~~t~~~~~v~~f~~~~~Ved~I~lt~~-P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~si  511 (944)
T KOG4307|consen  435 GALYVFQLPVMTPIVPPVNKFMGAAAVEDFIELTRL-PTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDSI  511 (944)
T ss_pred             ceEEeccCCccccccchhhhhhhhhhhhheeEeccC-CcccccchhhheeccccccchhhhcccccccCceEEEeech
Confidence            46999999999999999999998777776 555554 45788899999999988888888766667778888998754

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=95.92  E-value=0.0032  Score=48.29  Aligned_cols=80  Identities=19%  Similarity=0.321  Sum_probs=60.8

Q ss_pred             cEEEEcCCCCCCCHHHH---HHHHhcCCCeeEEEEeecCC--CCC-cceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           58 SFWRCISVSFSTTKEML---ADAFSQFGQVTEATIIMDIG--KNR-SKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l---~~~f~~~G~i~~~~~~~~~~--~~~-~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ..+||.+|+..+.++.+   .+.|.+||.|..+....++.  .+. ...-++|+|...++|..+|...+|..+.|+.++.
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka  157 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKA  157 (327)
T ss_pred             hhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHH
Confidence            34788889888766543   46788899999988877652  111 1223799999999999999999999999998887


Q ss_pred             EeecCC
Q 036791          132 DNVRPS  137 (157)
Q Consensus       132 ~~~~~~  137 (157)
                      .+...+
T Consensus       158 ~~gttk  163 (327)
T KOG2068|consen  158 SLGTTK  163 (327)
T ss_pred             hhCCCc
Confidence            776654

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=95.91  E-value=0.013  Score=46.06  Aligned_cols=77  Identities=17%  Similarity=0.175  Sum_probs=58.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGK---NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      -|-|.||.+..+.+++..+|...|.|..+.|......   ....-.|||.|.+...+..|...-|-..|+--.|.+-|..
T Consensus         9 vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~~~   88 (479)
T KOG4676|consen    9 VIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPYGD   88 (479)
T ss_pred             eeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEecCC
Confidence            5889999999999999999999999999988653322   2345689999999999999988554444444444444443

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=95.44  E-value=0.11  Score=35.41  Aligned_cols=72  Identities=15%  Similarity=0.099  Sum_probs=51.9

Q ss_pred             cccEEEEcCCCCCCCH-HH---HHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           56 NVSFWRCISVSFSTTK-EM---LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~-~~---l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      +-.+|-|.=|..++.. +|   +...++.||.|..+...       ++.-|.|.|.+...|-+|+.+++. ..-|..+.+
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~c-------GrqsavVvF~d~~SAC~Av~Af~s-~~pgtm~qC  156 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLC-------GRQSAVVVFKDITSACKAVSAFQS-RAPGTMFQC  156 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeec-------CCceEEEEehhhHHHHHHHHhhcC-CCCCceEEe
Confidence            3467878766655543 34   45556789999998653       234599999999999999999865 556777777


Q ss_pred             Eeec
Q 036791          132 DNVR  135 (157)
Q Consensus       132 ~~~~  135 (157)
                      .|-.
T Consensus       157 sWqq  160 (166)
T PF15023_consen  157 SWQQ  160 (166)
T ss_pred             eccc
Confidence            7643

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells

Probab=95.31  E-value=0.054  Score=38.73  Aligned_cols=61  Identities=20%  Similarity=0.212  Sum_probs=45.0

Q ss_pred             HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CCccCCcEEEEEeecCC
Q 036791           71 KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN--GKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        71 ~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--g~~~~g~~l~v~~~~~~  137 (157)
                      ...|+++|..++.+.....++..      +-..|.|.+.+.|.+|...|+  +..++|..+++-++.+.
T Consensus         9 ~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    9 LAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             HHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            47799999999988877666542      348899999999999999999  89999999999988543

Calcipressin 1 is a phosphoprotein that increases its capacity to inhibit calcineurin when phosphorylated at the FLISPP motif, and this phosphorylation also controls the half-life of calcipressin 1 by accelerating its degradation []. Calcineurin is a calcium-responsive enzyme that dephosphorylates the nuclear factor of activated T cells (NFAT). In so doing it promotes its nuclear translocation and uniquely links calcium signalling to transcriptional regulation []. Calcipressins are a family of proteins derived from three genes. Calcipressin 1 is also known as modulatory calcineurin-interacting protein 1 (MCIP1), Adapt78 and Down syndrome critical region 1 (DSCR1). Calcipressin 2 is variously known as MCIP2, ZAKI-4 and DSCR1-like 1. Calcipressin 3 is also called MCIP3 and DSCR1-like 2 []. DSCR1 (Adapt78) is associated with successful adaptation to oxidative stress and calcium stress as well as with diseases like Alzheimer's and Down syndrome. The DSCR1 (Adapt78) isoform 1 protein, calcipressin 1, inhibits calcineurin and protects against acute calcium-mediated stress damage, including transient oxidative stress []. Calcipressin 1 is encoded by DSCR1, a gene on human chromosome 21. Calcipressin 1 isoform 1 has an N-terminal coding region, which generates a new polypeptide of 252 amino acids. Endogenous calcipressin 1 exists as a complex together with the calcineurin A and B heterodimer []. ; GO: 0019722 calcium-mediated signaling; PDB: 1WEY_A.

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.09  E-value=0.55  Score=30.71  Aligned_cols=75  Identities=20%  Similarity=0.196  Sum_probs=51.8

Q ss_pred             cEEEE-cCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC---CcEEEEE
Q 036791           58 SFWRC-ISVSFSTTKEMLADAFSQF-GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD---GRVIFVD  132 (157)
Q Consensus        58 ~~l~V-~nl~~~~~~~~l~~~f~~~-G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~---g~~l~v~  132 (157)
                      ..+.| ...|..++.++|..+.+.+ ..|..++++++.  ..++-.+.+.|.+.++|..-.+.+||..++   ...++|-
T Consensus        13 ~~~~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~Chvv   90 (110)
T PF07576_consen   13 STLCCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPETCHVV   90 (110)
T ss_pred             ceEEEEEeCcccccHHHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCceeEEE
Confidence            33444 4445555556676555554 467788888872  336777889999999999999999999864   3445554


Q ss_pred             ee
Q 036791          133 NV  134 (157)
Q Consensus       133 ~~  134 (157)
                      +.
T Consensus        91 fV   92 (110)
T PF07576_consen   91 FV   92 (110)
T ss_pred             EE
Confidence            43

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

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

Probab=94.81  E-value=0.07  Score=43.68  Aligned_cols=78  Identities=17%  Similarity=0.199  Sum_probs=56.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHh-cCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc---C-CcEEEEEe
Q 036791           59 FWRCISVSFSTTKEMLADAFS-QFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL---D-GRVIFVDN  133 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~-~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~---~-g~~l~v~~  133 (157)
                      ++.|.|++-..|...|...-. ..|.-..+.++.|-.+..+.|||||.|.+.+++....+++||+..   + .+.+.+.|
T Consensus       390 t~~iknipNK~T~~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS~Kia~itY  469 (549)
T KOG4660|consen  390 TLMIKNIPNKYTSKMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNSEKIASITY  469 (549)
T ss_pred             hhHhhccCchhhHHhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcceeeeeeeh
Confidence            344555555544444433322 256667788888888888999999999999999999999999974   3 35677777


Q ss_pred             ecC
Q 036791          134 VRP  136 (157)
Q Consensus       134 ~~~  136 (157)
                      ++-
T Consensus       470 ArI  472 (549)
T KOG4660|consen  470 ARI  472 (549)
T ss_pred             hhh
Confidence            764

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=94.81  E-value=0.019  Score=46.17  Aligned_cols=72  Identities=25%  Similarity=0.266  Sum_probs=56.6

Q ss_pred             EEEcCCCCCCCH-HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           60 WRCISVSFSTTK-EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        60 l~V~nl~~~~~~-~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      |-+...++.... ++|...|.+||.|..|.+-..      --.|.|+|.+..+|-.|-. .++..|+|+.|+|.|-.+..
T Consensus       375 l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~------~~~a~vTF~t~aeag~a~~-s~~avlnnr~iKl~whnps~  447 (526)
T KOG2135|consen  375 LALEKSPFGLNTIADLNPHFAQFGEIENIQVDYS------SLHAVVTFKTRAEAGEAYA-SHGAVLNNRFIKLFWHNPSP  447 (526)
T ss_pred             hhhhccCCCCchHhhhhhhhhhcCccccccccCc------hhhheeeeeccccccchhc-cccceecCceeEEEEecCCc
Confidence            444445555544 889999999999999987554      2358999999999966655 48999999999999988744

>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=94.54  E-value=0.063  Score=38.10  Aligned_cols=79  Identities=9%  Similarity=-0.045  Sum_probs=49.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhc-CCCe---eEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCCccCC----
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQ-FGQV---TEATIIMDIGK--NRSKGYGYVTSSTEEEAQKALVDMNGKLLDG----  126 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~-~G~i---~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g----  126 (157)
                      ..+|-|++||++++++++.+.+.. +++.   ..+.-..+...  .....-|+|.|.+.+++..-...++|..+-+    
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg~   86 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKGN   86 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS-
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCCC
Confidence            357899999999999998886665 5544   33331222111  1234679999999999999999999987632    


Q ss_pred             -cEEEEEeec
Q 036791          127 -RVIFVDNVR  135 (157)
Q Consensus       127 -~~l~v~~~~  135 (157)
                       ....|.+|.
T Consensus        87 ~~~~~VE~Ap   96 (176)
T PF03467_consen   87 EYPAVVEFAP   96 (176)
T ss_dssp             EEEEEEEE-S
T ss_pred             CcceeEEEcc
Confidence             355666664

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.

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []

Probab=94.10  E-value=0.56  Score=28.20  Aligned_cols=60  Identities=22%  Similarity=0.336  Sum_probs=35.2

Q ss_pred             CCCCCHHHHHHHHhcCC-----CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           66 SFSTTKEMLADAFSQFG-----QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        66 ~~~~~~~~l~~~f~~~G-----~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      -..++..+|-.++...+     +|-.+.+...        |+||+-.. +.++.++..|++..+.|++++|+.|
T Consensus        10 ~dg~~~~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   10 KDGLTPRDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             GGT--HHHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             ccCCCHHHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            44577888888887664     4445665443        68888864 4788999999999999999999864

; PDB: 2G0C_A 3MOJ_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=93.81  E-value=0.052  Score=45.32  Aligned_cols=79  Identities=11%  Similarity=0.083  Sum_probs=63.9

Q ss_pred             CCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           46 PSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        46 ~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      |.........+..++||+|+...+..+-++.+...+|.|..+....         |||..|..+.....|+..+....++
T Consensus        29 p~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~   99 (668)
T KOG2253|consen   29 PIQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNID   99 (668)
T ss_pred             CCcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCC
Confidence            3334444445667899999999999999999999999886654332         7999999999999999999988898


Q ss_pred             CcEEEEEe
Q 036791          126 GRVIFVDN  133 (157)
Q Consensus       126 g~~l~v~~  133 (157)
                      |..+.+..
T Consensus       100 ~~kl~~~~  107 (668)
T KOG2253|consen  100 DQKLIENV  107 (668)
T ss_pred             cchhhccc
Confidence            88776655

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.25  E-value=0.38  Score=36.80  Aligned_cols=66  Identities=24%  Similarity=0.350  Sum_probs=48.0

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc-EEEEEe
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR-VIFVDN  133 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~-~l~v~~  133 (157)
                      |-|-++|+.-. ..+-.+|++||.|.+...      +.+..+-+|.|.+..+|++||.. +|..|+|. .|-|..
T Consensus       200 VTVfGFppg~~-s~vL~~F~~cG~Vvkhv~------~~ngNwMhirYssr~~A~KALsk-ng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  200 VTVFGFPPGQV-SIVLNLFSRCGEVVKHVT------PSNGNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGVKP  266 (350)
T ss_pred             EEEeccCccch-hHHHHHHHhhCeeeeeec------CCCCceEEEEecchhHHHHhhhh-cCeeeccceEEeeee
Confidence            44556766654 456678999999876532      33446889999999999999985 89999874 344544

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes

Probab=92.76  E-value=0.93  Score=26.79  Aligned_cols=55  Identities=15%  Similarity=0.181  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           68 STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        68 ~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      .++-.+++..+.+|+ ..++.  .+ .+|     -||.|.+..+|+++....+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~-~~~I~--~d-~tG-----fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYR-WDRIR--DD-RTG-----FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCC-cceEE--ec-CCE-----EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            456689999999995 44544  33 222     489999999999999999999888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=91.92  E-value=0.087  Score=40.29  Aligned_cols=80  Identities=20%  Similarity=-0.007  Sum_probs=63.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...++|++++.+.+.+.....++..+|................+|++.+.|...+.+..++.......+.+..+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            35679999999999999888888899987777666655678899999999999999999998654445666555554443

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=91.81  E-value=0.42  Score=39.52  Aligned_cols=66  Identities=17%  Similarity=0.203  Sum_probs=48.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhc--CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC--ccCCcEEE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQ--FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK--LLDGRVIF  130 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~--~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~--~~~g~~l~  130 (157)
                      +.+.++-||..+..++++.+|..  +-.+..|.+-.+-       -=||+|++..||+.|.+.|...  .|.|++|.
T Consensus       176 cIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKpIm  245 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKPIM  245 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcchh
Confidence            56778999999999999999975  6677777665431       1599999999999998766422  24444443

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=91.35  E-value=0.21  Score=43.18  Aligned_cols=77  Identities=25%  Similarity=0.219  Sum_probs=63.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc--CCcEEEEEeecC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL--DGRVIFVDNVRP  136 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~--~g~~l~v~~~~~  136 (157)
                      +.++.|.+-..+...|..+|++||.+.....+++.      ..+.|.|.+.+.|-.|+.+|+|.++  -|-+.+|.+++.
T Consensus       300 ~~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~------N~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  300 KQSLENNAVNLTSSSLATLCSDYGSVASAWTLRDL------NMALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhhhhcccccchHHHHHHHHHhhcchhhheecccc------cchhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            34455667778888999999999999988776663      3699999999999999999999985  578899999987


Q ss_pred             CCCCC
Q 036791          137 SRRYN  141 (157)
Q Consensus       137 ~~~~~  141 (157)
                      -+-+.
T Consensus       374 ~~~~e  378 (1007)
T KOG4574|consen  374 LPMYE  378 (1007)
T ss_pred             ccccc
Confidence            55443

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

Probab=91.14  E-value=0.097  Score=38.27  Aligned_cols=74  Identities=26%  Similarity=0.312  Sum_probs=60.7

Q ss_pred             cEEEEcC----CCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           58 SFWRCIS----VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        58 ~~l~V~n----l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .+++.|+    |...++++.+...|+.-|.+..+++..+.+ |+++.++|+++.-....-.++..+++..+--+++.+.
T Consensus        81 ~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~~~~~g  158 (267)
T KOG4454|consen   81 RTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELFQKKVTIG  158 (267)
T ss_pred             cccccCCCcchhhhhcchhhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhhhcccCcCCCCcccc
Confidence            4677888    888999999999999999999999988844 8899999999998888888888877766544444443

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

Probab=86.84  E-value=2  Score=31.19  Aligned_cols=105  Identities=18%  Similarity=0.166  Sum_probs=61.1

Q ss_pred             HHHHHHHhccccccCcccccccCCc--eeceeccc--cc--ccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcC
Q 036791            8 QTRKIQQFNSYFTEDSLLSFSSKPY--QVVNYFSL--HC--IVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQF   81 (157)
Q Consensus         8 ~~~a~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~--~~--~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~   81 (157)
                      -..|++.+++..+.++.+.+.....  ........  ..  .................+++++++..+....+...|..+
T Consensus       170 ~~~a~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (306)
T COG0724         170 AEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR  249 (306)
T ss_pred             HHHHHHHcCCCeECCceeEeeccccccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhcccc
Confidence            4678888999999999887665221  00000000  00  001111112222344679999999999999999999999


Q ss_pred             CCeeEEEEeecCCCCCcceEEEEEeCCHHHH
Q 036791           82 GQVTEATIIMDIGKNRSKGYGYVTSSTEEEA  112 (157)
Q Consensus        82 G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a  112 (157)
                      |.+....+.............++.+.....+
T Consensus       250 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  280 (306)
T COG0724         250 GDIVRASLPPSKDGKIPKSRSFVGNEASKDA  280 (306)
T ss_pred             ccceeeeccCCCCCcccccccccchhHHHhh
Confidence            9997776655533333333444443333333

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=86.48  E-value=5.4  Score=32.42  Aligned_cols=68  Identities=16%  Similarity=0.197  Sum_probs=56.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQF-GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~-G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      ...|+|-.+|-.++-.||-.+...+ -.|..+++++|.  --++=...+.|.+..+|..-.+.+||..+..
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~--~pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDG--MPNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecC--CCceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            6679999999999999998888765 578899999862  2345567899999999999999999998753

>KOG4410 consensus 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]

Probab=86.47  E-value=3.1  Score=31.85  Aligned_cols=46  Identities=7%  Similarity=-0.018  Sum_probs=35.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCe-eEEEEeecCCCCCcceEEEEEeCCH
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQV-TEATIIMDIGKNRSKGYGYVTSSTE  109 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~~~~~~~~~~~~~~g~afv~f~~~  109 (157)
                      +.||++||+.++.-.+|+..+.+.+.. .++.|      .-+.|-||+.|-+.
T Consensus       331 ~di~~~nl~rd~rv~dlk~~lr~~~~~pm~isw------kg~~~k~flh~~~~  377 (396)
T KOG4410|consen  331 TDIKLTNLSRDIRVKDLKSELRKRECTPMSISW------KGHFGKCFLHFGNR  377 (396)
T ss_pred             cceeeccCccccchHHHHHHHHhcCCCceeEee------ecCCcceeEecCCc
Confidence            569999999999999999999988633 34444      23456699999654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	157
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		2e-10
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		4e-09
2d9p_A	103	Solution Structure Of Rna Binding Domain 4 In Polya		1e-08
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		2e-08
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		3e-08
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		3e-08
2k8g_A	95	Solution Structure Of Rrm2 Domain Of Pabp1 Length =		4e-08
4f25_A	115	Crystal Structure Of The Second Rrm Domain Of Human		4e-08
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		6e-08
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		2e-07
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		2e-07
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		3e-07
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		3e-07
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		3e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		3e-07
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		4e-07
1p1t_A	104	Nmr Structure Of The N-Terminal Rrm Domain Of Cleav		5e-07
2fy1_A	116	A Dual Mode Of Rna Recognition By The Rbmy Protein		2e-06
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		2e-06
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		2e-06
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		2e-06
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-06
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		4e-06
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		4e-06
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		4e-06
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		4e-06
2cpf_A	98	Solution Structure Of The Penultimate Rna Recogniti		5e-06
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		6e-06
2dgu_A	103	Solution Structure Of The Rna Binding Domain In Het		1e-05
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		1e-05
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		1e-05
2cqd_A	116	Solution Structure Of The Rna Recognition Motif In		1e-05
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		1e-05
3bs9_A	87	X-Ray Structure Of Human Tia-1 Rrm2 Length = 87		1e-05
1x4g_A	109	Solution Structure Of Rrm Domain In Nucleolysin Tia		2e-05
2cqc_A	95	Solution Structure Of The Rna Recognition Motif In		2e-05
2dgv_A	92	Solution Structure Of The Rna Binding Domain In Het		3e-05
2dh9_A	89	Solution Structure Of The C-Terminal Rna Binding Do		4e-05
3md1_A	83	Crystal Structure Of The Second Rrm Domain Of Yeast		5e-05
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		6e-05
1whw_A	99	Solution Structure Of The N-Terminal Rna Binding Do		6e-05
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		1e-04
2kn4_A	158	The Structure Of The Rrm Domain Of Sc35 Length = 15		2e-04
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		2e-04
2e5h_A	94	Solution Structure Of Rna Binding Domain In Zinc Fi		2e-04
2err_A	109	Nmr Structure Of The Rna Binding Domain Of Human Fo		2e-04
2cq3_A	103	Solution Structure Of Rna Binding Domain In Rna Bin		2e-04
2lea_A	135	Solution Structure Of Human Srsf2 (Sc35) Rrm Length		2e-04
2xb2_D	90	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		3e-04
3cw1_K	216	Crystal Structure Of Human Spliceosomal U1 Snrnp Le		3e-04
2hyi_B	91	Structure Of The Human Exon Junction Complex With A		3e-04
2j0s_D	89	The Crystal Structure Of The Exon Junction Complex		3e-04
1p27_B	106	Crystal Structure Of The Human Y14MAGOH COMPLEX Len		4e-04
4a8x_A	88	Structure Of The Core Asap Complex Length = 88		4e-04
2j0q_D	109	The Crystal Structure Of The Exon Junction Complex		4e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		4e-04
3ex7_B	126	The Crystal Structure Of Ejc In Its Transition Stat		4e-04
3sde_A	261	Crystal Structure Of A Paraspeckle-Protein Heterodi		5e-04
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		5e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		7e-04
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		8e-04

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 47/74 (63%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF T ++ L   FS++GQ++E  ++ D    RS+G+G+VT    ++A+ A++ MNGK 
Sbjct: 19  GLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKS 78
Query: 124 LDGRVIFVDNVRPS 137
           +DGR I VD    S
Sbjct: 79  VDGRQIRVDQAGKS 92

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 57.0 bits (136), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 30/71 (42%), Positives = 44/71 (61%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+ F+ T++ML   F  FG++    ++MD    RSKGYG++T S  E A+KAL  +NG  
Sbjct: 33  SLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFE 92
Query: 124 LDGRVIFVDNV 134
           L GR + V +V
Sbjct: 93  LAGRPMKVGHV 103

>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In Polyadenylation Binding Protein 3 Length = 103

Iteration: 1
 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 42/60 (70%), Gaps = 2/60 (3%)
Query: 72  EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           E L  AFS FG +T A ++M+ G  RSKG+G+V  S+ EEA KA+ +MNG+++  + ++V
Sbjct: 30  ERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYV 87

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   + L D FS FG +    ++ D  +N SKGYG+V   T+E A++A+  MNG LL+ R
Sbjct: 109 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 166
Query: 128 VIFV 131
            +FV
Sbjct: 167 KVFV 170

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 54.3 bits (129), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   + L D FS FG +    ++ D  +N SKGYG+V   T+E A++A+  MNG LL+ R
Sbjct: 114 SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 171
Query: 128 VIFV 131
            +FV
Sbjct: 172 KVFV 175

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 40/60 (66%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T E +  AF+ FG++++A ++ D+   +SKGYG+V+   + +A+ A+V M G+ L GR I
Sbjct: 28  TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87

>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1 Length = 95

Iteration: 1
 Score = 53.9 bits (128), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   + L D FS FG +    ++ D  +N SKGYG+V   T+E A++A+  MNG LL+ R
Sbjct: 22  SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 79
Query: 128 VIFV 131
            +FV
Sbjct: 80  KVFV 83

>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1 At Ph 6.0 Length = 115

Iteration: 1
 Score = 53.5 bits (127), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           S   + L D FS FG +    ++ D  +N SKGYG+V   T+E A++A+  MNG LL+ R
Sbjct: 16  SIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLNDR 73
Query: 128 VIFV 131
            +FV
Sbjct: 74  KVFV 77

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 53.1 bits (126), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 28/71 (39%), Positives = 43/71 (60%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+ F+ T++ML   F  FG++    ++ D    RSKGYG++T S  E A++AL  +NG  
Sbjct: 12  SLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFE 71
Query: 124 LDGRVIFVDNV 134
           L GR + V +V
Sbjct: 72  LAGRPMRVGHV 82

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     
Sbjct: 20  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 78
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +DGRV     V P R      +++R+ +Q P
Sbjct: 79  VDGRV-----VEPKR------AVSREDSQRP 98

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     
Sbjct: 18  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 76
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +DGRV     V P R      +++R+ +Q P
Sbjct: 77  VDGRV-----VEPKR------AVSREDSQRP 96

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 51.2 bits (121), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/93 (35%), Positives = 50/93 (53%), Gaps = 16/93 (17%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK- 122
            +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A   MN + 
Sbjct: 13  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAA---MNARP 69
Query: 123 -LLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
             +DGRV     V P R      +++R+ +Q P
Sbjct: 70  HKVDGRV-----VEPKR------AVSREDSQRP 91

>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic Granule-Associated Rna Binding Protein 1 Length = 115

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 22/60 (36%), Positives = 39/60 (65%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T E +  AF+ FG++++A ++ D+   +SKGYG+V+   + +A+ A+  M G+ L GR I
Sbjct: 28  TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87

>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 = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     
Sbjct: 19  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 77
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +DGRV     V P R      +++R+ +Q P
Sbjct: 78  VDGRV-----VEPKR------AVSREDSQRP 97

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     
Sbjct: 20  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 78
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +DGRV     V P R      +++R+ +Q P
Sbjct: 79  VDGRV-----VEPKR------AVSREDSQRP 98

>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 = 50.4 bits (119), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/91 (34%), Positives = 49/91 (53%), Gaps = 12/91 (13%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     
Sbjct: 21  GLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHK 79
Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +DGRV     V P R      +++R+ +Q P
Sbjct: 80  VDGRV-----VEPKR------AVSREDSQRP 99

>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage Stimulation Factor 64 Kda Subunit Length = 104

Iteration: 1
 Score = 50.1 bits (118), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 38/71 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ +  T+E L D FS+ G V    ++ D    + KGYG+     +E A  A+ ++NG+ 
Sbjct: 15  NIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGRE 74
Query: 124 LDGRVIFVDNV 134
             GR + VDN 
Sbjct: 75  FSGRALRVDNA 85

>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein Length = 116

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 7/93 (7%)
Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
           T ++ML   F + G ++E  +I D   ++S+G+ ++T     +A+ A  DMNGK L G+ 
Sbjct: 19  TNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKA 77
Query: 129 IFVDNV-RPS-----RRYNTDASLARQPAQSPE 155
           I V+   +PS     RR    +S  R P+ S E
Sbjct: 78  IKVEQAKKPSFQSGGRRRPPASSRNRSPSGSLE 110

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 41/77 (53%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++ L   FS  G+V  A +I D     S GYG+V   T ++A++A+  +NG  L  + I
Sbjct: 15  TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 130 FVDNVRPSRRYNTDASL 146
            V   RPS     DA+L
Sbjct: 75  KVSYARPSSEVIKDANL 91

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 41/77 (53%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++ L   FS  G+V  A +I D     S GYG+V   T ++A++A+  +NG  L  + I
Sbjct: 15  TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 130 FVDNVRPSRRYNTDASL 146
            V   RPS     DA+L
Sbjct: 75  KVSYARPSSEVIKDANL 91

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           C+ V   S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A   
Sbjct: 14  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 119 MNGKLLDGRVIFVD 132
            NG  LDGR I VD
Sbjct: 74  ANGMELDGRRIRVD 87

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 47.8 bits (112), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           C+ V   S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A   
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 119 MNGKLLDGRVIFVD 132
            NG  LDGR I VD
Sbjct: 77  ANGMELDGRRIRVD 90

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +S+ TTK+ L D FS+FG+V + T+ +D    RS+G+G+V     E   K + D     
Sbjct: 6   GLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQKEHK 64
Query: 124 LDGRVI 129
           L+G+VI
Sbjct: 65  LNGKVI 70

>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15 A Resolution Length = 87

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +S+ T+K+ L D F++FG+V + TI  D    RS+G+G++        +K L D     
Sbjct: 18  GLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVL-DQKEHR 76
Query: 124 LDGRVI 129
           LDGRVI
Sbjct: 77  LDGRVI 82

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           C+ V   S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A   
Sbjct: 48  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 107
Query: 119 MNGKLLDGRVIFVD 132
            NG  LDGR I VD
Sbjct: 108 ANGMELDGRRIRVD 121

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 47.4 bits (111), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 4/77 (5%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DM 119
            +S+ TT+E L + F QFG+V E  ++ D    RS+G+G+VT   +    K L     ++
Sbjct: 32  GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 91
Query: 120 NGKLLDGRVIFVDNVRP 136
           + K +D +V F    +P
Sbjct: 92  DSKTIDPKVAFPRRAQP 108

>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition Motif Of Hypothetical Rna-Binding Protein Rbm19 Length = 98

Iteration: 1
 Score = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 47/95 (49%), Gaps = 17/95 (17%)
Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR-----SKGYGYVTSSTEEEAQKALVDM 119
           ++FSTT+E L   FS+ G +   TI     KN+     S G+G+V     E+AQKAL  +
Sbjct: 13  LNFSTTEETLKGVFSKVGAIKSCTISKK--KNKAGVLLSMGFGFVEYKKPEQAQKALKQL 70
Query: 120 NGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
            G  +DG  +    VR S R       A +PA  P
Sbjct: 71  QGHTVDGHKL---EVRISER-------ATKPASGP 95

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 40/66 (60%), Gaps = 1/66 (1%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +SF TT+E L + + Q+G++T+  ++ D    RS+G+G+VT S+  E   A+       
Sbjct: 34  GLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHS 92
Query: 124 LDGRVI 129
           +DGRV+
Sbjct: 93  IDGRVV 98

>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein Q Length = 103

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 50/103 (48%), Gaps = 10/103 (9%)
Query: 52  MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEE 111
           M  V V F R  +++ + T+E+L  AFSQFG++     + D        Y ++     + 
Sbjct: 8   MAKVKVLFVR--NLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHFDERDG 57
Query: 112 AQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           A KA+ +MNGK L+G  I +   +P  +   +    RQ A  P
Sbjct: 58  AVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAASGP 100

>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition Motif (Rrm1) Of The Au-Rich Element (Are) Binding Protein Hur At 2.0 Angstrom Resolution Length = 84

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++ L   FS  G+V  A +I D     S GYG+V   T ++A++A+  +NG  L  + I
Sbjct: 17  TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 76
Query: 130 FVDNVRPS 137
            V   RPS
Sbjct: 77  KVSYARPS 84

>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From Homo Sapiens At 1.90 A Resolution Length = 99

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 37/68 (54%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++ L   FS  G+V  A +I D     S GYG+V   T ++A++A+  +NG  L  + I
Sbjct: 32  TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 130 FVDNVRPS 137
            V   RPS
Sbjct: 92  KVSYARPS 99

>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna- Binding Region Containing Protein 1 Length = 116

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            + + TT   L   F  FG + EA +I D    +S+GYG+VT +    A++A  D N  +
Sbjct: 24  GLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPN-PI 82
Query: 124 LDGR 127
           +DGR
Sbjct: 83  IDGR 86

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV----DM 119
            +S+ TT+E L + F QFG+V E  ++ D    RS+G+G+VT   +    K L     ++
Sbjct: 7   GLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHEL 66
Query: 120 NGKLLDGRVIF 130
           + K +D +V F
Sbjct: 67  DSKTIDPKVAF 77

>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2 Length = 87

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 33/49 (67%)
Query: 81  FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           FG++++A ++ D+   +SKGYG+V+   + +A+ A+  M G+ L GR I
Sbjct: 30  FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78

>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar Length = 109

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 62  CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           C  ++   T +++   FS FGQ+ E  +  +      KGY +V  ST E A  A+V +NG
Sbjct: 30  CGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNG 83
Query: 122 KLLDGRVI 129
             ++G V+
Sbjct: 84  TTIEGHVV 91

>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In ArginineSERINE-Rich Splicing Factor 10 Length = 95

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 62  CISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           C+ V   S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A   
Sbjct: 17  CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 76
Query: 119 MNGKLLDGRVIFV 131
            NG  LDGR I V
Sbjct: 77  ANGMELDGRRIRV 89

>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 92

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ F  T +ML D F++ G V  A I M+ GK  SKG G V   + E A++A   MNG  
Sbjct: 15  NLPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMK 72
Query: 124 LDGRVIFV 131
           L GR I V
Sbjct: 73  LSGREIDV 80

>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In Heterogeneous Nuclear Ribonucleoprotein M Length = 89

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 2/68 (2%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ F  T +ML D F++ G V  A I M+ GK  SKG G V   + E A++A   MNG  
Sbjct: 12  NLPFDFTWKMLKDKFNECGHVLYADIKMENGK--SKGCGVVKFESPEVAERACRMMNGMK 69
Query: 124 LDGRVIFV 131
           L GR I V
Sbjct: 70  LSGREIDV 77

>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast Poly(U)-Binding Protein (Pub1) Length = 83

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 72  EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           E L +AF  F       ++ D+    S+GYG+V+ +++++AQ A+  M G+ L+GR +
Sbjct: 16  ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPL 73

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 37/63 (58%)
Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           ++ +   E L +AF  F       ++ D+    S+GYG+V+ +++++AQ A+  M G+ L
Sbjct: 95  LNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDL 154
Query: 125 DGR 127
           +GR
Sbjct: 155 NGR 157

>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain From Hypothetical Protein Bab23448 Length = 99

Iteration: 1
 Score = 43.1 bits (100), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 40/67 (59%)
Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+++++E L   FS +G ++E    +D    + KG+ +VT    E A KA  +++G++ 
Sbjct: 16  LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF 75
Query: 125 DGRVIFV 131
            GR++ V
Sbjct: 76  QGRMLHV 82

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKA----LVDM 119
            +S +TT E +   F QFG+V +A ++ D   NR +G+G+VT  +E+  +K       ++
Sbjct: 6   GLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEI 65
Query: 120 NGKLLDGR 127
           N K+++ +
Sbjct: 66  NNKMVECK 73

>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35 Length = 158

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 46/87 (52%)
Query: 52  MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEE 111
           M +  ++  +  ++++ T+ + L   F ++G+V +  I  D     S+G+ +V    + +
Sbjct: 65  MDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRD 124
Query: 112 AQKALVDMNGKLLDGRVIFVDNVRPSR 138
           A+ A+  M+G +LDGR + V   R  R
Sbjct: 125 AEDAMDAMDGAVLDGRELRVQMARYGR 151

>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2 Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori Length = 90

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           +S T E + + FSQFG+V    +I D    + KG+G+V    EE   +A+  ++     G
Sbjct: 11  YSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFV-EMQEESVSEAIAKLDNTDFMG 69
Query: 127 RVIFVDNVRPSR 138
           R I V    P +
Sbjct: 70  RTIRVTEANPKK 81

>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger Cchc-Type And Rna Binding Motif 1 Length = 94

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 36/66 (54%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ FS T   L   FS++G+V + TI+ D    +SKG  ++    ++ AQ     +N K 
Sbjct: 23  NLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQ 82
Query: 124 LDGRVI 129
           L GRVI
Sbjct: 83  LFGRVI 88

>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In Complex With Ugcaugu Length = 109

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN 133
           L   F QFG++ +  II +  +  SKG+G+VT     +A +A   ++G +++GR I V+N
Sbjct: 46  LRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 103

>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 9 Length = 103

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/60 (35%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 74  LADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN 133
           L   F QFG++ +  II +  +  SKG+G+VT     +A +A   ++G +++GR I V+N
Sbjct: 32  LRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN 89

>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm Length = 135

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 48/94 (51%), Gaps = 4/94 (4%)
Query: 45  RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
           RP  D+      ++  +  ++++ T+ + L   F ++G+V +  I  D     S+G+ +V
Sbjct: 39  RPPPDV----EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFV 94
Query: 105 TSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR 138
               + +A+ A+  M+G +LDGR + V   R  R
Sbjct: 95  RFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR 128

>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd Machinery Length = 90

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ 
Sbjct: 14  GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
Query: 124 LDGRVIFVD 132
           L G+ I VD
Sbjct: 74  LMGQPISVD 82

>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp Length = 216

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V++ TT+  L   F  +G +    ++      + +GY ++    E +   A    +GK +
Sbjct: 110 VNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKI 169
Query: 125 DGRVIFVD 132
           DGR + VD
Sbjct: 170 DGRRVLVD 177

>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A Trapped Dead-Box Helicase Bound To Rna Length = 91

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ 
Sbjct: 16  GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 75
Query: 124 LDGRVIFVD 132
           L G+ I VD
Sbjct: 76  LMGQPISVD 84

>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2 A Resolution Length = 89

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ 
Sbjct: 14  GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
Query: 124 LDGRVIFVD 132
           L G+ I VD
Sbjct: 74  LMGQPISVD 82

>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX Length = 106

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ 
Sbjct: 30  GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 89
Query: 124 LDGRVIFVD 132
           L G+ I VD
Sbjct: 90  LMGQPISVD 98

>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex Length = 88

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 68  STTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
           + TK+ + + FS +G++    + ++ +  + SKGY YV     +EA+KAL  M+G  +DG
Sbjct: 15  NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
Query: 127 RVI 129
           + I
Sbjct: 75  QEI 77

>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 109

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ 
Sbjct: 14  GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 73
Query: 124 LDGRVIFVD 132
           L G+ I VD
Sbjct: 74  LMGQPISVD 82

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T+E     F   G++    ++ D    +S GYG+V     ++A+KA+  +NG  L  + I
Sbjct: 15  TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 130 FVDNVRPSRRYNTDASL 146
            V   RPS     DA+L
Sbjct: 75  KVSYARPSSASIRDANL 91

>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State Length = 126

Iteration: 1
 Score = 40.4 bits (93), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/69 (33%), Positives = 37/69 (53%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ 
Sbjct: 29  GVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQD 88
Query: 124 LDGRVIFVD 132
           L G+ I VD
Sbjct: 89  LMGQPISVD 97

>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer, Pspc1NONO Length = 261

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 72  EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           E+L  AFSQFG V +A +++D  + R+ G G+V  + +  A+KAL     +  DG  +  
Sbjct: 111 ELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALE----RCGDGAFLLT 165
Query: 132 DNVRP 136
              RP
Sbjct: 166 TTPRP 170

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 28/41 (68%)
Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
            + +STT+E L   FSQ+G+V +  I+ D   N+S+G+G+V
Sbjct: 23  GLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFV 63

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 39.7 bits (91), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 72  EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV 131
           ++L  AF  FG +T+  I +D    + +G+ +V     E+A  A+ +MN   L GR I V
Sbjct: 27  KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV 86
Query: 132 DNVRPSR 138
           +  +P R
Sbjct: 87  NLAKPMR 93

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 39.7 bits (91), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 36/77 (46%)
Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
           T++     F   G +    ++ D    +S GYG+V  S   +A KA+  +NG  L  + I
Sbjct: 17  TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 130 FVDNVRPSRRYNTDASL 146
            V   RPS     DA+L
Sbjct: 77  KVSYARPSSASIRDANL 93

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	157
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	9e-27
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	1e-26
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	1e-26
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	2e-26
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	2e-26
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	6e-26
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	9e-26
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-26
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-25
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	2e-25
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	2e-25
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	2e-25
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	3e-25
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-25
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	8e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	8e-25
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	4e-23
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-24
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	3e-24
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-24
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	5e-24
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	6e-24
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	7e-24
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	2e-23
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-23
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-23
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-23
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-23
1x4e_A	85	RNA binding motif, single-stranded interacting pro	4e-23
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	4e-23
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	4e-23
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	5e-23
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	7e-23
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-23
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	1e-22
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	1e-22
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	2e-22
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	2e-22
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	2e-22
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-22
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-22
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-22
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	3e-22
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	6e-22
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-22
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	9e-22
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	9e-22
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	9e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	9e-22
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-17
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	9e-22
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	1e-21
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	2e-21
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	2e-21
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	2e-21
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	3e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	3e-21
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	2e-18
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	4e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	4e-21
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-19
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	6e-21
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-20
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-18
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	1e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-20
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-17
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-14
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-20
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-20
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	4e-17
1x5o_A	114	RNA binding motif, single-stranded interacting pro	5e-20
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	7e-20
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	7e-20
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	1e-16
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	8e-20
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-19
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	1e-19
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-19
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-19
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	2e-19
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	3e-19
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	3e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-19
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	4e-16
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-14
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	3e-19
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-19
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	4e-19
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-17
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	4e-19
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	5e-19
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-19
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	8e-19
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	8e-19
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	9e-19
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	1e-18
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	5e-18
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	2e-18
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	3e-18
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	5e-17
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	1e-17
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-17
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	3e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	3e-17
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	8e-16
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	3e-17
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	5e-17
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	7e-17
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	7e-17
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-16
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	1e-16
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-16
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	3e-16
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	4e-16
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	3e-16
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-16
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	3e-16
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	4e-16
1x5p_A	97	Negative elongation factor E; structure genomics,	5e-16
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-16
2div_A	99	TRNA selenocysteine associated protein; structural	1e-15
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	1e-15
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	3e-15
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	3e-15
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	6e-15
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	6e-15
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	8e-15
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-15
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	8e-15
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	9e-15
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	1e-14
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	2e-14
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-14
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	4e-14
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-14
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	2e-13
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	2e-13
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	2e-13
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-13
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	4e-07
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	8e-13
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	1e-12
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	3e-12
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-12
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	3e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-12
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	2e-08
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	4e-12
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	8e-12
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	8e-12
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-11
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	8e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	2e-11
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-11
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	5e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	9e-11
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-10
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	8e-09
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-10
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	2e-10
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	2e-10
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	3e-10
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-10
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	3e-10
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-10
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	5e-10
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	7e-10
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	9e-10
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	5e-09
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-09
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	9e-09
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-08
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	5e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	1e-07
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	1e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	3e-07
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	7e-07
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	8e-07
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	1e-06
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	1e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	3e-06
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	5e-06
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	3e-05
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	1e-04
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	2e-04
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	4e-04

>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 = 95.8 bits (239), Expect = 9e-27
 Identities = 29/74 (39%), Positives = 46/74 (62%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF T ++ L   FS++GQ++E  ++ D    RS+G+G+VT    ++A+ A++ MNGK +D
Sbjct: 21  SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD 80

Query: 126 GRVIFVDNVRPSRR 139
           GR I VD    S  
Sbjct: 81  GRQIRVDQAGKSSD 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 = 95.9 bits (239), Expect = 1e-26
 Identities = 26/88 (29%), Positives = 44/88 (50%), Gaps = 3/88 (3%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +  T ++ML   F + G ++E  +I D   ++S+G+ ++T     +A+ A  DMNGK L 
Sbjct: 16  NRETNEKMLKAVFGKHGPISEVLLIKD-RTSKSRGFAFITFENPADAKNAAKDMNGKSLH 74

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQS 153
           G+ I V+  +            R PA S
Sbjct: 75  GKAIKVEQAKK--PSFQSGGRRRPPASS 100

>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 = 95.4 bits (238), Expect = 1e-26
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMD---IGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           +FSTT+E L   FS+ G +   TI       G   S G+G+V     E+AQKAL  + G 
Sbjct: 14  NFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH 73

Query: 123 LLDGRVIFVDNVRPSRR 139
            +DG  + V     + +
Sbjct: 74  TVDGHKLEVRISERATK 90

>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 = 95.5 bits (238), Expect = 2e-26
 Identities = 28/90 (31%), Positives = 49/90 (54%), Gaps = 2/90 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S   T E +  AF+ FG++++A ++ D+   +SKGYG+V+   + +A+ A+  M G+ L 
Sbjct: 24  SPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG 83

Query: 126 GRVIFVD--NVRPSRRYNTDASLARQPAQS 153
           GR I  +    +P    +T  S  +Q   S
Sbjct: 84  GRQIRTNWATRKPPAPKSTYESNTKQSGPS 113

>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 = 94.5 bits (236), Expect = 2e-26
 Identities = 19/71 (26%), Positives = 39/71 (54%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           + +   E L +AF  F       ++ D+    S+GYG+V+ +++++AQ A+  M G+ L+
Sbjct: 10  NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 69

Query: 126 GRVIFVDNVRP 136
           GR + ++    
Sbjct: 70  GRPLRINWAAK 80

>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 = 93.4 bits (233), Expect = 6e-26
 Identities = 27/71 (38%), Positives = 41/71 (57%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F+ T++ML   F  FG++    ++ D    RSKGYG++T S  E A++AL  +NG  L 
Sbjct: 14  HFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELA 73

Query: 126 GRVIFVDNVRP 136
           GR + V +V  
Sbjct: 74  GRPMRVGHVTE 84

>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 = 92.6 bits (231), Expect = 9e-26
 Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 1/75 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + + TK+ + + FS +G++    + ++ +  + SKGY YV     +EA+KAL  M+G  +
Sbjct: 13  TRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQI 72

Query: 125 DGRVIFVDNVRPSRR 139
           DG+ I    V     
Sbjct: 73  DGQEITATAVLAPWP 87

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 93.1 bits (232), Expect = 9e-26
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F      L   F QFG++ +  II +  +  SKG+G+VT     +A +A   ++G +++
Sbjct: 24  PFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVE 81

Query: 126 GRVIFVDNVRPSRR 139
           GR I V+N      
Sbjct: 82  GRKIEVNNATARVM 95

>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 = 93.6 bits (233), Expect = 1e-25
 Identities = 25/73 (34%), Positives = 40/73 (54%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A    NG  LD
Sbjct: 55  SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 114

Query: 126 GRVIFVDNVRPSR 138
           GR I VD     R
Sbjct: 115 GRRIRVDFSITKR 127

>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 = 92.8 bits (231), Expect = 2e-25
 Identities = 30/73 (41%), Positives = 44/73 (60%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+ F+ T++ML   F  FG++    ++MD    RSKGYG++T S  E A+KAL  +NG  
Sbjct: 33  SLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFE 92

Query: 124 LDGRVIFVDNVRP 136
           L GR + V +V  
Sbjct: 93  LAGRPMKVGHVTE 105

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 92.8 bits (231), Expect = 2e-25
 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F      L   F QFG++ +  II +  +  SKG+G+VT     +A +A   ++G +++
Sbjct: 38  PFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVVE 95

Query: 126 GRVIFVDNVRP 136
           GR I V+N   
Sbjct: 96  GRKIEVNNATA 106

>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 = 91.9 bits (229), Expect = 2e-25
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A    NG  LD
Sbjct: 24  SLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 83

Query: 126 GRVIFVD 132
           GR I V 
Sbjct: 84  GRRIRVS 90

>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 = 91.5 bits (228), Expect = 3e-25
 Identities = 23/71 (32%), Positives = 41/71 (57%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S   T   +A AF+ FG++++A ++ D+   +SKGYG+V+   + +A+ A+  M G+ L 
Sbjct: 15  SPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLG 74

Query: 126 GRVIFVDNVRP 136
           GR I  +    
Sbjct: 75  GRQIRTNWATR 85

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 91.5 bits (228), Expect = 3e-25
 Identities = 20/74 (27%), Positives = 40/74 (54%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+++++E L   FS +G ++E    +D    + KG+ +VT    E A KA  +++G++  
Sbjct: 17  SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ 76

Query: 126 GRVIFVDNVRPSRR 139
           GR++ V      + 
Sbjct: 77  GRMLHVLPSTIKKE 90

>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 = 90.7 bits (226), Expect = 8e-25
 Identities = 22/74 (29%), Positives = 37/74 (50%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +     ++L  AF  FG +T+  I +D    + +G+ +V     E+A  A+ +MN   L 
Sbjct: 21  AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 80

Query: 126 GRVIFVDNVRPSRR 139
           GR I V+  +P R 
Sbjct: 81  GRTIRVNLAKPMRI 94

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 93.9 bits (234), Expect = 8e-25
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 2/92 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            +   ++ +  AF+ FG +    +  D    + KG+ +V     E AQ AL  MN  +L 
Sbjct: 37  YYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLG 96

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQSPEEN 157
           GR I V   RPS        + +   ++   N
Sbjct: 97  GRNIKVG--RPSNIGQAQPIIDQLAEEARAFN 126

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 89.7 bits (223), Expect = 4e-23
 Identities = 19/69 (27%), Positives = 33/69 (47%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           SV    + + +   F  FG++  AT+  D    + KGYG++     + +Q A+  MN   
Sbjct: 132 SVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFD 191

Query: 124 LDGRVIFVD 132
           L G+ + V 
Sbjct: 192 LGGQYLRVG 200

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 89.6 bits (223), Expect = 2e-24
 Identities = 29/76 (38%), Positives = 37/76 (48%), Gaps = 4/76 (5%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F  T +ML D F++ G V  A I M+ G  +SKG G V   + E A++A   MNG  L 
Sbjct: 17  PFDFTWKMLKDKFNECGHVLYADIKMENG--KSKGCGVVKFESPEVAERACRMMNGMKLS 74

Query: 126 GRVIFV--DNVRPSRR 139
           GR I V  D       
Sbjct: 75  GREIDVRIDRNASGPS 90

>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 = 89.2 bits (222), Expect = 3e-24
 Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 2/71 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                 E L  AFS FG +T A ++M+ G  RSKG+G+V  S+ EEA KA+ +MNG+++ 
Sbjct: 24  DDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEMNGRIVA 81

Query: 126 GRVIFVDNVRP 136
            + ++V   + 
Sbjct: 82  TKPLYVALAQR 92

>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 = 89.2 bits (222), Expect = 3e-24
 Identities = 21/74 (28%), Positives = 36/74 (48%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           ++ T+ + L   F ++G+V +  I  +      +G+ +V      +AQ A   M+G  LD
Sbjct: 22  TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELD 81

Query: 126 GRVIFVDNVRPSRR 139
           GR + V   R  RR
Sbjct: 82  GRELRVQVARYGRR 95

>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 = 88.8 bits (221), Expect = 5e-24
 Identities = 18/74 (24%), Positives = 38/74 (51%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  T +  L + F  FG ++   +  D    +SKG+ +++    E+A +A+  ++G   
Sbjct: 23  LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY 82

Query: 125 DGRVIFVDNVRPSR 138
           D  ++ V+  +PS 
Sbjct: 83  DHLILNVEWAKPST 96

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 90.4 bits (224), Expect = 6e-24
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 3/92 (3%)

Query: 66  SFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+ TT + L       G   V E     +    +SKGY  V  ++E    K L  + GK+
Sbjct: 64  SWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKV 123

Query: 124 LDGRVIFVDNVRP-SRRYNTDASLARQPAQSP 154
           L+G  + V      +       +  R+  + P
Sbjct: 124 LNGEKVDVRPATRQNLSQFEAQARKRECVRVP 155

>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 = 89.0 bits (221), Expect = 7e-24
 Identities = 26/90 (28%), Positives = 43/90 (47%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ L
Sbjct: 30  VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 89

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
            G+ I VD               R+ ++SP
Sbjct: 90  MGQPISVDWCFVRGPPKGKRRGGRRRSRSP 119

>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 = 87.7 bits (218), Expect = 2e-23
 Identities = 30/88 (34%), Positives = 46/88 (52%), Gaps = 4/88 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S   + L D FS FG +    ++ D  +N SKGYG+V   T+E A++A+  MNG LL+
Sbjct: 14  DKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLN 71

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQS 153
            R +FV   +   R   +A L  +  + 
Sbjct: 72  DRKVFVGRFKS--RKEREAELGARAKEF 97

>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 = 86.9 bits (216), Expect = 2e-23
 Identities = 23/67 (34%), Positives = 34/67 (50%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            FS T   L   FS++G+V + TI+ D    +SKG  ++    ++ AQ     +N K L 
Sbjct: 25  PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLF 84

Query: 126 GRVIFVD 132
           GRVI   
Sbjct: 85  GRVIKAS 91

>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 = 87.4 bits (217), Expect = 2e-23
 Identities = 25/90 (27%), Positives = 37/90 (41%), Gaps = 3/90 (3%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            +    + L + FS  G V  A I+ D    +S+G G VT     EA +A+   NG+LL 
Sbjct: 24  DYKVGWKKLKEVFSMAGVVVRADILED-KDGKSRGIGTVTFEQSIEAVQAISMFNGQLLF 82

Query: 126 GRVIFV--DNVRPSRRYNTDASLARQPAQS 153
            R + V  D     +         +Q   S
Sbjct: 83  DRPMHVKMDERALPKGDFFPPERPQQSGPS 112

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 86.6 bits (215), Expect = 3e-23
 Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 1/75 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + FS TKE L +     G V +  ++ +    + KG  YV    E +A +A++ M+G  +
Sbjct: 25  LPFSCTKEELEEICKAHGTVKDLRLVTN-RAGKPKGLAYVEYENESQASQAVMKMDGMTI 83

Query: 125 DGRVIFVDNVRPSRR 139
              +I V        
Sbjct: 84  KENIIKVAISNSGPS 98

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 86.5 bits (215), Expect = 4e-23
 Identities = 20/82 (24%), Positives = 33/82 (40%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S+ +  T+E + D  S  G V    ++ D    RSKGY ++     E +  A+ ++NG  
Sbjct: 9   SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68

Query: 124 LDGRVIFVDNVRPSRRYNTDAS 145
           L  R +       S        
Sbjct: 69  LGSRFLKCGYSSNSDISGVSLE 90

>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 = 86.0 bits (214), Expect = 4e-23
 Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
              TT + L      +G++     I+D   N+ KGYG+V   +   AQKA+  +    + 
Sbjct: 14  QPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQ 73

Query: 126 GRVIFVDNVRPS 137
            ++       PS
Sbjct: 74  AQMAKQS--GPS 83

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 86.5 bits (215), Expect = 4e-23
 Identities = 23/72 (31%), Positives = 37/72 (51%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V    T+E + D F+++G++    + +D      KGY  V   T +EAQ A+  +NG+ L
Sbjct: 31  VHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDL 90

Query: 125 DGRVIFVDNVRP 136
            G+ I VD    
Sbjct: 91  MGQPISVDWCFV 102

>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 = 85.7 bits (213), Expect = 4e-23
 Identities = 20/67 (29%), Positives = 34/67 (50%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +     ++L  AF  FG +T+  I +D    + +G+ +V     E+A  A+ +MN   L 
Sbjct: 16  AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 75

Query: 126 GRVIFVD 132
           GR I V+
Sbjct: 76  GRTIRVN 82

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 88.0 bits (218), Expect = 5e-23
 Identities = 21/74 (28%), Positives = 39/74 (52%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           ++ T+ + L   F ++G+V +  I  D     S+G+ +V    + +A+ A+  M+G +LD
Sbjct: 79  TYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLD 138

Query: 126 GRVIFVDNVRPSRR 139
           GR + V   R  R 
Sbjct: 139 GRELRVQMARYGRP 152

>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 = 87.1 bits (216), Expect = 7e-23
 Identities = 16/74 (21%), Positives = 33/74 (44%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             +  +  L   F ++G +    I+ D    +S+GYG+V   +   AQ+A+  +NG  + 
Sbjct: 51  PTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNIL 110

Query: 126 GRVIFVDNVRPSRR 139
            + + V       +
Sbjct: 111 NKRLKVALAASGHQ 124

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 86.8 bits (215), Expect = 8e-23
 Identities = 20/67 (29%), Positives = 34/67 (50%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +     ++L  AF  FG +T+  I +D    + +G+ +V     E+A  A+ +MN   L 
Sbjct: 72  AEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 131

Query: 126 GRVIFVD 132
           GR I V+
Sbjct: 132 GRTIRVN 138

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 86.3 bits (214), Expect = 1e-22
 Identities = 21/74 (28%), Positives = 40/74 (54%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +++ T+ + L   F ++G+V +  I  D     S+G+ +V    + +A+ A+  M+G +L
Sbjct: 55  LTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVL 114

Query: 125 DGRVIFVDNVRPSR 138
           DGR + V   R  R
Sbjct: 115 DGRELRVQMARYGR 128

>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 = 85.5 bits (212), Expect = 1e-22
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN---- 120
           +SF + +E L +   QFG +    +++      SKG  +    T+E AQK L   +    
Sbjct: 23  LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAE 82

Query: 121 --GKLLDGRVIFVDNVRP 136
             G  LDGR + VD    
Sbjct: 83  GGGLKLDGRQLKVDLAVT 100

>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 = 85.0 bits (211), Expect = 2e-22
 Identities = 25/85 (29%), Positives = 39/85 (45%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            +  T+E L D FS+ G V    ++ D    + KGYG+     +E A  A+ ++NG+   
Sbjct: 17  PYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFS 76

Query: 126 GRVIFVDNVRPSRRYNTDASLARQP 150
           GR + VDN    +      SL    
Sbjct: 77  GRALRVDNAASEKNKEELKSLGTGA 101

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 84.6 bits (210), Expect = 2e-22
 Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTE-ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
                +++L D FS FG + +   I+ D     SKGY ++  ++ + +  A+  MNG+ L
Sbjct: 14  DPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL 73

Query: 125 DGRVIFVDNVRP 136
             R I V     
Sbjct: 74  CNRPITVSYAFK 85

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 84.8 bits (210), Expect = 2e-22
 Identities = 14/93 (15%), Positives = 37/93 (39%), Gaps = 4/93 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           + +  +  L D   ++G+V E  I++     +  G   V  ++   A++ + +++   + 
Sbjct: 15  NDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVM 74

Query: 126 GRVIFV----DNVRPSRRYNTDASLARQPAQSP 154
           G +I         +  + Y    + +  P   P
Sbjct: 75  GNIIHAQLDIKGQQRMKYYELIVNGSYTPQTVP 107

>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 = 85.1 bits (211), Expect = 2e-22
 Identities = 22/81 (27%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           ++       L D FS  G+V +  II D    RSKG  YV     +    A+  + G+ L
Sbjct: 33  LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRL 91

Query: 125 DGRVIFVDNVRPSRRYNTDAS 145
            G  I V   +  +   +  S
Sbjct: 92  LGVPIIVQASQAEKNRLSGPS 112

>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 = 84.6 bits (210), Expect = 2e-22
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 1/69 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F  +   + + F++FG + +A +  D    RS G   V    + +A KA+   NG  LD
Sbjct: 38  DFGVSDADIQELFAEFGTLKKAAVHYD-RSGRSLGTADVHFERKADALKAMKQYNGVPLD 96

Query: 126 GRVIFVDNV 134
           GR + +  V
Sbjct: 97  GRPMNIQLV 105

>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 = 85.1 bits (211), Expect = 3e-22
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F  +   + + F++FG + +A +  D    RS G   V      +A KA+    G  LD
Sbjct: 44  DFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLD 102

Query: 126 GRVIFVDNVRPSR 138
           GR + +  V    
Sbjct: 103 GRPMDIQLVASQI 115

>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 = 84.2 bits (209), Expect = 3e-22
 Identities = 14/71 (19%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           + + +   L  A S+     +   ++D+    ++ +GYV   + E+ +KAL ++ G  + 
Sbjct: 26  NPNKSVAELKVAISELFAKNDL-AVVDVRTGTNRKFGYVDFESAEDLEKAL-ELTGLKVF 83

Query: 126 GRVIFVDNVRP 136
           G  I ++  + 
Sbjct: 84  GNEIKLEKPKG 94

>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 = 83.1 bits (206), Expect = 6e-22
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF+ T++ L + F    ++      +     +SKG  Y+   +E +A+K L +  G  +D
Sbjct: 25  SFNITEDELKEVFEDALEI-----RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID 79

Query: 126 GRVIFVDNVRP 136
           GR + +     
Sbjct: 80  GRSVSLYYTGE 90

>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 = 83.1 bits (206), Expect = 6e-22
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 1/67 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                +E+L + F Q G +T+ TI  D  + + K +G+V     E    A+  +NG  L 
Sbjct: 25  EARVREEILYELFLQAGPLTKVTICKD-REGKPKSFGFVCFKHPESVSYAIALLNGIRLY 83

Query: 126 GRVIFVD 132
           GR I V 
Sbjct: 84  GRPINVS 90

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 83.1 bits (206), Expect = 9e-22
 Identities = 19/74 (25%), Positives = 34/74 (45%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               ++ +L + F Q G V    +  D    + +GYG+V   +EE+A  A+  M+   L 
Sbjct: 24  DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY 83

Query: 126 GRVIFVDNVRPSRR 139
           G+ I V+      +
Sbjct: 84  GKPIRVNKASAHNK 97

>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 = 82.6 bits (205), Expect = 9e-22
 Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V +  T E L   F   G V   TI+ D      KG+ Y+  S +E  + +L  ++  L 
Sbjct: 14  VDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA-LDESLF 72

Query: 125 DGRVIFVDNVRPSR 138
            GR I V   R +R
Sbjct: 73  RGRQIKVIPKRTNR 86

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 82.6 bits (205), Expect = 9e-22
 Identities = 16/80 (20%), Positives = 30/80 (37%), Gaps = 7/80 (8%)

Query: 66  SFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ TT E L +A    G   + E     +    +SKG+  V   +E  ++K +  +  + 
Sbjct: 10  TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE 69

Query: 124 LDGRVIFVD-----NVRPSR 138
           L G+   V            
Sbjct: 70  LHGQNPVVTPSNKLEHHHHH 89

>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 = 84.9 bits (211), Expect = 9e-22
 Identities = 19/67 (28%), Positives = 39/67 (58%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           + +   E L +AF  F       ++ D+    S+GYG+V+ +++++AQ A+  M G+ L+
Sbjct: 96  NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155

Query: 126 GRVIFVD 132
           GR + ++
Sbjct: 156 GRPLRIN 162

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 72.6 bits (179), Expect = 5e-17
 Identities = 17/78 (21%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             + T+++L   F   G +    I++D   N++  Y +V      +A  AL  +NGK ++
Sbjct: 9   DKAITEDILKQYFQVGGPIANIKIMID-KNNKNVNYAFVEYHQSHDANIALQTLNGKQIE 67

Query: 126 GRVIFVDNVRPSRRYNTD 143
             ++ ++    S++ ++D
Sbjct: 68  NNIVKINWAFQSQQSSSD 85

>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 = 83.1 bits (206), Expect = 9e-22
 Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+S T+E L + F +   +     +      +SKGY ++  ++ E+A++AL   N + ++
Sbjct: 24  SYSATEETLQEVFEKATFI----KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIE 79

Query: 126 GRVIFVDNVRPSRRYN 141
           GR I ++   P    N
Sbjct: 80  GRAIRLELQGPRGSPN 95

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 86.3 bits (213), Expect = 1e-21
 Identities = 20/94 (21%), Positives = 40/94 (42%), Gaps = 3/94 (3%)

Query: 66  SFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++ TT E L +A    G   + E     +    +SKG+  V   +E  ++K +  +  + 
Sbjct: 77  TWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRE 136

Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN 157
           L G+   V  V   +  +     +R+  QS + +
Sbjct: 137 LHGQNPVVTPVNK-QFLSQFEMQSRKTTQSGQMS 169

>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 = 82.3 bits (204), Expect = 2e-21
 Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +     ++ + + F  +G++    + +D     SKGY  V   T ++A  A   +NG  +
Sbjct: 34  IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI 93

Query: 125 DGRVIFVD--NVRPSRR 139
            G+ I VD   V+  +R
Sbjct: 94  MGQTIQVDWCFVKGPKR 110

>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 = 83.7 bits (207), Expect = 2e-21
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 3/78 (3%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF TT+E + + FS+ G + +  + +D  K  + G+ +V   +  +A+ A+  +NG  LD
Sbjct: 48  SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLD 107

Query: 126 GRVIFVDNVRP---SRRY 140
            R+I  D        R+Y
Sbjct: 108 DRIIRTDWDAGFKEGRQY 125

>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 = 81.9 bits (203), Expect = 2e-21
 Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S  TT+E L ++F        A I+ D     SKG+G+V  ++EE+A+ A   M    +D
Sbjct: 24  SEDTTEETLKESF---DGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEID 80

Query: 126 GRVIFVDNVRP 136
           G  + +D  +P
Sbjct: 81  GNKVTLDWAKP 91

>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 = 83.7 bits (207), Expect = 3e-21
 Identities = 20/86 (23%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +     ++ + + F  +G++    + +D     SKGY  V   T ++A  A   +NG  +
Sbjct: 80  IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI 139

Query: 125 DGRVIFVD--NVRPSRRYNTDASLAR 148
            G+ I VD   V+  +R        R
Sbjct: 140 MGQTIQVDWCFVKGPKRVKKSEKRRR 165

>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 = 83.8 bits (208), Expect = 3e-21
 Identities = 20/81 (24%), Positives = 34/81 (41%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T   L   F   G +    I+ D     S GY +V  ++E ++Q+A+  +NG  + 
Sbjct: 12  PQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR 71

Query: 126 GRVIFVDNVRPSRRYNTDASL 146
            + + V   RP      D +L
Sbjct: 72  NKRLKVSYARPGGESIKDTNL 92

>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 = 76.1 bits (188), Expect = 2e-18
 Identities = 16/62 (25%), Positives = 31/62 (50%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             + T + L   F ++G + +  I+ D    R +G  +V  +  EEAQ+A+  +N  + +
Sbjct: 98  PRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE 157

Query: 126 GR 127
           G 
Sbjct: 158 GG 159

>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 = 82.0 bits (203), Expect = 4e-21
 Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 1/67 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            + TT   L   F  FG + EA +I D    +S+GYG+VT +    A++A  D N   +D
Sbjct: 26  PYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-ID 84

Query: 126 GRVIFVD 132
           GR   V+
Sbjct: 85  GRKANVN 91

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 83.4 bits (207), Expect = 4e-21
 Identities = 14/80 (17%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           + + +   L  A S+     +  ++       ++ +GYV   + E+ +KAL ++ G  + 
Sbjct: 22  NPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKAL-ELTGLKVF 79

Query: 126 GRVIFVDNVRPSRRYNTDAS 145
           G  I ++  +        A+
Sbjct: 80  GNEIKLEKPKGRDSKKVRAA 99

>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 = 79.6 bits (197), Expect = 1e-19
 Identities = 17/67 (25%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF+ T++ L + F    ++      +     +SKG  Y+   +E +A+K L +  G  +D
Sbjct: 108 SFNITEDELKEVFEDALEIR-----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEID 162

Query: 126 GRVIFVD 132
           GR + + 
Sbjct: 163 GRSVSLY 169

>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 = 81.2 bits (201), Expect = 6e-21
 Identities = 20/71 (28%), Positives = 30/71 (42%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                 + L   F  FG V  A + +D   N SK +G+V+      AQ A+  MNG  + 
Sbjct: 34  PQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIG 93

Query: 126 GRVIFVDNVRP 136
            + + V   R 
Sbjct: 94  MKRLKVQLKRS 104

>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 = 80.8 bits (200), Expect = 1e-20
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 8/89 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S   T+  L   F++F +     I   +   R +G  ++T   +E A +AL  +NG  L 
Sbjct: 34  SPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLY 93

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           G+++ ++  +  +         R    S 
Sbjct: 94  GKILVIEFGKNKK--------QRSSGPSS 114

>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 = 82.2 bits (204), Expect = 1e-20
 Identities = 24/82 (29%), Positives = 40/82 (48%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  + T+E     F   G++    ++ D    +S GYG+V     ++A+KA+  +NG  L
Sbjct: 10  LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69

Query: 125 DGRVIFVDNVRPSRRYNTDASL 146
             + I V   RPS     DA+L
Sbjct: 70  QTKTIKVSYARPSSASIRDANL 91

>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 = 74.9 bits (185), Expect = 7e-18
 Identities = 17/62 (27%), Positives = 34/62 (54%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             + T++ L   FSQ+G++  + I++D     S+G G++      EA++A+  +NG+   
Sbjct: 97  PKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS 156

Query: 126 GR 127
           G 
Sbjct: 157 GA 158

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 80.5 bits (199), Expect = 1e-20
 Identities = 20/66 (30%), Positives = 31/66 (46%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T   LA  F  FG V  A + +D   + SK +G+V+    + AQ A+  MNG  + 
Sbjct: 49  PQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVG 108

Query: 126 GRVIFV 131
            + + V
Sbjct: 109 TKRLKV 114

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 83.9 bits (208), Expect = 2e-20
 Identities = 17/67 (25%), Positives = 31/67 (46%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S T++   +    FG +    ++      +SKGYG+     ++ A +A  D+ GK L 
Sbjct: 104 PPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLG 163

Query: 126 GRVIFVD 132
            R ++V 
Sbjct: 164 PRTLYVH 170

>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 = 76.2 bits (188), Expect = 2e-17
 Identities = 19/86 (22%), Positives = 29/86 (33%), Gaps = 7/86 (8%)

Query: 69  TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
              + L  A S     T   +       + KG+  +   T E A++A    +G  L G  
Sbjct: 197 NDVDALCRALSAVHSPTFCQLACG-QDGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSH 255

Query: 129 IFVD--NVRPSRRYNTDASLARQPAQ 152
           + V      P  R    + LA   A 
Sbjct: 256 LRVSFCAPGPPGR----SMLAALIAA 277

>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 = 67.3 bits (165), Expect = 3e-14
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 7/66 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T + + D  S +        +     ++ KG  +VT    E+A+ A+   +   L 
Sbjct: 31  PGDVTNQEVHDLLSDYE-------LKYCFVDKYKGTAFVTLLNGEQAEAAINAFHQSRLR 83

Query: 126 GRVIFV 131
            R + V
Sbjct: 84  ERELSV 89

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 78.8 bits (195), Expect = 3e-20
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            +S T E + + FSQFG+V    +I D    + KG+G+V    EE   +A+  ++     
Sbjct: 10  VYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFM 68

Query: 126 GRVIFVDNVRP 136
           GR I V    P
Sbjct: 69  GRTIRVTEANP 79

>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 = 81.2 bits (201), Expect = 5e-20
 Identities = 12/69 (17%), Positives = 26/69 (37%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +      + + +  + FG +    ++ D     SKGY +          +A+  +NG  
Sbjct: 121 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 180

Query: 124 LDGRVIFVD 132
           L  + + V 
Sbjct: 181 LGDKKLLVQ 189

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 73.5 bits (181), Expect = 4e-17
 Identities = 15/97 (15%), Positives = 36/97 (37%), Gaps = 8/97 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEAT-----IIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
            F  T+E + D F+   ++   T      ++ +  N+ K + ++   + +E  +A+   +
Sbjct: 13  PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AFD 71

Query: 121 GKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSPEEN 157
           G +  G+ + +   RP                 P   
Sbjct: 72  GIIFQGQSLKIR--RPHDYQPLPGMSENPSVYVPGVV 106

>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 = 78.8 bits (195), Expect = 5e-20
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 1/71 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S  ++ L +    FGQV    I+ D     S+G G+    + E+ +  +   NGK + 
Sbjct: 34  PLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIK 92

Query: 126 GRVIFVDNVRP 136
                     P
Sbjct: 93  TPPGVSAPTEP 103

>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 = 78.1 bits (193), Expect = 7e-20
 Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 8/89 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           + + T+E+L  AFSQFG++     +        K Y ++     + A KA+ +MNGK L+
Sbjct: 20  ANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLE 71

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           G  I +   +P  +   +    RQ A  P
Sbjct: 72  GENIEIVFAKPPDQKRKERKAQRQAASGP 100

>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 = 80.0 bits (198), Expect = 7e-20
 Identities = 12/69 (17%), Positives = 26/69 (37%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +      + + +  + FG +    ++ D     SKGY +          +A+  +NG  
Sbjct: 101 GLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQ 160

Query: 124 LDGRVIFVD 132
           L  + + V 
Sbjct: 161 LGDKKLLVQ 169

>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 = 71.9 bits (177), Expect = 1e-16
 Identities = 14/83 (16%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 66  SFSTTKEMLADAFSQFGQVTEAT-----IIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
            F  T+E + D F+   ++   T      ++ +  N+ K + ++   + +E  +A+   +
Sbjct: 13  PFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FD 71

Query: 121 GKLLDGRVIFVDNVRPSRRYNTD 143
           G +  G+ + +   RP       
Sbjct: 72  GIIFQGQSLKIR--RPHDYQPLP 92

>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 = 78.0 bits (193), Expect = 8e-20
 Identities = 16/72 (22%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +     +  +   F+++G V E  II D     SKGYG+V+   + + QK +   +    
Sbjct: 17  IDVRMDETEIRSFFARYGSVKEVKIITD-RTGVSKGYGFVSFYNDVDVQKIV--ESQINF 73

Query: 125 DGRVIFVDNVRP 136
            G+ + +     
Sbjct: 74  HGKKLKLGPAIR 85

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 77.1 bits (191), Expect = 1e-19
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+ TT+E L + F QFG+V E  ++ D    RS+G+G+VT   +    K L   +   LD
Sbjct: 9   SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELD 67

Query: 126 GRVI 129
            + I
Sbjct: 68  SKTI 71

>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 = 77.2 bits (191), Expect = 1e-19
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+ T+K+ L D F++FG+V + TI MD    RS+G+G++        +K L     + LD
Sbjct: 20  SWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHR-LD 78

Query: 126 GRVIFVD 132
           GRVI   
Sbjct: 79  GRVIDPK 85

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 79.5 bits (196), Expect = 2e-19
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F  +   + + F++FG + +A +  D    RS G   V      +A KA+    G  LD
Sbjct: 97  DFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQYKGVPLD 155

Query: 126 GRVIFVDNVRPSR 138
           GR + +  V    
Sbjct: 156 GRPMDIQLVASQI 168

>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 = 77.8 bits (192), Expect = 2e-19
 Identities = 20/72 (27%), Positives = 30/72 (41%), Gaps = 1/72 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           V + +T + L   FS  G +   TI+ D      KGY Y+  +       A+  M+  + 
Sbjct: 44  VDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA-MDETVF 102

Query: 125 DGRVIFVDNVRP 136
            GR I V   R 
Sbjct: 103 RGRTIKVLPKRT 114

>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 = 76.9 bits (190), Expect = 2e-19
 Identities = 23/64 (35%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            +STT+E L   FSQ+G+V +  I+ D   N+S+G+G+V           L       LD
Sbjct: 25  DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL-ASRPHTLD 83

Query: 126 GRVI 129
           GR I
Sbjct: 84  GRNI 87

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 76.0 bits (188), Expect = 3e-19
 Identities = 19/64 (29%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S +TT E +   F QFG+V +A ++ D   NR +G+G+VT  +E+  +K   +++   ++
Sbjct: 8   SVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEIN 66

Query: 126 GRVI 129
            +++
Sbjct: 67  NKMV 70

>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 = 77.0 bits (190), Expect = 3e-19
 Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDM-NGK 122
           + F   +  + + FS FG++    +     G    +G+G+V   T+++A+KA   + +  
Sbjct: 23  IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST 82

Query: 123 LLDGRVIFVDNVRPSRRYNTDAS 145
            L GR + ++         +  S
Sbjct: 83  HLYGRRLVLEWADSEVTVQSGPS 105

>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 = 80.8 bits (200), Expect = 3e-19
 Identities = 14/84 (16%), Positives = 34/84 (40%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S T+  + D       V  +  +  +  N S+ + Y+  +++E+A+  +  +NG  ++
Sbjct: 126 PPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE 185

Query: 126 GRVIFVDNVRPSRRYNTDASLARQ 149
           G  +      P  +     S   +
Sbjct: 186 GYTLVTKVSNPLEKSKRTDSATLE 209

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 72.3 bits (178), Expect = 4e-16
 Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 3/69 (4%)

Query: 66  SFSTTKE-MLADAFSQFGQVTEATIIMDIGKN-RSKGYGYVTSSTEEEAQKALVDMNGKL 123
           S     E +L ++F  FG + +  I     ++  +    ++    ++ A++A + MN  L
Sbjct: 219 STELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERA-LQMNRSL 277

Query: 124 LDGRVIFVD 132
           L  R I V 
Sbjct: 278 LGNREISVS 286

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 68.1 bits (167), Expect = 2e-14
 Identities = 8/66 (12%), Positives = 21/66 (31%), Gaps = 3/66 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S  +  +   F   G +    +   + K  +  +  +  +  + A  A+   +   + 
Sbjct: 50  PKSYNQNKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAITKTHKV-VG 106

Query: 126 GRVIFV 131
              I V
Sbjct: 107 QNEIIV 112

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 76.7 bits (189), Expect = 3e-19
 Identities = 16/68 (23%), Positives = 30/68 (44%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                K+ L   FS+ G+V      +D    ++KG+ +V   +  +A+K +   +GK LD
Sbjct: 21  KVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80

Query: 126 GRVIFVDN 133
            +      
Sbjct: 81  LKHRLFLY 88

>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 = 76.1 bits (188), Expect = 3e-19
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             +  +  L + F +FG VTE  +I D  K R +G+G++T   E+   +A V+M+   + 
Sbjct: 19  PHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA-VNMHFHDIM 77

Query: 126 GRVIFVDNVRP 136
           G+ + V    P
Sbjct: 78  GKKVEVKRAEP 88

>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 = 78.9 bits (195), Expect = 4e-19
 Identities = 25/67 (37%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     +D
Sbjct: 22  SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVD 80

Query: 126 GRVIFVD 132
           GRV+   
Sbjct: 81  GRVVEPK 87

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 74.3 bits (183), Expect = 2e-17
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   T +  L D F Q+G++    I+ D G  + +G+ +VT    +   K ++      +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTV 170

Query: 125 DGRVIFVD 132
           +G    V 
Sbjct: 171 NGHNCEVR 178

>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 = 76.1 bits (188), Expect = 4e-19
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 6/80 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T+E +   F ++G+  E  I       + KG+G++   T   A+ A V+++   L 
Sbjct: 24  PPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETRTLAEIAKVELDNMPLR 77

Query: 126 GRVIFVDNVRPSRRYNTDAS 145
           G+ + V     S    +  S
Sbjct: 78  GKQLRVRFACHSASLTSGPS 97

>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 = 76.2 bits (188), Expect = 5e-19
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 3/79 (3%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +  +  ++ L   F +FG++ E T++ D      KG  ++T    E A KA   ++ + 
Sbjct: 20  QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQK 79

Query: 124 L---DGRVIFVDNVRPSRR 139
                 R I V       R
Sbjct: 80  TLPGMNRPIQVKPADSESR 98

>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 = 76.2 bits (188), Expect = 6e-19
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           SF TT+E L + + Q+G++T+  ++ D    RS+G+G+VT S+  E   A+       +D
Sbjct: 36  SFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSID 94

Query: 126 GRVI 129
           GRV+
Sbjct: 95  GRVV 98

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 75.4 bits (186), Expect = 8e-19
 Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 6/73 (8%)

Query: 66  SFSTTKEMLADAFSQFGQ--VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK- 122
           +  T  + +  A S +    V    +I D    +++G+ +V  S+  +A + L  +    
Sbjct: 18  APHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLH 77

Query: 123 ---LLDGRVIFVD 132
               +DG+ I VD
Sbjct: 78  PPLKIDGKTIGVD 90

>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 = 75.3 bits (186), Expect = 8e-19
 Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            + TT++ L + FS FG+V    +  D+    SKG+G+V  +  E   K +   +  ++D
Sbjct: 24  PWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRH--MID 81

Query: 126 GRVI 129
           GR  
Sbjct: 82  GRWC 85

>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 = 75.4 bits (186), Expect = 9e-19
 Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 1/64 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S+ TT+E L + F QFG+V E  ++ D    RS+G+G+VT   +    K L   +   LD
Sbjct: 34  SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHELD 92

Query: 126 GRVI 129
            + I
Sbjct: 93  SKTI 96

>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 = 76.8 bits (190), Expect = 1e-18
 Identities = 18/67 (26%), Positives = 37/67 (55%), Gaps = 2/67 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           ++ TT++ L + F ++G VT+  I+ D    RS+G+G+++        + +   +  +LD
Sbjct: 12  NWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQH--ILD 69

Query: 126 GRVIFVD 132
           G+VI   
Sbjct: 70  GKVIDPK 76

>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 = 75.3 bits (186), Expect = 5e-18
 Identities = 13/68 (19%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +      +   + FSQ+G + +A +++D    +S+G+G+VT  + +   +          
Sbjct: 95  IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDF 153

Query: 125 DGRVIFVD 132
             R I + 
Sbjct: 154 KDRKIEIK 161

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 74.7 bits (184), Expect = 2e-18
 Identities = 20/92 (21%), Positives = 30/92 (32%), Gaps = 8/92 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEAT--------IIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
             + T E +AD F Q G +            +  D    + KG   V+      A+ A+ 
Sbjct: 16  GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID 75

Query: 118 DMNGKLLDGRVIFVDNVRPSRRYNTDASLARQ 149
             +GK   G  I V        +N      R 
Sbjct: 76  WFDGKEFSGNPIKVSFATRRADFNRGGGNGRG 107

>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 = 74.2 bits (183), Expect = 2e-18
 Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             ST++EM+   F+         +       + + Y +V  S  E+A +A+  +NGK+LD
Sbjct: 24  MLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLD 77

Query: 126 GRVIFVDNVRPSRR 139
           G  I V   +P  +
Sbjct: 78  GSPIEVTLAKPVDK 91

>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 = 74.2 bits (183), Expect = 2e-18
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S   T+ ++   FSQ G      +I +     +  Y +V      +A  AL  MNG+ + 
Sbjct: 24  SRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAALAAMNGRKIL 81

Query: 126 GRVIFVDNVRPSRRYNTDAS 145
           G+ + V+         +  S
Sbjct: 82  GKEVKVNWATTPSSQKSGPS 101

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 76.5 bits (189), Expect = 3e-18
 Identities = 27/67 (40%), Positives = 39/67 (58%), Gaps = 2/67 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S   + L D FS FG +    ++ D  +N SKGYG+V   T+E A++A+  MNG LL+
Sbjct: 112 DKSIDNKALYDTFSAFGNILSCKVVCD--ENGSKGYGFVHFETQEAAERAIEKMNGMLLN 169

Query: 126 GRVIFVD 132
            R +FV 
Sbjct: 170 DRKVFVG 176

>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 = 73.5 bits (181), Expect = 5e-17
 Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T+ ML + FS  G +    +  D+   RS GY YV      +A++AL  MN  ++ 
Sbjct: 24  HPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK 83

Query: 126 GRVIFVD--NVRPSRRYNTDASL 146
           G+ + +      PS R +   ++
Sbjct: 84  GKPVRIMWSQRDPSLRKSGVGNI 106

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 72.2 bits (178), Expect = 1e-17
 Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S + T + L   F + G+V E  ++        K Y +V    E +A+ A+  +NGK + 
Sbjct: 18  SAACTSQELRSLFERRGRVIECDVV--------KDYAFVHMEKEADAKAAIAQLNGKEVK 69

Query: 126 GRVIFVDNVRPSRR 139
           G+ I V+     ++
Sbjct: 70  GKRINVELSTKGQK 83

>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 = 72.0 bits (177), Expect = 2e-17
 Identities = 22/72 (30%), Positives = 36/72 (50%), Gaps = 6/72 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +   T +++   FS FGQ+ E  +  +      KGY +V  ST E A  A+V +NG  ++
Sbjct: 34  ASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIE 87

Query: 126 GRVIFVDNVRPS 137
           G V+     + S
Sbjct: 88  GHVVKCYWGKES 99

>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 = 70.6 bits (174), Expect = 3e-17
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 1/65 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  T +E + + F  FG+V    + MD   N+ +G+ ++T   EE  +K +       +
Sbjct: 7   LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME-KKYHNV 65

Query: 125 DGRVI 129
                
Sbjct: 66  GLSKC 70

>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 = 73.4 bits (181), Expect = 3e-17
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMD--IGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           V  + +++ L + F Q+G V E  ++ D      +SKG  +VT  T + A +A   ++  
Sbjct: 11  VPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNM 70

Query: 123 LLDGRVIFVDNVRPSRR 139
            +   +     ++P+  
Sbjct: 71  KVLPGMHHPIQMKPADS 87

>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 = 69.6 bits (171), Expect = 8e-16
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
            +S   T+  +   FS FGQ+ E  I+       S+G  +VT +T   AQ A+  M+  
Sbjct: 102 MISKKCTENDIRVMFSSFGQIEECRILRG-PDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 72.1 bits (177), Expect = 3e-17
 Identities = 23/89 (25%), Positives = 34/89 (38%), Gaps = 8/89 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTE--------ATIIMDIGKNRSKGYGYVTSSTEEEAQKAL 116
           ++ S T + LAD F Q G V            I +D    + KG   V+      A+ A+
Sbjct: 23  LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAV 82

Query: 117 VDMNGKLLDGRVIFVDNVRPSRRYNTDAS 145
              +GK   G  + V   R     N+  S
Sbjct: 83  EWFDGKDFQGSKLKVSLARKKPPMNSGPS 111

>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 = 70.7 bits (174), Expect = 5e-17
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL- 123
           +S + T + L   F          ++         GY +V    +  A +A+  ++GK+ 
Sbjct: 16  LSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIETLSGKVE 69

Query: 124 LDGRVIFVDNVRPSRR 139
           L G+++ VD     + 
Sbjct: 70  LHGKIMEVDYSVSKKL 85

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 70.8 bits (174), Expect = 7e-17
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 8/74 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                +  L + F  FG + E  I+         G+ +V     E A KA+ +++GK   
Sbjct: 40  PLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFA 91

Query: 126 GRVIFVDNVRPSRR 139
            + + V   +   +
Sbjct: 92  NQPLEVVYSKLPAK 105

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 70.4 bits (173), Expect = 7e-17
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F+T +  +   F     +    ++ D   ++ KG+ YV     +  ++AL   +G LL 
Sbjct: 24  PFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLG 81

Query: 126 GRVIFVDNVRPSRR 139
            R + VD     ++
Sbjct: 82  DRSLRVDIAEGRKQ 95

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 69.5 bits (171), Expect = 1e-16
 Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 8/74 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T++ +   F Q+G+V E  II        K YG+V    +  A+ A+ +++   L 
Sbjct: 17  PREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLH 68

Query: 126 GRVIFVDNVRPSRR 139
           G  I V+  +   +
Sbjct: 69  GVNINVEASKNKSK 82

>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 = 69.3 bits (170), Expect = 2e-16
 Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 8/75 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEAT--------IIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
             + T E +AD F Q G +            +  D    + KG   V+      A+ A+ 
Sbjct: 22  GENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAID 81

Query: 118 DMNGKLLDGRVIFVD 132
             +GK   G  I V 
Sbjct: 82  WFDGKEFSGNPIKVS 96

>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 = 72.4 bits (178), Expect = 3e-16
 Identities = 15/66 (22%), Positives = 32/66 (48%), Gaps = 6/66 (9%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T+E     F ++G+ +E  I      NR +G+G++   +   A+ A  +++G +L 
Sbjct: 31  PTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAELDGTILK 84

Query: 126 GRVIFV 131
            R + +
Sbjct: 85  SRPLRI 90

>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 = 72.0 bits (177), Expect = 4e-16
 Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 3/94 (3%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK-LL 124
           S   + E+L  AFSQFG V +A +++D  + R+ G G+V  + +  A+KAL        L
Sbjct: 105 SPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFL 163

Query: 125 DGRVIFVDNVRP-SRRYNTDASLARQPAQSPEEN 157
                    V P  +  + D    +   ++ + +
Sbjct: 164 LTTTPRPVIVEPMEQFDDEDGLPEKLMQKTQQYH 197

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 68.9 bits (169), Expect = 3e-16
 Identities = 12/68 (17%), Positives = 30/68 (44%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F+ + + + D F  +  +  +  +    K    G   V   + +EA  A++D+N + +
Sbjct: 23  MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI 82

Query: 125 DGRVIFVD 132
             R + + 
Sbjct: 83  GSRKVKLV 90

>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 = 68.4 bits (168), Expect = 3e-16
 Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           S + T + L   F ++G V E  I+        K Y +V     E+A +A+  ++     
Sbjct: 19  SPTCTNQELRAKFEEYGPVIECDIV--------KDYAFVHMERAEDAVEAIRGLDNTEFQ 70

Query: 126 GRVIFVDNVRPSRR 139
           G+ + V       R
Sbjct: 71  GKRMHVQLSTSRLR 84

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 68.5 bits (168), Expect = 3e-16
 Identities = 12/67 (17%), Positives = 30/67 (44%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F+ + + + D F  +  +  +  +    K    G   V   + +EA  A++D+N + +
Sbjct: 23  MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI 82

Query: 125 DGRVIFV 131
             R + +
Sbjct: 83  GSRKVKL 89

>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 = 68.4 bits (168), Expect = 4e-16
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIG-KNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
            +  T+E + + F     ++   +  +     R KG+GY      +    AL  +N + L
Sbjct: 28  PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL 85

Query: 125 DGRVIFVDNVRPSR 138
             R I VD    ++
Sbjct: 86  GNRRIRVDVADQAQ 99

>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 = 68.1 bits (167), Expect = 5e-16
 Identities = 16/75 (21%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
              T  +L  AFS FG + + ++      +  +   +VT    E A +A+ ++NG  ++ 
Sbjct: 23  EDMTPTLLRGAFSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVES 76

Query: 127 RVIFVDNVRPSRRYN 141
             + V+  R     +
Sbjct: 77  VQLKVNIARKQPMLD 91

>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 = 67.8 bits (166), Expect = 9e-16
 Identities = 15/92 (16%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 61  RCISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
           R + +    +  T E + D F ++G + +  +        ++G  YV      +A+ A+ 
Sbjct: 9   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVD 65

Query: 118 DMNGKLLDGRVIFVDNVRPSRRYNTDASLARQ 149
            ++G  +  R + V     +R +    +  ++
Sbjct: 66  HLSGFNVSNRYLVVLYYNANRAFQKMDTKKKE 97

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 67.3 bits (165), Expect = 1e-15
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 1/67 (1%)

Query: 66  SFSTTKEMLADAFSQFGQ-VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
                +  ++ AF+  G+ V    II +       GY +V  +    A+K L  +NGK L
Sbjct: 18  EPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPL 77

Query: 125 DGRVIFV 131
            G     
Sbjct: 78  PGATPAK 84

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 66.9 bits (164), Expect = 1e-15
 Identities = 16/74 (21%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                K  L  AFS +G +    I          G+ +V      +A+ A+  ++GK++ 
Sbjct: 9   GTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRGLDGKVIC 63

Query: 126 GRVIFVDNVRPSRR 139
           G  + V+      R
Sbjct: 64  GSRVRVELSTGMPR 77

>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 = 66.5 bits (163), Expect = 3e-15
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGK-NRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
            +  T+E + + F     ++   +  +     R KG+GY      +    AL  +N + L
Sbjct: 24  PYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL 81

Query: 125 DGRVIFVDNVRPSRR 139
             + I VD    ++ 
Sbjct: 82  GNKRIRVDVADQAQD 96

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 66.2 bits (162), Expect = 3e-15
 Identities = 12/74 (16%), Positives = 27/74 (36%), Gaps = 3/74 (4%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                 + + D F ++G + +  +           + +V      +A+ A+   +G   D
Sbjct: 31  PPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYD 87

Query: 126 GRVIFVDNVRPSRR 139
           G  + V+  R  R 
Sbjct: 88  GYRLRVEFPRSGRG 101

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 66.0 bits (161), Expect = 6e-15
 Identities = 15/90 (16%), Positives = 33/90 (36%), Gaps = 1/90 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F    + + D F +   V ++  I      ++ G G+V    E + + AL   + + +
Sbjct: 33  LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYM 91

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
             R I V  +           + ++    P
Sbjct: 92  GNRFIQVHPITKKGMLEKIDMIRKRLQSGP 121

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 65.9 bits (161), Expect = 6e-15
 Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 4/89 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + FS TK  +            A  ++     +  G   V    E++A+K+   ++ K L
Sbjct: 23  IPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE-RLHRKKL 81

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQPAQS 153
           +GR  F   V      +        PAQ 
Sbjct: 82  NGREAF---VHVVTLEDMREIEKNPPAQG 107

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81

 Score = 64.7 bits (158), Expect = 8e-15
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
            K ++   FS+FG++T      + GK  +KGY ++  ++   A  A+ + +G  LD +  
Sbjct: 20  LKNVIHKIFSKFGKITNDFYPEEDGK--TKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 77

Query: 130 FVDN 133
           F  N
Sbjct: 78  FRVN 81

>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 = 66.4 bits (162), Expect = 8e-15
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             +  K  L  AF  +G +    +          G+ +V      +A  A+ +++G+ L 
Sbjct: 82  GNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRELDGRTLC 136

Query: 126 GRVIFVDNVRPSRR 139
           G  + V+     +R
Sbjct: 137 GCRVRVELSNGEKR 150

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 65.0 bits (159), Expect = 8e-15
 Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 6/65 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +    T+  L   F  FG + +            KG  ++   T E+A   +V +     
Sbjct: 35  IPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPF 88

Query: 125 DGRVI 129
            GR +
Sbjct: 89  QGRNL 93

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 65.1 bits (159), Expect = 9e-15
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR-VI 129
           K ++   FS+FG++T           ++KGY ++  ++   A  A+ + +G  LD +   
Sbjct: 35  KNVIHKIFSKFGKITN--DFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF 92

Query: 130 FVDNVRPSRRYNT 142
            V+      +Y T
Sbjct: 93  RVNLFTDFDKYMT 105

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 65.6 bits (160), Expect = 1e-14
 Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 5/72 (6%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATI-----IMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           +    ++ L   F ++   +  T      I  + + R KG  ++    E+ A KAL + N
Sbjct: 54  AKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEAN 113

Query: 121 GKLLDGRVIFVD 132
           G +L G+ + V 
Sbjct: 114 GYVLFGKPMVVQ 125

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 64.2 bits (157), Expect = 2e-14
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 5/87 (5%)

Query: 68  STTKEMLADAFSQ-FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK-LLD 125
                ML + F + +       +++D     SKGYG+V  + E E ++AL +  G   L 
Sbjct: 20  DVDDGMLYEFFVKVYPSCRGGKVVLD-QTGVSKGYGFVKFTDELEQKRALTECQGAVGLG 78

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQ 152
            + + +       + +    +   P+ 
Sbjct: 79  SKPVRLS--VAIPKASRVKPVESGPSS 103

>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 = 63.8 bits (156), Expect = 3e-14
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           ++   ++E +   F  FG + E T++       SKG  +V  S+  EAQ A+  ++G 
Sbjct: 23  LNKQQSEEDVLRLFQPFGVIDECTVLRG-PDGSSKGCAFVKFSSHTEAQAAIHALHGS 79

>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 = 63.7 bits (155), Expect = 4e-14
 Identities = 16/89 (17%), Positives = 27/89 (30%), Gaps = 7/89 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S + + L D   + G V  A +  D       G G V    +E+   A+  ++     
Sbjct: 24  PPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFR 76

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQSP 154
                   +R         S  R  +  P
Sbjct: 77  SHEGETAYIRVKVDGPRSPSYGRSRSSGP 105

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 63.2 bits (154), Expect = 4e-14
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 3/68 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +      E+L     Q+G V     +     +       VT S++++A++AL  +NG  L
Sbjct: 23  IPPHLQWEVLDSLLVQYGVVESCEQVNT---DSETAVVNVTYSSKDQARQALDKLNGFQL 79

Query: 125 DGRVIFVD 132
           +   + V 
Sbjct: 80  ENFTLKVA 87

>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 = 61.5 bits (150), Expect = 2e-13
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 10/78 (12%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  +T+   LA  F +FG +     +      +   + Y+   + + AQ A   M G  L
Sbjct: 25  LGPNTSLAALAREFDRFGSIRTIDHV------KGDSFAYIQYESLDAAQAACAKMRGFPL 78

Query: 125 DG--RVIFVD--NVRPSR 138
            G  R + VD     PS 
Sbjct: 79  GGPDRRLRVDFAKSGPSS 96

>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 = 61.1 bits (149), Expect = 2e-13
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 7/72 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
            +   T++ L + FSQ+G V +  I         + + +VT + ++ AQ         ++
Sbjct: 13  CTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLC--GEDLII 65

Query: 125 DGRVIFVDNVRP 136
            G  + + N  P
Sbjct: 66  KGISVHISNAEP 77

>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 = 61.6 bits (150), Expect = 2e-13
 Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 8/78 (10%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
              K  +   FS++G+V   ++         KGY +V  S E  A+ A++  NG++L G+
Sbjct: 39  LVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQ 90

Query: 128 VIFVDNVRPSRRYNTDAS 145
            + ++     +   +  S
Sbjct: 91  TLDINMAGEPKPDRSGPS 108

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 61.8 bits (150), Expect = 3e-13
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F  TKE +   FS    V     +    + +  G  +V  +++E A+KAL   + + +
Sbjct: 50  LPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKAL-GKHKERI 108

Query: 125 DGRVIFV 131
             R I V
Sbjct: 109 GHRYIEV 115

>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 = 62.8 bits (152), Expect = 5e-13
 Identities = 9/65 (13%), Positives = 23/65 (35%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
                T+E   +   + G     ++ +  GK+     G +   ++ +A + L  +N   +
Sbjct: 131 APLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQM 190

Query: 125 DGRVI 129
                
Sbjct: 191 KNPNG 195

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 47.0 bits (111), Expect = 4e-07
 Identities = 9/65 (13%), Positives = 22/65 (33%), Gaps = 5/65 (7%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
               + + + F  +G V +   +         G   V  +      +A+  +N   + G+
Sbjct: 16  KMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQ 70

Query: 128 VIFVD 132
            + V 
Sbjct: 71  KMNVC 75

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 60.1 bits (146), Expect = 8e-13
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
            F  +KE +   FS    V     +    + RS G  +V  +++E A+KAL   + + + 
Sbjct: 24  PFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKHKERIG 82

Query: 126 GRVIFV 131
            R I +
Sbjct: 83  HRYIEI 88

>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 = 59.5 bits (144), Expect = 1e-12
 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 6/77 (7%)

Query: 62  CISVSFSTTKEML---ADAFSQFGQVTEATIIMDI---GKNRSKGYGYVTSSTEEEAQKA 115
            + +S       +    + F +FG++ +  I       G        YVT    E+A +A
Sbjct: 20  VVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRA 79

Query: 116 LVDMNGKLLDGRVIFVD 132
           +  +N  ++DGR +   
Sbjct: 80  IQCVNNVVVDGRTLKAS 96

>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 = 58.4 bits (142), Expect = 3e-12
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 3/62 (4%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           K+ L   FS+FGQ+ +  +       + +G  +V       A  AL  M G     + + 
Sbjct: 26  KKSLHAIFSRFGQILDILVSRS---LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR 82

Query: 131 VD 132
           + 
Sbjct: 83  IQ 84

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 59.1 bits (143), Expect = 3e-12
 Identities = 16/89 (17%), Positives = 28/89 (31%), Gaps = 7/89 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             S + + L D   + G V  A +  D       G G V    +E+   A+  ++     
Sbjct: 25  PPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFR 77

Query: 126 GRVIFVDNVRPSRRYNTDASLARQPAQSP 154
                   +R         S  R  ++S 
Sbjct: 78  SHEGETAYIRVKVDGPRSPSYGRSRSRSR 106

>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 = 58.0 bits (141), Expect = 3e-12
 Identities = 15/72 (20%), Positives = 29/72 (40%), Gaps = 7/72 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
            +   T E L   F Q+G+V +  I         + + +VT + ++ AQ         ++
Sbjct: 19  CTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLC--GEDLII 71

Query: 125 DGRVIFVDNVRP 136
            G  + + N  P
Sbjct: 72  KGISVHISNAEP 83

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 60.3 bits (146), Expect = 4e-12
 Identities = 23/95 (24%), Positives = 35/95 (36%), Gaps = 10/95 (10%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
              T + L   F  +G V    I+ +      K    V  +   +AQ A+  +NG  L G
Sbjct: 14  ERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHG 68

Query: 127 RVIFV-----DNVRPSRRYNTDASLARQPAQSPEE 156
           + I +      NV+  R    D  L +    SP  
Sbjct: 69  KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLH 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 = 50.3 bits (120), Expect = 2e-08
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG-KL 123
           +  S ++E L   FS  G V +          + +    +   + EEA +AL+D++   L
Sbjct: 128 IPPSVSEEDLKVLFSSNGGVVK----GFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDL 183

Query: 124 LDGRVIFVD 132
            +   + V 
Sbjct: 184 GENHHLRVS 192

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 58.2 bits (141), Expect = 4e-12
 Identities = 17/86 (19%), Positives = 32/86 (37%), Gaps = 3/86 (3%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + FS  +  + D F    +V    ++ D    R+ G G V   + ++  +AL   N  L+
Sbjct: 24  MPFSAMENDVRDFFHGL-RVDAVHLLKD-HVGRNNGNGLVKFLSPQDTFEAL-KRNRMLM 80

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQP 150
             R + V      +       +   P
Sbjct: 81  IQRYVEVSPATERQWVAAGGHITSGP 106

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 57.2 bits (139), Expect = 8e-12
 Identities = 12/76 (15%), Positives = 31/76 (40%), Gaps = 8/76 (10%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           + +KE L   FS +G + +  I           +G++     +  + A+   + ++  G+
Sbjct: 22  NVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIECESQEMNFGK 73

Query: 128 VIFVDNVRPSRRYNTD 143
            + ++    + R   D
Sbjct: 74  KLILEVSSSNARPQFD 89

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 57.5 bits (139), Expect = 8e-12
 Identities = 19/77 (24%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               + + L D   +    T       +      G G +   +EE   +AL  +N     
Sbjct: 37  PEGCSWQDLKDLARENSLET---TFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFR 93

Query: 126 GRVIFV---DNVRPSRR 139
           G VI V   DN  P RR
Sbjct: 94  GSVITVERDDNPPPIRR 110

>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 = 59.9 bits (144), Expect = 1e-11
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 3/62 (4%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           K+ L   FSQFGQ+ +  +       + +G  +V       A  AL  M G     + + 
Sbjct: 27  KKSLYAIFSQFGQILDILVSRS---LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR 83

Query: 131 VD 132
           + 
Sbjct: 84  IQ 85

>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 = 49.1 bits (116), Expect = 8e-08
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 6/65 (9%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG-KLLDG 126
            T + ML+  F+QF    E  ++            +V    E +A  A   + G K+   
Sbjct: 218 ETNELMLSMLFNQFPGFKEVRLVPG-----RHDIAFVEFDNEVQAGAARDALQGFKITQN 272

Query: 127 RVIFV 131
             + +
Sbjct: 273 NAMKI 277

>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 = 56.7 bits (137), Expect = 2e-11
 Identities = 14/85 (16%), Positives = 30/85 (35%), Gaps = 4/85 (4%)

Query: 65  VSFSTTKEMLADAFSQFG-QVTEATIIMDIG-KNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           +     +E + +  ++    V +  +      K +++G+ +V   +   A  A   +   
Sbjct: 16  IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG 75

Query: 123 --LLDGRVIFVDNVRPSRRYNTDAS 145
              L G  I VD   P    + D  
Sbjct: 76  RIQLWGHQIAVDWAEPEIDVDEDVM 100

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 55.8 bits (135), Expect = 3e-11
 Identities = 11/72 (15%), Positives = 30/72 (41%), Gaps = 8/72 (11%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
           + +KE L   FS +G + +  I           +G++     +  + A+   + ++  G+
Sbjct: 34  NVSKEDLFRIFSPYGHIMQINI--------KNAFGFIQFDNPQSVRDAIEXESQEMNFGK 85

Query: 128 VIFVDNVRPSRR 139
            + ++    + R
Sbjct: 86  KLILEVSSSNAR 97

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 55.0 bits (133), Expect = 5e-11
 Identities = 16/86 (18%), Positives = 28/86 (32%), Gaps = 9/86 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
                    L++ F  FG V    ++MD  K     +  V        +  L   +   L
Sbjct: 16  FPRGVDSAQLSEYFLAFGPVAS--VVMDKDKGV---FAIVEMGDVGAREAVL-SQSQHSL 69

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQP 150
            G  +    VRP  +    +  ++ P
Sbjct: 70  GGHRL---RVRPREQKEFQSPASKSP 92

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 54.2 bits (131), Expect = 9e-11
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
             F+ T++ + +  +         I+ +       GY +V  S EEE ++AL   N + +
Sbjct: 18  APFNVTEKNVMEFLAPLK-PVAIRIVRNA-HGNKTGYIFVDFSNEEEVKQAL-KCNREYM 74

Query: 125 DGRVIFVDNVRPS 137
            GR I V   +  
Sbjct: 75  GGRYIEVFREKSG 87

>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 = 56.2 bits (135), Expect = 2e-10
 Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 10/93 (10%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
              T + L   F  +G V    I+ +      K    V  +   +AQ A+  +NG  L G
Sbjct: 45  ERVTPQSLFILFGVYGDVQRVKILFN-----KKENALVQMADGNQAQLAMSHLNGHKLHG 99

Query: 127 RVIFV-----DNVRPSRRYNTDASLARQPAQSP 154
           + I +      NV+  R    D  L +    SP
Sbjct: 100 KPIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 132

>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 = 51.5 bits (123), Expect = 8e-09
 Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG-KL 123
           +  S ++E L   FS  G V +          + +    +   + EEA +AL+D++   L
Sbjct: 159 IPPSVSEEDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDL 214

Query: 124 LDGRVIFVD 132
            +   + V 
Sbjct: 215 GENHHLRVS 223

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 12/66 (18%), Positives = 25/66 (37%), Gaps = 1/66 (1%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T + + +     GQV    +   + K   KG  +V   + E A+K +     K  +
Sbjct: 20  PTDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVETPGQKYKE 78

Query: 126 GRVIFV 131
             ++ +
Sbjct: 79  TDLLIL 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 53.2 bits (128), Expect = 2e-10
 Identities = 14/78 (17%), Positives = 37/78 (47%), Gaps = 8/78 (10%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATI-----IMDIGKNRSKGYGYVTSSTEEEAQKALVD 118
           ++ F  T+E + D F+   ++   T      ++ +  N+ K + ++   + +E  +A+  
Sbjct: 13  NIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-A 71

Query: 119 MNGKLLDGRVIFVDNVRP 136
            +G +  G+ + +   RP
Sbjct: 72  FDGIIFQGQSLKIR--RP 87

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 54.1 bits (130), Expect = 2e-10
 Identities = 23/91 (25%), Positives = 32/91 (35%), Gaps = 7/91 (7%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKN---RSKGYGYVTSSTEEEAQKALVDMNGK 122
            F+ T E +   F Q   +T     +        R  G  +V  + EE AQ AL   +  
Sbjct: 32  PFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL-RKHKD 90

Query: 123 LLDGRVIFVDNVRPSRRYNTDASLARQPAQS 153
           LL  R I    +  S        L R  + S
Sbjct: 91  LLGKRYI---ELFRSTAAEVQQVLNRFSSAS 118

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 54.5 bits (131), Expect = 2e-10
 Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +  T+  + + FS         I +     R  G   V  +T EEA  A+   +   +
Sbjct: 54  LPYKATENDIYNFFSPLN-PVRVHIEIG-PDGRVTGEADVEFATHEEAVAAM-SKDRANM 110

Query: 125 DGRVIFV 131
             R I +
Sbjct: 111 QHRYIEL 117

>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 = 56.4 bits (135), Expect = 3e-10
 Identities = 17/76 (22%), Positives = 32/76 (42%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           ++ TT+  L   F  +G +    ++      + +GY ++    E +   A    +GK +D
Sbjct: 111 NYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKID 170

Query: 126 GRVIFVDNVRPSRRYN 141
           GR + VD  R      
Sbjct: 171 GRRVLVDVERGRTVKG 186

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 53.8 bits (129), Expect = 3e-10
 Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 3/69 (4%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            V     + +L    S  G + +   I+    + + G  Y+  +T+E AQ  +    G  
Sbjct: 40  EVPKEKLQALLYALASSQGDILD---IVVDLSDDNSGKAYIVFATQESAQAFVEAFQGYP 96

Query: 124 LDGRVIFVD 132
             G  + + 
Sbjct: 97  FQGNPLVIT 105

>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 = 52.7 bits (127), Expect = 3e-10
 Identities = 13/66 (19%), Positives = 31/66 (46%), Gaps = 7/66 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM-NGKL 123
           +  + T+  L + F QFG++   T++        +   ++  +T + A+ A     N  +
Sbjct: 20  LGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLI 73

Query: 124 LDGRVI 129
           ++GR +
Sbjct: 74  VNGRRL 79

>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 = 53.3 bits (128), Expect = 4e-10
 Identities = 13/92 (14%), Positives = 27/92 (29%), Gaps = 7/92 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   T    + + FS+FG +    +              V      EA+KA   +     
Sbjct: 18  LPAGTLAAEIQETFSRFGSLGRVLL------PEGGITAIVEFLEPLEARKAFRHLAYSKF 71

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQPAQSPEE 156
               ++++   P   +           + P E
Sbjct: 72  HHVPLYLEWA-PIGVFGAAPQKKDSQHEQPAE 102

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 52.8 bits (127), Expect = 5e-10
 Identities = 12/67 (17%), Positives = 25/67 (37%), Gaps = 3/67 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +  T+  + + FS         I +     R  G   V  +T E+A  A+   +   +
Sbjct: 23  LPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAM-AKDKANM 79

Query: 125 DGRVIFV 131
             R + +
Sbjct: 80  QHRYVEL 86

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.6 bits (126), Expect = 7e-10
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 6/61 (9%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +    ++  L     + G V    ++M   K     Y +    T EE+++A V +NGK 
Sbjct: 34  GLGNGVSRNQLLPVLEKCGLVDA--LLMPPNK----PYSFARYRTTEESKRAYVTLNGKE 87

Query: 124 L 124
           +
Sbjct: 88  V 88

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 51.6 bits (124), Expect = 9e-10
 Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 7/67 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   +  + + D    +        +     +R+K   +VT    E+AQ A+   +    
Sbjct: 13  LPQDSNCQEVHDLLKDYD-------LKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 125 DGRVIFV 131
            G+ + V
Sbjct: 66  RGKDLIV 72

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 49.8 bits (119), Expect = 5e-09
 Identities = 12/74 (16%), Positives = 22/74 (29%), Gaps = 5/74 (6%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
                   L  A  + G V      + +     +   ++       AQ+A+  + G  L 
Sbjct: 28  PRDARVSDLKRALRELGSVP-----LRLTWQGPRRRAFLHYPDSAAAQQAVSCLQGLRLG 82

Query: 126 GRVIFVDNVRPSRR 139
              + V   R  R 
Sbjct: 83  TDTLRVALARQQRD 96

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 49.9 bits (119), Expect = 9e-09
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 6/91 (6%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGK--NRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +S + E + +  S          +  I     R  G  +V   +E++ + AL   + + 
Sbjct: 26  PWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL-KKDRES 84

Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +  R I    V  S R   D  L      S 
Sbjct: 85  MGHRYI---EVFKSHRTEMDWVLKHSGPNSA 112

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 50.0 bits (119), Expect = 9e-09
 Identities = 14/73 (19%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 61  RCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKN--RSKGYGYVTSSTEEEAQKALVD 118
           +   + +S + E + +  S       A  +  I     R  G  +V   +E++ + AL  
Sbjct: 48  KLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL-K 106

Query: 119 MNGKLLDGRVIFV 131
            + + +  R I V
Sbjct: 107 KDRESMGHRYIEV 119

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 48.2 bits (115), Expect = 2e-08
 Identities = 11/70 (15%), Positives = 22/70 (31%), Gaps = 8/70 (11%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK-- 122
           +     +  L +A  +FG ++   ++        K    V       A  A+        
Sbjct: 29  LIDGVVEADLVEALQEFGPISYVVVM------PKKRQALVEFEDVLGACNAVNYAADNQI 82

Query: 123 LLDGRVIFVD 132
            + G   FV+
Sbjct: 83  YIAGHPAFVN 92

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 47.5 bits (113), Expect = 5e-08
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 6/90 (6%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGK--NRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +S T E + + FS          I  +     + +G   +   +E++ QKAL + +   
Sbjct: 20  PWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL-EKHRMY 78

Query: 124 LDGRVIFVDNVRPSRRYNTDASLARQPAQS 153
           +  R +    V      + DA +     +S
Sbjct: 79  MGQRYVE---VYEINNEDVDALMKSLQVKS 105

>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 = 46.3 bits (110), Expect = 1e-07
 Identities = 10/70 (14%), Positives = 23/70 (32%), Gaps = 8/70 (11%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL--VDMNGK 122
           +  S  +  L +A  +FG +    +         K    V     + A++ +        
Sbjct: 23  LCESVVEADLVEALEKFGTICYVMM------MPFKRQALVEFENIDSAKECVTFAADVPV 76

Query: 123 LLDGRVIFVD 132
            + G+  F +
Sbjct: 77  YIAGQQAFFN 86

>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 = 46.4 bits (110), Expect = 1e-07
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL--VDMNGK 122
           +    T+  +      FG+VT   ++      + K   ++  +TEE A   +        
Sbjct: 39  LPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYYTSVTP 92

Query: 123 LLDGRVIFVD 132
           +L G+ I++ 
Sbjct: 93  VLRGQPIYIQ 102

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 8/70 (11%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL--VDMNGK 122
           +    T+  +      FG+VT   ++      + K   ++  +TEE A   +        
Sbjct: 24  LPIDVTEGEVISLGLPFGKVTNLLML------KGKNQAFIEMNTEEAANTMVNYYTSVTP 77

Query: 123 LLDGRVIFVD 132
           +L G+ I++ 
Sbjct: 78  VLRGQPIYIQ 87

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 44.6 bits (105), Expect = 7e-07
 Identities = 16/98 (16%), Positives = 32/98 (32%), Gaps = 8/98 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR--SKGYGYVTSSTEEEAQKALVD---M 119
           +     ++ +  +F +FG +          K+    KGY ++    E   Q  +      
Sbjct: 16  LPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEE 75

Query: 120 NGKL---LDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
           +GKL   +    I    V+      +D+        S 
Sbjct: 76  DGKLYLCVSSPTIKDKPVQIRPWNLSDSDFVMDSGPSS 113

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 45.9 bits (108), Expect = 8e-07
 Identities = 12/72 (16%), Positives = 25/72 (34%), Gaps = 6/72 (8%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +  +  +  +   FS+ G +     +       SK  G+V    +  A+ A   M+ + 
Sbjct: 150 HLKPAQIESRIRFVFSRLGDIDRIRYV------ESKNCGFVKFKYQANAEFAKEAMSNQT 203

Query: 124 LDGRVIFVDNVR 135
           L        + R
Sbjct: 204 LLLPSDKEWDDR 215

>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 Length = 112

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 4/70 (5%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           +E L    S+FGQ+ +    + +      G   V+    EEA   +  ++G+   GR I 
Sbjct: 40  REDLRVECSKFGQIRK----LLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 95

Query: 131 VDNVRPSRRY 140
                 +  Y
Sbjct: 96  AQAWDGTTDY 105

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 45.2 bits (106), Expect = 1e-06
 Identities = 16/128 (12%), Positives = 35/128 (27%), Gaps = 4/128 (3%)

Query: 4   QSLIQTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCI 63
             L     +       ++  L+  S    ++    S                   + +  
Sbjct: 58  NRLTTDFNVIVEALSKSKAELMEISEDKTKIRRSPSKPLPEVTDEYKNDVKNRSVYIKGF 117

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
                 T + + +     GQV    +   + K   KG  +V   + E A+K +     K 
Sbjct: 118 P--TDATLDDIKEWLEDKGQVLNIQMRRTLHK-AFKGSIFVVFDSIESAKKFVETPGQK- 173

Query: 124 LDGRVIFV 131
                + +
Sbjct: 174 YKETDLLI 181

>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 = 42.9 bits (101), Expect = 3e-06
 Identities = 12/70 (17%), Positives = 25/70 (35%), Gaps = 8/70 (11%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKAL--VDMNGK 122
           +    T+  +      FG+VT   +       + K   ++  +TEE A   +        
Sbjct: 23  LPGEVTETEVIALGLPFGKVTNILM------LKGKNQAFLELATEEAAITMVNYYSAVTP 76

Query: 123 LLDGRVIFVD 132
            L  + I++ 
Sbjct: 77  HLRNQPIYIQ 86

>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 Length = 104

 Score = 42.2 bits (99), Expect = 5e-06
 Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF 130
           +E+  +   ++G+V E   + D   +   G  YV    EE+A+KA++D+N +  +G+ I 
Sbjct: 41  EEVFTEMEEKYGEVEEM-NVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH 99

Query: 131 VD 132
            +
Sbjct: 100 AE 101

>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 Length = 105

 Score = 40.2 bits (94), Expect = 3e-05
 Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)

Query: 71  KEMLADAFSQFGQVTEATI--IMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV 128
            E + D  S++G V    I   +D  +    G  +V  ++  + QKA+  + G+    RV
Sbjct: 29  VEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRV 88

Query: 129 I 129
           +
Sbjct: 89  V 89

>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 Length = 114

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 78  FSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS 137
            ++ G V      + + KN ++G  YV   +   A  A+  ++G+   G++I    V   
Sbjct: 38  CNKHGGVIH----IYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLP 93

Query: 138 RRYNT---DASLARQPAQS 153
             Y+    D+  A Q    
Sbjct: 94  -TYHNLFPDSMTATQLLVP 111

>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 Length = 96

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 11/74 (14%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 64  SVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
            +S    +++L +AF++ G+V    +         +    V     ++A  A+  ++   
Sbjct: 20  RLSRKELQQLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMENLQDAIGAVNSLHRYK 76

Query: 124 LDGRVIFVDNVRPS 137
           +  + I V     +
Sbjct: 77  IGSKKILVSLATGA 90

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.1 bits (90), Expect = 3e-04
 Identities = 26/179 (14%), Positives = 54/179 (30%), Gaps = 48/179 (26%)

Query: 3   AQSLIQTRKIQQFNSYFTEDSLLSFSSKPY-------------QVVNYFSLHC----IVR 45
           ++S   +    + +S   E   L   SKPY             +  N F+L C      R
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRL-LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTR 273

Query: 46  PSSDLIMQLVNVSFWRCISVSFS----TTKEMLADAFSQFGQVT------EA-------- 87
                +   ++ +    IS+       T  E+      ++          E         
Sbjct: 274 FKQ--VTDFLSAATTTHISLDHHSMTLTPDEVK-SLLLKYLDCRPQDLPREVLTTNPRRL 330

Query: 88  TII---MDIGKNRSKGYGYVTSSTEEEAQKALVDM-----NGKLLDGRVIFVDNVR-PS 137
           +II   +  G      + +V         ++ +++       K+ D   +F  +   P+
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPT 389

>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} PDB: 3us5_A 2dny_A Length = 118

 Score = 37.0 bits (86), Expect = 4e-04
 Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 4/63 (6%)

Query: 71  KEMLADAFSQFGQVTEATIIMDIGKNRSKGYG----YVTSSTEEEAQKALVDMNGKLLDG 126
           +  + +   +FG V    I  +              +V  S   E  KA+  +NG+   G
Sbjct: 39  EGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG 98

Query: 127 RVI 129
           R +
Sbjct: 99  RKV 101

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	157
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.92
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.9
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.89
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.89
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.89
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.89
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.89
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.89
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.89
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.89
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.89
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.89
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.88
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.88
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.88
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.88
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.88
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.88
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.88
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.88
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.88
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.88
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.88
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.88
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.88
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.88
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.88
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.88
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.88
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.88
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.88
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.87
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.87
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.87
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.87
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.87
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.87
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.87
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.87
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.87
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.87
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.87
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.87
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.87
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.86
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.86
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.86
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.86
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.86
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.86
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.86
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.86
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.86
2div_A	99	TRNA selenocysteine associated protein; structural	99.86
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.86
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.86
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.86
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.86
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.86
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.86
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.85
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.85
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.85
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.85
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.85
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.85
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.85
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.85
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.85
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.85
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.85
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.85
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.85
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.84
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.84
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.75
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.84
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.84
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.84
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.84
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.84
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.84
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.84
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.84
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.83
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.83
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.83
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.83
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.83
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.83
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.83
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.83
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.83
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.83
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.83
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.83
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.83
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.83
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.83
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.82
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.82
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.82
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.82
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.82
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.82
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.82
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.82
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.82
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.82
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.82
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.82
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.82
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.82
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.81
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.81
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.81
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.81
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.81
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.81
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.81
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.81
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.81
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.81
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.81
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.81
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.81
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.8
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.8
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.8
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.8
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.8
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.8
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.8
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.8
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.8
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.8
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.8
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.8
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.8
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.8
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.8
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.79
1x5p_A	97	Negative elongation factor E; structure genomics,	99.79
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.79
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.79
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.79
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.79
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.79
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.79
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.79
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.78
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.78
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.78
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.78
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.77
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.77
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.77
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.77
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.77
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.76
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.76
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.76
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.75
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.75
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.75
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.75
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.75
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.74
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.74
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.74
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.74
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.73
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.73
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.73
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.73
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.72
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.71
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.71
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.71
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.7
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.7
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.7
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.7
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.7
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.69
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.69
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.69
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.67
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.67
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.66
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.64
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.64
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.62
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.61
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.6
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.6
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.58
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.57
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.56
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.5
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.4
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.35
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.25
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.16
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.13
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.82
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.97
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.81
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.71
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.55
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.55
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.66
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.55
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	96.37
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.29
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	95.32
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.27
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	91.47
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	86.98

>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=99.92  E-value=1.9e-24  Score=138.91  Aligned_cols=81  Identities=30%  Similarity=0.416  Sum_probs=78.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|++|+|.+++
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            35689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      |
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            6

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.90  E-value=9.5e-23  Score=133.96  Aligned_cols=91  Identities=26%  Similarity=0.379  Sum_probs=84.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA   92 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCC
Q 036791          135 RPSRRYNTDAS  145 (157)
Q Consensus       135 ~~~~~~~~~~~  145 (157)
                      +++........
T Consensus        93 ~~~~~~~~~~~  103 (115)
T 2dgo_A           93 TRKPPAPKSTY  103 (115)
T ss_dssp             SCCCCCSCCCC
T ss_pred             cCCCCCCcccc
Confidence            98766554433

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.89  E-value=1e-22  Score=133.15  Aligned_cols=84  Identities=13%  Similarity=0.203  Sum_probs=79.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +..+|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a~   84 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLDI   84 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECS
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      .+..
T Consensus        85 ~~~~   88 (110)
T 3s8s_A           85 KGQQ   88 (110)
T ss_dssp             TTHH
T ss_pred             CCcH
Confidence            6543

>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=99.89  E-value=1.6e-22  Score=129.48  Aligned_cols=88  Identities=23%  Similarity=0.373  Sum_probs=82.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|++|+..|||..+.|++|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   85 (99)
T 1whw_A            6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            35678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      .++.....
T Consensus        86 ~~~~~~~~   93 (99)
T 1whw_A           86 TIKKEASQ   93 (99)
T ss_dssp             CCCSTTCC
T ss_pred             CCCccccc
Confidence            98766543

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.89  E-value=1.9e-22  Score=128.10  Aligned_cols=87  Identities=33%  Similarity=0.471  Sum_probs=81.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|++|+|.++.
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   83 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHVT   83 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEESS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            45789999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 036791          136 PSRRYNT  142 (157)
Q Consensus       136 ~~~~~~~  142 (157)
                      ++..+..
T Consensus        84 ~~~~~~~   90 (95)
T 2dnz_A           84 ERLDGGS   90 (95)
T ss_dssp             CCCCCCC
T ss_pred             cccCCCC
Confidence            8765543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.89  E-value=2.3e-22  Score=136.29  Aligned_cols=92  Identities=17%  Similarity=0.244  Sum_probs=84.7

Q ss_pred             hccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           52 MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        52 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ......++|||+|||.++++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|.+|++.|||..|.|+.|+|
T Consensus        37 ~~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           37 PEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             CCTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            33455689999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeecCCCCCCCC
Q 036791          132 DNVRPSRRYNTD  143 (157)
Q Consensus       132 ~~~~~~~~~~~~  143 (157)
                      .+++++..+...
T Consensus       117 ~~a~~~~~~~~~  128 (139)
T 1u6f_A          117 ALAASGHQRPGI  128 (139)
T ss_dssp             EESSCCCCCCCS
T ss_pred             EECCCCCCCCCC
Confidence            999987666543

>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=99.89  E-value=2.7e-22  Score=124.32  Aligned_cols=81  Identities=23%  Similarity=0.410  Sum_probs=78.3

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      .+|||+|||.++++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|++|+|.+++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~~   81 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAKL   81 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCcC
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q 036791          138 R  138 (157)
Q Consensus       138 ~  138 (157)
                      .
T Consensus        82 ~   82 (83)
T 3md1_A           82 E   82 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.89  E-value=2.2e-22  Score=130.10  Aligned_cols=87  Identities=22%  Similarity=0.226  Sum_probs=81.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..||+..|.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   92 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   92 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        93 ~~~~~~~   99 (105)
T 1x5u_A           93 SAHNKNL   99 (105)
T ss_dssp             TTTSCCC
T ss_pred             CCCCcCC
Confidence            9876544

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.89  E-value=3e-22  Score=129.10  Aligned_cols=87  Identities=22%  Similarity=0.355  Sum_probs=81.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..||+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   92 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEC
Confidence            45678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        93 ~~~~~~~   99 (103)
T 2cq0_A           93 KPSTNSG   99 (103)
T ss_dssp             SCCCCSC
T ss_pred             CCCCCCC
Confidence            9876543

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.89  E-value=2e-23  Score=132.11  Aligned_cols=84  Identities=14%  Similarity=0.239  Sum_probs=77.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CCccCCcEEEEEeec
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFG-QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN-GKLLDGRVIFVDNVR  135 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~-g~~~~g~~l~v~~~~  135 (157)
                      .+|||+|||+++++++|+++|++|| .|..+.++.++.+|+++|||||+|.+.++|++|++.++ +..++|++|+|.++.
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a~   81 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYSD   81 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEcC
Confidence            4799999999999999999999999 89999999999999999999999999999999999874 557999999999999


Q ss_pred             CCCCCC
Q 036791          136 PSRRYN  141 (157)
Q Consensus       136 ~~~~~~  141 (157)
                      ++....
T Consensus        82 ~~~~~~   87 (91)
T 2lxi_A           82 PKPKIN   87 (91)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            876543

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.89  E-value=4.6e-22  Score=127.38  Aligned_cols=87  Identities=23%  Similarity=0.370  Sum_probs=81.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ |++..++|+.|+|.++
T Consensus         8 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            8 SKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeEEEEEEC
Confidence            356789999999999999999999999999999999999999999999999999999999999 9999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      .++.....
T Consensus        87 ~~~~~~~~   94 (99)
T 2dgs_A           87 EPRDSKSS   94 (99)
T ss_dssp             CCCCCCCC
T ss_pred             CCCcccCC
Confidence            98765443

>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=99.89  E-value=4.8e-22  Score=130.62  Aligned_cols=87  Identities=23%  Similarity=0.256  Sum_probs=81.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  102 (115)
T 2cpz_A           23 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK  102 (115)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus       103 ~~~~~~~  109 (115)
T 2cpz_A          103 RSKNDSK  109 (115)
T ss_dssp             CCSCCCC
T ss_pred             CCCCcCC
Confidence            9876543

>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=99.88  E-value=4.3e-22  Score=131.29  Aligned_cols=85  Identities=26%  Similarity=0.402  Sum_probs=79.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||.++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            5 DHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             CSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            446789999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      +++...
T Consensus        84 ~~~~~~   89 (116)
T 2fy1_A           84 KKPSFQ   89 (116)
T ss_dssp             CCSSCS
T ss_pred             CCCCCC
Confidence            876543

>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=99.88  E-value=3.5e-22  Score=124.85  Aligned_cols=82  Identities=28%  Similarity=0.441  Sum_probs=77.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +..+|||+|||.++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|+.|+|.+++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            45789999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ++
T Consensus        85 ~k   86 (87)
T 3bs9_A           85 RK   86 (87)
T ss_dssp             --
T ss_pred             CC
Confidence            75

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=1.2e-21  Score=128.41  Aligned_cols=88  Identities=26%  Similarity=0.226  Sum_probs=80.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|.+||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           13 RLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            345789999999999999999999999999999999996 5999999999999999999999999999999999999999


Q ss_pred             cCCCCCCCC
Q 036791          135 RPSRRYNTD  143 (157)
Q Consensus       135 ~~~~~~~~~  143 (157)
                      +....+...
T Consensus        92 ~~~~~~~~~  100 (114)
T 2do0_A           92 ERALPKGDF  100 (114)
T ss_dssp             SCCCCCSCC
T ss_pred             ccCCCCCCC
Confidence            876555443

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.88  E-value=5.2e-22  Score=128.72  Aligned_cols=89  Identities=19%  Similarity=0.358  Sum_probs=82.2

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEE
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDM-NGKLLDGRVIFV  131 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~ai~~l-~g~~~~g~~l~v  131 (157)
                      ....++|||+|||+.+++++|+++|+.||.|..+.++.+ +.+++++|||||+|.+.++|++|+..| |+..+.|+.|+|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~v   91 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   91 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEEE
Confidence            345678999999999999999999999999999999998 788999999999999999999999999 999999999999


Q ss_pred             EeecCCCCCCC
Q 036791          132 DNVRPSRRYNT  142 (157)
Q Consensus       132 ~~~~~~~~~~~  142 (157)
                      .+++++.....
T Consensus        92 ~~a~~~~~~~~  102 (107)
T 2cph_A           92 EWADSEVTVQS  102 (107)
T ss_dssp             EECCCCCCCCC
T ss_pred             EeCCCCCCCCC
Confidence            99998765443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2.4e-22  Score=127.86  Aligned_cols=88  Identities=24%  Similarity=0.311  Sum_probs=81.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEA-TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ...++|||+|||..+++++|+++|++||.|..+ .++.++.+++++|||||+|.+.++|++|+..||+..++|++|+|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            346789999999999999999999999999999 9999989999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 036791          134 VRPSRRYNT  142 (157)
Q Consensus       134 ~~~~~~~~~  142 (157)
                      +.++..+..
T Consensus        83 a~~~~~~~~   91 (96)
T 1x5t_A           83 AFKKDSKGS   91 (96)
T ss_dssp             SCCCCCCCC
T ss_pred             ecccCCCCC
Confidence            998765543

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.88  E-value=8.2e-22  Score=126.40  Aligned_cols=85  Identities=22%  Similarity=0.332  Sum_probs=79.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..++|++|+|.++
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   93 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAIS   93 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            445789999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      +++..+
T Consensus        94 ~~~~~~   99 (100)
T 2do4_A           94 NSGPSS   99 (100)
T ss_dssp             CCCSCC
T ss_pred             CCCCCC
Confidence            987653

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=3.4e-22  Score=128.56  Aligned_cols=88  Identities=33%  Similarity=0.541  Sum_probs=81.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|++|+|.++
T Consensus        10 ~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   89 (102)
T 1x5s_A           10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA   89 (102)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            35678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      +++.....
T Consensus        90 ~~~~~~~~   97 (102)
T 1x5s_A           90 GKSSDNRS   97 (102)
T ss_dssp             ECCCCCCC
T ss_pred             CCCCCCCC
Confidence            98765433

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=2.6e-22  Score=129.16  Aligned_cols=88  Identities=25%  Similarity=0.381  Sum_probs=82.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus        10 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   89 (102)
T 2cqb_A           10 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   89 (102)
T ss_dssp             CCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEeC
Confidence            35678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      +++.....
T Consensus        90 ~~~~~~~~   97 (102)
T 2cqb_A           90 KPMRIKES   97 (102)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCCCC
Confidence            98765443

>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=99.88  E-value=3.6e-22  Score=129.32  Aligned_cols=87  Identities=21%  Similarity=0.192  Sum_probs=81.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc---CCcEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL---DGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~---~g~~l~v  131 (157)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..+   .|++|+|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l~v   90 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPIQV   90 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceEEE
Confidence            4567899999999999999999999999999999999999999999999999999999999999999987   8999999


Q ss_pred             EeecCCCCCC
Q 036791          132 DNVRPSRRYN  141 (157)
Q Consensus       132 ~~~~~~~~~~  141 (157)
                      .++.++..+.
T Consensus        91 ~~a~~~~~~~  100 (106)
T 2dgp_A           91 KPADSESRGG  100 (106)
T ss_dssp             EECCCCSCCC
T ss_pred             EECCcccccC
Confidence            9999876544

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=5.6e-22  Score=128.41  Aligned_cols=84  Identities=29%  Similarity=0.321  Sum_probs=80.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|+..|||..++|+.|+|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      .++.
T Consensus       101 ~~~~  104 (106)
T 1p27_B          101 FVRG  104 (106)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            8765

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=9.6e-22  Score=126.73  Aligned_cols=86  Identities=31%  Similarity=0.514  Sum_probs=80.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+  +++++|||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            45678999999999999999999999999999999987  7999999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      .++..+..
T Consensus        91 ~~~~~~~~   98 (103)
T 2d9p_A           91 QRKEERQS   98 (103)
T ss_dssp             SSCCCCCC
T ss_pred             cccccCCC
Confidence            98765543

>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=99.88  E-value=8.5e-22  Score=128.49  Aligned_cols=88  Identities=26%  Similarity=0.360  Sum_probs=82.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CCccCCcE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN------GKLLDGRV  128 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~------g~~~~g~~  128 (157)
                      ...++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|++|+..||      +..++|+.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g~~   92 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   92 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcCEE
Confidence            456789999999999999999999999999999999999999999999999999999999999999      99999999


Q ss_pred             EEEEeecCCCCCCC
Q 036791          129 IFVDNVRPSRRYNT  142 (157)
Q Consensus       129 l~v~~~~~~~~~~~  142 (157)
                      |+|.++.++.....
T Consensus        93 l~v~~a~~~~~~~~  106 (111)
T 1x4h_A           93 LKVDLAVTRDEAAS  106 (111)
T ss_dssp             EEEECCCCCCCCCC
T ss_pred             EEEEECCCCccCCC
Confidence            99999998765443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.88  E-value=3.9e-22  Score=128.55  Aligned_cols=87  Identities=24%  Similarity=0.379  Sum_probs=81.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|+.|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2dnm_A           11 DGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVA   90 (103)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus        91 ~~~~~~~   97 (103)
T 2dnm_A           91 RYGRRDL   97 (103)
T ss_dssp             SSCCSCC
T ss_pred             CcCCCCC
Confidence            8765443

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.88  E-value=1.3e-21  Score=128.73  Aligned_cols=84  Identities=29%  Similarity=0.429  Sum_probs=78.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.+++ .|.|+.|+|.++
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~~a   93 (116)
T 2cqd_A           15 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   93 (116)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEEEc
Confidence            4568899999999999999999999999999999999999999999999999999999999999998 899999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .++..
T Consensus        94 ~~~~~   98 (116)
T 2cqd_A           94 YLGAK   98 (116)
T ss_dssp             TTTCC
T ss_pred             ccCCC
Confidence            76543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.88  E-value=8.6e-23  Score=130.13  Aligned_cols=80  Identities=20%  Similarity=0.310  Sum_probs=74.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCC--eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC----ccCCcEEE
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQ--VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK----LLDGRVIF  130 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~--i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~----~~~g~~l~  130 (157)
                      -.+|||+|||+++++++|+++|++||.  +..|.+++|+.+|+++|||||+|.+.++|++|++.|||.    .|+|++|.
T Consensus         9 m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i~   88 (95)
T 2lkz_A            9 MDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIG   88 (95)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEEE
T ss_pred             cCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEEE
Confidence            457999999999999999999999995  678999999999999999999999999999999999997    48999999


Q ss_pred             EEeecC
Q 036791          131 VDNVRP  136 (157)
Q Consensus       131 v~~~~~  136 (157)
                      |+|+++
T Consensus        89 V~~Aks   94 (95)
T 2lkz_A           89 VDFAKS   94 (95)
T ss_dssp             EEECCC
T ss_pred             EEEccC
Confidence            999975

>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=99.88  E-value=1.6e-21  Score=126.10  Aligned_cols=87  Identities=20%  Similarity=0.212  Sum_probs=80.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC---cEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG---RVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g---~~l~v  131 (157)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++ +++++|||||+|.+.++|++|++.||+..+.|   ++|+|
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            456789999999999999999999999999999999996 79999999999999999999999999999988   99999


Q ss_pred             EeecCCCCCCC
Q 036791          132 DNVRPSRRYNT  142 (157)
Q Consensus       132 ~~~~~~~~~~~  142 (157)
                      .++.++..+..
T Consensus        92 ~~a~~~~~~~~  102 (105)
T 2dnh_A           92 KFADTDKESGP  102 (105)
T ss_dssp             EESCSSCCCSC
T ss_pred             EECccCcccCC
Confidence            99998765543

>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=99.88  E-value=8.9e-23  Score=128.67  Aligned_cols=81  Identities=20%  Similarity=0.242  Sum_probs=72.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      .+|||+|||+++++++|+++|++||  .|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            4699999999999999999999999  99999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      +..
T Consensus        82 ~~~   84 (90)
T 3p5t_L           82 KLE   84 (90)
T ss_dssp             ---
T ss_pred             CCc
Confidence            764

>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=99.88  E-value=3.6e-22  Score=133.17  Aligned_cols=87  Identities=28%  Similarity=0.298  Sum_probs=81.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..|+|+.|+|.++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            44678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus       100 ~~~~~~~  106 (126)
T 3ex7_B          100 FVRGPPK  106 (126)
T ss_dssp             EESSSCC
T ss_pred             cCCCCCC
Confidence            8765543

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.88  E-value=1.8e-21  Score=125.54  Aligned_cols=85  Identities=19%  Similarity=0.287  Sum_probs=79.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|+.|| |..+.++.++.+++++|||||+|.+.++|++|+ .||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEECEEEEC
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEEEEEEe
Confidence            4467899999999999999999999997 999999999999999999999999999999999 89999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2dng_A           91 EGRKQDK   97 (103)
T ss_dssp             CCCCCCC
T ss_pred             cCCCCCC
Confidence            9876543

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=9.6e-22  Score=126.98  Aligned_cols=86  Identities=17%  Similarity=0.250  Sum_probs=80.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGK-NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      .+..+|||+|||+.+++++|+++|..|| |..+.++.++.+ ++++|||||+|.+.++|++|+ .||+..|.|+.|+|.+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcEEEEEE
Confidence            3457899999999999999999999999 999999999887 999999999999999999999 8999999999999999


Q ss_pred             ecCCCCCCC
Q 036791          134 VRPSRRYNT  142 (157)
Q Consensus       134 ~~~~~~~~~  142 (157)
                      +.++....+
T Consensus        91 a~~~~~~~~   99 (104)
T 1wi8_A           91 ADQAQDKDS   99 (104)
T ss_dssp             CCCCCCCCC
T ss_pred             ccCCCCCCC
Confidence            998766554

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.87  E-value=9.2e-22  Score=125.67  Aligned_cols=86  Identities=30%  Similarity=0.370  Sum_probs=79.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC---CCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIG---KNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~---~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.   +++++|||||+|.+.++|++|+..||+..+.|++|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   83 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVR   83 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            456899999999999999999999999999999998876   66899999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 036791          133 NVRPSRRYN  141 (157)
Q Consensus       133 ~~~~~~~~~  141 (157)
                      ++.++....
T Consensus        84 ~a~~~~~~~   92 (98)
T 2cpf_A           84 ISERATKPA   92 (98)
T ss_dssp             CSSCSSCCC
T ss_pred             EccCCCCCC
Confidence            998875443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=6.5e-22  Score=129.57  Aligned_cols=87  Identities=26%  Similarity=0.236  Sum_probs=81.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVT--------EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      .+.++|||+|||+.+++++|+++|++||.|.        .+.++.++.+++++|||||+|.+.++|++|++.||+..|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   92 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   92 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCccCC
Confidence            4567899999999999999999999999998        69999999999999999999999999999999999999999


Q ss_pred             cEEEEEeecCCCCCC
Q 036791          127 RVIFVDNVRPSRRYN  141 (157)
Q Consensus       127 ~~l~v~~~~~~~~~~  141 (157)
                      +.|+|.+++++....
T Consensus        93 ~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           93 SKLKVSLARKKPPMN  107 (113)
T ss_dssp             EECEEECSSCCCCST
T ss_pred             CEEEEEECCCCCCCC
Confidence            999999999876544

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=1.5e-21  Score=123.93  Aligned_cols=82  Identities=28%  Similarity=0.433  Sum_probs=78.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..|||..++|++|+|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   92 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVSGP   92 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEec
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cC
Q 036791          135 RP  136 (157)
Q Consensus       135 ~~  136 (157)
                      ++
T Consensus        93 ~~   94 (95)
T 2cqc_A           93 SS   94 (95)
T ss_dssp             SC
T ss_pred             CC
Confidence            75

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.87  E-value=1.2e-21  Score=125.44  Aligned_cols=81  Identities=22%  Similarity=0.208  Sum_probs=77.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTE--------ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      ....+|||+|||.++++++|+++|++||.|..        +.++.++.+|+++|||||+|.+.++|++|++.|||..+.|
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~g   90 (99)
T 2la6_A           11 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   90 (99)
T ss_dssp             CCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCC
Confidence            45678999999999999999999999999999        9999999999999999999999999999999999999999


Q ss_pred             cEEEEEeec
Q 036791          127 RVIFVDNVR  135 (157)
Q Consensus       127 ~~l~v~~~~  135 (157)
                      +.|+|.+++
T Consensus        91 ~~l~V~~A~   99 (99)
T 2la6_A           91 NPIKVSFAT   99 (99)
T ss_dssp             SBCEEEECC
T ss_pred             cEEEEEecC
Confidence            999999874

>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=99.87  E-value=1.5e-21  Score=134.78  Aligned_cols=86  Identities=24%  Similarity=0.292  Sum_probs=81.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.++
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  116 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD  116 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      ++....
T Consensus       117 ~~~~~~  122 (156)
T 1h2v_Z          117 AGFKEG  122 (156)
T ss_dssp             SCCCTT
T ss_pred             CCCCCc
Confidence            875543

>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=99.87  E-value=1.3e-21  Score=127.48  Aligned_cols=84  Identities=36%  Similarity=0.514  Sum_probs=80.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|.++
T Consensus        24 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  103 (108)
T 2jrs_A           24 AGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHV  103 (108)
T ss_dssp             SSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEECS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      +++.
T Consensus       104 ~~k~  107 (108)
T 2jrs_A          104 TERT  107 (108)
T ss_dssp             CSSC
T ss_pred             ccCC
Confidence            8865

>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=99.87  E-value=1.1e-21  Score=125.02  Aligned_cols=83  Identities=24%  Similarity=0.329  Sum_probs=79.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||..+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            46899999999999999999999999999999999998999999999999999999999999999999999999999988


Q ss_pred             CCC
Q 036791          137 SRR  139 (157)
Q Consensus       137 ~~~  139 (157)
                      +..
T Consensus        82 ~~~   84 (96)
T 2x1f_A           82 SDI   84 (96)
T ss_dssp             SSG
T ss_pred             CCC
Confidence            653

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A

Probab=99.87  E-value=1e-21  Score=129.24  Aligned_cols=83  Identities=33%  Similarity=0.523  Sum_probs=75.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+++++++|+++|++||.|..+.|+.++  +.++|||||+|.+.++|++|++.|+|..|+|++|+|.++.+
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4679999999999999999999999999999999985  45899999999999999999999999999999999999988


Q ss_pred             CCCCC
Q 036791          137 SRRYN  141 (157)
Q Consensus       137 ~~~~~  141 (157)
                      +..+.
T Consensus        83 ~~~~~   87 (115)
T 4f25_A           83 RKERE   87 (115)
T ss_dssp             CCC--
T ss_pred             ccccc
Confidence            65543

>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=99.87  E-value=8.8e-22  Score=122.49  Aligned_cols=81  Identities=25%  Similarity=0.377  Sum_probs=77.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|++|+|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            35678999999999999999999999999999999999899999999999999999999999999999999999999997


Q ss_pred             c
Q 036791          135 R  135 (157)
Q Consensus       135 ~  135 (157)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.87  E-value=9.7e-22  Score=128.13  Aligned_cols=85  Identities=22%  Similarity=0.284  Sum_probs=80.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|+..|||..++|+.|+|.++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .++..
T Consensus       104 ~~~~~  108 (110)
T 1oo0_B          104 FVKGP  108 (110)
T ss_dssp             EESSC
T ss_pred             ccCCC
Confidence            87654

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.87  E-value=9.4e-22  Score=129.41  Aligned_cols=87  Identities=26%  Similarity=0.413  Sum_probs=81.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|++|+.. ++..|+|+.|+|.++
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V~~a  103 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEPKRA  103 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEEEEC
Confidence            4457899999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      .++.....
T Consensus       104 ~~~~~~~~  111 (116)
T 1x4b_A          104 VAREESGS  111 (116)
T ss_dssp             SSCCCCCC
T ss_pred             CCCccCCC
Confidence            98766543

>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=99.87  E-value=1.3e-22  Score=130.86  Aligned_cols=86  Identities=27%  Similarity=0.475  Sum_probs=80.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||..+++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            35789999999999999999999999999999999999899999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 036791          136 PSRRYN  141 (157)
Q Consensus       136 ~~~~~~  141 (157)
                      ++....
T Consensus        87 ~~~~~~   92 (104)
T 1p1t_A           87 SEKNKE   92 (104)
T ss_dssp             CTTHHH
T ss_pred             Cccchh
Confidence            875543

>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=99.86  E-value=1.5e-21  Score=122.07  Aligned_cols=84  Identities=26%  Similarity=0.380  Sum_probs=78.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC-cceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR-SKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~-~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ..++|||+|||.++++++|+++|++||.|..+.++.++.++. ++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            356899999999999999999999999999999999987766 8999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .+...
T Consensus        83 ~~~~~   87 (88)
T 4a8x_A           83 LAPWP   87 (88)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=2.1e-21  Score=125.27  Aligned_cols=87  Identities=20%  Similarity=0.284  Sum_probs=80.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhc-CCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc-cCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQ-FGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL-LDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~-~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~-~~g~~l~v~  132 (157)
                      .+..+|||+|||+++++++|+++|+. ||.|..+.++.++ +++++|||||+|.+.++|.+|++.|++.. ++|++|+|.
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            7 GPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            34578999999999999999999999 9999999999997 89999999999999999999999999999 999999999


Q ss_pred             eecCCCCCCC
Q 036791          133 NVRPSRRYNT  142 (157)
Q Consensus       133 ~~~~~~~~~~  142 (157)
                      ++.++..+..
T Consensus        86 ~a~~~~~~~~   95 (104)
T 2dhg_A           86 VAIPKASRVK   95 (104)
T ss_dssp             BCCCCCSCCC
T ss_pred             EccCCCcCCC
Confidence            9988765443

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=2.1e-21  Score=122.98  Aligned_cols=81  Identities=30%  Similarity=0.352  Sum_probs=77.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|++|+|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   93 (94)
T 2e5h_A           14 PSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASIA   93 (94)
T ss_dssp             CCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEec
Confidence            45578999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q 036791          135 R  135 (157)
Q Consensus       135 ~  135 (157)
                      +
T Consensus        94 k   94 (94)
T 2e5h_A           94 I   94 (94)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.86  E-value=6e-21  Score=122.96  Aligned_cols=86  Identities=20%  Similarity=0.251  Sum_probs=78.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++.  .++|||||+|.+.++|++|+..||+..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHT--SNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCC--SSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCC--CCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            4567899999999999999999999999999999998854  36899999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      +++.....
T Consensus        91 ~~~~~~~~   98 (103)
T 2cqi_A           91 TTPSSQKS   98 (103)
T ss_dssp             CCTTCCCC
T ss_pred             CCCccccc
Confidence            98665443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=1.9e-21  Score=125.79  Aligned_cols=86  Identities=28%  Similarity=0.384  Sum_probs=80.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|+.. ++..|+|+.|+|.++
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~l~V~~a   92 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDPKPC   92 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEEEBCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEc
Confidence            4567899999999999999999999999999999999999999999999999999999999998 999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        93 ~~~~~~~   99 (105)
T 2dh8_A           93 TPRGMQP   99 (105)
T ss_dssp             CCSSCCT
T ss_pred             cCCCCCC
Confidence            9876544

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.86  E-value=5.5e-22  Score=127.47  Aligned_cols=82  Identities=21%  Similarity=0.357  Sum_probs=78.3

Q ss_pred             ccEEEEcCCCC------CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC-cEE
Q 036791           57 VSFWRCISVSF------STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG-RVI  129 (157)
Q Consensus        57 ~~~l~V~nl~~------~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g-~~l  129 (157)
                      .++|||+|||.      .+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..+.| +.|
T Consensus         6 ~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r~l   85 (100)
T 3ns6_A            6 DQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRL   85 (100)
T ss_dssp             GGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCeEE
Confidence            56899999999      99999999999999999999999999999999999999999999999999999999999 999


Q ss_pred             EEEeecCCC
Q 036791          130 FVDNVRPSR  138 (157)
Q Consensus       130 ~v~~~~~~~  138 (157)
                      +|.++.++.
T Consensus        86 ~V~~a~~~~   94 (100)
T 3ns6_A           86 FLYTMKDVE   94 (100)
T ss_dssp             EEEESHHHH
T ss_pred             EEEECchhh
Confidence            999997653

>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=99.86  E-value=6.6e-21  Score=124.00  Aligned_cols=85  Identities=15%  Similarity=0.203  Sum_probs=76.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+   +.++|||||+|.+.++|++|++.||+..|+|+.|+|.++
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            45678999999999999999999999999999998654   568999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      +++.....
T Consensus        97 ~~~~~~~~  104 (109)
T 1x4a_A           97 RSGRGTGS  104 (109)
T ss_dssp             CCCCCCCC
T ss_pred             ccCCCCCC
Confidence            98765443

>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=99.86  E-value=1.1e-20  Score=121.70  Aligned_cols=85  Identities=27%  Similarity=0.446  Sum_probs=78.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+++++++|+++|++||.|..+.++.++.  .++|||||+|.+.++|++|+..||+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            4567899999999999999999999999999999998853  38999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2cq3_A           91 TARVMTN   97 (103)
T ss_dssp             CSSCCCC
T ss_pred             ccCCCCC
Confidence            9876544

>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=99.86  E-value=3.5e-21  Score=120.72  Aligned_cols=82  Identities=28%  Similarity=0.396  Sum_probs=77.7

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+ .|||..+.|+.|+|.+++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~~a~   83 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVIPKR   83 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEEETT
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEEEcc
Confidence            3568999999999999999999999999999999999889999999999999999999999 899999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ++.
T Consensus        84 ~~~   86 (89)
T 3ucg_A           84 TNR   86 (89)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            753

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.86  E-value=2.7e-21  Score=123.71  Aligned_cols=84  Identities=20%  Similarity=0.229  Sum_probs=79.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCee-EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE----E
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVT-EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV----I  129 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~-~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~----l  129 (157)
                      ...++|||+|||+++++++|+++|++||.|. .+.++.++.+++++|||||+|.+.++|++|++.|||..+.|+.    |
T Consensus         7 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~l   86 (99)
T 2div_A            7 GMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRF   86 (99)
T ss_dssp             SSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEEC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCcceeE
Confidence            3467899999999999999999999999999 9999999999999999999999999999999999999999999    9


Q ss_pred             EEEeecCCC
Q 036791          130 FVDNVRPSR  138 (157)
Q Consensus       130 ~v~~~~~~~  138 (157)
                      +|.++++..
T Consensus        87 ~v~~a~~~~   95 (99)
T 2div_A           87 KLNYATYSG   95 (99)
T ss_dssp             CEEETTCCS
T ss_pred             EEeecCCCC
Confidence            999998754

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.86  E-value=6.9e-22  Score=132.86  Aligned_cols=86  Identities=19%  Similarity=0.254  Sum_probs=79.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeE--EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC----ccCCcE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTE--ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK----LLDGRV  128 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~----~~~g~~  128 (157)
                      ....+|||+|||+++++++|+++|.+||.|..  |.|+.++.+|+++|||||+|.+. +|.+|+..|||.    .++|+.
T Consensus        21 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr~   99 (131)
T 2m2b_A           21 NANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGKT   99 (131)
T ss_dssp             CCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCEE
Confidence            44578999999999999999999999999976  99999999999999999999999 999999999999    999999


Q ss_pred             EEEEeecCCCCCC
Q 036791          129 IFVDNVRPSRRYN  141 (157)
Q Consensus       129 l~v~~~~~~~~~~  141 (157)
                      |+|.+++++....
T Consensus       100 l~V~~a~~~~~~~  112 (131)
T 2m2b_A          100 INVEFAKGSKRDM  112 (131)
T ss_dssp             CCCEECCCSCCCC
T ss_pred             EEEEECCCCCCCC
Confidence            9999999875543

>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=99.86  E-value=1.8e-21  Score=130.57  Aligned_cols=85  Identities=29%  Similarity=0.429  Sum_probs=80.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+++.+|||||+|.+.++|++|++.|+|..|+|++|+|.++
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~~a  123 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFS  123 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEESCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            45578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .++..
T Consensus       124 ~~~~p  128 (129)
T 2kxn_B          124 ITKRP  128 (129)
T ss_dssp             SSSSC
T ss_pred             cCCCC
Confidence            88653

>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=99.86  E-value=1.1e-20  Score=121.63  Aligned_cols=85  Identities=24%  Similarity=0.357  Sum_probs=78.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|++|+.  ++..++|+.|+|.++
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~--~~~~~~g~~l~v~~a   90 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS--QRHMIDGRWCDCKLP   90 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH--SCEEETTEEEEEECC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH--cCCeeCCeEEEEEec
Confidence            456789999999999999999999999999999999999999999999999999999999998  477899999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        91 ~~~~~~~   97 (103)
T 2cqg_A           91 NSKQSQD   97 (103)
T ss_dssp             CTTCCCC
T ss_pred             CCCCcCC
Confidence            9876544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.86  E-value=2.3e-21  Score=134.10  Aligned_cols=82  Identities=26%  Similarity=0.301  Sum_probs=77.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ..++|||+|||+++++++|+++|+.||  .|..+.++.|+.+|+++|||||+|.+.++|++||+.|||..|+|+.|+|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            346899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecCC
Q 036791          134 VRPS  137 (157)
Q Consensus       134 ~~~~  137 (157)
                      +.++
T Consensus       134 a~~~  137 (156)
T 3n9u_C          134 ATRQ  137 (156)
T ss_dssp             CCHH
T ss_pred             cCCC
Confidence            9764

>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=99.86  E-value=4.7e-21  Score=122.12  Aligned_cols=82  Identities=13%  Similarity=0.156  Sum_probs=76.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLA----DAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      .+.++|||+|||+.+++++|+    ++|++||.|..+.++.++.+   +|||||+|.+.++|++|++.|||..++|++|+
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~   83 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGSKKIL   83 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            355789999999999999999    99999999999999988665   88999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 036791          131 VDNVRPSRR  139 (157)
Q Consensus       131 v~~~~~~~~  139 (157)
                      |.+++++..
T Consensus        84 V~~a~~~~~   92 (96)
T 2dgx_A           84 VSLATGASG   92 (96)
T ss_dssp             EEECCCSSC
T ss_pred             EEEcCCCCC
Confidence            999987654

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.86  E-value=2.9e-21  Score=127.33  Aligned_cols=82  Identities=24%  Similarity=0.263  Sum_probs=77.3

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ..+.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|++|+|++
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~  116 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQL  116 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            34567899999999999999999999999999999999988999999999999999999999999999999999999998


Q ss_pred             ec
Q 036791          134 VR  135 (157)
Q Consensus       134 ~~  135 (157)
                      ++
T Consensus       117 ak  118 (118)
T 2khc_A          117 KK  118 (118)
T ss_dssp             C-
T ss_pred             cC
Confidence            74

>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=99.85  E-value=3.7e-21  Score=122.82  Aligned_cols=84  Identities=14%  Similarity=0.209  Sum_probs=78.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            34578999999999999999999999999998888888899999999999999999999999999999999999999998


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      ..+.
T Consensus        93 ~~~~   96 (98)
T 2cqp_A           93 SGPS   96 (98)
T ss_dssp             SCSS
T ss_pred             CCCC
Confidence            7654

>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=99.85  E-value=6.2e-21  Score=131.75  Aligned_cols=87  Identities=24%  Similarity=0.429  Sum_probs=81.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|+..|||..+.|++|+|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            44678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus       148 ~~~~~~~  154 (158)
T 2kn4_A          148 RYGRPPD  154 (158)
T ss_dssp             CCSSCCC
T ss_pred             CCCCCCC
Confidence            9865443

>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=99.85  E-value=7.3e-21  Score=120.73  Aligned_cols=81  Identities=26%  Similarity=0.272  Sum_probs=76.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++. ++++|||||+|.+.++|++|++.||+..++|++|+|.++
T Consensus        14 ~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           14 EADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             TGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            4457899999999999999999999999999999999975 999999999999999999999999999999999999998


Q ss_pred             cC
Q 036791          135 RP  136 (157)
Q Consensus       135 ~~  136 (157)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=9.6e-21  Score=121.74  Aligned_cols=86  Identities=27%  Similarity=0.328  Sum_probs=77.7

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ..+.++|||+|||+.+++++|+++|+.|+   .+.++.++.+++++|||||+|.+.++|++|++.||+..|.|+.|+|.+
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDW   88 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            34567899999999999999999999774   677888888999999999999999999999999999999999999999


Q ss_pred             ecCCCCCCC
Q 036791          134 VRPSRRYNT  142 (157)
Q Consensus       134 ~~~~~~~~~  142 (157)
                      ++++..+..
T Consensus        89 a~~~~~~~~   97 (102)
T 2fc8_A           89 AKPKGEGGS   97 (102)
T ss_dssp             CCCCCSSSC
T ss_pred             ecCCCCCCC
Confidence            998766544

>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=99.85  E-value=1.1e-20  Score=122.49  Aligned_cols=81  Identities=25%  Similarity=0.341  Sum_probs=76.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|.+||.|..+.++.++ +++++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  105 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLV  105 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            456789999999999999999999999999999999997 8999999999999999999999999999999999999998


Q ss_pred             cC
Q 036791          135 RP  136 (157)
Q Consensus       135 ~~  136 (157)
                      .+
T Consensus       106 ~s  107 (107)
T 3ulh_A          106 TS  107 (107)
T ss_dssp             CC
T ss_pred             CC
Confidence            63

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.85  E-value=4.7e-21  Score=124.95  Aligned_cols=86  Identities=29%  Similarity=0.338  Sum_probs=77.4

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ..+.++|||+|||.++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|+..+ +..++|+.|+|.+
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~-~~~l~g~~l~V~~  100 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS-RHELDSKTIDPKV  100 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSS-CEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHC-CCcCCCEEEEEEE
Confidence            345678999999999999999999999999999999999999999999999999999999999986 5889999999999


Q ss_pred             ecCCCCC
Q 036791          134 VRPSRRY  140 (157)
Q Consensus       134 ~~~~~~~  140 (157)
                      +.++..+
T Consensus       101 a~~~~~~  107 (109)
T 2rs2_A          101 AFPRRAQ  107 (109)
T ss_dssp             CCCCCCC
T ss_pred             ccCCCCC
Confidence            9987644

>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=99.85  E-value=6.8e-22  Score=129.72  Aligned_cols=84  Identities=26%  Similarity=0.374  Sum_probs=79.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|++|+ .||+..|+|+.|+|.++
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEEEEH
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEEEec
Confidence            34578999999999999999999999999999999999999999999999999999999999 89999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .++..
T Consensus       102 ~~~~~  106 (114)
T 2cq4_A          102 QAEKN  106 (114)
T ss_dssp             HHHHH
T ss_pred             CCCcc
Confidence            87543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.85  E-value=1.2e-20  Score=119.09  Aligned_cols=83  Identities=34%  Similarity=0.365  Sum_probs=77.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|++||.|..+.+..+  +++++|||||+|.+.++|++|++.||+..++|+.|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   83 (92)
T 2dgv_A            6 SGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRID   83 (92)
T ss_dssp             SSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            34678999999999999999999999999999999874  7899999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      ++...
T Consensus        84 ~~~~~   88 (92)
T 2dgv_A           84 RNASG   88 (92)
T ss_dssp             SCCSS
T ss_pred             CCCCC
Confidence            88654

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.85  E-value=6.3e-21  Score=126.78  Aligned_cols=84  Identities=24%  Similarity=0.348  Sum_probs=79.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||.++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+ .|||..|+|+.|+|.++
T Consensus        34 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~~a  112 (124)
T 2jwn_A           34 IDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPK  112 (124)
T ss_dssp             HHHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEEC
Confidence            34678999999999999999999999999999999999999999999999999999999999 79999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      ++...
T Consensus       113 ~~~~~  117 (124)
T 2jwn_A          113 RTNMP  117 (124)
T ss_dssp             SCCCS
T ss_pred             CCCCC
Confidence            87543

>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=99.85  E-value=1.2e-20  Score=117.93  Aligned_cols=79  Identities=32%  Similarity=0.476  Sum_probs=74.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++. ++..++|+.|+|++|
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~i~v~~A   87 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPKKA   87 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEEEEEEeC
Confidence            4567899999999999999999999999999999999999999999999999999999999975 788899999999875

>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=99.85  E-value=6.9e-21  Score=124.49  Aligned_cols=84  Identities=19%  Similarity=0.249  Sum_probs=77.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHH---HHHhcCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCCccCCcE
Q 036791           55 VNVSFWRCISVSFSTTKEMLA---DAFSQFGQVTEATIIMDIGKN---RSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV  128 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~---~~f~~~G~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~  128 (157)
                      ....+|||+|||+.+++++|+   ++|++||.|..+.++.++.++   +++|||||+|.+.++|++|++.|||..|+|++
T Consensus        13 ~~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~   92 (111)
T 2cpi_A           13 VQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   92 (111)
T ss_dssp             CCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEE
Confidence            445689999999999999999   999999999999999887654   45699999999999999999999999999999


Q ss_pred             EEEEeecCCC
Q 036791          129 IFVDNVRPSR  138 (157)
Q Consensus       129 l~v~~~~~~~  138 (157)
                      |+|.++.++.
T Consensus        93 l~V~~a~~k~  102 (111)
T 2cpi_A           93 LKASLGTTKY  102 (111)
T ss_dssp             EEEESCCCCS
T ss_pred             EEEEeccccc
Confidence            9999999876

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A

Probab=99.85  E-value=9e-21  Score=132.08  Aligned_cols=87  Identities=22%  Similarity=0.271  Sum_probs=79.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+.+|++||.|..|.++.++.+|+++|||||+|.+.++|.+||..|||..|.|+.|.|.++
T Consensus        70 ~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  149 (165)
T 1rk8_A           70 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  149 (165)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++..+.
T Consensus       150 ~~~~~~~  156 (165)
T 1rk8_A          150 FVKGPKR  156 (165)
T ss_dssp             EECC---
T ss_pred             cCCCCCC
Confidence            8765543

>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=99.85  E-value=1.4e-20  Score=122.41  Aligned_cols=87  Identities=15%  Similarity=0.165  Sum_probs=79.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEe-ecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CCccCCcEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQ-VTEATII-MDIGKNRSKGYGYVTSSTEEEAQKALVDMN--GKLLDGRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~-~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--g~~~~g~~l~  130 (157)
                      .+.++|||+|||+.+++++|+++|..||. |..+.++ .++.+++++|||||+|.+.++|++|+..|+  +..+.|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            34678999999999999999999999998 9999998 788889999999999999999999999996  5899999999


Q ss_pred             EEeecCCCCCC
Q 036791          131 VDNVRPSRRYN  141 (157)
Q Consensus       131 v~~~~~~~~~~  141 (157)
                      |.++.++....
T Consensus        86 V~~a~~~~~~~   96 (109)
T 2dis_A           86 VDWAEPEIDVD   96 (109)
T ss_dssp             EEESCSSCSTT
T ss_pred             EEEcCCCCCcC
Confidence            99999876543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.84  E-value=3.5e-20  Score=127.84  Aligned_cols=112  Identities=20%  Similarity=0.314  Sum_probs=92.5

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEAT   88 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~   88 (157)
                      ++|+..+++..+.++.+.+...                ............+|||+|||..+++++|+++|++||.|..+.
T Consensus        55 ~~A~~~l~~~~~~g~~i~v~~~----------------~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  118 (166)
T 3md3_A           55 NIALQTLNGKQIENNIVKINWA----------------FQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGH  118 (166)
T ss_dssp             HHHHHHHTTCEETTEECEEEEC----------------CCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEE
T ss_pred             HHHHHHcCCCccCCCeeEEEEc----------------CCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEE
Confidence            4566677777777666654321                000111223456899999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           89 IIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        89 ~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ++.++.+|.++|||||+|.+.++|.+|+..|||..++|++|+|.|+++
T Consensus       119 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          119 VMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             EEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESCC
T ss_pred             EEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEecCC
Confidence            999999999999999999999999999999999999999999999864

>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=99.84  E-value=2.2e-21  Score=124.58  Aligned_cols=83  Identities=19%  Similarity=0.248  Sum_probs=75.6

Q ss_pred             cccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           54 LVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDI-GKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        54 ~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ....++|||+|||.++++++|+++|+.|| |..+.++.++ .+|+++|||||+|.+.++|.+|+ .|+|..++|+.|+|.
T Consensus        16 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           16 KSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNRRIRVD   93 (100)
T ss_dssp             ----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTBCCCCE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCeEEEEE
Confidence            34568899999999999999999999999 9999999998 58999999999999999999999 899999999999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      +++++.
T Consensus        94 ~a~~~~   99 (100)
T 2j76_E           94 VADQAQ   99 (100)
T ss_dssp             ECCCSC
T ss_pred             eccCCC
Confidence            998764

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.7e-20  Score=120.37  Aligned_cols=82  Identities=23%  Similarity=0.355  Sum_probs=74.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+++++++|+++|.+||.|   .++.+ .+++.+|||||+|.+.++|++|+..||+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   88 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLELQ   88 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEc
Confidence            456789999999999999999999999977   55665 67899999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      +++...
T Consensus        89 ~~~~~~   94 (101)
T 2fc9_A           89 GPRGSP   94 (101)
T ss_dssp             SSCCCC
T ss_pred             CCCCCC
Confidence            987543

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=8.8e-23  Score=134.41  Aligned_cols=93  Identities=20%  Similarity=0.200  Sum_probs=84.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeE--------EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTE--------ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~--------~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      .+.++|||+|||..+++++|+++|++||.|..        +.++.++.+++++|||||+|.+.++|++|+..||+..+.|
T Consensus         5 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   84 (116)
T 2lcw_A            5 SDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSG   84 (116)
Confidence            34578999999999999999999999999998        8999998899999999999999999999999999999999


Q ss_pred             cEEEEEeecCCCCCCCCCCCC
Q 036791          127 RVIFVDNVRPSRRYNTDASLA  147 (157)
Q Consensus       127 ~~l~v~~~~~~~~~~~~~~~~  147 (157)
                      ++|+|.+++++..+.+++.++
T Consensus        85 ~~l~V~~a~~~~~~~~ggg~~  105 (116)
T 2lcw_A           85 NPIKVSFATRRADFNRGGGNG  105 (116)
Confidence            999999999887765544333

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=9.6e-21  Score=122.33  Aligned_cols=80  Identities=15%  Similarity=0.075  Sum_probs=75.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|++||.|..+.++.++. |+++|||||+|.+.++|++|+. +++..++|+.|.|.++
T Consensus         9 ~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            9 VKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFK   86 (103)
T ss_dssp             SGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTCEEEEH
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEEEEEEc
Confidence            3457899999999999999999999999999999999977 9999999999999999999999 8999999999999987


Q ss_pred             cC
Q 036791          135 RP  136 (157)
Q Consensus       135 ~~  136 (157)
                      ..
T Consensus        87 ~~   88 (103)
T 1s79_A           87 DD   88 (103)
T ss_dssp             HH
T ss_pred             hH
Confidence            54

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.84  E-value=4.2e-21  Score=116.77  Aligned_cols=75  Identities=25%  Similarity=0.395  Sum_probs=72.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ +++..++|++|+|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~-~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            48999999999999999999999999999999998899999999999999999999998 8999999999999875

>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=99.84  E-value=6.4e-21  Score=120.99  Aligned_cols=81  Identities=15%  Similarity=0.262  Sum_probs=75.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..++|++|+|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            35789999999999999999999999999989899988999999999999999999999999999999999999999986


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      +
T Consensus        94 s   94 (95)
T 2ek1_A           94 S   94 (95)
T ss_dssp             -
T ss_pred             C
Confidence            5

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.84  E-value=4.3e-21  Score=129.71  Aligned_cols=87  Identities=24%  Similarity=0.429  Sum_probs=81.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|++|+..|||..|.|++|+|.++
T Consensus        45 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a  124 (135)
T 2lea_A           45 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  124 (135)
T ss_dssp             GGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            44678999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus       125 ~~~~~~~  131 (135)
T 2lea_A          125 RYGRPPD  131 (135)
T ss_dssp             CCCCCCT
T ss_pred             CCCCCCc
Confidence            8865443

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=3.9e-20  Score=116.53  Aligned_cols=81  Identities=21%  Similarity=0.304  Sum_probs=76.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|+.| .|..+.++.+ .+|+++|||||+|.+.++|++|+. ||+..++|+.|+|.++
T Consensus         8 ~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i~v~~a   84 (91)
T 2dgw_A            8 TTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYIEVFRE   84 (91)
T ss_dssp             CCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEEEEEEE
T ss_pred             CCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEEEEEEC
Confidence            345789999999999999999999999 9999999999 789999999999999999999999 9999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      .++.
T Consensus        85 ~~~~   88 (91)
T 2dgw_A           85 KSGP   88 (91)
T ss_dssp             SSCC
T ss_pred             CcCC
Confidence            8864

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.6e-21  Score=121.41  Aligned_cols=81  Identities=21%  Similarity=0.295  Sum_probs=75.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|+.|++.+.+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~~   83 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGPS   83 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCCC
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999998877655


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      +
T Consensus        84 s   84 (85)
T 1x4e_A           84 S   84 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=5e-20  Score=115.87  Aligned_cols=79  Identities=23%  Similarity=0.338  Sum_probs=72.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||.++++++|+++|++||.|..+.++        +|||||+|.+.++|++|++.||+..++|++|+|.++
T Consensus         6 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   77 (90)
T 2dnq_A            6 SGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEAS   77 (90)
T ss_dssp             SCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECS
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEEC
Confidence            456789999999999999999999999999999886        579999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus        78 ~~~~~~~   84 (90)
T 2dnq_A           78 KNKSKAS   84 (90)
T ss_dssp             SCCCCCC
T ss_pred             CCCCCCC
Confidence            9876544

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.84  E-value=5.4e-20  Score=122.32  Aligned_cols=84  Identities=23%  Similarity=0.294  Sum_probs=79.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|++||.|..+.++.++ +|+++|||||+|.+.++|++|++.|||..+.|+.|+|.++
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  111 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  111 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEe
Confidence            456789999999999999999999999999999999997 8999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .+...
T Consensus       112 ~~~~~  116 (124)
T 2kt5_A          112 ASQID  116 (124)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87543

>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=99.83  E-value=6e-20  Score=120.31  Aligned_cols=83  Identities=20%  Similarity=0.364  Sum_probs=77.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc--------CC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL--------DG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~--------~g  126 (157)
                      .+.++|||+|||+.+++++|+++|+.||.|..+.++.++ +++++|||||+|.+.++|++|+..|||..+        .+
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~~  101 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT  101 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCCC
Confidence            455789999999999999999999999999999999997 899999999999999999999999999999        57


Q ss_pred             cEEEEEeecCCC
Q 036791          127 RVIFVDNVRPSR  138 (157)
Q Consensus       127 ~~l~v~~~~~~~  138 (157)
                      ++|.|.++.++.
T Consensus       102 ~~l~v~~a~p~~  113 (114)
T 1x5o_A          102 EPLLCKFSGPSS  113 (114)
T ss_dssp             SCBEEEECCCSC
T ss_pred             CceeEEccCCCC
Confidence            889999998753

>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=99.83  E-value=5.2e-20  Score=118.64  Aligned_cols=81  Identities=28%  Similarity=0.463  Sum_probs=73.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|.+||.|..+.++        ++||||+|.+.++|++|++.||+..|.|+.|+|.++
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~--------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   80 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL--------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFA   80 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC--------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEc
Confidence            356789999999999999999999999999999886        358999999999999999999999999999999999


Q ss_pred             cCCCCCCCC
Q 036791          135 RPSRRYNTD  143 (157)
Q Consensus       135 ~~~~~~~~~  143 (157)
                      +++......
T Consensus        81 ~~~~~~~~~   89 (103)
T 2dgu_A           81 KPPDQKRKE   89 (103)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCcccchh
Confidence            887665443

>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=99.83  E-value=2.3e-20  Score=120.29  Aligned_cols=82  Identities=15%  Similarity=0.115  Sum_probs=75.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|+.|| +..+.++.++ +++++|||||+|.+.++|++||+ +|+..|+|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V~~~   89 (102)
T 1wez_A           13 TTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-ceEEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            4457899999999999999999999999 4599999997 89999999999999999999995 7999999999999998


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .+...
T Consensus        90 ~~~~~   94 (102)
T 1wez_A           90 STAGT   94 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87653

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.6e-20  Score=121.24  Aligned_cols=81  Identities=17%  Similarity=0.222  Sum_probs=72.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--CccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG--KLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~~~g~~l~v~  132 (157)
                      ....+|||+|||+++++++|+++|++||.|..+.++.+      +|||||+|.+.++|++|++.|++  ..+.|++|+|.
T Consensus        14 ~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           14 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34678999999999999999999999999999999865      69999999999999999998864  68999999999


Q ss_pred             eecCCCCCC
Q 036791          133 NVRPSRRYN  141 (157)
Q Consensus       133 ~~~~~~~~~  141 (157)
                      +++++....
T Consensus        88 ~A~~~~~~~   96 (105)
T 1sjq_A           88 FSNHKELKT   96 (105)
T ss_dssp             CCSSSSCCC
T ss_pred             EcCCCCCCc
Confidence            998865444

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.83  E-value=2e-20  Score=120.13  Aligned_cols=80  Identities=20%  Similarity=0.268  Sum_probs=73.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      ++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++|++.|++..++|+.|+|.+++++
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            47999999999999999999999999999999876     6899999999999999999999999999999999999987


Q ss_pred             CCCCC
Q 036791          138 RRYNT  142 (157)
Q Consensus       138 ~~~~~  142 (157)
                      .....
T Consensus        76 ~~~~~   80 (101)
T 2hvz_A           76 PRRSR   80 (101)
T ss_dssp             CCSSC
T ss_pred             CCccc
Confidence            65433

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.83  E-value=7.8e-20  Score=129.80  Aligned_cols=130  Identities=14%  Similarity=0.202  Sum_probs=98.0

Q ss_pred             HHHHHHhccccccCcccccccC-Cceecee-cccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSK-PYQVVNY-FSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTE   86 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~   86 (157)
                      ++|+ ++|+..+.++.+.+... .+....- ........+............+|||+|||..+++++|+++|++||.|..
T Consensus        65 ~~Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~  143 (198)
T 2yh0_A           65 TQAM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKA  143 (198)
T ss_dssp             HHHG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEE
T ss_pred             HHHH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccE
Confidence            4556 78888888888766531 1100000 0000011111111112245578999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCC
Q 036791           87 ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRR  139 (157)
Q Consensus        87 ~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~  139 (157)
                      +.++.++.+|.++|||||+|.+.++|.+|++.|||..++|+.|+|.++.++..
T Consensus       144 ~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          144 FNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             EEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            99999988999999999999999999999999999999999999999998754

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.83  E-value=5.1e-20  Score=132.43  Aligned_cols=122  Identities=20%  Similarity=0.259  Sum_probs=94.5

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCC-cchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPS-SDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEA   87 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~   87 (157)
                      ++|++.+++..+.++.+.+....        ......+. ...........+|||+|||..+++++|+++|++||.|..+
T Consensus        84 ~~A~~~l~~~~~~g~~l~v~~~~--------~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v  155 (216)
T 2qfj_A           84 QLALEQMNSVMLGGRNIKVGRPS--------NIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSA  155 (216)
T ss_dssp             HHHHHHHSSCCCC-CCCEEECCS--------CCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEE
T ss_pred             HHHHHHccCCeeCCeeEEEecCC--------CccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEE
Confidence            55666677777777776553200        00000000 0011122345789999999999999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           88 TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        88 ~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      .++.++.+|+++|||||+|.+.++|.+|++.|||..|+|+.|+|.++.++.
T Consensus       156 ~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~  206 (216)
T 2qfj_A          156 TLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPP  206 (216)
T ss_dssp             EEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCS
T ss_pred             EEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCC
Confidence            999998899999999999999999999999999999999999999998864

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=1.9e-20  Score=121.98  Aligned_cols=84  Identities=26%  Similarity=0.451  Sum_probs=77.1

Q ss_pred             hccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           52 MQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        52 ~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ......++|||+|||.++++++|+++|++||.|..+.++.++  +.++|||||+|.+.++|++|++.|||..++|+.|+|
T Consensus        24 ~~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  101 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEV  101 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBT--TBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEE
T ss_pred             cCCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECC--CCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            333556889999999999999999999999999999999884  458999999999999999999999999999999999


Q ss_pred             EeecCC
Q 036791          132 DNVRPS  137 (157)
Q Consensus       132 ~~~~~~  137 (157)
                      .+++++
T Consensus       102 ~~a~~~  107 (109)
T 2err_A          102 NNATAR  107 (109)
T ss_dssp             EECCCS
T ss_pred             EECCCC
Confidence            999875

>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=99.83  E-value=2.6e-21  Score=121.69  Aligned_cols=80  Identities=28%  Similarity=0.480  Sum_probs=74.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      ++|||+|||.++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.+ |.+|+..|||..++|++|+|.++.++
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999999999999999999999999 99999999999999999999999875


Q ss_pred             C
Q 036791          138 R  138 (157)
Q Consensus       138 ~  138 (157)
                      .
T Consensus        81 ~   81 (90)
T 2ki2_A           81 K   81 (90)
T ss_dssp             -
T ss_pred             C
Confidence            4

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A

Probab=99.83  E-value=2.8e-20  Score=127.55  Aligned_cols=123  Identities=12%  Similarity=0.117  Sum_probs=92.1

Q ss_pred             HHHHHHHh-ccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeE
Q 036791            8 QTRKIQQF-NSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTE   86 (157)
Q Consensus         8 ~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~   86 (157)
                      -++|++++ |+..+.+ .+.+....-.....  ..................++|||+|||+.+++++|+++|++||.|..
T Consensus        26 A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~  102 (150)
T 2i2y_A           26 AEKVFKQYANDNGVDG-EWTYDDATKTFTVT--EGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERAFGYYGPLRS  102 (150)
T ss_dssp             HTTTHHHHHHHHTCCC-EEEEETTTTEEEEE--CSSSSCCCCSCSSSSTTSCEEEEESCCSCCSCHHHHHHHHHHSCEEE
T ss_pred             HHHHHHHHhcCCCCCC-ceecccccCccccc--cccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEE
Confidence            35677788 8888888 66544311111100  00011111122223345679999999999999999999999999999


Q ss_pred             EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           87 ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        87 ~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      +.++.+     ++|||||+|.+.++|.+|+..|||..++|++|+|.+++++.
T Consensus       103 v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A          103 VWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             EEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             EEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999875     57999999999999999999999999999999999998864

>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=99.83  E-value=8.8e-21  Score=124.43  Aligned_cols=88  Identities=19%  Similarity=0.255  Sum_probs=75.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|..||.|..+.+..+..+++++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a  102 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG  102 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEc
Confidence            34578999999999999999999999999843322222236889999999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      +++..+..
T Consensus       103 ~~~~~~~~  110 (115)
T 2cpx_A          103 KNKKQRSS  110 (115)
T ss_dssp             CCCSCCCC
T ss_pred             cCCCCCCC
Confidence            98765443

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.83  E-value=4.1e-20  Score=125.01  Aligned_cols=80  Identities=25%  Similarity=0.371  Sum_probs=76.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||..+++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..+.|++|+|++|
T Consensus        61 ~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~A  140 (140)
T 2ku7_A           61 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA  140 (140)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEEC-
T ss_pred             CCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            45678999999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.83  E-value=1.6e-19  Score=117.36  Aligned_cols=79  Identities=19%  Similarity=0.139  Sum_probs=73.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC-----cEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG-----RVI  129 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g-----~~l  129 (157)
                      ....+|||+|||+++++++|+++|.+||.|..+.++.+       |||||+|.+.++|++||+.||+..|+|     +.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i   85 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   85 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEE
Confidence            34678999999999999999999999999999999875       899999999999999999999999999     999


Q ss_pred             EEEeecCCCCC
Q 036791          130 FVDNVRPSRRY  140 (157)
Q Consensus       130 ~v~~~~~~~~~  140 (157)
                      +|.++.++...
T Consensus        86 ~V~~a~~~~~~   96 (108)
T 1x4c_A           86 RVKVDGPRSPS   96 (108)
T ss_dssp             EEEESSCCSCC
T ss_pred             EEEeCCCCCCC
Confidence            99999986543

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.83  E-value=8.2e-21  Score=115.94  Aligned_cols=76  Identities=30%  Similarity=0.393  Sum_probs=72.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.++ ..++|++|+|+++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            369999999999999999999999999999999998899999999999999999999999998 9999999999986

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.83  E-value=2.4e-21  Score=124.42  Aligned_cols=84  Identities=17%  Similarity=0.186  Sum_probs=76.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|+.||.|.. .++.++.+++++|||||+|.+.++|++|++ ||+..+.|+.|+|.++
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEEEEEc
Confidence            34678999999999999999999999998887 667777788999999999999999999999 9999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      .++..+
T Consensus        93 ~~~~~~   98 (101)
T 1fj7_A           93 KGRDGT   98 (101)
T ss_dssp             SCCCCS
T ss_pred             CCCCCC
Confidence            987544

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.82  E-value=3.1e-20  Score=120.20  Aligned_cols=82  Identities=21%  Similarity=0.254  Sum_probs=75.2

Q ss_pred             cccEEEEcCCCCCC------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc-E
Q 036791           56 NVSFWRCISVSFST------TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR-V  128 (157)
Q Consensus        56 ~~~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~-~  128 (157)
                      ..++|||+|||+.+      ++++|+++|++||.|..+.++  +.+|+++|||||+|.+.++|.+|+..|||..+.|+ +
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            35789999999999      789999999999999999887  46799999999999999999999999999999998 9


Q ss_pred             EEEEeecCCCC
Q 036791          129 IFVDNVRPSRR  139 (157)
Q Consensus       129 l~v~~~~~~~~  139 (157)
                      |+|.++.....
T Consensus        92 l~V~~a~~~~k  102 (105)
T 2nlw_A           92 FRVNLFTDFDK  102 (105)
T ss_dssp             EEEECSCCCCC
T ss_pred             EEEEEcchHhh
Confidence            99999986543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.82  E-value=5.7e-20  Score=117.63  Aligned_cols=78  Identities=14%  Similarity=0.144  Sum_probs=71.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc--cCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL--LDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~--~~g~~l~v~  132 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.+++      .+|+|||+|.+.++|.+|++.|++..  +.|++|.|.
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~------~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~   92 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP------KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVN   92 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc------CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEE
Confidence            4567899999999999999999999999999998875      36899999999999999999999876  789999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      ++++++
T Consensus        93 ~S~~k~   98 (100)
T 3r27_A           93 YSTSQK   98 (100)
T ss_dssp             ECSCSC
T ss_pred             eccccc
Confidence            998764

>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=99.82  E-value=1.7e-19  Score=116.07  Aligned_cols=81  Identities=15%  Similarity=0.118  Sum_probs=72.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM--NGKLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~l~v~  132 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|  ++..+.|++|+|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            45578999999999999999999999999999988764      799999999999999999987  4677999999999


Q ss_pred             eecCCCCCC
Q 036791          133 NVRPSRRYN  141 (157)
Q Consensus       133 ~~~~~~~~~  141 (157)
                      +++++.-..
T Consensus        87 ~a~~~~~~~   95 (101)
T 2cq1_A           87 YSNHKELKT   95 (101)
T ss_dssp             ECSCSSCCC
T ss_pred             EcCcccCcC
Confidence            999765443

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=1.7e-19  Score=113.87  Aligned_cols=80  Identities=20%  Similarity=0.322  Sum_probs=72.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.+++        +||||+|.+.++|++|++.||+..+.|+.|+|.++
T Consensus         8 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            8 KASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK--------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS--------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            4567899999999999999999999999999998863        39999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 036791          135 RPSRRYNT  142 (157)
Q Consensus       135 ~~~~~~~~  142 (157)
                      +++.....
T Consensus        80 ~~~~~~~~   87 (92)
T 2dgt_A           80 TSRLRTAS   87 (92)
T ss_dssp             SCCCSCCC
T ss_pred             cCCCCCCC
Confidence            98765443

>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=99.82  E-value=2.6e-20  Score=136.25  Aligned_cols=81  Identities=21%  Similarity=0.263  Sum_probs=76.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCC--CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFG--QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G--~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ..++|||+||++++++++|+++|++||  .|..|.|+.++.+++++|||||+|.+.++|++||+.||+..|+|+.|+|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            456899999999999999999999999  999999999999999999999999999999999999999999999999999


Q ss_pred             ecC
Q 036791          134 VRP  136 (157)
Q Consensus       134 ~~~  136 (157)
                      +.+
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            753

>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=99.82  E-value=1e-19  Score=118.35  Aligned_cols=81  Identities=28%  Similarity=0.450  Sum_probs=74.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|+.||.|..+.++.+      +|||||+|.+.++|++|+..|+|..+.|++|+|.++
T Consensus        23 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           23 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            45678999999999999999999999999999999875      689999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus        97 ~~~~~~~  103 (109)
T 1x4g_A           97 KESPDMT  103 (109)
T ss_dssp             CCCCSSC
T ss_pred             CCCCCCC
Confidence            9876443

>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=99.82  E-value=1.3e-19  Score=115.52  Aligned_cols=79  Identities=20%  Similarity=0.266  Sum_probs=72.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC--CcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD--GRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~--g~~l~v~  132 (157)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.||+..+.  |+.|+|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            34578999999999999999999999999999988653      689999999999999999999999999  9999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      +++++..
T Consensus        89 ~a~~~~~   95 (97)
T 1why_A           89 FAKSGPS   95 (97)
T ss_dssp             ECCCCCC
T ss_pred             ECCCCCC
Confidence            9998754

>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=99.82  E-value=1.5e-19  Score=128.11  Aligned_cols=90  Identities=19%  Similarity=0.311  Sum_probs=75.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|+.. ++..++|+.|.|.++.
T Consensus       103 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v~~a~  181 (196)
T 1l3k_A          103 TVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEVRKAL  181 (196)
T ss_dssp             CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEEEECC
T ss_pred             CcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEEEecC
Confidence            457899999999999999999999999999999999988999999999999999999999986 7999999999999999


Q ss_pred             CCCCCCCCCCC
Q 036791          136 PSRRYNTDASL  146 (157)
Q Consensus       136 ~~~~~~~~~~~  146 (157)
                      ++.........
T Consensus       182 ~k~~~~~~~~~  192 (196)
T 1l3k_A          182 SKQEMASASSS  192 (196)
T ss_dssp             -----------
T ss_pred             ChhHhcccccc
Confidence            98776554433

>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=99.82  E-value=1.4e-19  Score=116.84  Aligned_cols=82  Identities=27%  Similarity=0.321  Sum_probs=75.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeE-EEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTE-ATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~-~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      .+..+|||+|||+++++++|+++|..||.|.. +.++.+ .+|+++|||||+|.+.++|++|+.. ++..++|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~i~v~~   90 (104)
T 1wg5_A           13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRYIEIFK   90 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSCCEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcEEEEEE
Confidence            34578999999999999999999999999987 888888 7899999999999999999999997 99999999999999


Q ss_pred             ecCCC
Q 036791          134 VRPSR  138 (157)
Q Consensus       134 ~~~~~  138 (157)
                      +.++.
T Consensus        91 ~~~~~   95 (104)
T 1wg5_A           91 SSRAE   95 (104)
T ss_dssp             ECTTT
T ss_pred             CCHHH
Confidence            87654

>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=99.82  E-value=1.4e-19  Score=115.69  Aligned_cols=81  Identities=23%  Similarity=0.291  Sum_probs=74.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            45678999999999999999999999999999988754      689999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus        87 ~~~~~~~   93 (99)
T 2cpj_A           87 CHSASLT   93 (99)
T ss_dssp             SCCSCCC
T ss_pred             CCCCCCC
Confidence            9865443

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.82  E-value=9e-20  Score=118.68  Aligned_cols=80  Identities=19%  Similarity=0.311  Sum_probs=72.2

Q ss_pred             ccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           53 QLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        53 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .....++|||+|||.++++++|+++|++||.|..+.++        +|||||+|.+.++|++|++.|||..++|+.|+|.
T Consensus        27 ~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   98 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV   98 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            33556899999999999999999999999999999887        6899999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 036791          133 NVRPSRRY  140 (157)
Q Consensus       133 ~~~~~~~~  140 (157)
                      +++++..+
T Consensus        99 ~a~~~~~r  106 (108)
T 2jvo_A           99 YSKLPAKR  106 (108)
T ss_dssp             SCSCCC--
T ss_pred             EecCCCCC
Confidence            99886543

>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=99.82  E-value=1.7e-19  Score=119.02  Aligned_cols=81  Identities=17%  Similarity=0.222  Sum_probs=73.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC--CccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG--KLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g--~~~~g~~l~v~  132 (157)
                      .+.++|||+|||+++++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|++  ..+.|++|+|.
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~  102 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ  102 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEE
Confidence            44678999999999999999999999999999999875      69999999999999999999874  68999999999


Q ss_pred             eecCCCCCC
Q 036791          133 NVRPSRRYN  141 (157)
Q Consensus       133 ~~~~~~~~~  141 (157)
                      +++++.-..
T Consensus       103 ~a~~k~~~~  111 (119)
T 2ad9_A          103 FSNHKELKT  111 (119)
T ss_dssp             ECSSSSCCC
T ss_pred             EccCCCCCc
Confidence            998876544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.82  E-value=4.4e-20  Score=114.76  Aligned_cols=73  Identities=21%  Similarity=0.253  Sum_probs=68.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..-|||+||++.+++++|+++|.+||+|..+.+..      ++|||||+|.+.++|++|++.||+..++|++|+|.++.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            45699999999999999999999999999999865      58999999999999999999999999999999999984

>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=99.82  E-value=2e-19  Score=116.32  Aligned_cols=80  Identities=14%  Similarity=0.141  Sum_probs=71.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC--ccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK--LLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~--~~~g~~l~v~  132 (157)
                      .+..+|||+|||+.+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|++.  .+.|++|+|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            34578999999999999999999999999999988753      689999999999999999988754  5899999999


Q ss_pred             eecCCCCC
Q 036791          133 NVRPSRRY  140 (157)
Q Consensus       133 ~~~~~~~~  140 (157)
                      +++++...
T Consensus        87 ~a~~~~~~   94 (104)
T 1wex_A           87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EccCcccc
Confidence            99876543

>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=99.81  E-value=5.2e-20  Score=118.55  Aligned_cols=78  Identities=17%  Similarity=0.202  Sum_probs=70.5

Q ss_pred             cccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC--ccCCcEEEEE
Q 036791           56 NVSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK--LLDGRVIFVD  132 (157)
Q Consensus        56 ~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~--~~~g~~l~v~  132 (157)
                      +..+|||+|||+ .+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|++.|++.  .|.|++|+|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            467899999999 9999999999999999999999765      479999999999999999999864  5999999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      ++++...
T Consensus        88 ~a~~~~~   94 (102)
T 1x4d_A           88 LSQKYKR   94 (102)
T ss_dssp             EECCCTT
T ss_pred             ECCCCCC
Confidence            9987543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.81  E-value=8e-20  Score=122.18  Aligned_cols=81  Identities=16%  Similarity=0.231  Sum_probs=73.0

Q ss_pred             cccEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLA----DAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      +..+|||+|||+.+++++|+    ++|++||.|..|.+..   +++++|||||+|.+.++|.+|+..|||..+.|++|+|
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            45789999999999999876    6999999999887743   5889999999999999999999999999999999999


Q ss_pred             EeecCCCC
Q 036791          132 DNVRPSRR  139 (157)
Q Consensus       132 ~~~~~~~~  139 (157)
                      .|++++..
T Consensus       105 ~~a~~~~~  112 (127)
T 2a3j_A          105 TFSETPQS  112 (127)
T ss_dssp             EECCCCCH
T ss_pred             EEccCcch
Confidence            99987643

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.81  E-value=1.4e-19  Score=130.73  Aligned_cols=82  Identities=34%  Similarity=0.553  Sum_probs=75.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+.+++++|+++|++||.|..+.|+.++  +.++|||||+|.+.++|++|++.|||..|+|++|+|.++.
T Consensus       102 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~~a~  179 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK  179 (213)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             ccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999884  4579999999999999999999999999999999999998


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      ++.+
T Consensus       180 ~~~~  183 (213)
T 4f02_A          180 SRKE  183 (213)
T ss_dssp             CHHH
T ss_pred             CCcc
Confidence            7643

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.81  E-value=2.8e-20  Score=122.91  Aligned_cols=81  Identities=17%  Similarity=0.162  Sum_probs=75.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQ---VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ....+|||+|||+++++++|+++|+.||.   |..+.++.++. |+++|||||+|.+.++|++|++ +|+..|+|+.|+|
T Consensus        15 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V   92 (118)
T 2db1_A           15 GEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGHRYIEV   92 (118)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECCeEEEE
Confidence            34578999999999999999999999998   89999999976 9999999999999999999999 9999999999999


Q ss_pred             EeecCC
Q 036791          132 DNVRPS  137 (157)
Q Consensus       132 ~~~~~~  137 (157)
                      .++.++
T Consensus        93 ~~a~~~   98 (118)
T 2db1_A           93 FKSHRT   98 (118)
T ss_dssp             EEECHH
T ss_pred             EECCHH
Confidence            999764

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=4.4e-19  Score=113.39  Aligned_cols=78  Identities=31%  Similarity=0.494  Sum_probs=71.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcC--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQF--GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .+.++|||+|||+.+++++|+++|++|  |.|..+.+.        +|||||+|.+.++|++|+..|||..++|++|+|.
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   84 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   84 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            456789999999999999999999999  899888764        5799999999999999999999999999999999


Q ss_pred             eecCCCCC
Q 036791          133 NVRPSRRY  140 (157)
Q Consensus       133 ~~~~~~~~  140 (157)
                      +++++...
T Consensus        85 ~a~~~~~~   92 (99)
T 2cpd_A           85 LAKPVDKD   92 (99)
T ss_dssp             CCCCCCCC
T ss_pred             ECCCCCCC
Confidence            99987543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.81  E-value=7.2e-20  Score=116.37  Aligned_cols=81  Identities=21%  Similarity=0.292  Sum_probs=73.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||..+++++|+++|+.||.|..+     ..+++++|||||+|.+.++|.+|+..|+|..++|+.|+|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            356789999999999999999999999988666     256889999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      .++...
T Consensus        89 ~~~~~~   94 (96)
T 1fjc_A           89 GEKGGT   94 (96)
T ss_dssp             SSSCCC
T ss_pred             CCCCCC
Confidence            886543

>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=99.81  E-value=3e-20  Score=121.99  Aligned_cols=82  Identities=21%  Similarity=0.208  Sum_probs=76.5

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCe-eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQV-TEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i-~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      .+..+|||+|||+++++++|+++|+.||.| ..+.++.++ +|+++|||||+|.+.++|++||+. |+..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeEEEEEE
Confidence            345789999999999999999999999999 889999997 899999999999999999999997 99999999999999


Q ss_pred             ecCCC
Q 036791          134 VRPSR  138 (157)
Q Consensus       134 ~~~~~  138 (157)
                      +.++.
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            98654

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.81  E-value=1.2e-19  Score=115.57  Aligned_cols=79  Identities=15%  Similarity=0.245  Sum_probs=71.1

Q ss_pred             ccccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      .+.++|||+|||+ .+++++|+++|++||.|..+.+.        +|||||+|.+.++|++|++.|||..+.|++|+|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            4567899999998 99999999999999999999884        68999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 036791          134 VRPSRRYN  141 (157)
Q Consensus       134 ~~~~~~~~  141 (157)
                      ++++....
T Consensus        80 a~~~~~~~   87 (96)
T 2kvi_A           80 SSSNARPQ   87 (96)
T ss_dssp             EECCCC--
T ss_pred             cCcCCCCC
Confidence            98765443

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.81  E-value=2e-19  Score=114.67  Aligned_cols=80  Identities=15%  Similarity=0.129  Sum_probs=71.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|+.||.|. +.++.    ++++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus        17 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~----~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           17 PLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTW----QGPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEE----ETTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEc----CCCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            3457899999999999999999999999996 66654    367899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      +++..
T Consensus        92 ~~~~~   96 (97)
T 2e5j_A           92 RQQRD   96 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            88653

>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=99.81  E-value=8.2e-20  Score=116.25  Aligned_cols=82  Identities=17%  Similarity=0.201  Sum_probs=75.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLA----DAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      .+.++|||+|||.++++++|+    ++|++||.|..+.+..   +|+++|||||+|.+.++|.+|++.|||..++|+.|+
T Consensus         6 ~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   82 (97)
T 1nu4_A            6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   82 (97)
T ss_dssp             CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEE
Confidence            456789999999999999999    9999999999998864   478899999999999999999999999999999999


Q ss_pred             EEeecCCCC
Q 036791          131 VDNVRPSRR  139 (157)
Q Consensus       131 v~~~~~~~~  139 (157)
                      |.+++++..
T Consensus        83 v~~a~~~~~   91 (97)
T 1nu4_A           83 IQYAKTDSD   91 (97)
T ss_dssp             EEECSSCCT
T ss_pred             EEEccCCCc
Confidence            999988653

>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=99.81  E-value=5.5e-20  Score=124.30  Aligned_cols=81  Identities=16%  Similarity=0.151  Sum_probs=75.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQ---VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ....+|||+|||+++++++|+++|+.||.   |..+.++.++. |+++|||||+|.+.++|++|++ +|+..|+|+.|+|
T Consensus        42 ~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~gr~i~V  119 (136)
T 2hgl_A           42 GEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGHRYIEV  119 (136)
T ss_dssp             CTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSSSEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECCEEEEE
Confidence            34578999999999999999999999999   88999999977 9999999999999999999999 9999999999999


Q ss_pred             EeecCC
Q 036791          132 DNVRPS  137 (157)
Q Consensus       132 ~~~~~~  137 (157)
                      .++.++
T Consensus       120 ~~a~~~  125 (136)
T 2hgl_A          120 FKSHRT  125 (136)
T ss_dssp             EECCHH
T ss_pred             EECChH
Confidence            998654

>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=99.81  E-value=1.2e-19  Score=114.70  Aligned_cols=80  Identities=18%  Similarity=0.247  Sum_probs=70.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC-CccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQ-VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG-KLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g-~~~~g~~l~v~  132 (157)
                      ...++|||+|||+++++++|+++|++||. |..+.+.       ++|||||+|.+.++|++|++.||| ..++|+.|+|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~   78 (93)
T 2cqh_A            6 SGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVD   78 (93)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEE
Confidence            34578999999999999999999999999 5555542       478999999999999999999999 99999999999


Q ss_pred             eecCCCCCC
Q 036791          133 NVRPSRRYN  141 (157)
Q Consensus       133 ~~~~~~~~~  141 (157)
                      +++++..+.
T Consensus        79 ~a~~~~~~~   87 (93)
T 2cqh_A           79 YSVSKKLRS   87 (93)
T ss_dssp             ECCCCCCCC
T ss_pred             EccCccccC
Confidence            999876543

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.81  E-value=8.7e-20  Score=119.25  Aligned_cols=79  Identities=18%  Similarity=0.098  Sum_probs=70.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFG-QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...+|||+|||+++++++|+++|++|| .|..+.+..    .+++|||||+|.+.++|++|++.|||..++|+.|+|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~----~~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNT----RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSS----CSSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEc----CCCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            457899999999999999999999999 899988753    347899999999999999999999999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      +.+.
T Consensus       103 ~~~p  106 (111)
T 2jvr_A          103 DNPP  106 (111)
T ss_dssp             CC--
T ss_pred             CCCC
Confidence            7543

>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=99.80  E-value=3.9e-19  Score=113.46  Aligned_cols=77  Identities=14%  Similarity=0.242  Sum_probs=71.1

Q ss_pred             cccccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           54 LVNVSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        54 ~~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ....++|||+|||+ ++++++|+++|+.||.|..+.+.        +|||||+|.+.++|.+|+..|||..++|+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34567899999998 99999999999999999999883        6899999999999999999999999999999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      +++++.
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            998754

>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=99.80  E-value=2.8e-20  Score=123.80  Aligned_cols=82  Identities=17%  Similarity=0.222  Sum_probs=75.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|..||.|..+.++.+..+|+++|||||+|.+.++|++||. ||+..|+|+.|.|.++
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEEEEEC
Confidence            345789999999999999999999999999887677777889999999999999999999999 9999999999999999


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      .++
T Consensus       102 ~~~  104 (124)
T 1wel_A          102 TKK  104 (124)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            764

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.80  E-value=7.1e-20  Score=117.71  Aligned_cols=82  Identities=20%  Similarity=0.282  Sum_probs=75.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+.+++++|+++|+.||.|..+.++.++ +|+++|||||+|.+.++|++|+.  ++..++|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEEEEEECC
Confidence            45789999999999999999999999999999999997 89999999999999999999998  8999999999999998


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++...
T Consensus        85 ~~~~~   89 (102)
T 2xs2_A           85 RKQNL   89 (102)
T ss_dssp             ECC--
T ss_pred             cCcch
Confidence            76544

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=3.2e-19  Score=112.12  Aligned_cols=78  Identities=26%  Similarity=0.339  Sum_probs=71.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.+++        +||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK--------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS--------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC--------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            4567899999999999999999999999999998874        38999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      .++...
T Consensus        79 ~~~~~~   84 (90)
T 2dnp_A           79 TKGQKK   84 (90)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            886543

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.80  E-value=1.5e-19  Score=115.99  Aligned_cols=76  Identities=18%  Similarity=0.208  Sum_probs=70.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||.++++++|+++|++||.|..+.+.      +++|||||+|.+.++|++|+..|||..++|+.|+|.+++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            45789999999999999999999999999999887      357999999999999999999999999999999999998


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ++
T Consensus       100 ~~  101 (101)
T 2la4_A          100 ER  101 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.80  E-value=5.6e-20  Score=113.49  Aligned_cols=72  Identities=24%  Similarity=0.324  Sum_probs=67.1

Q ss_pred             cEEEEcCCCCCC------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc-EEE
Q 036791           58 SFWRCISVSFST------TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR-VIF  130 (157)
Q Consensus        58 ~~l~V~nl~~~~------~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~-~l~  130 (157)
                      ++|||+|||..+      ++++|+++|++||.|..+.++  +.+|+++|||||+|.+.++|++|++.|||..++|+ +|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            579999999999      679999999999999999887  46899999999999999999999999999999999 887


Q ss_pred             E
Q 036791          131 V  131 (157)
Q Consensus       131 v  131 (157)
                      |
T Consensus        80 V   80 (81)
T 2krb_A           80 V   80 (81)
T ss_dssp             C
T ss_pred             e
Confidence            6

>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=99.80  E-value=4.2e-19  Score=123.40  Aligned_cols=79  Identities=15%  Similarity=0.273  Sum_probs=76.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..+|||+|||..+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|.+|++.|||..++|++|+|+++.
T Consensus        94 ~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~As  172 (172)
T 2g4b_A           94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS  172 (172)
T ss_dssp             TTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEEEeCC
Confidence            5789999999999999999999999999999999998899999999999999999999999999999999999999873

>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=99.80  E-value=2.8e-20  Score=113.07  Aligned_cols=75  Identities=20%  Similarity=0.232  Sum_probs=71.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++. ++..+.|+.|+|+++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            589999999999999999999999999999999999999999999999999999999995 899999999999875

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B

Probab=99.80  E-value=2.7e-19  Score=117.35  Aligned_cols=80  Identities=18%  Similarity=0.268  Sum_probs=74.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||..+++++|+++|+.||.|..+.++.+   +.++|||||+|.+.++|.+|+..|||..++|+.|+|.++.
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            4568999999999999999999999999999999875   5569999999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ++.
T Consensus        84 ~~~   86 (115)
T 3lqv_A           84 ANR   86 (115)
T ss_dssp             HHH
T ss_pred             CCh
Confidence            644

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.80  E-value=4.2e-19  Score=112.54  Aligned_cols=79  Identities=16%  Similarity=0.167  Sum_probs=70.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|+.||.|..|  +.++.+++   ||||+|.+.++|++|+. |++..++|+.|+|.++.
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~V~~a~   80 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLRVRPRE   80 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECCCBCSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEEEEECC
Confidence            45689999999999999999999999999987  66666665   99999999999999999 99999999999999887


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++...
T Consensus        81 ~~~~~   85 (94)
T 2e5g_A           81 QKEFQ   85 (94)
T ss_dssp             CSCCC
T ss_pred             cCCCC
Confidence            65543

>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=99.80  E-value=3.6e-19  Score=110.61  Aligned_cols=75  Identities=20%  Similarity=0.275  Sum_probs=69.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM-NGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l-~g~~~~g~~l~v~~  133 (157)
                      ...++|||+|||..+++++|+++|++||.|..+.++.+      +|||||+|.+.++|++|++.| ++..+.|++|+|+|
T Consensus        10 ~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~   83 (85)
T 2ytc_A           10 KTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKW   83 (85)
T ss_dssp             SSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEE
T ss_pred             CCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEe
Confidence            45678999999999999999999999999999998864      689999999999999999999 99999999999999


Q ss_pred             ec
Q 036791          134 VR  135 (157)
Q Consensus       134 ~~  135 (157)
                      ++
T Consensus        84 ak   85 (85)
T 2ytc_A           84 GR   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>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=99.80  E-value=5.8e-19  Score=139.90  Aligned_cols=84  Identities=21%  Similarity=0.413  Sum_probs=79.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+.+|.+||.|..|.|+.++.+++++|||||+|.+.++|.+||..|||..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      .++.
T Consensus       180 ~~~~  183 (437)
T 3pgw_S          180 RGRT  183 (437)
T ss_pred             CCCC
Confidence            8653

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5.6e-20  Score=119.86  Aligned_cols=78  Identities=21%  Similarity=0.261  Sum_probs=72.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||+|||+++++++|+++|+.| .|..+.|+.++. |+++|||||+|.+.++|++|+ .+|+..|+|+.|.|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEEECCc
Confidence            4689999999999999999999999 899999999965 999999999999999999999 5899999999999988875


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      +
T Consensus        93 ~   93 (109)
T 2dnn_A           93 R   93 (109)
T ss_dssp             H
T ss_pred             c
Confidence            4

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.80  E-value=5.6e-19  Score=127.51  Aligned_cols=82  Identities=23%  Similarity=0.303  Sum_probs=77.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||+++++++|+++|++||.|..|.|+.++.+++++|||||+|.+.++|++|++.+++..+.|+.|++.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ..
T Consensus        94 ~~   95 (213)
T 4f02_A           94 RD   95 (213)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>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=99.80  E-value=5.3e-19  Score=115.16  Aligned_cols=76  Identities=24%  Similarity=0.382  Sum_probs=70.2

Q ss_pred             cccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFS-TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ..++|||+|||+. +++++|+++|++||.|..+.+        .+|||||+|.+.++|++|++.||+..++|+.|+|.++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            3478999999999 999999999999999999988        4789999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      +++..
T Consensus        98 ~~~~~  102 (110)
T 1wf1_A           98 GEPKP  102 (110)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            86443

>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=99.79  E-value=1.4e-18  Score=120.26  Aligned_cols=108  Identities=21%  Similarity=0.334  Sum_probs=89.1

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEAT   88 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~   88 (157)
                      ++|+..+++..+.++.+.+....              +.    .......+|||+|||..+++++|+++|++||.|..+.
T Consensus        59 ~~a~~~l~~~~~~g~~l~v~~~~--------------~~----~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  120 (168)
T 1b7f_A           59 QRAIKVLNGITVRNKRLKVSYAR--------------PG----GESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKN  120 (168)
T ss_dssp             HHHHHHHTTCEETTEECEEEECC--------------CC----SSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEE
T ss_pred             HHHHHhcCCCEeCCcEEEEEecC--------------CC----cccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEE
Confidence            45666677777766666443210              00    1123457899999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEee
Q 036791           89 IIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDNV  134 (157)
Q Consensus        89 ~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~~  134 (157)
                      ++.++.+++++|||||+|.+.++|.+|++.|||..+.|  ++|+|.+|
T Consensus       121 i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          121 ILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeEEEEEeC
Confidence            99998889999999999999999999999999999988  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.79  E-value=1.2e-18  Score=120.19  Aligned_cols=83  Identities=25%  Similarity=0.373  Sum_probs=78.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|++.|+|..+.|++|+|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            46899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 036791          137 SRR  139 (157)
Q Consensus       137 ~~~  139 (157)
                      ...
T Consensus        82 ~~~   84 (167)
T 1fxl_A           82 SSA   84 (167)
T ss_dssp             CCG
T ss_pred             Ccc
Confidence            543

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.3e-18  Score=109.73  Aligned_cols=79  Identities=20%  Similarity=0.307  Sum_probs=71.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+||  ++++++|+++|++||.|..+.+.      +.+|||||+|.+.++|++|+..||+..++|++|+|.++
T Consensus        13 ~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           13 RKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            35578999995  89999999999999999999884      46789999999999999999999999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      +++....
T Consensus        85 ~~~~~~~   91 (97)
T 1x5p_A           85 RKQPMLD   91 (97)
T ss_dssp             SSCCCCC
T ss_pred             CCCCCCC
Confidence            8876544

>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=99.79  E-value=2.2e-19  Score=124.27  Aligned_cols=110  Identities=14%  Similarity=0.193  Sum_probs=90.4

Q ss_pred             cccCCceeceecccccccCCC---------------cchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEee
Q 036791           27 FSSKPYQVVNYFSLHCIVRPS---------------SDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIM   91 (157)
Q Consensus        27 ~~~~~~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~   91 (157)
                      ..+.+++++.|.+...+...-               ...........+|||+|||..+++++|+++|++||.|..+.++.
T Consensus        42 g~~~g~afV~f~~~~~a~~A~~~~~~~~g~~i~v~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~  121 (167)
T 2cjk_A           42 GRSRGFGFLSFEKPSSVDEVVKTQHILDGKVIDPKRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLML  121 (167)
T ss_dssp             SSCCSCEEEEESSTHHHHHHHHSCCEETTEECCCEECCCHHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCC
T ss_pred             CCccceEEEEEccHHHHHHHHhcccccCCeEcccccccchhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEE
Confidence            345678888887665421110               00111112346899999999999999999999999999999999


Q ss_pred             cCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           92 DIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        92 ~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      ++.+|.++|||||+|.+.++|.+|++ +++..++|++|+|.++.|+
T Consensus       122 ~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          122 DKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             SSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEEECCCC
T ss_pred             cCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEeecCCC
Confidence            98899999999999999999999998 8999999999999999886

>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=99.79  E-value=5.4e-20  Score=119.46  Aligned_cols=81  Identities=19%  Similarity=0.253  Sum_probs=75.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCC---eeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQ---VTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~---i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ....+|||+|||+++++++|+++|+.||.   |..+.++.++. |+++|||||+|.+.++|++|+. +|+..++|+.|+|
T Consensus         9 ~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i~V   86 (107)
T 2lmi_A            9 DDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQRYVEV   86 (107)
T ss_dssp             SSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSSSCCCC
T ss_pred             CCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCCeEEEE
Confidence            45678999999999999999999999988   89999999977 9999999999999999999999 9999999999999


Q ss_pred             EeecCC
Q 036791          132 DNVRPS  137 (157)
Q Consensus       132 ~~~~~~  137 (157)
                      .++.++
T Consensus        87 ~~a~~~   92 (107)
T 2lmi_A           87 YEINNE   92 (107)
T ss_dssp             EECCHH
T ss_pred             EECCHH
Confidence            998764

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.79  E-value=3.6e-19  Score=117.79  Aligned_cols=79  Identities=10%  Similarity=0.064  Sum_probs=72.1

Q ss_pred             cEEEEcCC----CCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCC----HHH----HHHHHH--HhCCCc
Q 036791           58 SFWRCISV----SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSST----EEE----AQKALV--DMNGKL  123 (157)
Q Consensus        58 ~~l~V~nl----~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~----~~~----a~~ai~--~l~g~~  123 (157)
                      ++|||+||    |+.+++.+|+++|+.||+|.++.++.|+.||.++|||||+|.+    .++    |.+|+.  .|+|..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            57999999    9999999999999999999999999999999999999999996    333    888988  789999


Q ss_pred             cCCcEEEEEeecC
Q 036791          124 LDGRVIFVDNVRP  136 (157)
Q Consensus       124 ~~g~~l~v~~~~~  136 (157)
                      |+|++|+|.+.+.
T Consensus        83 I~Gr~irV~ln~~   95 (136)
T 2j8a_A           83 IMGFKFEVILNKH   95 (136)
T ss_dssp             ETTEEEEEEECCT
T ss_pred             ecCcEEEEEECcc
Confidence            9999999998764

>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=99.79  E-value=1e-18  Score=120.87  Aligned_cols=83  Identities=22%  Similarity=0.305  Sum_probs=79.1

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|++.|+|..+.|++|+|.++.+
T Consensus         3 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   82 (168)
T 1b7f_A            3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   82 (168)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecCC
Confidence            56899999999999999999999999999999999988999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 036791          137 SRR  139 (157)
Q Consensus       137 ~~~  139 (157)
                      ...
T Consensus        83 ~~~   85 (168)
T 1b7f_A           83 GGE   85 (168)
T ss_dssp             CSS
T ss_pred             Ccc
Confidence            654

>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=99.79  E-value=6.1e-19  Score=115.25  Aligned_cols=77  Identities=13%  Similarity=0.099  Sum_probs=70.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.      .+|||||+|.+.++|++|+..|||..++|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            457899999999999999999999999999998764      46899999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ...
T Consensus        83 ~~~   85 (111)
T 1whx_A           83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.79  E-value=1.2e-18  Score=121.58  Aligned_cols=79  Identities=22%  Similarity=0.312  Sum_probs=72.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||..+++++|+++|+.||.|..+     ..++.++|||||+|.+.++|.+|+..|||..+.|+.|+|.++
T Consensus        97 ~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v~~a  171 (175)
T 1fje_B           97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT  171 (175)
T ss_dssp             GGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEEEEC
T ss_pred             ccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEec
Confidence            345789999999999999999999999987665     467899999999999999999999999999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      .+++
T Consensus       172 ~~k~  175 (175)
T 1fje_B          172 GEKG  175 (175)
T ss_dssp             SSCC
T ss_pred             CCCC
Confidence            8863

>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=99.79  E-value=2.2e-18  Score=118.84  Aligned_cols=108  Identities=23%  Similarity=0.339  Sum_probs=88.9

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEAT   88 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~   88 (157)
                      ++|++.+++..+.++.+.+....              +..    ......+|||+|||..+++++|+++|++||.|..+.
T Consensus        58 ~~a~~~l~~~~~~g~~l~v~~~~--------------~~~----~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~  119 (167)
T 1fxl_A           58 EKAINTLNGLRLQTKTIKVSYAR--------------PSS----ASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSR  119 (167)
T ss_dssp             HHHHHHHTTCEETTEECEEEECC--------------CCC----GGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEE
T ss_pred             HHHHHHcCCCccCCceEEEEecC--------------CCc----ccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEE
Confidence            56666777777777766543210              111    113456799999999999999999999999999999


Q ss_pred             EeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE--EEEEee
Q 036791           89 IIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV--IFVDNV  134 (157)
Q Consensus        89 ~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~--l~v~~~  134 (157)
                      ++.++.+|.++|||||+|.+.++|.+|++.|||..+.|+.  |+|.||
T Consensus       120 i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          120 ILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             EEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             EEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccceEEEeC
Confidence            9999889999999999999999999999999999999964  888875

>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=99.78  E-value=7.1e-20  Score=124.17  Aligned_cols=83  Identities=17%  Similarity=0.117  Sum_probs=75.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+++++++|+++|++|| +..|.|+.++. ++++|||||+|.+.++|++|| .+|+..|.|+.|+|..+
T Consensus        44 ~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~V~~a  120 (139)
T 2hgn_A           44 TTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIELFLN  120 (139)
T ss_dssp             -CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCCCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEEEEEC
Confidence            4557899999999999999999999999 77999999976 999999999999999999999 78999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      .++...
T Consensus       121 ~~~~~~  126 (139)
T 2hgn_A          121 STTGAS  126 (139)
T ss_dssp             CCSCC-
T ss_pred             CCCCCC
Confidence            876544

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.78  E-value=6.7e-19  Score=124.01  Aligned_cols=82  Identities=23%  Similarity=0.310  Sum_probs=77.7

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+.+++++|+++|+.||.|..|.++.++ +++++|||||+|.+.++|++|++.||+..|.|+.|+|.++.
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45789999999999999999999999999999999997 89999999999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      +..
T Consensus       166 ~~~  168 (177)
T 2f3j_A          166 SQI  168 (177)
T ss_dssp             SGG
T ss_pred             CCC
Confidence            653

>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=99.78  E-value=1.9e-18  Score=119.63  Aligned_cols=80  Identities=16%  Similarity=0.193  Sum_probs=72.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~  132 (157)
                      .+..+|||+||++.+++++|+++|++||.|.++.+...    ..+|||||+|.+.++|++|++.|||..|.|  ++|+|.
T Consensus        44 s~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k----~~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~  119 (164)
T 1sjr_A           44 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID  119 (164)
T ss_dssp             CCEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEES----SSCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEE
T ss_pred             CceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEE
Confidence            34567999999999999999999999999999998643    257999999999999999999999999966  999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      |++++.
T Consensus       120 ~Ak~~~  125 (164)
T 1sjr_A          120 FSKLTS  125 (164)
T ss_dssp             ECSSSS
T ss_pred             EecCCc
Confidence            999863

>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=99.78  E-value=1.5e-18  Score=113.35  Aligned_cols=80  Identities=13%  Similarity=0.167  Sum_probs=70.9

Q ss_pred             ccccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC--CCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFS-TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN--GKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~--g~~~~g~~l~v  131 (157)
                      .+.++|||+|||++ +++++|+++|++||.|..+.++.      .+|||||+|.+.++|++|++.|+  +..|.|++|+|
T Consensus        23 ~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~------~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V   96 (112)
T 1x4f_A           23 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR------MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   96 (112)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec------CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEE
Confidence            34678999999998 99999999999999999999864      37899999999999999999886  45699999999


Q ss_pred             EeecCCCCC
Q 036791          132 DNVRPSRRY  140 (157)
Q Consensus       132 ~~~~~~~~~  140 (157)
                      .++.++...
T Consensus        97 ~~a~~~~~~  105 (112)
T 1x4f_A           97 DLSEKYKKL  105 (112)
T ss_dssp             EEECSCSSS
T ss_pred             EECcccccc
Confidence            999876543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=1e-18  Score=110.97  Aligned_cols=78  Identities=21%  Similarity=0.222  Sum_probs=71.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEA-TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ..++|||+|||+++++++|+++|++||.|..+ .++.++.++.    |||+|.+.++|++|++.|||..++|++|+|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45789999999999999999999999999999 5887765543    999999999999999999999999999999999


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      .++
T Consensus        90 ~~~   92 (96)
T 2e44_A           90 PDE   92 (96)
T ss_dssp             CCC
T ss_pred             Ccc
Confidence            986

>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=99.77  E-value=1.2e-18  Score=118.53  Aligned_cols=87  Identities=23%  Similarity=0.275  Sum_probs=73.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEE--E---eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEAT--I---IMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI  129 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~--~---~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l  129 (157)
                      ...++|||+|||+.+++++|+++|+.||.|..+.  +   +....+|+++|||||+|.+.++|.+|+..|||..+.|+.|
T Consensus        43 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l  122 (143)
T 3egn_A           43 EPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPM  122 (143)
T ss_dssp             SCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEETTEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCcEE
Confidence            3457899999999999999999999999887631  0   1112468999999999999999999999999999999999


Q ss_pred             EEEeecCCCCCC
Q 036791          130 FVDNVRPSRRYN  141 (157)
Q Consensus       130 ~v~~~~~~~~~~  141 (157)
                      +|.++++...+.
T Consensus       123 ~V~~a~~~~~~~  134 (143)
T 3egn_A          123 VVQFARSARPKQ  134 (143)
T ss_dssp             EEEECCCSCC--
T ss_pred             EEEECCCCCCcc
Confidence            999998765443

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.77  E-value=4.5e-18  Score=113.66  Aligned_cols=79  Identities=16%  Similarity=0.238  Sum_probs=71.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCCccCC--cEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGY-GYVTSSTEEEAQKALVDMNGKLLDG--RVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v  131 (157)
                      .+...|||+||++.+++++|+++|++||.|.++.+...     .+|+ |||+|.+.++|++|++.|||..|+|  +.|+|
T Consensus        26 s~VL~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~-----~~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI  100 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTK-----NNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRI  100 (130)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEE-----TTEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEE
T ss_pred             CceEEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcC-----CCCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEE
Confidence            45667999999999999999999999999999988754     2577 9999999999999999999999988  89999


Q ss_pred             EeecCCC
Q 036791          132 DNVRPSR  138 (157)
Q Consensus       132 ~~~~~~~  138 (157)
                      .|++++.
T Consensus       101 ~~ak~~~  107 (130)
T 3zzy_A          101 DFSKLTS  107 (130)
T ss_dssp             EECSCSS
T ss_pred             EecCCCc
Confidence            9998763

>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=99.77  E-value=1.5e-18  Score=114.03  Aligned_cols=77  Identities=19%  Similarity=0.161  Sum_probs=67.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE-----EE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV-----IF  130 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~-----l~  130 (157)
                      ...+|||+|||+++++++|+++|.+||.|..+.++.+       |||||+|.+.++|++||+.||+..|+|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            3568999999999999999999999999999998765       89999999999999999999999999988     88


Q ss_pred             EEeecCCCC
Q 036791          131 VDNVRPSRR  139 (157)
Q Consensus       131 v~~~~~~~~  139 (157)
                      |..+.++..
T Consensus        88 v~~~~~~~~   96 (115)
T 3beg_B           88 VKVDGPRSP   96 (115)
T ss_dssp             EEECC----
T ss_pred             eccCCCCCC
Confidence            888776543

>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=99.77  E-value=3.4e-18  Score=121.14  Aligned_cols=84  Identities=30%  Similarity=0.434  Sum_probs=77.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|+.. ++..+.|+.|.|.++
T Consensus        11 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l~v~~~   89 (196)
T 1l3k_A           11 EQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRA   89 (196)
T ss_dssp             GGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEeeeecc
Confidence            4567899999999999999999999999999999999999999999999999999999999986 899999999999998


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .+...
T Consensus        90 ~~~~~   94 (196)
T 1l3k_A           90 VSRED   94 (196)
T ss_dssp             CC---
T ss_pred             cCccc
Confidence            77543

>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=99.77  E-value=4.6e-18  Score=127.26  Aligned_cols=116  Identities=16%  Similarity=0.088  Sum_probs=94.9

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCC-CHHHHHHHHhcCCCeeEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFST-TKEMLADAFSQFGQVTEA   87 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~-~~~~l~~~f~~~G~i~~~   87 (157)
                      ++|+..+++..+.++.+.+....        ..       ..........+|||+|||..+ ++++|+++|+.||.|..+
T Consensus       151 ~~A~~~l~~~~~~g~~i~v~~a~--------~~-------~~~~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~G~i~~v  215 (284)
T 3smz_A          151 ARAKSDLLGKPLGPRTLYVHWTD--------AG-------QLTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFC  215 (284)
T ss_dssp             HHHHHHHTTCEETTEECEEEECC--------GG-------GCCTTTTSCSEEEEECCCTTCCCHHHHHHHTCSSSCCSEE
T ss_pred             HHHHHHhCCCEeCCcEEEEEECC--------CC-------CCCcccCCccEEEEecCCcccCCHHHHHHHhhCCCCeEEE
Confidence            56777788888877777554211        10       011122345789999999995 999999999999999999


Q ss_pred             EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCCC
Q 036791           88 TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRY  140 (157)
Q Consensus        88 ~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~~  140 (157)
                      .++.++ +|+++|+|||+|.+.++|.+|+..|||..++|++|+|.++.++..+
T Consensus       216 ~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~~  267 (284)
T 3smz_A          216 QLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPPG  267 (284)
T ss_dssp             EEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSCH
T ss_pred             EEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCcc
Confidence            999985 7999999999999999999999999999999999999999987653

>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=99.76  E-value=2.4e-18  Score=107.79  Aligned_cols=76  Identities=16%  Similarity=0.151  Sum_probs=70.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||+.+++++|+++|++| .|..+.+.      +++|||||+|.+.++|++|++.|||..++|++|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            45689999999999999999999999 99999884      578999999999999999999999999999999999997


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      .+.
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            653

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=7.5e-19  Score=116.79  Aligned_cols=81  Identities=25%  Similarity=0.252  Sum_probs=73.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCe----eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQV----TEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i----~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      .+..+|||+|||+++++++|+++|++||.|    ..|.|+.+ .+|+++|||||+|.+.++|++|++. |+..|.|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d-~~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTY-PDGRPTGDAFVLFACEEYAQNALRK-HKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEEC-TTSCEEEEEEECCSSHHHHHHHHTT-TTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEEC-CCCCEeeEEEEEECCHHHHHHHHHh-CCCeeCCeEEE
Confidence            445789999999999999999999999875    68999998 5899999999999999999999996 99999999999


Q ss_pred             EEeecCC
Q 036791          131 VDNVRPS  137 (157)
Q Consensus       131 v~~~~~~  137 (157)
                      |..+.++
T Consensus        99 V~~a~~~  105 (123)
T 2dha_A           99 LFRSTAA  105 (123)
T ss_dssp             CEEECHH
T ss_pred             EEECCHH
Confidence            9998654

>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=99.76  E-value=1.5e-17  Score=115.58  Aligned_cols=79  Identities=24%  Similarity=0.211  Sum_probs=73.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC---CcEEEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD---GRVIFVD  132 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~---g~~l~v~  132 (157)
                      ...+|||+|||..+++++|+++|++||.|..+.++.++ +|+++|||||+|.+.++|.+|++.|||..+.   |++|+|.
T Consensus        94 ~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~l~V~  172 (175)
T 3nmr_A           94 EDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSPMVVK  172 (175)
T ss_dssp             GGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSCCEEE
T ss_pred             CCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCCeEEE
Confidence            45689999999999999999999999999999999985 5899999999999999999999999998876   4999999


Q ss_pred             eec
Q 036791          133 NVR  135 (157)
Q Consensus       133 ~~~  135 (157)
                      |+.
T Consensus       173 ~ad  175 (175)
T 3nmr_A          173 FAD  175 (175)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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=99.75  E-value=9.7e-19  Score=116.64  Aligned_cols=80  Identities=26%  Similarity=0.311  Sum_probs=72.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCee--EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVT--EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .+..+|||+|||+++++++|+++|+.| .|.  .|.|+.++. |+++|||||+|.+.++|++|++. ++..|+|+.|.|.
T Consensus        40 ~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~I~V~  116 (126)
T 2hgm_A           40 ANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRYIEVF  116 (126)
T ss_dssp             SSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBCCCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEEEEEE
Confidence            455789999999999999999999999 677  899999976 99999999999999999999985 7899999999999


Q ss_pred             eecCC
Q 036791          133 NVRPS  137 (157)
Q Consensus       133 ~~~~~  137 (157)
                      .+.++
T Consensus       117 ~a~~~  121 (126)
T 2hgm_A          117 KSSQE  121 (126)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            88653

>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=99.75  E-value=5.7e-18  Score=127.21  Aligned_cols=118  Identities=17%  Similarity=0.148  Sum_probs=91.6

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEE
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFS-TTKEMLADAFSQFGQVTEA   87 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~   87 (157)
                      ++|+..+++..+.++.+.+....        ....   ............+|||+|||.. +++++|+++|+.||.|..+
T Consensus       173 ~~A~~~l~g~~~~g~~l~v~~a~--------~~~~---~~~~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~G~v~~v  241 (292)
T 2ghp_A          173 RYCVEKLNGLKIEGYTLVTKVSN--------PLEK---SKRTDSATLEGREIMIRNLSTELLDENLLRESFEGFGSIEKI  241 (292)
T ss_dssp             HHHHHHHTTCEETTEECEEEECC--------CC------------CCTTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEE
T ss_pred             HHHHHHhCCCEeCCcEEEEEECC--------CCcc---cccccccCCCCceEEEECCCcccCCHHHHHHHHhccCCeeEE
Confidence            56777788888887777544211        0000   0000122345678999999999 9999999999999999999


Q ss_pred             EEeecCC-CCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           88 TIIMDIG-KNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        88 ~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      .++.+.. ||.++|||||+|.+.++|.+|+ .|||..|.|++|+|.++.+++
T Consensus       242 ~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i~V~~a~~k~  292 (292)
T 2ghp_A          242 NIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREISVSLADKKP  292 (292)
T ss_dssp             ECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEEEEEECCCCC
T ss_pred             EEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEEEEEEecCCC
Confidence            9999866 5999999999999999999999 999999999999999999863

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=1.3e-17  Score=104.62  Aligned_cols=74  Identities=14%  Similarity=0.126  Sum_probs=66.2

Q ss_pred             cEEEEcCCCCCCCHHH----HHHHHhcC-CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           58 SFWRCISVSFSTTKEM----LADAFSQF-GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~----l~~~f~~~-G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      +.|||+|||+.+++++    |+++|++| |.|..|       ++   |+|||.|.+.++|.+|++.|+|..+.|++|+|.
T Consensus        10 T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~   79 (96)
T 2diu_A           10 TLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNRIIVS   79 (96)
T ss_dssp             EEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             eEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCceEEEE
Confidence            3499999999999987    56899999 599887       23   999999999999999999999999999999999


Q ss_pred             eecCCCCCC
Q 036791          133 NVRPSRRYN  141 (157)
Q Consensus       133 ~~~~~~~~~  141 (157)
                      +++.+..--
T Consensus        80 ~A~~~sd~~   88 (96)
T 2diu_A           80 FTPKNRELC   88 (96)
T ss_dssp             SSCCSCCCC
T ss_pred             ecCCCccee
Confidence            999876543

>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=99.75  E-value=2.5e-17  Score=123.23  Aligned_cols=85  Identities=20%  Similarity=0.337  Sum_probs=79.7

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+.+++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|+..|+|..++|+.|.|.++.
T Consensus        94 ~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~a~  173 (284)
T 3smz_A           94 TDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD  173 (284)
T ss_dssp             CSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECC
Confidence            34689999999999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++...
T Consensus       174 ~~~~~  178 (284)
T 3smz_A          174 AGQLT  178 (284)
T ss_dssp             GGGCC
T ss_pred             CCCCC
Confidence            76543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.75  E-value=2.4e-17  Score=109.54  Aligned_cols=78  Identities=22%  Similarity=0.253  Sum_probs=69.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceE-EEEEeCCHHHHHHHHHHhCCCccCC--cEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGY-GYVTSSTEEEAQKALVDMNGKLLDG--RVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~-afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v  131 (157)
                      .+...|||+||++.+++++|+++|++||.|..|.+.. +     .|| |||+|.+.++|.+|++.|||..|.|  +.|+|
T Consensus        23 s~vl~l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~-~-----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V   96 (124)
T 2e5i_A           23 NKVLLLSIQNPLYPITVDVLYTVCNPVGKVQRIVIFK-R-----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI   96 (124)
T ss_dssp             CSEEEEEEESCCSCCCHHHHHHHHTTTSCEEEEEEEE-S-----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEE
T ss_pred             CcEEEEEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEe-C-----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEE
Confidence            3445689999999999999999999999999998864 2     275 9999999999999999999999988  68999


Q ss_pred             EeecCCC
Q 036791          132 DNVRPSR  138 (157)
Q Consensus       132 ~~~~~~~  138 (157)
                      .+++++.
T Consensus        97 ~~Ak~~~  103 (124)
T 2e5i_A           97 EYARPTR  103 (124)
T ss_dssp             ECCSCSC
T ss_pred             EEecCCc
Confidence            9999864

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.74  E-value=1.4e-17  Score=114.72  Aligned_cols=81  Identities=20%  Similarity=0.352  Sum_probs=75.0

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      ++|||+|||.++++++|+++|++||.|..+.++.++ +++++|||||+|.+.++|.+|++.|+|..+.|+.|.|.++.+.
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~   79 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQS   79 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCC
Confidence            479999999999999999999999999999999985 4789999999999999999999999999999999999999775


Q ss_pred             CC
Q 036791          138 RR  139 (157)
Q Consensus       138 ~~  139 (157)
                      ..
T Consensus        80 ~~   81 (166)
T 3md3_A           80 QQ   81 (166)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.74  E-value=6.5e-18  Score=110.49  Aligned_cols=76  Identities=18%  Similarity=0.267  Sum_probs=68.3

Q ss_pred             cccEEEE--cCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc-----CCcE
Q 036791           56 NVSFWRC--ISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL-----DGRV  128 (157)
Q Consensus        56 ~~~~l~V--~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~-----~g~~  128 (157)
                      +..+|||  +||++++++++|+++|++||.|..+.++.      .+|||||+|.+.++|++|++.|||..+     .|++
T Consensus        24 pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~------~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~   97 (114)
T 2cq2_A           24 ATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   97 (114)
T ss_dssp             CCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT------TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcE
Confidence            4567999  77999999999999999999999987753      268999999999999999999999988     6899


Q ss_pred             EEEEeecCC
Q 036791          129 IFVDNVRPS  137 (157)
Q Consensus       129 l~v~~~~~~  137 (157)
                      |.|.++...
T Consensus        98 l~v~~a~~~  106 (114)
T 2cq2_A           98 LYLNFVEKV  106 (114)
T ss_dssp             CEEEEESCC
T ss_pred             EEEEecccC
Confidence            999999754

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.74  E-value=9.7e-18  Score=120.43  Aligned_cols=84  Identities=26%  Similarity=0.330  Sum_probs=75.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||.++++++|+++|+.||.|..+.++.++.+++++|||||+|.+.++|.+|++.|++..+.|+.|+|.++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~  105 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRP  105 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECC
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecC
Confidence            34578999999999999999999999999999999999889999999999999999999999999999999999999887


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      ....
T Consensus       106 ~~~~  109 (216)
T 2qfj_A          106 SNIG  109 (216)
T ss_dssp             SCCG
T ss_pred             CCcc
Confidence            6543

>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=99.74  E-value=1.2e-17  Score=104.85  Aligned_cols=76  Identities=22%  Similarity=0.298  Sum_probs=62.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc--cCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL--LDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~--~~g~~l~v~  132 (157)
                      ....+|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++    +++..  +.|+.|.|.
T Consensus         9 ~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~----~~~~~~~~~g~~v~v~   79 (89)
T 3d2w_A            9 HHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQS----LCGEDLIIKGISVHIS   79 (89)
T ss_dssp             --CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHH----HTTCEEEETTEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHH----HcCCCcccCCEEEEEE
Confidence            34578999999999999999999999999999998764     68999999999999983    45665  459999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      ++.++..
T Consensus        80 ~a~~k~~   86 (89)
T 3d2w_A           80 NAEPKHN   86 (89)
T ss_dssp             ECC----
T ss_pred             EcCCCCc
Confidence            9988654

>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=99.73  E-value=5.2e-18  Score=106.11  Aligned_cols=80  Identities=21%  Similarity=0.279  Sum_probs=66.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+     ++|||||+|.+.++|++++..  ...+.|++|.|.++.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v~~a~   76 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEEEecC
Confidence            4578999999999999999999999999999988754     689999999999999764321  234589999999999


Q ss_pred             CCCCCCC
Q 036791          136 PSRRYNT  142 (157)
Q Consensus       136 ~~~~~~~  142 (157)
                      ++.....
T Consensus        77 ~~~~~~~   83 (88)
T 1wf0_A           77 PKHNSNS   83 (88)
T ss_dssp             CCCCCCS
T ss_pred             CCCCCCC
Confidence            8765443

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.1e-17  Score=108.30  Aligned_cols=76  Identities=13%  Similarity=0.152  Sum_probs=64.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCC---CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGK---NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~---~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ..++|||+|||+++++++|+++|++||.|. +.++.++.+   |+++|||||+|.+.++|++|++.|+  .++|+.+.+.
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEec
Confidence            457899999999999999999999999999 888888777   7999999999999999999999983  2555555554


Q ss_pred             ee
Q 036791          133 NV  134 (157)
Q Consensus       133 ~~  134 (157)
                      .+
T Consensus        84 ~~   85 (114)
T 2dnl_A           84 SS   85 (114)
T ss_dssp             CC
T ss_pred             cC
Confidence            43

>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=99.73  E-value=3e-17  Score=114.06  Aligned_cols=83  Identities=22%  Similarity=0.223  Sum_probs=75.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCCccC---CcEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKN--RSKGYGYVTSSTEEEAQKALVDMNGKLLD---GRVIF  130 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~ai~~l~g~~~~---g~~l~  130 (157)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.++  +++|||||+|.+.++|++|++.|++..+.   ++.+.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            45789999999999999999999999999999999998877  89999999999999999999999998875   67888


Q ss_pred             EEeecCCC
Q 036791          131 VDNVRPSR  138 (157)
Q Consensus       131 v~~~~~~~  138 (157)
                      +.++.+..
T Consensus        82 ~~~~~~~~   89 (175)
T 3nmr_A           82 MKPADSEK   89 (175)
T ss_dssp             EEECGGGC
T ss_pred             Eccccccc
Confidence            88877654

>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=99.72  E-value=2.4e-17  Score=118.53  Aligned_cols=77  Identities=12%  Similarity=0.220  Sum_probs=71.1

Q ss_pred             cccEEEEcCCC-CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVS-FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...+|||+||| +.+++++|+++|++||.|.++.++.+     .+|||||+|.+.++|++|++.|||..+.|++|+|.++
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s   77 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS-----KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVS   77 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT-----STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC-----CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEc
Confidence            35689999999 89999999999999999999999765     3799999999999999999999999999999999998


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      +.+
T Consensus        78 ~~~   80 (205)
T 3tyt_A           78 KQP   80 (205)
T ss_dssp             SCS
T ss_pred             cCC
Confidence            754

>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=99.71  E-value=3.9e-17  Score=101.66  Aligned_cols=71  Identities=20%  Similarity=0.382  Sum_probs=65.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQF----G-------QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL  124 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~  124 (157)
                      ..++|||+|||+++++++|+++|++|    |       .|..+.+..+      +|||||+|.+.++|++|+ .|||..+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~g~~~   77 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDGIIF   77 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcCCCEE
Confidence            46789999999999999999999999    8       8999888654      799999999999999999 9999999


Q ss_pred             CCcEEEEEe
Q 036791          125 DGRVIFVDN  133 (157)
Q Consensus       125 ~g~~l~v~~  133 (157)
                      +|+.|+|+.
T Consensus        78 ~g~~l~V~r   86 (87)
T 2hzc_A           78 QGQSLKIRR   86 (87)
T ss_dssp             TTEECEEEC
T ss_pred             CCeEEEEeC
Confidence            999999974

>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=99.71  E-value=1.4e-16  Score=119.12  Aligned_cols=76  Identities=16%  Similarity=0.161  Sum_probs=70.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-GRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~v~~~  134 (157)
                      ...+|||+|||..+++++|+++|++||.|..+.++.++     +|||||+|.+.++|.+|++.|||..+. |+.|+|.|+
T Consensus       206 ~~~~l~v~nl~~~~~~~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a  280 (282)
T 3pgw_A          206 PNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFA  280 (282)
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEe
Confidence            45789999999999999999999999999999998653     589999999999999999999999999 999999998


Q ss_pred             cC
Q 036791          135 RP  136 (157)
Q Consensus       135 ~~  136 (157)
                      +.
T Consensus       281 kk  282 (282)
T 3pgw_A          281 KK  282 (282)
T ss_pred             cC
Confidence            63

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.71  E-value=1.6e-16  Score=102.76  Aligned_cols=81  Identities=19%  Similarity=0.176  Sum_probs=71.7

Q ss_pred             cccEEEEcCCCC-----CCCHHHHHHHHhcCCCeeEEEEeecCCC-CCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q 036791           56 NVSFWRCISVSF-----STTKEMLADAFSQFGQVTEATIIMDIGK-NRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI  129 (157)
Q Consensus        56 ~~~~l~V~nl~~-----~~~~~~l~~~f~~~G~i~~~~~~~~~~~-~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l  129 (157)
                      ..+.|+|.||..     +-.+++|++.|++||.|..+.++.++.+ ++++|++||+|.+.++|.+|++.|||..++|+.|
T Consensus         7 ~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~i   86 (105)
T 2pe8_A            7 PTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVV   86 (105)
T ss_dssp             CCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcEE
Confidence            456799999863     2367999999999999999999988654 6889999999999999999999999999999999


Q ss_pred             EEEeecC
Q 036791          130 FVDNVRP  136 (157)
Q Consensus       130 ~v~~~~~  136 (157)
                      +|.++.+
T Consensus        87 ~v~~a~~   93 (105)
T 2pe8_A           87 KACFYNL   93 (105)
T ss_dssp             EEEECCH
T ss_pred             EEEEcCH
Confidence            9999875

>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=99.70  E-value=1e-16  Score=119.86  Aligned_cols=81  Identities=19%  Similarity=0.209  Sum_probs=74.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHH----HHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLA----DAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~----~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      ...++|||+|||+++++++|+    ++|+.||.|..|.+..   +++++|||||+|.+.++|.+|++.|||..+.|+.|+
T Consensus         7 ~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            456789999999999999976    8999999999998875   588999999999999999999999999999999999


Q ss_pred             EEeecCCC
Q 036791          131 VDNVRPSR  138 (157)
Q Consensus       131 v~~~~~~~  138 (157)
                      |.+++.+.
T Consensus        84 v~~a~~~~   91 (282)
T 3pgw_A           84 IQYAKTDS   91 (282)
T ss_pred             EEEeccCc
Confidence            99997654

>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=99.70  E-value=9.3e-17  Score=115.47  Aligned_cols=125  Identities=12%  Similarity=0.077  Sum_probs=89.2

Q ss_pred             HHHHHHHhccccccCcccccccCCceec-eec--cccc------------ccCCCcc---h-hhccccccEEEEcCCCCC
Q 036791            8 QTRKIQQFNSYFTEDSLLSFSSKPYQVV-NYF--SLHC------------IVRPSSD---L-IMQLVNVSFWRCISVSFS   68 (157)
Q Consensus         8 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~------------~~~~~~~---~-~~~~~~~~~l~V~nl~~~   68 (157)
                      -++|++.||+..+.++.+++........ ...  ....            ..+-...   . .....+..+|||+|||++
T Consensus        55 A~~Ai~~lng~~~~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~  134 (205)
T 3tyt_A           55 VDRAITHLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLE  134 (205)
T ss_dssp             HHHHHHHHTTCEETTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTT
T ss_pred             HHHHHHHhCCCEECCceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCC
Confidence            3678889999999999987764221110 000  0000            0000000   0 000123568999999999


Q ss_pred             CCHHHHHHHHhcCCCe--eEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCc----EEEEEee
Q 036791           69 TTKEMLADAFSQFGQV--TEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR----VIFVDNV  134 (157)
Q Consensus        69 ~~~~~l~~~f~~~G~i--~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~----~l~v~~~  134 (157)
                      +++++|+++|++||.|  ..+.+..++  +..+|+|||+|.+.++|.+||..|||..|.|+    ++.|+++
T Consensus       135 ~t~~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          135 VTEENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CCHHHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCHHHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            9999999999999999  888888764  56679999999999999999999999999875    6777665

>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=99.70  E-value=3.7e-17  Score=112.98  Aligned_cols=80  Identities=24%  Similarity=0.436  Sum_probs=74.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|+..  +..+.|+.|.|.++.
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~~~~   79 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPKRAI   79 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEccccccc
Confidence            357899999999999999999999999999999999999999999999999999999999984  678999999999886


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ++
T Consensus        80 ~~   81 (167)
T 2cjk_A           80 PR   81 (167)
T ss_dssp             CH
T ss_pred             ch
Confidence            54

>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=99.70  E-value=4.2e-16  Score=113.55  Aligned_cols=124  Identities=17%  Similarity=0.159  Sum_probs=91.1

Q ss_pred             HHHHHHhccccccCcccccccCCceeceeccc----------------ccccCCCcc-hhhccccccEEEEcCCCCCCCH
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSL----------------HCIVRPSSD-LIMQLVNVSFWRCISVSFSTTK   71 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~-~~~~~~~~~~l~V~nl~~~~~~   71 (157)
                      ++|++.+|+..+.++.+.+.............                .....+... ......+..+|||+|||..+++
T Consensus        86 ~~Ai~~l~g~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~  165 (229)
T 2adc_A           86 QLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSE  165 (229)
T ss_dssp             HHHHHHHTTCBCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCH
T ss_pred             HHHHHHhCCCeECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCH
Confidence            67788899999999988765422111000000                000001100 0111233578999999999999


Q ss_pred             HHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEeecCC
Q 036791           72 EMLADAFSQFG-QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-GRVIFVDNVRPS  137 (157)
Q Consensus        72 ~~l~~~f~~~G-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~v~~~~~~  137 (157)
                      ++|+++|++|| .|..+.++.+     .+|||||+|.+.++|.+|+..|||..+. |+.|+|.|++++
T Consensus       166 ~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~  228 (229)
T 2adc_A          166 EDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  228 (229)
T ss_dssp             HHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSC
T ss_pred             HHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCC
Confidence            99999999999 9999988653     3689999999999999999999999999 999999999874

>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=99.70  E-value=1.4e-16  Score=113.56  Aligned_cols=79  Identities=14%  Similarity=0.066  Sum_probs=72.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.+. +++++|||||+|.+.++|++|+..+ +..++|+.|.|.++.
T Consensus       108 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~-~~~~~Gr~l~V~~~~  185 (193)
T 2voo_A          108 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETP-GQKYKETDLLILFKD  185 (193)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCT-TCEETTEECEEEETT
T ss_pred             ccCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhC-CCeECCEEEEEEEhH
Confidence            45789999999999999999999999999999999985 5899999999999999999999876 458999999999876


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      .
T Consensus       186 ~  186 (193)
T 2voo_A          186 D  186 (193)
T ss_dssp             T
T ss_pred             H
Confidence            5

>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=99.69  E-value=2.1e-16  Score=117.26  Aligned_cols=81  Identities=30%  Similarity=0.451  Sum_probs=73.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC-CCccC---CcEEEEE
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN-GKLLD---GRVIFVD  132 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~-g~~~~---g~~l~v~  132 (157)
                      ..+|||+|||..+++++|+++|+.||.|..+.++.+ .+|+++|||||+|.+.++|.+|+..|| +..+.   +++|.|.
T Consensus        96 ~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r~i~v~  174 (261)
T 3sde_A           96 GAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPRPVIVE  174 (261)
T ss_dssp             SSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCCBCEEE
T ss_pred             CCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCceEEEe
Confidence            468999999999999999999999999999999999 689999999999999999999999995 44444   9999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      ++.+..
T Consensus       175 ~~~~~~  180 (261)
T 3sde_A          175 PMEQFD  180 (261)
T ss_dssp             ECCCEE
T ss_pred             eccccC
Confidence            998753

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.69  E-value=6.7e-17  Score=118.42  Aligned_cols=79  Identities=16%  Similarity=0.186  Sum_probs=70.0

Q ss_pred             ccccEEEEcCCCCCC---------CHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc-
Q 036791           55 VNVSFWRCISVSFST---------TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL-  124 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~---------~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~-  124 (157)
                      ...++|||+||+..+         ++++|+++|++||.|..|.++.      ++|||||+|.+.++|+.|++.|+|..| 
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~------~kG~AFV~F~~~~~Ae~A~~am~g~~l~  205 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE------SKNCGFVKFKYQANAEFAKEAMSNQTLL  205 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG------GGTEEEEEESSHHHHHHHHHHHTTCCCC
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC------CCCEEEEEeCCHHHHHHHHHHhCCCEEe
Confidence            356799999999998         7999999999999999999985      379999999999999999999999999 


Q ss_pred             -----------CCcEEEEEeecCCCC
Q 036791          125 -----------DGRVIFVDNVRPSRR  139 (157)
Q Consensus       125 -----------~g~~l~v~~~~~~~~  139 (157)
                                 .|+.|.|.|++....
T Consensus       206 ~~~~~e~~~~~~gr~L~V~wA~~~pn  231 (240)
T 3u1l_A          206 LPSDKEWDDRREGTGLLVKWANEDPD  231 (240)
T ss_dssp             CTTSTTGGGGGGSCCCEEEECC----
T ss_pred             ccccccccccCCCCEEEEEEccCCCC
Confidence                       899999999987643

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.69  E-value=2.3e-16  Score=112.09  Aligned_cols=125  Identities=16%  Similarity=0.138  Sum_probs=91.2

Q ss_pred             HHHHHHHhccccccCcccccccCCceeceecccc----------------cccCCCcc-hhhccccccEEEEcCCCCCCC
Q 036791            8 QTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLH----------------CIVRPSSD-LIMQLVNVSFWRCISVSFSTT   70 (157)
Q Consensus         8 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~~-~~~~~~~~~~l~V~nl~~~~~   70 (157)
                      -++|+..+++..+.++.+.+..............                ....+... ......+..+|||+|||..++
T Consensus        54 a~~A~~~l~~~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~  133 (198)
T 1qm9_A           54 AQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVS  133 (198)
T ss_dssp             HHHHHHHHTTCCCSSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCC
T ss_pred             HHHHHHHhCCCeecCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCC
Confidence            3677888999999998887653211110000000                00000000 001113367899999999999


Q ss_pred             HHHHHHHHhcCC-CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC-CcEEEEEeecCC
Q 036791           71 KEMLADAFSQFG-QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD-GRVIFVDNVRPS  137 (157)
Q Consensus        71 ~~~l~~~f~~~G-~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~-g~~l~v~~~~~~  137 (157)
                      +++|+++|++|| .|..+.+..+     .+|+|||+|.+.++|.+|+..|||..+. |+.|+|.|++++
T Consensus       134 ~~~l~~~f~~~G~~v~~v~i~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~  197 (198)
T 1qm9_A          134 EEDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKST  197 (198)
T ss_dssp             HHHHHHHHHHTTSCCCEEEESST-----TSSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCC
T ss_pred             HHHHHHHHHHcCCCceEEEEEeC-----CCcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeeccc
Confidence            999999999999 9999988654     2689999999999999999999999999 999999999874

>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=99.67  E-value=2.5e-16  Score=118.24  Aligned_cols=110  Identities=12%  Similarity=0.198  Sum_probs=82.7

Q ss_pred             CCceeceecccccccCCCc---------chhhccccccEEEEcCCCCCCCHHHHHHHHhcCC-CeeEEEEeecCCCCCcc
Q 036791           30 KPYQVVNYFSLHCIVRPSS---------DLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFG-QVTEATIIMDIGKNRSK   99 (157)
Q Consensus        30 ~~~~~~~~~~~~~~~~~~~---------~~~~~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G-~i~~~~~~~~~~~~~~~   99 (157)
                      .+++++.|.....+..+-.         .......+..+|||+|||+.+++++|+++|+.|| .|..+.++.++. +.++
T Consensus        81 ~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~-~~~~  159 (292)
T 2ghp_A           81 FRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRF-NTSR  159 (292)
T ss_dssp             SEEEEEEESSHHHHHHHHTTTTCEETTEECEEEECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC--------C
T ss_pred             cEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCC-CCcc
Confidence            5677777776655322210         0111123457899999999999999999999999 999999998855 8899


Q ss_pred             eEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCCC
Q 036791          100 GYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRY  140 (157)
Q Consensus       100 g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~~  140 (157)
                      |||||+|.+.++|.+|+..|+|..+.|+.|.|.++.+....
T Consensus       160 g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~~  200 (292)
T 2ghp_A          160 RFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNPLEKS  200 (292)
T ss_dssp             CEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCCC---
T ss_pred             eEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEECCCCccc
Confidence            99999999999999999999999999999999999876543

>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=99.67  E-value=2.6e-16  Score=114.68  Aligned_cols=78  Identities=22%  Similarity=0.278  Sum_probs=72.9

Q ss_pred             ccccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           55 VNVSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ....+|||+|||+ .+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|++|++.|+|..+.|+.|.|.+
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~  106 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITL  106 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEEC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            4567899999999 99999999999999999999998874     78999999999999999999999999999999999


Q ss_pred             ecCC
Q 036791          134 VRPS  137 (157)
Q Consensus       134 ~~~~  137 (157)
                      ++++
T Consensus       107 a~~~  110 (229)
T 2adc_A          107 SKHQ  110 (229)
T ss_dssp             CSCC
T ss_pred             ecCc
Confidence            9865

>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=99.66  E-value=1.2e-15  Score=99.58  Aligned_cols=83  Identities=20%  Similarity=0.282  Sum_probs=70.7

Q ss_pred             ccccEEEEcCCCCCCC-----------HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 036791           55 VNVSFWRCISVSFSTT-----------KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL  123 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~-----------~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~  123 (157)
                      ....+|+|.||.....           +++|+++|++||.|..+.+ .++   .++|||||+|.+.++|++|+..|||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            4567899999944432           5799999999999999955 553   379999999999999999999999999


Q ss_pred             cCCcEEEEEeecCCCCCC
Q 036791          124 LDGRVIFVDNVRPSRRYN  141 (157)
Q Consensus       124 ~~g~~l~v~~~~~~~~~~  141 (157)
                      ++|++|+|.++.++....
T Consensus        89 ~~gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           89 FGGRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             ETTEECEEEECCSCCCSS
T ss_pred             ECCcEEEEEEeCCCCCcc
Confidence            999999999998876543

>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=99.64  E-value=6.3e-17  Score=112.79  Aligned_cols=83  Identities=17%  Similarity=0.199  Sum_probs=72.6

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||.++++++|+++|..||.+.. .++.+..+++++|||||+|.+.++|.+|++ |+|..+.|+.|+|.++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEEEEecC
Confidence            45678999999999999999999999987765 334444678899999999999999999995 9999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .++..
T Consensus        89 ~~~~~   93 (175)
T 1fje_B           89 KGRDS   93 (175)
T ss_dssp             CCSSC
T ss_pred             CCccc
Confidence            87654

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.64  E-value=3.8e-16  Score=110.98  Aligned_cols=76  Identities=22%  Similarity=0.283  Sum_probs=71.2

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      .++|||+|||+ .+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|++.|||..+.|+.|+|.++.
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~   77 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   77 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEec
Confidence            46899999999 99999999999999999999998764     7899999999999999999999999999999999998


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      +.
T Consensus        78 ~~   79 (198)
T 1qm9_A           78 HQ   79 (198)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

>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=99.62  E-value=2.4e-15  Score=111.57  Aligned_cols=77  Identities=17%  Similarity=0.295  Sum_probs=71.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+++++++|+++|+.||.|..+.+..      .+|||||.|.+.++|.+|+..|+|..+.|+.|.|.++
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~------~kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           20 TQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINR------DRGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             CGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEET------TTTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeC------CCcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            4567899999999999999999999999999998854      3689999999999999999999999999999999998


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      .+.
T Consensus        94 ~~~   96 (261)
T 3sde_A           94 THG   96 (261)
T ss_dssp             CCS
T ss_pred             ccC
Confidence            763

>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=99.61  E-value=4e-16  Score=100.69  Aligned_cols=72  Identities=21%  Similarity=0.417  Sum_probs=63.6

Q ss_pred             EcCCCCCCCHHHHHHHH------------hcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEE
Q 036791           62 CISVSFSTTKEMLADAF------------SQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI  129 (157)
Q Consensus        62 V~nl~~~~~~~~l~~~f------------~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l  129 (157)
                      +.+|++.+++++|++.|            ++||.|..+.++.++ +++++|||||.|.+.++|.+|+..|||..++|++|
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~-~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i   98 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI   98 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSS-SSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCC-CCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEE
Confidence            56677777777776666            999999999999885 47899999999999999999999999999999999


Q ss_pred             EEEee
Q 036791          130 FVDNV  134 (157)
Q Consensus       130 ~v~~~  134 (157)
                      +|.++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99986

>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=99.60  E-value=6.6e-15  Score=96.99  Aligned_cols=81  Identities=16%  Similarity=0.203  Sum_probs=69.7

Q ss_pred             cccEEEEcCCCC--CC---CHHHHHHHHhcCCCeeEEEEeecCC----CCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           56 NVSFWRCISVSF--ST---TKEMLADAFSQFGQVTEATIIMDIG----KNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        56 ~~~~l~V~nl~~--~~---~~~~l~~~f~~~G~i~~~~~~~~~~----~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      +.+.|++.|+-.  .+   -+++|++.|++||.|..+.|+.++.    +++++|++||+|.+.++|.+|++.|||..++|
T Consensus        19 ps~vl~L~Nm~~~~el~ddleedl~eef~k~G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~f~G   98 (118)
T 3ue2_A           19 ESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAG   98 (118)
T ss_dssp             SCCEEEEESCSCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHHHhccCCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            456788888732  22   2588999999999999999998864    45778999999999999999999999999999


Q ss_pred             cEEEEEeecC
Q 036791          127 RVIFVDNVRP  136 (157)
Q Consensus       127 ~~l~v~~~~~  136 (157)
                      +.|+|.++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999999864

>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=99.60  E-value=5.2e-15  Score=95.58  Aligned_cols=81  Identities=19%  Similarity=0.233  Sum_probs=68.8

Q ss_pred             cccEEEEcCC--CCCCC--------HHHHHHHHhcCCCeeEEEEeecCCC--CCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 036791           56 NVSFWRCISV--SFSTT--------KEMLADAFSQFGQVTEATIIMDIGK--NRSKGYGYVTSSTEEEAQKALVDMNGKL  123 (157)
Q Consensus        56 ~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~--~~~~g~afv~f~~~~~a~~ai~~l~g~~  123 (157)
                      +.+.|.+.|+  |..+.        +++|++.|++||.|.++.|+.++.+  +.++|++||+|.+.++|.+|+..|||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            3456778887  33333        3689999999999999999988654  3678999999999999999999999999


Q ss_pred             cCCcEEEEEeecC
Q 036791          124 LDGRVIFVDNVRP  136 (157)
Q Consensus       124 ~~g~~l~v~~~~~  136 (157)
                      ++|+.|+|.++..
T Consensus        84 f~GR~i~v~~~~~   96 (105)
T 3v4m_A           84 FANRVVVTKYCDP   96 (105)
T ss_dssp             ETTEECEEEEECH
T ss_pred             eCCCEEEEEEeCH
Confidence            9999999999864

>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=99.58  E-value=7.5e-15  Score=101.73  Aligned_cols=76  Identities=17%  Similarity=0.340  Sum_probs=66.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQF----G-------QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL  124 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~  124 (157)
                      +.++|||+|||+++++++|+++|++|    |       .|..+.+.      +.+|||||+|.+.++|.+|+ .|+|..+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~------~~~g~afV~f~~~~~A~~A~-~~~~~~~   75 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDGIIF   75 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEE------TTTTEEEEEESSHHHHHHHG-GGTTCEE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEec------CCCCEEEEEeCCHHHHHHHH-HhCCcEe
Confidence            45789999999999999999999999    6       66666553      44799999999999999999 8999999


Q ss_pred             CCcEEEEEeecCCC
Q 036791          125 DGRVIFVDNVRPSR  138 (157)
Q Consensus       125 ~g~~l~v~~~~~~~  138 (157)
                      .|+.|+|.++.+..
T Consensus        76 ~g~~i~v~~~~~~~   89 (172)
T 2g4b_A           76 QGQSLKIRRPHDYQ   89 (172)
T ss_dssp             TTEECEEECCSSCC
T ss_pred             cCceeeecCCcccC
Confidence            99999999877643

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.57  E-value=1.6e-14  Score=102.23  Aligned_cols=75  Identities=19%  Similarity=0.369  Sum_probs=66.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcC----C-------CeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQF----G-------QVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~----G-------~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      .++|||+|||+++++++|+++|+.|    |       .|..+.+      ++++|||||+|.+.++|++|+ .|||..+.
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~------~~~~g~afV~F~~~~~A~~Al-~l~g~~~~   76 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQI------NQDKNFAFLEFRSVDETTQAM-AFDGIIFQ   76 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEE------ETTTTEEEEEESCSHHHHHHG-GGTTEEET
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEe------cCCCCEEEEEeCCHHHHHHHH-HhcCCEEc
Confidence            5689999999999999999999999    4       4555544      456899999999999999999 89999999


Q ss_pred             CcEEEEEeecCCC
Q 036791          126 GRVIFVDNVRPSR  138 (157)
Q Consensus       126 g~~l~v~~~~~~~  138 (157)
                      |+.|+|.++.+..
T Consensus        77 g~~i~v~~~~~~~   89 (198)
T 2yh0_A           77 GQSLKIRRPHDYQ   89 (198)
T ss_dssp             TEEEEEECCCCCC
T ss_pred             CceEEEeCCCCCC
Confidence            9999999987653

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=2.7e-14  Score=91.36  Aligned_cols=67  Identities=16%  Similarity=0.207  Sum_probs=58.9

Q ss_pred             CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCCCC
Q 036791           67 FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRY  140 (157)
Q Consensus        67 ~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~~~  140 (157)
                      ..+++++|+++|++||.|..+.++     ++++|||||+|.+.++|++|++.+++  +.|++|+|.|++++...
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~   93 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQD   93 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCC
Confidence            568999999999999999999887     46789999999999999999998544  67999999999876543

>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=99.50  E-value=6e-14  Score=107.72  Aligned_cols=75  Identities=20%  Similarity=0.326  Sum_probs=64.1

Q ss_pred             ccccEEEEcC--CCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC---Cc--
Q 036791           55 VNVSFWRCIS--VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD---GR--  127 (157)
Q Consensus        55 ~~~~~l~V~n--l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~---g~--  127 (157)
                      .+..+|||+|  |+..+++++|+++|++||.|..+.+..      +||||||+|.+.++|++|++.|||..+.   |+  
T Consensus        16 ~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~   89 (345)
T 3tht_A           16 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   89 (345)
T ss_dssp             SCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccccCCce
Confidence            4556899999  578999999999999999999886643      4799999999999999999999999873   45  


Q ss_pred             EEEEEeec
Q 036791          128 VIFVDNVR  135 (157)
Q Consensus       128 ~l~v~~~~  135 (157)
                      .|.|.++.
T Consensus        90 ~ly~~~~~   97 (345)
T 3tht_A           90 TLYLNFVE   97 (345)
T ss_dssp             ECEEEECS
T ss_pred             EEEEEEee
Confidence            57777774

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A

Probab=99.40  E-value=6.3e-13  Score=86.94  Aligned_cols=61  Identities=18%  Similarity=0.285  Sum_probs=55.7

Q ss_pred             HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        72 ~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ++|++.|++||.|..+.+..+.    .+|++||.|.+.++|.+|++.|||..++|+.|+|.++..
T Consensus        32 edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f~GR~i~v~~~~~   92 (114)
T 3s6e_A           32 DDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL   92 (114)
T ss_dssp             HHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEETTEECEEEEECH
T ss_pred             HHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEEcH
Confidence            5789999999999999886542    489999999999999999999999999999999999864

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.35  E-value=5.8e-12  Score=78.26  Aligned_cols=77  Identities=25%  Similarity=0.186  Sum_probs=64.8

Q ss_pred             ccccEEEEcCCC----CCCCH----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           55 VNVSFWRCISVS----FSTTK----EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~----~~~~~----~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      .+..||+|.-.+    .++-+    .+|.+.|..||.|..++++.++        +||+|.+.++|.+|++ |||..++|
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~G   75 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLN   75 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETT
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCC
Confidence            345677777665    23333    6799999999999999998874        8999999999999999 99999999


Q ss_pred             cEEEEEeecCCCCC
Q 036791          127 RVIFVDNVRPSRRY  140 (157)
Q Consensus       127 ~~l~v~~~~~~~~~  140 (157)
                      +.|+|+++++.+..
T Consensus        76 r~LkV~lkt~dW~~   89 (91)
T 2dnr_A           76 RTITIALKSPSGPS   89 (91)
T ss_dssp             EEEEEEECCCSSCS
T ss_pred             eEEEEEeCCCCccc
Confidence            99999999997643

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.25  E-value=3.7e-11  Score=78.99  Aligned_cols=75  Identities=16%  Similarity=0.088  Sum_probs=66.2

Q ss_pred             ccccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCC-HHHHHHHHHHhC--CCccCCcEEE
Q 036791           55 VNVSFWRCISVSFS-TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSST-EEEAQKALVDMN--GKLLDGRVIF  130 (157)
Q Consensus        55 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~-~~~a~~ai~~l~--g~~~~g~~l~  130 (157)
                      .....|||+||++. +++++|+++|+.||.|..|.+..+..      .|||.|.+ ..+|..|+..|+  +..|.|..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            45678999999999 99999999999999999999988754      39999999 899999999995  7778998888


Q ss_pred             EEeec
Q 036791          131 VDNVR  135 (157)
Q Consensus       131 v~~~~  135 (157)
                      ++...
T Consensus        90 ~evL~   94 (121)
T 1owx_A           90 WEVLE   94 (121)
T ss_dssp             EEECC
T ss_pred             EEECC
Confidence            87654

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=99.16  E-value=1.5e-10  Score=83.63  Aligned_cols=68  Identities=19%  Similarity=0.283  Sum_probs=60.5

Q ss_pred             CCHHHHHHHHhcCCCeeEEEEeecC----CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           69 TTKEMLADAFSQFGQVTEATIIMDI----GKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        69 ~~~~~l~~~f~~~G~i~~~~~~~~~----~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      -.+++|++.|++||.|..+.++.+.    .+++++|++||+|.+.++|.+|+..|||..++||.|++.++..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            3457899999999999999998554    3458999999999999999999999999999999999999753

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.13  E-value=1.1e-10  Score=72.88  Aligned_cols=73  Identities=15%  Similarity=0.090  Sum_probs=62.2

Q ss_pred             ccccEEEEcCCCCC-----CCH----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           55 VNVSFWRCISVSFS-----TTK----EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        55 ~~~~~l~V~nl~~~-----~~~----~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      .+..||+|.-++..     +-+    .+|.+.|..||.+..++++.++        +||+|.+.++|.+||+ |||..++
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~v~   83 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMKVK   83 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSEET
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCeeeC
Confidence            45678888877642     322    5689999999999999999884        9999999999999999 9999999


Q ss_pred             CcEEEEEeecC
Q 036791          126 GRVIFVDNVRP  136 (157)
Q Consensus       126 g~~l~v~~~~~  136 (157)
                      |+.|+|.+..+
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998765

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.82  E-value=2.5e-08  Score=63.63  Aligned_cols=72  Identities=14%  Similarity=0.184  Sum_probs=65.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcC-----CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQF-----GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~-----G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      +.++|-+-|||..+++..++.+...+     |.+..+.+..|-      +-|+|+|.+...|-+|.-+|+|..|.|++|+
T Consensus        20 ~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~gr~Lr   93 (117)
T 2l9w_A           20 LETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQGKVIR   93 (117)
T ss_dssp             TTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEETTEEEE
T ss_pred             CCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeecCeEEE
Confidence            35678899999999999999999999     999999988873      4599999999999999999999999999999


Q ss_pred             EEe
Q 036791          131 VDN  133 (157)
Q Consensus       131 v~~  133 (157)
                      +.-
T Consensus        94 ~gT   96 (117)
T 2l9w_A           94 SGT   96 (117)
T ss_dssp             EEC
T ss_pred             ecC
Confidence            864

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.97  E-value=0.00041  Score=43.70  Aligned_cols=76  Identities=16%  Similarity=0.118  Sum_probs=61.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhc---C--CCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQ---F--GQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~---~--G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      ..+|.|.|||+.+.++.|+-+|++   .  |.|..+....        +-|+|+|.+.+.|++.++. ....|+|.+|.|
T Consensus         8 ~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~~~LsV   78 (104)
T 2dhx_A            8 GVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHGAQLSL   78 (104)
T ss_dssp             CCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSSSBCEE
T ss_pred             ccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecCeEEEE
Confidence            457999999999999999999986   2  5777776533        3589999999999999874 367899999999


Q ss_pred             EeecCCCCCC
Q 036791          132 DNVRPSRRYN  141 (157)
Q Consensus       132 ~~~~~~~~~~  141 (157)
                      .-..++..+.
T Consensus        79 ~P~~~~~~~r   88 (104)
T 2dhx_A           79 RPAPPRAPAR   88 (104)
T ss_dssp             EECCCCCCCC
T ss_pred             EcCCCCCcce
Confidence            8877665443

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.81  E-value=5.4e-05  Score=47.88  Aligned_cols=74  Identities=9%  Similarity=-0.019  Sum_probs=61.2

Q ss_pred             cEEEEcCCCCCCCH-----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           58 SFWRCISVSFSTTK-----EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        58 ~~l~V~nl~~~~~~-----~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .+|+|.||+.++-.     ..++.+|..|+++..-...+.-      .-..|.|.+.++|.+|-..||+..++|++|+|-
T Consensus         6 ntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSF------RRirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            6 SGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSF------KRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTT------TEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             ceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcc------eEEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            46899999886521     5679999999988887666542      136899999999999999999999999999999


Q ss_pred             eecCC
Q 036791          133 NVRPS  137 (157)
Q Consensus       133 ~~~~~  137 (157)
                      ++.+.
T Consensus        80 Fgq~~   84 (104)
T 1wey_A           80 FAQTL   84 (104)
T ss_dssp             CCCCS
T ss_pred             ecCCC
Confidence            98854

>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=97.71  E-value=0.00015  Score=45.19  Aligned_cols=53  Identities=23%  Similarity=0.218  Sum_probs=45.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM  119 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l  119 (157)
                      .-+++ ++|..+...||.++|+.|| -..|.++.|-       .|||.|.+++.|..|+..+
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTTC-SCCCEEEETT-------EEEEECSCHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhc
Confidence            34555 9999999999999999999 4577888772       5999999999999999876

>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=97.55  E-value=0.00063  Score=42.09  Aligned_cols=68  Identities=12%  Similarity=0.010  Sum_probs=56.9

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR--SKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      ++|-|++||+.++++++.+.+.....+.....+..+.+.+  ...-|+|.|.+.+++..-.+.++|..+-
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            4688999999999999999999988777667766654433  3467999999999999999999999863

>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=97.55  E-value=0.00014  Score=45.49  Aligned_cols=52  Identities=21%  Similarity=0.220  Sum_probs=45.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN  120 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~  120 (157)
                      +++ ++|..+...||.++|+.|| -..|.++.|-       -|||.|.+++.|..|+..+.
T Consensus         9 ~~l-~FP~ewKt~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            9 LHV-TFPKEWKTSDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEE-ECCTTCCHHHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             EEE-eCChhhhhHHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            455 9999999999999999999 5678888872       59999999999999999774

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.09  E-value=0.0045  Score=40.07  Aligned_cols=70  Identities=14%  Similarity=0.274  Sum_probs=55.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC-cEEEEEee
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG-RVIFVDNV  134 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g-~~l~v~~~  134 (157)
                      ..-|.|-+.|+... ..+-..|++||.|.+....      ....+-.|.|.+..+|++||.. ||..+.| -.|-|...
T Consensus        24 ~~wVtVFGFp~~~~-~~VL~~F~~~G~Iv~~~~~------~~~NWihI~Y~s~~~A~rAL~k-NG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQASA-SYILLQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALSK-DGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGGH-HHHHHHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHTT-TTCEETTTEECEEEEC
T ss_pred             CCEEEEECCCHHHH-HHHHHHHHhhCcEEEeccC------CCCCeEEEEeCCHHHHHHHHHh-CCeEecCCEEEEEEEC
Confidence            45688889999864 5667789999999987651      2346899999999999999985 9999975 56667664

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP}

Probab=96.66  E-value=0.0028  Score=42.59  Aligned_cols=44  Identities=11%  Similarity=0.004  Sum_probs=32.2

Q ss_pred             EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           86 EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        86 ~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      .+.+.++.  ++.+|||||+|.+.++|++|+..+++....+..+.+
T Consensus         2 ~~kl~ln~--~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~   45 (158)
T 2kn4_A            2 QYKLILNG--KTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTY   45 (158)
T ss_dssp             EEEEEEEC--SSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEE
T ss_pred             cEEEEecC--ccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccc
Confidence            34566653  468999999999999999999988765443333333

>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=96.55  E-value=0.0011  Score=44.35  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=38.0

Q ss_pred             CCCcceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEEEeecCC
Q 036791           95 KNRSKGYGYVTSSTEEEAQKALVDM-NGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        95 ~~~~~g~afv~f~~~~~a~~ai~~l-~g~~~~g~~l~v~~~~~~  137 (157)
                      ..+.+|+++|+|.+.++|++|++.+ ||..++| .+.+.++.++
T Consensus         9 g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~   51 (150)
T 2i2y_A            9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKT   51 (150)
T ss_dssp             CSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTE
T ss_pred             cccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCc
Confidence            3577899999999999999999999 9999999 9999988764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=96.37  E-value=0.008  Score=37.45  Aligned_cols=68  Identities=9%  Similarity=-0.028  Sum_probs=49.5

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR--SKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      -+|-|+.||+.+|++++.+.+...-.+.....+..+.+.+  .-.-|+|.|.+.++...-.+.++|..+-
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            3588999999999999888777654443322333222221  2356899999999999999999999863

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.29  E-value=0.0037  Score=41.10  Aligned_cols=76  Identities=16%  Similarity=0.270  Sum_probs=54.2

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeec--------CCCC-----CcceEEEEEeCCHHHHHHHHHHhCCCc
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEA-TIIMD--------IGKN-----RSKGYGYVTSSTEEEAQKALVDMNGKL  123 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~--------~~~~-----~~~g~afv~f~~~~~a~~ai~~l~g~~  123 (157)
                      .-|.|-+.|++.... +-+.|++||.|.+- ....+        +...     ....+-.|.|.+..+|.+||.. ||..
T Consensus         8 ~~VtVFGFp~~~~~~-VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-NG~i   85 (132)
T 3p3d_A            8 LAILVFGYPETMANQ-VIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-NGAV   85 (132)
T ss_dssp             CEEEEECCCGGGHHH-HHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-TTCE
T ss_pred             eEEEEEecCHHHHHH-HHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-CCeE
Confidence            457788888887655 55679999998762 11100        0001     1356789999999999999985 9999


Q ss_pred             cCCcEEEEEeec
Q 036791          124 LDGRVIFVDNVR  135 (157)
Q Consensus       124 ~~g~~l~v~~~~  135 (157)
                      +.|..|-|....
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999888887764

>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=95.32  E-value=0.0083  Score=38.23  Aligned_cols=55  Identities=11%  Similarity=0.060  Sum_probs=17.0

Q ss_pred             HHHHHHhccccccCcccccccCCceeceecccccccCCCcchhhccccccEEEEcCCCCCCCHHH
Q 036791            9 TRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVSFSTTKEM   73 (157)
Q Consensus         9 ~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~   73 (157)
                      ++|+++|++..+.++.+.+...        ....  ..............+|||+|||+++|++.
T Consensus        59 ~~Ai~~l~~~~~~g~~i~V~~a--------~~~~--~~~~~~~~~~~~~~~lyv~Nl~~~~T~~a  113 (115)
T 4f25_A           59 ERAIEKMNGMLLNDRKVFVGRF--------KSRK--EREAELGARAKEFTNVYIKNFGPGSTRAA  113 (115)
T ss_dssp             HHHHHHHTTCEETTEECEEEES--------SCCC--C----------------------------
T ss_pred             HHHHHHcCCCEECCEEEEEEEC--------CCcc--ccccccccccCCCCceEeCCCCCCccccc
Confidence            6788889999998888865421        1100  00111112223445799999999999763

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.27  E-value=0.012  Score=46.74  Aligned_cols=55  Identities=13%  Similarity=0.032  Sum_probs=40.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHH
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVD  118 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~  118 (157)
                      ++|+|. .|..+++.+|.++|++||.|..+..-.+  .   .-|+.|+|.+.+++.+++..
T Consensus        54 rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~--~---g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           54 RTVLIH-CPEKISENKFLKYLSQFGPINNHFFYES--F---GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             TEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECS--S---SEEEEEECC---CCHHHHSS
T ss_pred             ceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEcc--C---CeEEEEEeCCHHHHHHHHhc
Confidence            689997 7999999999999999999999866543  2   37999999999998877543

>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=91.47  E-value=0.86  Score=36.58  Aligned_cols=54  Identities=22%  Similarity=0.198  Sum_probs=44.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG  121 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g  121 (157)
                      .++|+ +|..+...+|.++|+.||. ..|.++-+       ..|||.|.+.+.|..++..+..
T Consensus       442 vl~v~-f~~~~~~~~i~~~fs~fg~-v~V~widd-------t~a~V~~~~~~~a~~~l~~~~~  495 (507)
T 3d45_A          442 VLHVT-FPKEWKTSDLYQLFSAFGN-IQISWIDD-------TSAFVSLSQPEQVQIAVNTSKY  495 (507)
T ss_dssp             EEEEE-CCTTCCHHHHHHHGGGGCC-CEEEECSS-------SEEEEECSCHHHHHHHHHHHTT
T ss_pred             EEEEe-CCCCCCHHHHHHHHHhcCC-EEEEEEcC-------CeEEEEECCHHHHHHHHHHHHh
Confidence            45555 9999999999999999995 46666554       3599999999999999998853

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=86.98  E-value=0.39  Score=29.20  Aligned_cols=21  Identities=5%  Similarity=0.059  Sum_probs=15.8

Q ss_pred             HHHHHHHhccccccCcccccc
Q 036791            8 QTRKIQQFNSYFTEDSLLSFS   28 (157)
Q Consensus         8 ~~~a~~~~~~~~~~~~~~~~~   28 (157)
                      -++|+.++++..+.++.+++.
T Consensus        50 a~~A~~~l~g~~~~g~~l~V~   70 (101)
T 2hvz_A           50 AEDAVRGLDGKVICGSRVRVE   70 (101)
T ss_dssp             HHHHHHHHHHSCSSSCCCEEE
T ss_pred             HHHHHHHHCCCeECCcEEEEE
Confidence            366777888888888887655

---

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	157
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-16
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	8e-15
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-14
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	5e-14
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-14
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	9e-14
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-13
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	1e-13
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-13
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	4e-13
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	5e-13
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	5e-13
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-12
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-12
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-12
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	5e-12
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	6e-12
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-12
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	9e-12
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	1e-11
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	1e-11
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-11
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-11
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	1e-11
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-11
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-11
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	3e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	4e-06
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	3e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	3e-11
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-11
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	7e-11
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-11
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	8e-11
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	9e-11
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-10
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-10
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	2e-10
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-10
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-10
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	3e-10
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	5e-10
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-10
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	6e-10
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-09
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	3e-09
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-09
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-09
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:) 7e-09
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-08
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-08
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	3e-08
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	3e-08
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	4e-08
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	5e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	8e-08
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	2e-07
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	3e-07
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	3e-07
d1wg4a_	98	d.58.7.1 (A:) Splicing factor, arginine/serine-ric	3e-07
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	4e-07
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	5e-07
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	8e-07
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-06
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	2e-06
d1fjeb1	91	d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesoc	3e-06
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	3e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	3e-06
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-05
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	6e-05
d2adca1	109	d.58.7.1 (A:335-443) Polypyrimidine tract-binding	7e-05
d3begb1	87	d.58.7.1 (B:121-207) Splicing factor, arginine/ser	2e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	2e-04
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	0.001
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.001
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	0.003

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.7 bits (160), Expect = 9e-16
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +    T+ ML + FS  G +    +  D+   RS GY YV      +A++AL  MN  ++
Sbjct: 8   LHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI 67

Query: 125 DGRVIFVDNVRPSRR 139
            G+ +    +  S+R
Sbjct: 68  KGKPV---RIMWSQR 79

>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 = 63.8 bits (155), Expect = 8e-15
 Identities = 23/79 (29%), Positives = 43/79 (54%), Gaps = 3/79 (3%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF TT+E + + FS+ G + +  + +D  K  + G+ +V   +  +A+ A+  +NG  L
Sbjct: 15  LSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRL 74

Query: 125 DGRVIFVD---NVRPSRRY 140
           D R+I  D     +  R+Y
Sbjct: 75  DDRIIRTDWDAGFKEGRQY 93

>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 = 62.7 bits (152), Expect = 2e-14
 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 3/78 (3%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMD---IGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           ++FSTT+E L   FS+ G +   TI       G   S G+G+V     E+AQKAL  + G
Sbjct: 6   LNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQG 65

Query: 122 KLLDGRVIFVDNVRPSRR 139
             +DG  + V     + +
Sbjct: 66  HTVDGHKLEVRISERATK 83

>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 = 61.8 bits (150), Expect = 5e-14
 Identities = 13/80 (16%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
           +    K  +   FS++G++   ++          G+ +V    E  A+ A+   +G+++ 
Sbjct: 25  TLVVKKSDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVAGEDGRMIA 76

Query: 126 GRVIFVDNVRPSRRYNTDAS 145
           G+V+ ++     +   +  S
Sbjct: 77  GQVLDINLAAEPKVNRSGPS 96

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 61.2 bits (148), Expect = 7e-14
 Identities = 18/72 (25%), Positives = 32/72 (44%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +    T   L   F   G +    I+ D     S GY +V  ++E ++Q+A+  +NG  +
Sbjct: 10  LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV 69

Query: 125 DGRVIFVDNVRP 136
             + + V   RP
Sbjct: 70  RNKRLKVSYARP 81

>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 = 60.8 bits (147), Expect = 9e-14
 Identities = 22/74 (29%), Positives = 38/74 (51%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           ++     ++L  AF  FG +T+  I +D    + +G+ +V     E+A  A+ +MN   L
Sbjct: 13  LAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESEL 72

Query: 125 DGRVIFVDNVRPSR 138
            GR I V+  +P R
Sbjct: 73  FGRTIRVNLAKPMR 86

>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 = 60.4 bits (146), Expect = 1e-13
 Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ TT+E L + F QFG+V E  ++ D    RS+G+G+VT   +    K L   +   L
Sbjct: 8   LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVL-AQSRHEL 66

Query: 125 DGRVIFVD 132
           D + I   
Sbjct: 67  DSKTIDPK 74

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-13
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +  T E + D F ++G + +   I       ++G  YV      +A+ A   ++G  +
Sbjct: 15  LPYKITAEEMYDIFGKYGPIRQ---IRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNV 71

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQ 149
             R + V     +R +    +  ++
Sbjct: 72  CNRYLVVLYYNANRAFQKMDTKKKE 96

>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 = 59.6 bits (144), Expect = 4e-13
 Identities = 16/70 (22%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDI-GKNRSKGYGYVTSSTEEEAQKALVDM-NGK 122
           + F   +  + + FS FG++    +   + G    +G+G+V   T+++A+KA   + +  
Sbjct: 16  IPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHST 75

Query: 123 LLDGRVIFVD 132
            L GR + ++
Sbjct: 76  HLYGRRLVLE 85

>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 = 59.2 bits (143), Expect = 4e-13
 Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  + T + L   F ++G + +  I+ D    R +G  +V  +  EEAQ+A+  +N  + 
Sbjct: 14  LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP 73

Query: 125 DG--RVIFVD 132
           +G  + + V 
Sbjct: 74  EGGSQPLSVR 83

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 59.3 bits (143), Expect = 5e-13
 Identities = 19/75 (25%), Positives = 35/75 (46%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +    ++ +L + F Q G V    +  D    + +GYG+V   +EE+A  A+  M+   L
Sbjct: 17  LDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKL 76

Query: 125 DGRVIFVDNVRPSRR 139
            G+ I V+      +
Sbjct: 77  YGKPIRVNKASAHNK 91

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 58.9 bits (142), Expect = 5e-13
 Identities = 23/67 (34%), Positives = 39/67 (58%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  TT+  L + FS++G + + +I+ D    RS+G+ +V     ++A++A    NG  L
Sbjct: 17  LSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL 76

Query: 125 DGRVIFV 131
           DGR I V
Sbjct: 77  DGRRIRV 83

>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 = 57.2 bits (138), Expect = 2e-12
 Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F  +   + + F++FG + +A +  D    RS G   V    + +A KA+   NG  L
Sbjct: 8   LDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPL 66

Query: 125 DGRVIFVD 132
           DGR + + 
Sbjct: 67  DGRPMNIQ 74

>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 = 57.3 bits (138), Expect = 2e-12
 Identities = 12/75 (16%), Positives = 27/75 (36%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +      + + +  + FG +    ++ D     SKGY +          +A+  +NG  L
Sbjct: 9   LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQL 68

Query: 125 DGRVIFVDNVRPSRR 139
             + + V       +
Sbjct: 69  GDKKLLVQRASVGAK 83

>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 = 56.9 bits (137), Expect = 2e-12
 Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 1/67 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+ TTK+ L D FS+FG+V + T+ +D    RS+G+G+V     E   K + D     L
Sbjct: 7   LSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM-DQKEHKL 65

Query: 125 DGRVIFV 131
           +G+VI  
Sbjct: 66  NGKVIDP 72

>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 = 56.3 bits (135), Expect = 5e-12
 Identities = 21/73 (28%), Positives = 36/73 (49%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  + T+E     F   G++    ++ D    +S GYG+V     ++A+KA+  +NG  L
Sbjct: 10  LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRL 69

Query: 125 DGRVIFVDNVRPS 137
             + I V   RPS
Sbjct: 70  QTKTIKVSYARPS 82

>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 = 56.0 bits (134), Expect = 6e-12
 Identities = 13/72 (18%), Positives = 31/72 (43%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
              S T+  + D       V  +  +  +  N S+ + Y+  +++E+A+  +  +NG  +
Sbjct: 9   FPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKI 68

Query: 125 DGRVIFVDNVRP 136
           +G  +      P
Sbjct: 69  EGYTLVTKVSNP 80

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.1 bits (135), Expect = 8e-12
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 6/74 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           ++   T +++   FS FGQ+ E  +         KGY +V  ST E A  A+V +NG  +
Sbjct: 26  IASGLTDQLMRQTFSPFGQIMEIRVF------PEKGYSFVRFSTHESAAHAIVSVNGTTI 79

Query: 125 DGRVIFVDNVRPSR 138
           +G V+     + S 
Sbjct: 80  EGHVVKCYWGKESP 93

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 9e-12
 Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 2/77 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F      L   F QFG++ +  II +  +  SKG+G+VT     +A +A   ++G ++
Sbjct: 19  IPFRFRDPDLRQMFGQFGKILDVEIIFN--ERGSKGFGFVTFENSADADRAREKLHGTVV 76

Query: 125 DGRVIFVDNVRPSRRYN 141
           +GR I V+N       N
Sbjct: 77  EGRKIEVNNATARVMTN 93

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.5 bits (133), Expect = 1e-11
 Identities = 12/79 (15%), Positives = 35/79 (44%), Gaps = 6/79 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATI-----IMDIGKNRSKGYGYVTSSTEEEAQKALVDM 119
           + F  T+E + D F+   ++   T      ++ +  N+ K + ++   + +E  +A+   
Sbjct: 9   IPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAM-AF 67

Query: 120 NGKLLDGRVIFVDNVRPSR 138
           +G +  G+ + +      +
Sbjct: 68  DGIIFQGQSLKIRRPHDYQ 86

>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 = 55.5 bits (133), Expect = 1e-11
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 1/73 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIM-DIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           +     +++L D FS FG + +   IM D     SKGY ++  ++ + +  A+  MNG+ 
Sbjct: 6   LDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQY 65

Query: 124 LDGRVIFVDNVRP 136
           L  R I V     
Sbjct: 66  LCNRPITVSYAFK 78

>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 = 55.0 bits (132), Expect = 1e-11
 Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 1/67 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  T +E + + F  FG+V    + MD   N+ +G+ ++T   EE  +K + +     +
Sbjct: 7   LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKYHNV 65

Query: 125 DGRVIFV 131
                 +
Sbjct: 66  GLSKCEI 72

>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 = 55.8 bits (134), Expect = 1e-11
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF TT+E L + + Q+G++T+  ++ D    RS+G+G+VT S+  E   A+       +
Sbjct: 28  LSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM-AARPHSI 86

Query: 125 DGRVIFVDNVRP 136
           DGRV+       
Sbjct: 87  DGRVVEPKRAVA 98

>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 = 55.4 bits (133), Expect = 1e-11
 Identities = 18/73 (24%), Positives = 38/73 (52%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S  T +  L + F  FG ++   +  D    +SKG+ +++    E+A +A+  ++G   
Sbjct: 16  LSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGY 75

Query: 125 DGRVIFVDNVRPS 137
           D  ++ V+  +PS
Sbjct: 76  DHLILNVEWAKPS 88

>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 = 55.5 bits (133), Expect = 2e-11
 Identities = 12/74 (16%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +      + + D F ++G + +  +           + +V      +A+ A+   +G   
Sbjct: 22  LPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDY 78

Query: 125 DGRVIFVDNVRPSR 138
           DG  + V+  R  R
Sbjct: 79  DGYRLRVEFPRSGR 92

>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 = 55.4 bits (133), Expect = 2e-11
 Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 1/74 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           ++       L D FS  G+V +  II D    RSKG  YV     +    A + + G+ L
Sbjct: 26  LAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLA-IGLTGQRL 84

Query: 125 DGRVIFVDNVRPSR 138
            G  I V   +  +
Sbjct: 85  LGVPIIVQASQAEK 98

>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 = 54.9 bits (132), Expect = 2e-11
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 4/74 (5%)

Query: 67  FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG 126
            +  +E L    S+FGQ+ +  +          G   V+    EEA   +  ++G+   G
Sbjct: 29  LNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRWFGG 84

Query: 127 RVIFVDNVRPSRRY 140
           R I       +  Y
Sbjct: 85  RQITAQAWDGTTDY 98

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.5 bits (135), Expect = 3e-11
 Identities = 22/132 (16%), Positives = 47/132 (35%), Gaps = 4/132 (3%)

Query: 8   QTRKIQQFNSYFTEDSLLSFSSKPYQVVNYFSLHCIVRPSSDLIMQLVNVSFWRCISVS- 66
           +  +   F +Y T + + +  +     V+   +      S +   +       + I V  
Sbjct: 45  KRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGG 104

Query: 67  --FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
               T +  L D F Q+G++    I+ D G  + +G+ +VT    +   K +       +
Sbjct: 105 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTV 163

Query: 125 DGRVIFVDNVRP 136
           +G    V     
Sbjct: 164 NGHNCEVRKALS 175

>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 = 42.3 bits (98), Expect = 4e-06
 Identities = 21/57 (36%), Positives = 32/57 (56%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
           +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+     
Sbjct: 14  LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH 70

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 3e-11
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S   + L D FS FG +    ++ D   N SKGYG+V   T+E A++A+  MNG LL
Sbjct: 16  LDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLL 73

Query: 125 DGRVIFVDNVRPSRR 139
           + R +FV   +  + 
Sbjct: 74  NDRKVFVGRFKSRKE 88

>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 = 54.3 bits (130), Expect = 3e-11
 Identities = 25/68 (36%), Positives = 39/68 (57%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF TT E L   F Q+G +T+  ++ D    RS+G+G+VT +T EE   A+ +     +
Sbjct: 14  LSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKV 72

Query: 125 DGRVIFVD 132
           DGRV+   
Sbjct: 73  DGRVVEPK 80

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.9 bits (129), Expect = 5e-11
 Identities = 17/63 (26%), Positives = 35/63 (55%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  + T++ L   FSQ+G++  + I++D     S+G G++      EA++A+  +NG+  
Sbjct: 14  LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKP 73

Query: 125 DGR 127
            G 
Sbjct: 74  SGA 76

>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 = 53.9 bits (129), Expect = 7e-11
 Identities = 20/75 (26%), Positives = 41/75 (54%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S+++++E L   FS +G ++E    +D    + KG+ +VT    E A KA  +++G++ 
Sbjct: 16  LSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVF 75

Query: 125 DGRVIFVDNVRPSRR 139
            GR++ V      + 
Sbjct: 76  QGRMLHVLPSTIKKE 90

>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 = 53.4 bits (128), Expect = 7e-11
 Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + + TT++ L + FS FG+V    +  D+    SKG+G+V  +  E   K +   +   +
Sbjct: 16  LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHM--I 73

Query: 125 DGRVIFVDNVRP 136
           DGR         
Sbjct: 74  DGRWCDCKLPNS 85

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.1 bits (127), Expect = 8e-11
 Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 6/75 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  ST++EM+   F+         +       + + Y +V  S  E+A +A+  +NGK+L
Sbjct: 16  LMLSTSEEMIEKEFNNIKPGAVERV------KKIRDYAFVHFSNREDAVEAMKALNGKVL 69

Query: 125 DGRVIFVDNVRPSRR 139
           DG  I V   +P  +
Sbjct: 70  DGSPIEVTLAKPVDK 84

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.5 bits (128), Expect = 9e-11
 Identities = 15/76 (19%), Positives = 29/76 (38%), Gaps = 2/76 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDI--GKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
             +    E + D  S++G V    I   +   +    G  +V  ++  + QKA+  + G+
Sbjct: 22  EEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR 81

Query: 123 LLDGRVIFVDNVRPSR 138
               RV+      P  
Sbjct: 82  KFANRVVVTKYCDPDS 97

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.2 bits (127), Expect = 1e-10
 Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 4/83 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIM--DIGKNRSKGYGYVTSSTEEEAQKALVDMNGK 122
           +     +E + +  ++  +     I+      K +++G+ +V   +   A  A   +   
Sbjct: 9   IPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPG 68

Query: 123 --LLDGRVIFVDNVRPSRRYNTD 143
              L G  I VD   P    + D
Sbjct: 69  RIQLWGHQIAVDWAEPEIDVDED 91

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 52.8 bits (126), Expect = 1e-10
 Identities = 12/67 (17%), Positives = 30/67 (44%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F+ + + + D F  +  +  +  +    K    G   V   + +EA  A++D+N + +
Sbjct: 17  MPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPI 76

Query: 125 DGRVIFV 131
             R + +
Sbjct: 77  GSRKVKL 83

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 52.4 bits (125), Expect = 2e-10
 Identities = 17/68 (25%), Positives = 32/68 (47%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +     ++ + + F  +G++    + +D     SKGY  V   T ++A  A   +NG  +
Sbjct: 15  IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEI 74

Query: 125 DGRVIFVD 132
            G+ I VD
Sbjct: 75  MGQTIQVD 82

>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 = 51.9 bits (124), Expect = 2e-10
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 6/71 (8%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
               T  +L  AFS FG       I+D+  +  +   +VT    E A +A+ ++NG  ++
Sbjct: 12  GEDMTPTLLRGAFSPFGN------IIDLSMDPPRNCAFVTYEKMESADQAVAELNGTQVE 65

Query: 126 GRVIFVDNVRP 136
              + V+  R 
Sbjct: 66  SVQLKVNIARK 76

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (123), Expect = 2e-10
 Identities = 19/68 (27%), Positives = 40/68 (58%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S +TT E +   F QFG+V +A ++ D   NR +G+G+VT  +E+  +K   +++   +
Sbjct: 7   LSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVC-EIHFHEI 65

Query: 125 DGRVIFVD 132
           + +++   
Sbjct: 66  NNKMVECK 73

>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 = 52.0 bits (124), Expect = 2e-10
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S   T+ ++   FSQ G      +I +     +  Y +V      +A  AL  MNG+ +
Sbjct: 16  LSRDVTEVLILQLFSQIGPCKSCKMITE--HTSNDPYCFVEFYEHRDAAAALAAMNGRKI 73

Query: 125 DGRVIFVDNVRP 136
            G+ + V+    
Sbjct: 74  LGKEVKVNWATT 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 52.0 bits (124), Expect = 3e-10
 Identities = 18/74 (24%), Positives = 34/74 (45%), Gaps = 5/74 (6%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF+ T++ L + F    +     I +     +SKG  Y+   +E +A+K L +  G  +
Sbjct: 24  LSFNITEDELKEVFEDALE-----IRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEI 78

Query: 125 DGRVIFVDNVRPSR 138
           DGR + +       
Sbjct: 79  DGRSVSLYYTGEKG 92

>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 = 51.6 bits (123), Expect = 5e-10
 Identities = 20/75 (26%), Positives = 31/75 (41%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +      + L   F  FG V  A + +D   N SK +G+V+      AQ A+  MNG  +
Sbjct: 26  LPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQI 85

Query: 125 DGRVIFVDNVRPSRR 139
             + + V   R    
Sbjct: 86  GMKRLKVQLKRSKND 100

>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 = 51.7 bits (123), Expect = 5e-10
 Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 8/86 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATII--------MDIGKNRSKGYGYVTSSTEEEAQKAL 116
           ++ S T + LAD F Q G V              +D    + KG   V+      A+ A+
Sbjct: 16  LNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAV 75

Query: 117 VDMNGKLLDGRVIFVDNVRPSRRYNT 142
              +GK   G  + V   R     N+
Sbjct: 76  EWFDGKDFQGSKLKVSLARKKPPMNS 101

>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 = 51.3 bits (122), Expect = 6e-10
 Identities = 29/74 (39%), Positives = 47/74 (63%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +SF T ++ L   FS++GQ++E  ++ D    RS+G+G+VT    ++A+ A++ MNGK +
Sbjct: 13  LSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSV 72

Query: 125 DGRVIFVDNVRPSR 138
           DGR I VD    S 
Sbjct: 73  DGRQIRVDQAGKSS 86

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.7 bits (118), Expect = 2e-09
 Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 1/81 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +  T+E + + F                  R KG+GY      +    AL  +N + L
Sbjct: 23  LPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESL 81

Query: 125 DGRVIFVDNVRPSRRYNTDAS 145
             + I VD    ++  ++  S
Sbjct: 82  GNKRIRVDVADQAQDKDSGPS 102

>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 = 49.8 bits (118), Expect = 3e-09
 Identities = 25/86 (29%), Positives = 40/86 (46%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + +  T+E L D FS+ G V    ++ D    + KGYG+     +E A  A+ ++NG+  
Sbjct: 16  IPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREF 75

Query: 125 DGRVIFVDNVRPSRRYNTDASLARQP 150
            GR + VDN    +      SL    
Sbjct: 76  SGRALRVDNAASEKNKEELKSLGTGA 101

>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 = 49.4 bits (117), Expect = 3e-09
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + + TT   L   F  FG + EA +I D    +S+GYG+VT +    A++A  D N   +
Sbjct: 18  LPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNPI-I 76

Query: 125 DGRVIFVDNVRPSRR 139
           DGR   V+      +
Sbjct: 77  DGRKANVNLAYLGAK 91

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.4 bits (115), Expect = 6e-09
 Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 6/68 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +    T+E +   F ++G+  E  I  D G      +G++   T   A+ A V+++   L
Sbjct: 16  LPPDITEEEMRKLFEKYGKAGEVFIHKDKG------FGFIRLETRTLAEIAKVELDNMPL 69

Query: 125 DGRVIFVD 132
            G+ + V 
Sbjct: 70  RGKQLRVR 77

>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 = 48.5 bits (115), Expect = 7e-09
 Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 1/63 (1%)

Query: 70  TKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVI 129
            +E+  +   ++G+V E  +  ++  +   G  YV    EE+A+KA++D+N +  +G+ I
Sbjct: 40  FEEVFTEMEEKYGEVEEMNVCDNL-GDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPI 98

Query: 130 FVD 132
             +
Sbjct: 99  HAE 101

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 2e-08
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 7/81 (8%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
            +   T++ L + FSQ+G V +  I         + + +VT + ++ AQ         ++
Sbjct: 13  CTGDMTEDELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLC--GEDLII 65

Query: 125 DGRVIFVDNVRPSRRYNTDAS 145
            G  + + N  P    N+  S
Sbjct: 66  KGISVHISNAEPKHNSNSGPS 86

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.6 bits (110), Expect = 3e-08
 Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 65  VSFSTTKEMLAD-AFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL 123
           ++    K+ L     + F +  +   I+     + +G  +V       A  AL  M G  
Sbjct: 11  LNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFP 70

Query: 124 LDGRVIFVD 132
              + + + 
Sbjct: 71  FYDKPMRIQ 79

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 3e-08
 Identities = 15/76 (19%), Positives = 31/76 (40%), Gaps = 7/76 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL- 123
           +S + T + L   F          ++         GY +V    +  A +A+  ++GK+ 
Sbjct: 9   LSPAVTADDLRQLFGDRKLPLAGQVL------LKSGYAFVDYPDQNWAIRAIETLSGKVE 62

Query: 124 LDGRVIFVDNVRPSRR 139
           L G+++ VD     + 
Sbjct: 63  LHGKIMEVDYSVSKKL 78

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.8 bits (110), Expect = 3e-08
 Identities = 19/92 (20%), Positives = 33/92 (35%), Gaps = 4/92 (4%)

Query: 61  RCISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
            C  +    FS TK  +            A  ++     +  G   V    E++A+K+  
Sbjct: 9   VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE- 67

Query: 118 DMNGKLLDGRVIFVDNVRPSRRYNTDASLARQ 149
            ++ K L+GR  FV  V        + +   Q
Sbjct: 68  RLHRKKLNGREAFVHVVTLEDMREIEKNPPAQ 99

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (110), Expect = 4e-08
 Identities = 17/74 (22%), Positives = 36/74 (48%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +S   T+  L   F++F +     I   +   R +G  ++T   +E A +AL  +NG  L
Sbjct: 26  LSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKL 85

Query: 125 DGRVIFVDNVRPSR 138
            G+++ ++  +  +
Sbjct: 86  YGKILVIEFGKNKK 99

>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 = 45.5 bits (107), Expect = 5e-08
 Identities = 16/65 (24%), Positives = 30/65 (46%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   TT + L      +G++     I+D   N+ KGYG+V   +   AQKA+  +    +
Sbjct: 6   LQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGV 65

Query: 125 DGRVI 129
             ++ 
Sbjct: 66  QAQMA 70

>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 = 45.1 bits (106), Expect = 8e-08
 Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   T +  L D F Q+G++    I+ D G  + +G+ +VT    +   K +       +
Sbjct: 10  IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV-IQKYHTV 68

Query: 125 DGRVIFVD 132
           +G    V 
Sbjct: 69  NGHNCEVR 76

>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 = 44.8 bits (105), Expect = 2e-07
 Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN---- 120
           +SF + +E L +   QFG +    +++      SKG  +    T+E AQK L   +    
Sbjct: 16  LSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAE 75

Query: 121 --GKLLDGRVIFVDNVRP 136
             G  LDGR + VD    
Sbjct: 76  GGGLKLDGRQLKVDLAVT 93

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.6 bits (105), Expect = 3e-07
 Identities = 16/85 (18%), Positives = 35/85 (41%), Gaps = 9/85 (10%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL- 124
            +  T ++L   FS+FG V +           ++    +  +    AQ A + ++G+ + 
Sbjct: 16  FYPVTLDVLHQIFSKFGTVLKIITFT----KNNQFQALLQYADPVSAQHAKLSLDGQNIY 71

Query: 125 -DGRVIFVDNVRPSR---RYNTDAS 145
                + +D  + +    +YN D S
Sbjct: 72  NACCTLRIDFSKLTSLNVKYNNDKS 96

>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 = 44.4 bits (104), Expect = 3e-07
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 1/72 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S  ++ L +   +      +T I+      S+G G+    + E+ +  +   NGK +
Sbjct: 26  LPLSMDEQELEN-MLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFI 84

Query: 125 DGRVIFVDNVRP 136
                      P
Sbjct: 85  KTPPGVSAPTEP 96

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 3e-07
 Identities = 10/75 (13%), Positives = 22/75 (29%), Gaps = 7/75 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S + + L D   +          +     +  G G V    +E+ + AL  ++    
Sbjct: 23  LPPSGSWQDLKDHMREA-------GDVCYADVQKDGMGMVEYLRKEDMEYALRKLDDTKF 75

Query: 125 DGRVIFVDNVRPSRR 139
                    +R    
Sbjct: 76  RSHEGETSYIRVYPE 90

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 44.0 bits (103), Expect = 4e-07
 Identities = 15/110 (13%), Positives = 30/110 (27%), Gaps = 12/110 (10%)

Query: 45  RPSSDLIMQLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYV 104
             SS LI  + N   +       S T+      F  + + T                  +
Sbjct: 3   SGSSGLIACVANDDVFSE-----SETRAKFESLFRTYDKDTTFQYFKS------FKRVRI 51

Query: 105 TSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSRRYNTDASLARQPAQSP 154
             S    A  A + ++     G+ + +   +      +       P +S 
Sbjct: 52  NFSNPLSAADARLRLHKTEFLGKEMKLYFAQT-LHIGSSHLAPPNPDKSG 100

>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 = 43.6 bits (102), Expect = 5e-07
 Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 7/67 (10%)

Query: 62  CISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNG 121
              +    ++  L     + G       +  +    +K Y +    T EE+++A V +NG
Sbjct: 25  NGGLGNGVSRNQLLPVLEKCGL------VDALLMPPNKPYSFARYRTTEESKRAYVTLNG 78

Query: 122 K-LLDGR 127
           K ++D  
Sbjct: 79  KEVVDDL 85

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.3 bits (101), Expect = 8e-07
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 61  RCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN 120
           R   + F  +KE +   FS    V     +    + RS G  +V  +++E A+KAL   +
Sbjct: 19  RLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKAL-KKH 77

Query: 121 GKLLDGRVIFVDNVRPSRRYNTDAS 145
            + +  R I +     +    +  S
Sbjct: 78  KERIGHRYIEIFKSSRAEVRTSGPS 102

>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 = 43.4 bits (101), Expect = 1e-06
 Identities = 16/75 (21%), Positives = 34/75 (45%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  +  +  L   F ++G +    I+ D    +S+GYG+V   +   AQ+A+  +NG  +
Sbjct: 50  IPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNI 109

Query: 125 DGRVIFVDNVRPSRR 139
             + + V       +
Sbjct: 110 LNKRLKVALAASGHQ 124

>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 = 42.0 bits (98), Expect = 1e-06
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 65  VSFSTTKE-MLADAFSQFGQVTEATIIMDIGKN-RSKGYGYVTSSTEEEAQKALVDMNGK 122
           +S     E +L ++F  FG + +  I     ++  +    ++    ++ A++AL  MN  
Sbjct: 12  LSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRS 70

Query: 123 LLDGRVIFVDNVRP 136
           LL  R I V     
Sbjct: 71  LLGNREISVSLADK 84

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 2e-06
 Identities = 15/71 (21%), Positives = 28/71 (39%), Gaps = 6/71 (8%)

Query: 65  VSFSTTKEMLADAF---SQFGQVTEATIIMDIGKNRS---KGYGYVTSSTEEEAQKALVD 118
           +S       +        +FG++ +  I        S       YVT    E+A +A+  
Sbjct: 16  LSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQC 75

Query: 119 MNGKLLDGRVI 129
           +N  ++DGR +
Sbjct: 76  VNNVVVDGRTL 86

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 41.5 bits (96), Expect = 3e-06
 Identities = 13/72 (18%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           ++ + +   L  A S+     +  ++       ++ +GYV   + E+ +KAL ++ G  +
Sbjct: 21  LNPNKSVAELKVAISELFAKNDLAVVDVR-TGTNRKFGYVDFESAEDLEKAL-ELTGLKV 78

Query: 125 DGRVIFVDNVRP 136
            G  I ++  + 
Sbjct: 79  FGNEIKLEKPKG 90

>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 = 41.2 bits (96), Expect = 3e-06
 Identities = 19/77 (24%), Positives = 30/77 (38%), Gaps = 8/77 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  +T+   LA  F +FG       I  I   +   + Y+   + + AQ A   M G  L
Sbjct: 25  LGPNTSLAALAREFDRFGS------IRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPL 78

Query: 125 DG--RVIFVDNVRPSRR 139
            G  R + VD  +    
Sbjct: 79  GGPDRRLRVDFAKSGPS 95

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.7 bits (95), Expect = 3e-06
 Identities = 12/73 (16%), Positives = 33/73 (45%), Gaps = 10/73 (13%)

Query: 66  SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLD 125
             ++   +L   F+Q+G       I+    + +  + ++   ++ +A+KAL   +G++  
Sbjct: 13  PQASASYIL-LQFAQYGN------ILKHVMSNTGNWMHIRYQSKLQARKAL-SKDGRIFG 64

Query: 126 GRVIFVDNVRPSR 138
             ++    V+P  
Sbjct: 65  ESIMI--GVKPCI 75

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 4e-05
 Identities = 12/82 (14%), Positives = 28/82 (34%), Gaps = 6/82 (7%)

Query: 61  RCISV---SFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV 117
            C+ +    +  T+  + + FS    +     I   G+        V  +T E+A  A+ 
Sbjct: 16  HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTG--EADVEFATHEDAVAAM- 72

Query: 118 DMNGKLLDGRVIFVDNVRPSRR 139
             +   +  R + +     +  
Sbjct: 73  AKDKANMQHRYVELFLNSTAGT 94

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 6e-05
 Identities = 11/68 (16%), Positives = 24/68 (35%), Gaps = 7/68 (10%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +   +  + + D    +              +R+K   +VT    E+AQ A+   +    
Sbjct: 13  LPQDSNCQEVHDLLKDYDL-------KYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSF 65

Query: 125 DGRVIFVD 132
            G+ + V 
Sbjct: 66  RGKDLIVQ 73

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 109

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.8 bits (87), Expect = 7e-05
 Identities = 22/92 (23%), Positives = 35/92 (38%), Gaps = 10/92 (10%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
             T + L   F  +G V    I+ +  +        V  +   +AQ A+  +NG  L G+
Sbjct: 14  RVTPQSLFILFGVYGDVQRVKILFNKKE-----NALVQMADGNQAQLAMSHLNGHKLHGK 68

Query: 128 VIFVD-----NVRPSRRYNTDASLARQPAQSP 154
            I +      NV+  R    D  L +    SP
Sbjct: 69  PIRITLSKHQNVQLPREGQEDQGLTKDYGNSP 100

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 87

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.4 bits (83), Expect = 2e-04
 Identities = 9/74 (12%), Positives = 20/74 (27%), Gaps = 7/74 (9%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S + + L D   +          +        G G V    +E+   A+  ++    
Sbjct: 8   LPPSGSWQDLKDHMREA-------GDVCYADVYRDGTGVVEFVRKEDMTYAVRKLDNTKF 60

Query: 125 DGRVIFVDNVRPSR 138
                    +R   
Sbjct: 61  RSHEGETAYIRVKV 74

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.8 bits (84), Expect = 2e-04
 Identities = 14/72 (19%), Positives = 29/72 (40%), Gaps = 1/72 (1%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           + F    + + D F +   V ++  I      ++ G G+V    E + + AL   + + +
Sbjct: 26  LPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL-CRHKQYM 84

Query: 125 DGRVIFVDNVRP 136
             R I V  +  
Sbjct: 85  GNRFIQVHPITK 96

>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 = 34.1 bits (77), Expect = 0.001
 Identities = 9/68 (13%), Positives = 19/68 (27%), Gaps = 3/68 (4%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
           +  S  +  +   F   G +    +   + KN              +   A +    K++
Sbjct: 8   LPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFAR---YDGALAAITKTHKVV 64

Query: 125 DGRVIFVD 132
               I V 
Sbjct: 65  GQNEIIVS 72

>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 = 33.9 bits (77), Expect = 0.001
 Identities = 11/67 (16%), Positives = 23/67 (34%), Gaps = 2/67 (2%)

Query: 65  VSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL 124
                T + + +     GQV     +        KG  +V   + E A+K + +  G+  
Sbjct: 14  FPTDATLDDIKEWLEDKGQVLN-IQMRRTLHKAFKGSIFVVFDSIESAKKFV-ETPGQKY 71

Query: 125 DGRVIFV 131
               + +
Sbjct: 72  KETDLLI 78

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 33.1 bits (75), Expect = 0.003
 Identities = 9/73 (12%), Positives = 26/73 (35%), Gaps = 4/73 (5%)

Query: 68  STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGR 127
              +  L      FG ++   I+       ++ +  + ++ + +A          L+ G+
Sbjct: 20  KNLRYQLLQLVEPFGVISNHLILN----KINEAFIEMATTEDAQAAVDYYTTTPALVFGK 75

Query: 128 VIFVDNVRPSRRY 140
            + V   +  +R 
Sbjct: 76  PVRVHLSQKYKRI 88

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	157
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.92
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.92
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.91
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.91
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.91
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.91
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.91
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.91
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.91
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.9
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.9
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.9
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.9
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.9
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.9
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.9
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.9
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.9
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.89
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.89
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.89
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.89
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.89
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.89
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.88
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.88
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.88
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.88
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.88
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.88
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.88
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.87
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.87
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.87
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.86
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.86
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.86
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.86
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.86
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.85
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.85
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.85
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.84
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.84
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.83
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.83
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.83
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.83
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.83
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.83
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.83
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.83
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.82
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.82
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.82
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.82
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.82
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.82
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.82
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.82
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.81
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.81
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.81
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.81
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.8
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.8
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.79
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.79
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.77
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.77
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.77
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.76
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.75
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.74
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.71
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.7
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	99.68
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.62
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.59
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.56
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.56
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.55
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.43
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.77
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.72
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.56
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.26

>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=99.92  E-value=7.3e-25  Score=134.65  Aligned_cols=81  Identities=22%  Similarity=0.315  Sum_probs=77.9

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|++|+|.+++|
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            45799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      .
T Consensus        82 g   82 (82)
T d1b7fa1          82 G   82 (82)
T ss_dssp             C
T ss_pred             C
Confidence            4

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.92  E-value=2.5e-24  Score=136.77  Aligned_cols=87  Identities=23%  Similarity=0.381  Sum_probs=81.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+.+++++|+++|.+||.|..+.++.++.+++++|||||+|.+.++|++|++.||+..|+|++|+|.++.
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a~   86 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPST   86 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEECC
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            35679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 036791          136 PSRRYNT  142 (157)
Q Consensus       136 ~~~~~~~  142 (157)
                      ++.+...
T Consensus        87 ~~~~~~~   93 (99)
T d1whwa_          87 IKKEASQ   93 (99)
T ss_dssp             CCSTTCC
T ss_pred             CCCccCC
Confidence            8765444

>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=99.91  E-value=1.9e-24  Score=134.52  Aligned_cols=83  Identities=23%  Similarity=0.298  Sum_probs=78.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||.++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|++|+..|||..++|++|+|+|+
T Consensus         5 ~~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a   84 (88)
T d1rk8a_           5 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC   84 (88)
T ss_dssp             C-CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            44578999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      .++
T Consensus        85 ~~k   87 (88)
T d1rk8a_          85 FVK   87 (88)
T ss_dssp             EEC
T ss_pred             cCC
Confidence            875

>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=99.91  E-value=1.9e-24  Score=135.01  Aligned_cols=84  Identities=23%  Similarity=0.373  Sum_probs=80.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+..+|||+|||.++++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..++|++|+|.|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            34568999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      +|+.
T Consensus        86 kp~~   89 (90)
T d2cq0a1          86 KPST   89 (90)
T ss_dssp             SCCC
T ss_pred             eCCC
Confidence            9875

>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=99.91  E-value=3.8e-24  Score=131.34  Aligned_cols=79  Identities=25%  Similarity=0.393  Sum_probs=76.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++.|||..++|++|+|.+++|
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            5699999999999999999999999999999999989999999999999999999999999999999999999999986

>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=99.91  E-value=6.3e-24  Score=133.43  Aligned_cols=84  Identities=25%  Similarity=0.322  Sum_probs=79.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|..|++.|||..++|++|+|.|+.
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a~   85 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDA   85 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEES
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45689999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      +...
T Consensus        86 ~~~~   89 (93)
T d1h2vz_          86 GFKE   89 (93)
T ss_dssp             CCCT
T ss_pred             CCCC
Confidence            6543

>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=99.91  E-value=1.4e-24  Score=135.39  Aligned_cols=83  Identities=27%  Similarity=0.400  Sum_probs=79.2

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|+..|||..++|++|+|.+++|
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~p   84 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP   84 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCC
Q 036791          137 SRR  139 (157)
Q Consensus       137 ~~~  139 (157)
                      +..
T Consensus        85 ~~~   87 (89)
T d2cqba1          85 MRI   87 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            643

>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=99.91  E-value=2.4e-24  Score=135.34  Aligned_cols=83  Identities=23%  Similarity=0.253  Sum_probs=79.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||..+++++|+++|++||.|..+.++.++.+|.++|||||+|.+.++|++|++.|||..++|++|+|++++
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ++.
T Consensus        88 ~~~   90 (93)
T d1x5ua1          88 AHN   90 (93)
T ss_dssp             TTS
T ss_pred             CCC
Confidence            865

>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=99.91  E-value=8.6e-24  Score=142.02  Aligned_cols=86  Identities=19%  Similarity=0.303  Sum_probs=81.1

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|.+|++.|||..|+|++|+|.+++
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~a~  120 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVALAA  120 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 036791          136 PSRRYN  141 (157)
Q Consensus       136 ~~~~~~  141 (157)
                      ++..+.
T Consensus       121 ~~~~~p  126 (139)
T d1u6fa1         121 SGHQRP  126 (139)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            876554

>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=99.90  E-value=6.9e-24  Score=129.67  Aligned_cols=78  Identities=24%  Similarity=0.309  Sum_probs=75.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      +|||+|||+.+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|..|++.|||..+.|++|+|.|++.
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~~   79 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQR   79 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECCC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            599999999999999999999999999999999999999999999999999999999999999999999999999853

>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=99.90  E-value=9.6e-24  Score=134.72  Aligned_cols=85  Identities=24%  Similarity=0.266  Sum_probs=80.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|+.||.|..+.++.++.+|.++|||||+|.+.++|+.|++.|||..|+|++|+|+|++
T Consensus        17 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a~   96 (102)
T d2cpza1          17 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLKR   96 (102)
T ss_dssp             TTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEeC
Confidence            34579999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++.++
T Consensus        97 ~k~~~  101 (102)
T d2cpza1          97 SKNDS  101 (102)
T ss_dssp             CSCCC
T ss_pred             CCCCC
Confidence            87654

>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=99.90  E-value=4.4e-24  Score=132.01  Aligned_cols=82  Identities=15%  Similarity=0.265  Sum_probs=78.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      .+|||+|||+++++++|+++|++||.|..+.++.|+.+|+++|||||+|.+.++|..|++.|||..++|++|.|.++.+.
T Consensus         2 ~rlfV~nlp~~~te~~l~~~F~~~G~v~~v~i~~d~~tg~~rg~aFV~f~~~~~A~~a~~~l~~~~l~g~~l~V~~A~~~   81 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG   81 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             CC
Q 036791          138 RR  139 (157)
Q Consensus       138 ~~  139 (157)
                      ..
T Consensus        82 ~~   83 (85)
T d2u2fa_          82 AK   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.90  E-value=2.1e-23  Score=133.37  Aligned_cols=83  Identities=29%  Similarity=0.424  Sum_probs=77.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||+.+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.+++ .|+|++|+|.++
T Consensus         8 ~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a   86 (103)
T d2cqda1           8 TTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLA   86 (103)
T ss_dssp             CSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEES
T ss_pred             CCCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEc
Confidence            3456899999999999999999999999999999999999999999999999999999999999876 799999999999


Q ss_pred             cCCC
Q 036791          135 RPSR  138 (157)
Q Consensus       135 ~~~~  138 (157)
                      .++.
T Consensus        87 ~~~~   90 (103)
T d2cqda1          87 YLGA   90 (103)
T ss_dssp             TTTC
T ss_pred             CCCC
Confidence            7654

>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=99.90  E-value=1e-23  Score=129.72  Aligned_cols=81  Identities=25%  Similarity=0.349  Sum_probs=76.1

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEE-EEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEA-TIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~-~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      |||+|||+++++++|+++|++||.|..+ .++.++.+|+++|||||+|.+.++|++|++.|+|..++|++|+|.++.++.
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~k~   80 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKD   80 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCCCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecCCC
Confidence            7999999999999999999999999765 788899999999999999999999999999999999999999999999876


Q ss_pred             CC
Q 036791          139 RY  140 (157)
Q Consensus       139 ~~  140 (157)
                      .+
T Consensus        81 ~k   82 (83)
T d1x5ta1          81 SK   82 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            54

>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=99.90  E-value=2.5e-24  Score=137.97  Aligned_cols=84  Identities=27%  Similarity=0.479  Sum_probs=79.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..|.|++|+|.++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CCCC
Q 036791          137 SRRY  140 (157)
Q Consensus       137 ~~~~  140 (157)
                      +..+
T Consensus        88 ~~~~   91 (104)
T d1p1ta_          88 EKNK   91 (104)
T ss_dssp             TTHH
T ss_pred             CCCc
Confidence            6543

>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=99.90  E-value=3.3e-23  Score=128.00  Aligned_cols=79  Identities=24%  Similarity=0.359  Sum_probs=74.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~  133 (157)
                      ..++|||+|||+.+++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++.|||..++|  ++|+|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            45679999999999999999999999999999999999999999999999999999999999999999987  5699988


Q ss_pred             e
Q 036791          134 V  134 (157)
Q Consensus       134 ~  134 (157)
                      |
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.90  E-value=3.8e-23  Score=127.71  Aligned_cols=79  Identities=22%  Similarity=0.360  Sum_probs=75.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~  133 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.+++++.+|+++|||||+|.+.++|.+|++.|||..+.|  ++|+|+|
T Consensus         5 ~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~~   84 (85)
T d1b7fa2           5 KDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRL   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEEE
Confidence            45679999999999999999999999999999999999999999999999999999999999999999876  8899998


Q ss_pred             e
Q 036791          134 V  134 (157)
Q Consensus       134 ~  134 (157)
                      |
T Consensus        85 A   85 (85)
T d1b7fa2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.90  E-value=2.9e-23  Score=130.59  Aligned_cols=85  Identities=19%  Similarity=0.360  Sum_probs=78.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHh-CCCccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIG-KNRSKGYGYVTSSTEEEAQKALVDM-NGKLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l-~g~~~~g~~l~v~  132 (157)
                      ...++|||+|||+.+++++|+++|++||.|..+.++.++. +|+++|||||+|.+.++|.+|++.| ||..++|++|+|+
T Consensus         6 ~~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~   85 (94)
T d2cpha1           6 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLE   85 (94)
T ss_dssp             SCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEE
Confidence            3456799999999999999999999999999999988754 7899999999999999999999998 8999999999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      |+.++..
T Consensus        86 ~A~~~~~   92 (94)
T d2cpha1          86 WADSEVT   92 (94)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCCC
Confidence            9988653

>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=99.89  E-value=4e-23  Score=128.89  Aligned_cols=83  Identities=24%  Similarity=0.363  Sum_probs=76.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.|+.+|+++|||||.|.+.++|++|++.  ...|+|+.|.|+++.
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~--~~~l~Gr~i~v~~a~   84 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWCDCKLPN   84 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEEEEECCC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhc--CCccCCEEeEEEeCC
Confidence            456799999999999999999999999999999999999999999999999999999999985  457999999999998


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++..+
T Consensus        85 ~k~~~   89 (90)
T d2cqga1          85 SKQSQ   89 (90)
T ss_dssp             TTCCC
T ss_pred             CCCCC
Confidence            87643

>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=99.89  E-value=2.5e-23  Score=129.87  Aligned_cols=84  Identities=35%  Similarity=0.569  Sum_probs=79.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|+.||.|..+.++.++.++.++|||||+|.++++|+.|++.|||..++|++|+|.++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45679999999999999999999999999999999998999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      ++..
T Consensus        84 ~~~~   87 (90)
T d1x5sa1          84 KSSD   87 (90)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7654

>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=99.89  E-value=2.1e-23  Score=133.23  Aligned_cols=84  Identities=27%  Similarity=0.426  Sum_probs=79.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.|+.++.++.++|||||+|.+.++|++|++ +++..|+|+.|.|+++.
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~a~   97 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKRAV   97 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEECCS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEECc
Confidence            34689999999999999999999999999999999999999999999999999999999997 69999999999999999


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++.+.
T Consensus        98 ~ke~~  102 (103)
T d1x4ba1          98 AREES  102 (103)
T ss_dssp             SCCCC
T ss_pred             ccCCC
Confidence            88754

>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=99.89  E-value=9e-23  Score=125.74  Aligned_cols=80  Identities=31%  Similarity=0.462  Sum_probs=75.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++ +++..|+|+.|+|+.|.
T Consensus         5 ~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~-~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN-ARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-TCSCEETTEECEEEECC
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEeee
Confidence            45689999999999999999999999999999999999999999999999999999999998 58999999999999875


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      +
T Consensus        84 s   84 (84)
T d1l3ka1          84 S   84 (84)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.89  E-value=2.4e-23  Score=127.45  Aligned_cols=79  Identities=16%  Similarity=0.277  Sum_probs=69.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ++|||+|||+++++++|+++|++||.|..+.++.+..+|+++|||||+|.+.++|++|++.|||..++|++|+|++++|
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            5899999999999999999999999999888888888899999999999999999999999999999999999999987

>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=99.89  E-value=7.3e-23  Score=125.86  Aligned_cols=76  Identities=30%  Similarity=0.482  Sum_probs=73.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEE
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFV  131 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v  131 (157)
                      +.++|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|+..|||..++|++|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            3567999999999999999999999999999999999999999999999999999999999999999999999987

>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=99.88  E-value=7.8e-23  Score=124.33  Aligned_cols=77  Identities=26%  Similarity=0.377  Sum_probs=73.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      +|||+|||+++++++|+++|++||.|..+.+..++ +|+++|||||+|.+.++|++|++.|||..++|++|+|+++.+
T Consensus         2 rl~V~nLp~~~~~~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~S   78 (78)
T d1no8a_           2 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTS   78 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEECC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            59999999999999999999999999999999985 799999999999999999999999999999999999999864

>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=99.88  E-value=7.5e-24  Score=134.94  Aligned_cols=81  Identities=27%  Similarity=0.370  Sum_probs=76.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.++.+|+++|||||+|.+.++|.+|+. |||..|+|+.|+|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~-l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEEECC
Confidence            34689999999999999999999999999999999999999999999999999999999995 99999999999999986


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ++
T Consensus        96 ~~   97 (101)
T d2cq4a1          96 AE   97 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            54

>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=99.88  E-value=1.5e-22  Score=126.26  Aligned_cols=83  Identities=20%  Similarity=0.258  Sum_probs=75.8

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+.++|||+|||.++++++|+++|+.||.|..+.++.++.+  .+|||||+|.+.++|++|++.|||..+.|+.|+|.|+
T Consensus         6 ~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~--~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a   83 (90)
T d2cqia1           6 GQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   83 (90)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCc--cceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            34568999999999999999999999999999999988654  4799999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      +++..
T Consensus        84 ~~~~~   88 (90)
T d2cqia1          84 TTPSS   88 (90)
T ss_dssp             CCTTC
T ss_pred             CCCCC
Confidence            87654

>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=99.88  E-value=1.3e-22  Score=125.24  Aligned_cols=79  Identities=33%  Similarity=0.453  Sum_probs=73.5

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCC---CcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKN---RSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~---~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      |||+|||+++++++|+++|++||.|..+.++.++.++   +++|||||+|.+.++|.+|++.|||..++|++|+|+++.+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            7999999999999999999999999999999887765   4689999999999999999999999999999999999865


Q ss_pred             CC
Q 036791          137 SR  138 (157)
Q Consensus       137 ~~  138 (157)
                      ..
T Consensus        81 ~~   82 (85)
T d2cpfa1          81 AT   82 (85)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>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=99.88  E-value=5.8e-23  Score=127.92  Aligned_cols=83  Identities=34%  Similarity=0.539  Sum_probs=76.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|+.||.|..+.++.++  +.++|||||+|.+.++|++|++.|||..++|++|+|.+++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~--~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBT--TBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeec--CCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            45679999999999999999999999999999999885  4478999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++.++
T Consensus        85 ~~~~R   89 (89)
T d1cvja2          85 SRKER   89 (89)
T ss_dssp             CTTTC
T ss_pred             CCCCC
Confidence            87653

>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=99.88  E-value=5.1e-22  Score=124.55  Aligned_cols=83  Identities=27%  Similarity=0.454  Sum_probs=76.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ...++|||+|||+.+++++|+++|+.||.|..+.++.++  +.++|||||+|.+.++|.+|++.|||..++|+.|+|+++
T Consensus         9 ~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~--~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A   86 (93)
T d2cq3a1           9 STPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   86 (93)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCT--TTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccc--cCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEec
Confidence            345679999999999999999999999999999999875  346899999999999999999999999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      +++..
T Consensus        87 ~~r~~   91 (93)
T d2cq3a1          87 TARVM   91 (93)
T ss_dssp             CSSCC
T ss_pred             CcCCC
Confidence            98753

>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=99.88  E-value=1e-22  Score=122.88  Aligned_cols=75  Identities=32%  Similarity=0.446  Sum_probs=71.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +|||+|||+++++++|+++|++||.|..+.++.++.+++++|||||+|.+.++|++|++ +++..|+|+.|.|+.|
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~-~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            48999999999999999999999999999999999999999999999999999999998 6999999999998654

>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=99.88  E-value=3.9e-23  Score=125.33  Aligned_cols=76  Identities=30%  Similarity=0.389  Sum_probs=72.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ++|||+|||+++++++|+++|++||.|..+.++.++.+|+++|||||+|.+.++|++|++ +++..++|+.|.|+.|
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~-~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLA-QSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHH-TTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHH-cCCCEECCeEEEEEEC
Confidence            369999999999999999999999999999999999999999999999999999999997 6999999999999876

>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=99.87  E-value=4.2e-22  Score=125.95  Aligned_cols=85  Identities=27%  Similarity=0.376  Sum_probs=78.1

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC------CCccCCcE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN------GKLLDGRV  128 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~------g~~~~g~~  128 (157)
                      ...++|||+|||+++++++|+++|.+||.+..+.++.++.+++++|||||+|.+.++|.+|++.|+      |..+.|++
T Consensus         6 ~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr~   85 (98)
T d1x4ha1           6 TEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGRQ   85 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSCE
T ss_pred             CCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCEE
Confidence            345689999999999999999999999999999999998899999999999999999999999987      56689999


Q ss_pred             EEEEeecCCCC
Q 036791          129 IFVDNVRPSRR  139 (157)
Q Consensus       129 l~v~~~~~~~~  139 (157)
                      |+|+++.++.+
T Consensus        86 l~v~~a~~k~~   96 (98)
T d1x4ha1          86 LKVDLAVTRDE   96 (98)
T ss_dssp             EEEECCCCCCC
T ss_pred             EEEEECCCCCc
Confidence            99999988654

>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=99.87  E-value=2.9e-22  Score=127.39  Aligned_cols=86  Identities=26%  Similarity=0.224  Sum_probs=78.0

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCee--------EEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVT--------EATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG  126 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~--------~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g  126 (157)
                      ...++|||+|||..+++++|+++|+.||.|.        .+.+..++.+|+.+|||||+|.++++|.+|++.|||..|+|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            4567899999999999999999999999874        56677888889999999999999999999999999999999


Q ss_pred             cEEEEEeecCCCCC
Q 036791          127 RVIFVDNVRPSRRY  140 (157)
Q Consensus       127 ~~l~v~~~~~~~~~  140 (157)
                      +.|+|++++++..+
T Consensus        86 r~i~V~~a~~~~p~   99 (101)
T d2cpea1          86 SKLKVSLARKKPPM   99 (101)
T ss_dssp             EECEEECSSCCCCS
T ss_pred             EEEEEEEcCCCCCC
Confidence            99999999886543

>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=99.87  E-value=6.7e-22  Score=120.35  Aligned_cols=77  Identities=21%  Similarity=0.344  Sum_probs=73.3

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .++|||+|||+++++++|+++|++||.|..+.+..++.+++++|||||+|.+.+++++|++ ++|..|+|+.|+|+.|
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEEC
Confidence            4679999999999999999999999999999999999999999999999999999999996 7999999999999876

>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=99.86  E-value=4.1e-22  Score=123.26  Aligned_cols=82  Identities=20%  Similarity=0.238  Sum_probs=71.2

Q ss_pred             cccEEEEcCCCCCCC-HHHHHHHHhcCCCeeEEEEeec-CCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEe
Q 036791           56 NVSFWRCISVSFSTT-KEMLADAFSQFGQVTEATIIMD-IGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~-~~~l~~~f~~~G~i~~~~~~~~-~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~  133 (157)
                      ..++|||+|||++++ +++|+++|++||.|..+.++.+ +.+++++|||||+|.+.++|++|++ ||+..++|+.|+|.+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~V~~   81 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREISVSL   81 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEEEEE
Confidence            356899999999876 5669999999999999998764 5678999999999999999999996 999999999999999


Q ss_pred             ecCCC
Q 036791          134 VRPSR  138 (157)
Q Consensus       134 ~~~~~  138 (157)
                      +.+++
T Consensus        82 a~~kP   86 (86)
T d2ghpa3          82 ADKKP   86 (86)
T ss_dssp             CCCCC
T ss_pred             cCCCC
Confidence            98763

>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=99.86  E-value=1.8e-22  Score=121.76  Aligned_cols=75  Identities=20%  Similarity=0.232  Sum_probs=71.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +|||+|||+++++++|+++|++||.|..+.|+.++.+++++|||||+|.+.++|++|++. ++..|+|+.|.|+.|
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~-~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            599999999999999999999999999999999999999999999999999999999975 778899999999865

>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=99.86  E-value=1.5e-22  Score=129.04  Aligned_cols=85  Identities=20%  Similarity=0.262  Sum_probs=79.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||.++++++|+++|+.||.|..+.+..+..+|+++|||||+|.+.++|.+|++.|||..|.|++|+|.|++
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~ak   96 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGK   96 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeCC
Confidence            35689999999999999999999999999999888887889999999999999999999999999999999999999999


Q ss_pred             CCCCC
Q 036791          136 PSRRY  140 (157)
Q Consensus       136 ~~~~~  140 (157)
                      ++.++
T Consensus        97 ~k~~r  101 (102)
T d2cpxa1          97 NKKQR  101 (102)
T ss_dssp             CCSCC
T ss_pred             CcccC
Confidence            87654

>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=99.86  E-value=6.4e-22  Score=119.22  Aligned_cols=75  Identities=25%  Similarity=0.395  Sum_probs=72.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +|||+|||+++++++|+++|+.||.+..+.++.++.+++++|||||+|.+.++|++|++ +||..|+|++|+|++|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            48999999999999999999999999999999999999999999999999999999997 8999999999999876

>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=99.86  E-value=2.5e-21  Score=121.82  Aligned_cols=79  Identities=15%  Similarity=0.212  Sum_probs=72.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||+++++++|+++|+.||.|..+.+..+   +.++|||||+|.+.++|+.||+.||+..|+|++|+|++++
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            4567999999999999999999999999998887544   5678999999999999999999999999999999999998


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      +.
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.85  E-value=4.5e-21  Score=124.39  Aligned_cols=78  Identities=17%  Similarity=0.234  Sum_probs=72.5

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||.++++++|+++|++||.|..|.+..+   +.++|||||+|.+.++|..|++.|||..|.|++|+|.++.+
T Consensus         7 ~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~~   83 (114)
T d2f9da1           7 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA   83 (114)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCH
T ss_pred             CCEEEEECCCCCCCHHHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            468999999999999999999999999999988754   67789999999999999999999999999999999999865


Q ss_pred             C
Q 036791          137 S  137 (157)
Q Consensus       137 ~  137 (157)
                      .
T Consensus        84 ~   84 (114)
T d2f9da1          84 N   84 (114)
T ss_dssp             H
T ss_pred             C
Confidence            3

>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=99.85  E-value=3.6e-21  Score=121.30  Aligned_cols=78  Identities=29%  Similarity=0.473  Sum_probs=72.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||..+++++|+++|++||.|..+.++.+      +|||||+|.+.++|.+|+..|||..|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            4568999999999999999999999999999999865      6899999999999999999999999999999999998


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      +++.
T Consensus        91 ~~p~   94 (96)
T d1x4ga1          91 ESPD   94 (96)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            7653

>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=99.85  E-value=8e-21  Score=121.31  Aligned_cols=84  Identities=18%  Similarity=0.243  Sum_probs=73.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecC-CCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDI-GKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~-~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +..+|||+|||+++++++|+++|+.|| +..+.++.++ .+++++|||||+|.+.++|++|+. ||+..|+|+.|+|.++
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~-~~~~~~~gr~l~V~~a   91 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS-LNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHG-GGTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHH-cCCCEECCEEEEEEEC
Confidence            347899999999999999999999999 7777777655 468899999999999999987775 9999999999999999


Q ss_pred             cCCCCCC
Q 036791          135 RPSRRYN  141 (157)
Q Consensus       135 ~~~~~~~  141 (157)
                      .++....
T Consensus        92 ~~~~~~~   98 (104)
T d1wi8a_          92 DQAQDKD   98 (104)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8865443

>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=99.84  E-value=3.7e-21  Score=122.30  Aligned_cols=80  Identities=20%  Similarity=0.358  Sum_probs=73.9

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      +.++|||+|||.++++++|+++|+.||.|..+.+..+ .+++++|||||+|.+.++|.+|++.|||..|.|+++.|.++.
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~-~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~~   95 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRD-SSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE   95 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEEC-SSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecc-cccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCCC
Confidence            3468999999999999999999999999999998887 578999999999999999999999999999999998887766


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      |
T Consensus        96 P   96 (101)
T d1x5oa1          96 P   96 (101)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.84  E-value=7.1e-21  Score=119.92  Aligned_cols=81  Identities=21%  Similarity=0.306  Sum_probs=72.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+..+|||+|||+++++++|+++|.+||.|..+.     .+++++|||||+|.+.++|++|++.|||..|+|++|+|.|+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a   88 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            3457899999999999999999999999876553     35789999999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 036791          135 RPSRRY  140 (157)
Q Consensus       135 ~~~~~~  140 (157)
                      .++...
T Consensus        89 ~~k~~~   94 (96)
T d1fjca_          89 GEKGGT   94 (96)
T ss_dssp             SSSCCC
T ss_pred             CCCCCC
Confidence            987653

>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=99.84  E-value=3.1e-22  Score=125.03  Aligned_cols=80  Identities=16%  Similarity=0.164  Sum_probs=73.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|+.||.|..+.++.+ .+|+++|||||+|.+.++|++|++ |||..++|++|+|++++
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEEEECCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEEEEecC
Confidence            4568999999999999999999999999988877654 679999999999999999999996 99999999999999998


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ++
T Consensus        90 ~k   91 (91)
T d1fjeb1          90 GR   91 (91)
T ss_dssp             CS
T ss_pred             CC
Confidence            74

>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=99.83  E-value=9.4e-21  Score=119.33  Aligned_cols=83  Identities=16%  Similarity=0.184  Sum_probs=73.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCC-eeEEEEeecCC-CCCcceEEEEEeCCHHHHHHHHHHhCCC--ccCCcEEEEEe
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQ-VTEATIIMDIG-KNRSKGYGYVTSSTEEEAQKALVDMNGK--LLDGRVIFVDN  133 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~-i~~~~~~~~~~-~~~~~g~afv~f~~~~~a~~ai~~l~g~--~~~g~~l~v~~  133 (157)
                      ++|||+|||.++++++|+++|+.||. |..+.++.++. +++++|||||+|.++++|..|++.|++.  .+.|+.|+|.|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~~   81 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVDW   81 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEEE
Confidence            47999999999999999999999995 88999988753 5889999999999999999999999754  45799999999


Q ss_pred             ecCCCCC
Q 036791          134 VRPSRRY  140 (157)
Q Consensus       134 ~~~~~~~  140 (157)
                      ++|+.+.
T Consensus        82 A~p~~~~   88 (96)
T d2disa1          82 AEPEIDV   88 (96)
T ss_dssp             SCSSCST
T ss_pred             cCCCCCC
Confidence            9986654

>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=99.83  E-value=1.3e-20  Score=119.05  Aligned_cols=74  Identities=19%  Similarity=0.387  Sum_probs=67.3

Q ss_pred             ccEEEEcCCC-CCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVS-FSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~-~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..+|||+||+ ..+++.+|+++|++||.|..+.+        ++|||||+|.+.++|++|++.|||..|.|++|+|++++
T Consensus        15 ~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i--------~rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   86 (98)
T d1wf2a_          15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAA   86 (98)
T ss_dssp             CCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEE--------ETEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETT
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEE--------eCCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            4569999997 56888999999999999999987        36899999999999999999999999999999999997


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ++.
T Consensus        87 ~~~   89 (98)
T d1wf2a_          87 EPK   89 (98)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            643

>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=99.83  E-value=1.3e-20  Score=116.32  Aligned_cols=78  Identities=27%  Similarity=0.440  Sum_probs=70.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|+.||.+..+.+.      +++|||||+|.+.++|.+|+..|||..|.|+.|+|.|++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~------~~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEE------ECSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEc------cccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            34689999999999999999999999998877663      357899999999999999999999999999999999998


Q ss_pred             CCCC
Q 036791          136 PSRR  139 (157)
Q Consensus       136 ~~~~  139 (157)
                      |+..
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7653

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=2.7e-20  Score=114.66  Aligned_cols=78  Identities=14%  Similarity=0.043  Sum_probs=72.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||.++++++|+++|+.||.|..+.+..+ .+|+++|||||+|.+.++|++|++ +++..++|+.|.|.+..
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~-~~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRT-LHKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEEC-TTCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeee-ccCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEEEcC
Confidence            3468999999999999999999999999999999887 479999999999999999999996 69999999999999853

>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=99.83  E-value=5.5e-21  Score=116.56  Aligned_cols=76  Identities=20%  Similarity=0.265  Sum_probs=68.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCC-ccCCcEEEEEeecCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGK-LLDGRVIFVDNVRPS  137 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~-~~~g~~l~v~~~~~~  137 (157)
                      +|||+|||.++++++|+++|++||.+..+.+..      .+|||||+|.+.++|++|++.|||. .+.|++|+|+++.|+
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~------~rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEec------ccceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            599999999999999999999999887765554      4689999999999999999999996 599999999999987


Q ss_pred             CCC
Q 036791          138 RRY  140 (157)
Q Consensus       138 ~~~  140 (157)
                      ..+
T Consensus        77 ~~r   79 (80)
T d2cqha1          77 KLR   79 (80)
T ss_dssp             CCC
T ss_pred             CcC
Confidence            654

>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=99.83  E-value=1.4e-20  Score=116.16  Aligned_cols=76  Identities=25%  Similarity=0.305  Sum_probs=71.0

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..+|||+|||.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|++.|||..++|++|+|+|+.+
T Consensus         8 ~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           8 RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             TTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            457999999999999999999999999999998754      57999999999999999999999999999999999987


Q ss_pred             CC
Q 036791          137 SR  138 (157)
Q Consensus       137 ~~  138 (157)
                      +.
T Consensus        82 ~~   83 (86)
T d2cpja1          82 SA   83 (86)
T ss_dssp             CS
T ss_pred             cC
Confidence            64

>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=99.83  E-value=2.5e-21  Score=119.93  Aligned_cols=76  Identities=17%  Similarity=0.093  Sum_probs=68.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCCC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPSR  138 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~~  138 (157)
                      +|||+|||+++++++|+++|++||.|..+.+..+       |||||+|.+.++|++||..|||..|.|+.|+|.+++++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~~   74 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVKV   74 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecCc
Confidence            4999999999999999999999999999987653       799999999999999999999999999999999887655


Q ss_pred             CCC
Q 036791          139 RYN  141 (157)
Q Consensus       139 ~~~  141 (157)
                      ...
T Consensus        75 ~~~   77 (87)
T d3begb1          75 DGP   77 (87)
T ss_dssp             CC-
T ss_pred             CCC
Confidence            443

>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=99.83  E-value=2.4e-21  Score=115.84  Aligned_cols=71  Identities=23%  Similarity=0.363  Sum_probs=68.3

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      |||+|||.++++++|+++|++||.|..+.+..++.++.++|||||+|.+.++|++|++.|||..++|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            79999999999999999999999999999999999999999999999999999999999999999998764

>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=99.82  E-value=1.2e-20  Score=117.73  Aligned_cols=80  Identities=18%  Similarity=0.221  Sum_probs=71.8

Q ss_pred             ccEEEEcCCCCCCCHHHHHH----HHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           57 VSFWRCISVSFSTTKEMLAD----AFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~----~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      .++|||+|||+++++++|++    +|++||.|..+.+..   +++++|||||+|.+.++|.+|++.|||..++|+.|+|.
T Consensus         3 ~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~   79 (91)
T d1nu4a_           3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQ   79 (91)
T ss_dssp             CSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            56899999999999988864    689999999988754   47789999999999999999999999999999999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      |++++.+
T Consensus        80 ~ak~~~~   86 (91)
T d1nu4a_          80 YAKTDSD   86 (91)
T ss_dssp             ECSSCCT
T ss_pred             EeCCCch
Confidence            9988654

>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=99.82  E-value=8.3e-20  Score=116.55  Aligned_cols=84  Identities=24%  Similarity=0.238  Sum_probs=75.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      .+...|||+|||+++++++|+++|..+|.+....++.+..+++.+|||||+|.+.++|++|++ +|+..|+|+.|+|.++
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYIEIFKS   91 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCCEEEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEEEEEEC
Confidence            345679999999999999999999999998887677777889999999999999999999996 8999999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .+...
T Consensus        92 ~~~~~   96 (104)
T d1wg5a_          92 SRAEV   96 (104)
T ss_dssp             CTTTS
T ss_pred             CHHHh
Confidence            87653

>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=99.82  E-value=4.8e-20  Score=118.82  Aligned_cols=77  Identities=13%  Similarity=0.110  Sum_probs=70.3

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+.+++++|+++|+.||.|..|.+.      +.+|||||+|.+.++|.+|++.|||..|.|++|.|+|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~------~~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLP------EGGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECC------SSSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEee------ccCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            34689999999999999999999999999998774      346899999999999999999999999999999999997


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ...
T Consensus        83 ~~~   85 (111)
T d1whxa_          83 IGV   85 (111)
T ss_dssp             TTT
T ss_pred             CCc
Confidence            643

>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=99.82  E-value=1.2e-20  Score=117.20  Aligned_cols=76  Identities=21%  Similarity=0.306  Sum_probs=69.4

Q ss_pred             ccEEEEcCCCCCCCHHHH---HHHHhcCCCeeEEEEeecCCCCCc---ceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           57 VSFWRCISVSFSTTKEML---ADAFSQFGQVTEATIIMDIGKNRS---KGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l---~~~f~~~G~i~~~~~~~~~~~~~~---~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      ..+|||+|||+++++++|   +++|++||.|..+.++.++.++..   +|||||+|.+.++|.+|++.|||..++|++|+
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~lk   87 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLK   87 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEEE
Confidence            346999999999999999   778999999999999998877654   49999999999999999999999999999999


Q ss_pred             EE
Q 036791          131 VD  132 (157)
Q Consensus       131 v~  132 (157)
                      |.
T Consensus        88 vS   89 (89)
T d2cpia1          88 AS   89 (89)
T ss_dssp             EE
T ss_pred             EC
Confidence            84

>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=99.82  E-value=4.4e-20  Score=114.38  Aligned_cols=78  Identities=19%  Similarity=0.243  Sum_probs=69.8

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc-CCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL-DGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~-~g~~l~v~~~  134 (157)
                      +..+|||+|||.++++++|+++|++||.|..+.+..    ++.+|||||+|.+.++|.+|+..|||..+ +|+.|+|.++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~----~~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFF----QKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEEC----SSSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEee----ecccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            356899999999999999999999999998876654    44578999999999999999999999988 5899999999


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            864

>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=99.82  E-value=2.8e-20  Score=113.10  Aligned_cols=75  Identities=21%  Similarity=0.318  Sum_probs=68.4

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|++  +++++|+++|++||.|..+.+.++      +|||||+|.+.++|.+|++.|||..++|++|+|.|++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            45689999986  899999999999999999988653      5799999999999999999999999999999999998


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      +++
T Consensus        76 ~~P   78 (79)
T d2bz2a1          76 KQP   78 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            753

>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=99.82  E-value=4.6e-20  Score=113.11  Aligned_cols=77  Identities=16%  Similarity=0.180  Sum_probs=69.4

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc-CCcEEEEEe
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL-DGRVIFVDN  133 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~-~g~~l~v~~  133 (157)
                      .+.++|||+|||..+++++|+++|+.||.|..+.++.+     .+|||||+|.+.++|.+|++.|||..+ .|++|+|.|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPN-----RHDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTT-----TCSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeecc-----cceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            34578999999999999999999999999999998754     368999999999999999999999988 468999999


Q ss_pred             ecC
Q 036791          134 VRP  136 (157)
Q Consensus       134 ~~~  136 (157)
                      ++.
T Consensus        81 akk   83 (83)
T d2b0ga1          81 AKK   83 (83)
T ss_dssp             CCC
T ss_pred             ecC
Confidence            873

>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=99.82  E-value=4.9e-20  Score=117.23  Aligned_cols=84  Identities=15%  Similarity=0.119  Sum_probs=74.0

Q ss_pred             ccccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           53 QLVNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        53 ~~~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ......+|||+|||+++++++|+++|..+| +..+.++.+ .++..+|||||+|.+.++|++|++ +|+..|+|+.|+|.
T Consensus        11 ~~~~~~~v~v~nLp~~~te~dl~~~F~~~~-~~~v~~~~~-~~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I~V~   87 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIG-PDGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYVELF   87 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCHHHHHHSSCSCC-CSEEEEEES-SSSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCCEEE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHhccC-cceeeeEEe-cCCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEEEEE
Confidence            334556899999999999999999999997 557878777 458999999999999999999986 89999999999999


Q ss_pred             eecCCCC
Q 036791          133 NVRPSRR  139 (157)
Q Consensus       133 ~~~~~~~  139 (157)
                      ++.++..
T Consensus        88 ~s~~~~~   94 (102)
T d1weza_          88 LNSTAGT   94 (102)
T ss_dssp             EECCCCC
T ss_pred             EcCCCCC
Confidence            9987653

>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=99.82  E-value=2.2e-20  Score=115.26  Aligned_cols=79  Identities=15%  Similarity=0.237  Sum_probs=70.6

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ..+.|||+|||+++++++|+++|..||.+....++.+..+++++|+|||+|.+.++|++|++.||+..|.|++|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3457999999999999999999999999876444444478999999999999999999999999999999999999874

>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=99.81  E-value=8.1e-20  Score=117.42  Aligned_cols=76  Identities=22%  Similarity=0.283  Sum_probs=69.5

Q ss_pred             ccEEEEcCCCC-CCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSF-STTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~-~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      .++|||+||++ .+++++|+++|+.||.|..+.++.++     +|||||+|.+.++|.+|++.|||..|+|+.|+|.+++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            35799999965 59999999999999999999998763     6899999999999999999999999999999999987


Q ss_pred             CC
Q 036791          136 PS  137 (157)
Q Consensus       136 ~~  137 (157)
                      ..
T Consensus        77 ~~   78 (109)
T d2adca1          77 HQ   78 (109)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.81  E-value=6.1e-20  Score=113.79  Aligned_cols=76  Identities=16%  Similarity=0.174  Sum_probs=66.5

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|.+|| +..+.+      ++.+|||||+|.+.++|++|++.||+..++|++|+|++++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~------~~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV------DRNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEE------EGGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeee------eccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            346799999999999999999999999 223322      4568999999999999999999999999999999999997


Q ss_pred             CCC
Q 036791          136 PSR  138 (157)
Q Consensus       136 ~~~  138 (157)
                      ++.
T Consensus        77 ~~~   79 (88)
T d1wg1a_          77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.81  E-value=6.7e-20  Score=115.76  Aligned_cols=79  Identities=16%  Similarity=0.092  Sum_probs=71.7

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|++||.|..+.+..       +|||||+|.+.++|++||+.|||..+.|+.|+|.+.+
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            456799999999999999999999999999998753       4799999999999999999999999999999999998


Q ss_pred             CCCCCC
Q 036791          136 PSRRYN  141 (157)
Q Consensus       136 ~~~~~~  141 (157)
                      ++..+.
T Consensus        87 ~~~~~~   92 (98)
T d1wg4a_          87 VYPERS   92 (98)
T ss_dssp             EECCCS
T ss_pred             cCCCCC
Confidence            765443

>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=99.81  E-value=2.7e-20  Score=115.37  Aligned_cols=80  Identities=21%  Similarity=0.280  Sum_probs=70.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ..++|||+|||+++++++|+++|++||.|..+.+.     ..++|||||+|.+.++|++|+.  ++..|+|++|+|+++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~-----~~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v~~a~   76 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHISNAE   76 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECC-----SSCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEe-----eccCceEEEEECCHHHHHHHHh--CCCEECCEEeEEEeCC
Confidence            45689999999999999999999999999998654     3467899999999999999985  7888999999999998


Q ss_pred             CCCCCCC
Q 036791          136 PSRRYNT  142 (157)
Q Consensus       136 ~~~~~~~  142 (157)
                      ++.....
T Consensus        77 ~k~~~~~   83 (88)
T d1wf0a_          77 PKHNSNS   83 (88)
T ss_dssp             CCCCCCS
T ss_pred             CCCCCCC
Confidence            8664433

>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=99.80  E-value=1.4e-19  Score=108.83  Aligned_cols=74  Identities=11%  Similarity=0.152  Sum_probs=67.8

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ++|||+|||+++++++|+++|+.||.|..+.+..++.  ..++||||+|.+.++|++|+. +|+..|+|++|.|..+
T Consensus         1 Ttv~V~nlp~~~t~~~l~~~F~~~G~I~~v~~~~~~~--~~~~~afV~F~~~~~a~~Al~-~~~~~i~g~~i~V~~~   74 (75)
T d2ghpa2           1 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLK--KNFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTT--SSSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeecc--ccceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            4799999999999999999999999999999998864  345799999999999999996 8999999999999865

>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=99.80  E-value=1.9e-19  Score=108.30  Aligned_cols=71  Identities=18%  Similarity=0.202  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecCC
Q 036791           60 WRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRPS  137 (157)
Q Consensus        60 l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~~  137 (157)
                      |||+|||+++++++|+++|++|| +..+.+      ++++|||||+|.+.++|++|+..|||..+.|++|+|++++.+
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~------~~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFV------DKYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEE------ETTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceee------cccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            79999999999999999999999 444433      456899999999999999999999999999999999999765

>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=99.79  E-value=3.5e-19  Score=112.21  Aligned_cols=77  Identities=22%  Similarity=0.311  Sum_probs=69.7

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCC--cEEEEEe
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDG--RVIFVDN  133 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g--~~l~v~~  133 (157)
                      +.++|||+|||+++++++|+++|++||.|..+.+..+      ++||||+|.+.++|.+|++.||+..|.|  ++|+|+|
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~   89 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEe
Confidence            4568999999999999999999999999999988654      5799999999999999999999999976  5899999


Q ss_pred             ecCCC
Q 036791          134 VRPSR  138 (157)
Q Consensus       134 ~~~~~  138 (157)
                      +++.+
T Consensus        90 ak~~~   94 (97)
T d1whya_          90 AKSGP   94 (97)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            98754

>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=99.79  E-value=3.1e-19  Score=114.59  Aligned_cols=80  Identities=16%  Similarity=0.181  Sum_probs=71.9

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc--CCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL--DGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~--~g~~l~v~  132 (157)
                      .+...|||+|||+.+++++|+++|++||.|..+.+..++    .+|||||+|.+.++|++|+..|||..|  .+..|+|.
T Consensus         5 s~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~   80 (108)
T d2adba1           5 SPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRID   80 (108)
T ss_dssp             CCEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEE
T ss_pred             CCeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEE
Confidence            345679999999999999999999999999999998763    579999999999999999999999998  57889999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      +++++.
T Consensus        81 ~s~~~~   86 (108)
T d2adba1          81 FSKLTS   86 (108)
T ss_dssp             ECSSCS
T ss_pred             ecCCcc
Confidence            987653

>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=99.77  E-value=3.8e-19  Score=113.21  Aligned_cols=78  Identities=22%  Similarity=0.222  Sum_probs=70.4

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .+|||+|||+++++++|+++|..||.+..+.++....+|+++|+|||+|.+.++|++|+. +|+..|+|+.|.|.++..
T Consensus         9 ~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~~~~~   86 (103)
T d2cpya1           9 VCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVHVVTL   86 (103)
T ss_dssp             CEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEEEECH
T ss_pred             eEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEEECCH
Confidence            569999999999999999999999988775555555789999999999999999999996 899999999999999754

>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=99.77  E-value=7.2e-19  Score=112.06  Aligned_cols=82  Identities=10%  Similarity=-0.022  Sum_probs=71.2

Q ss_pred             cccEEEEcCCCCCC-CH----HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Q 036791           56 NVSFWRCISVSFST-TK----EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIF  130 (157)
Q Consensus        56 ~~~~l~V~nl~~~~-~~----~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~  130 (157)
                      ...+|||+||+.++ ++    ++|+++|+.||.|..+.+.+      +++||||.|.+.++|.+|++.|||..|+|++|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k------~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK------SFKRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET------TTTEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec------CCCEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45679999999986 33    56999999999999998864      467999999999999999999999999999999


Q ss_pred             EEeecCCCCCCCC
Q 036791          131 VDNVRPSRRYNTD  143 (157)
Q Consensus       131 v~~~~~~~~~~~~  143 (157)
                      |.|+++.......
T Consensus        78 v~~a~~~~~~~~~   90 (104)
T d1weya_          78 LYFAQTLHIGSSH   90 (104)
T ss_dssp             EECCCCSSCCSCC
T ss_pred             EeecccCCCCCcc
Confidence            9999887655443

>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=99.77  E-value=7e-18  Score=107.43  Aligned_cols=78  Identities=14%  Similarity=0.147  Sum_probs=69.2

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM--NGKLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~l~v~  132 (157)
                      .+..+|||+|||..+++++|.++|++||.|..+.+.++      +|+|||+|.+.++|++|+..|  ++..+.|++|+|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            45678999999999999999999999999999988653      679999999999999999988  4566889999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      |++.++
T Consensus        87 ~s~~~~   92 (104)
T d1wexa_          87 YSTSKR   92 (104)
T ss_dssp             ECSSSS
T ss_pred             EcCCCc
Confidence            997654

>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=99.76  E-value=2.6e-18  Score=106.27  Aligned_cols=78  Identities=15%  Similarity=0.139  Sum_probs=69.7

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEEEE
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM--NGKLLDGRVIFVD  132 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~l~v~  132 (157)
                      .+.++|||+|||.++++++|+++|++||.|..+.+..+      +|||||+|.+.++|++|+..+  ++..+.|++|+|.
T Consensus         6 ~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~   79 (88)
T d2cq1a1           6 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   79 (88)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEE
Confidence            45678999999999999999999999999999988754      479999999999999999865  5678999999999


Q ss_pred             eecCCC
Q 036791          133 NVRPSR  138 (157)
Q Consensus       133 ~~~~~~  138 (157)
                      +++.+.
T Consensus        80 ~sk~~~   85 (88)
T d2cq1a1          80 YSNHKE   85 (88)
T ss_dssp             ECSCSS
T ss_pred             ECCCCC
Confidence            998654

>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=99.76  E-value=1.6e-18  Score=120.47  Aligned_cols=84  Identities=19%  Similarity=0.326  Sum_probs=78.3

Q ss_pred             ccccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           55 VNVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        55 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      ....+|||+|||+.+++++|+++|..||.|..+.++.++.+++++|||||+|.+.++|.+|++ +++..++|++|+|.++
T Consensus        95 ~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i~V~~A  173 (183)
T d1u1qa_          95 LTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRKA  173 (183)
T ss_dssp             CCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEEEEEEC
T ss_pred             cccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEec
Confidence            445789999999999999999999999999999999999999999999999999999999997 6889999999999999


Q ss_pred             cCCCC
Q 036791          135 RPSRR  139 (157)
Q Consensus       135 ~~~~~  139 (157)
                      .++.+
T Consensus       174 ~~k~e  178 (183)
T d1u1qa_         174 LSKQE  178 (183)
T ss_dssp             CCHHH
T ss_pred             CCccc
Confidence            88654

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=2.2e-18  Score=108.86  Aligned_cols=78  Identities=13%  Similarity=0.148  Sum_probs=69.2

Q ss_pred             ccccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHH--HhCCCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFS-TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALV--DMNGKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~--~l~g~~~~g~~l~v  131 (157)
                      ...++|||+|||.. +++++|.++|+.||.|..+.++.+      +|+|||+|.+.++|.+|++  .+++..++|++|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            44578999999985 899999999999999999998754      5799999999999999997  57888999999999


Q ss_pred             EeecCCC
Q 036791          132 DNVRPSR  138 (157)
Q Consensus       132 ~~~~~~~  138 (157)
                      .+++.+.
T Consensus        90 ~~s~~~~   96 (99)
T d1x4fa1          90 DLSEKYK   96 (99)
T ss_dssp             EEECSCS
T ss_pred             EEcCCcc
Confidence            9997654

>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=99.74  E-value=1.2e-18  Score=112.47  Aligned_cols=80  Identities=18%  Similarity=0.235  Sum_probs=72.2

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      ...+|||+|||+++++++|+++|+.+|.+..+.++.+..+|+.+|+|||+|.+.++|++|++ ||+..|+|+.|.|..+.
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBEEEEEC
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEEEEEcC
Confidence            35589999999999999999999999988776666666789999999999999999999996 89999999999999875


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      +
T Consensus        96 ~   96 (112)
T d1wela1          96 K   96 (112)
T ss_dssp             H
T ss_pred             h
Confidence            4

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=2.1e-17  Score=102.33  Aligned_cols=78  Identities=15%  Similarity=0.171  Sum_probs=68.4

Q ss_pred             ccccEEEEcCCCCC-CCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHh--CCCccCCcEEEE
Q 036791           55 VNVSFWRCISVSFS-TTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDM--NGKLLDGRVIFV  131 (157)
Q Consensus        55 ~~~~~l~V~nl~~~-~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l--~g~~~~g~~l~v  131 (157)
                      .....|||+|||.. +++++|.++|++||.|..+.++.+      +++|||.|.+.++|.+|++.|  ++..+.|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~------k~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeecc------ceEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            34567999999986 789999999999999999998765      358999999999999999966  677899999999


Q ss_pred             EeecCCC
Q 036791          132 DNVRPSR  138 (157)
Q Consensus       132 ~~~~~~~  138 (157)
                      .|+++..
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9998643

>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=99.70  E-value=1.4e-19  Score=112.58  Aligned_cols=75  Identities=16%  Similarity=0.338  Sum_probs=65.7

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEE-----eecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEE
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATI-----IMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVD  132 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~-----~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~  132 (157)
                      ++|||+|||.++++++|+++|+.||.+..+.+     +.+..+++++|||||+|.+.++|++|+. |||..++|++|+|+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l~V~   80 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSLKIR   80 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCCCCB
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEEEEC
Confidence            57999999999999999999999997765544     2345667899999999999999999985 99999999999996


Q ss_pred             e
Q 036791          133 N  133 (157)
Q Consensus       133 ~  133 (157)
                      .
T Consensus        81 r   81 (90)
T d1u2fa_          81 R   81 (90)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.68  E-value=2.6e-18  Score=109.46  Aligned_cols=76  Identities=22%  Similarity=0.288  Sum_probs=71.6

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEee
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNV  134 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~  134 (157)
                      +.++|.+++..+++++|+++|++||.|..+.|+.+ .+++.+|+|||+|.+.++|.+|+..|||..++|++|+|+++
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            56889999999999999999999999999999877 67999999999999999999999999999999999999986

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=2.4e-15  Score=104.11  Aligned_cols=82  Identities=30%  Similarity=0.449  Sum_probs=74.4

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .++|||+|||+.+++++|+++|++||.|..+.++.++.++.++|||||+|.+.++|.+|+.. ++..++++.+.+....+
T Consensus         6 ~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           6 LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhhhhh
Confidence            36899999999999999999999999999999999999999999999999999999999985 67778888888888765


Q ss_pred             CCC
Q 036791          137 SRR  139 (157)
Q Consensus       137 ~~~  139 (157)
                      ...
T Consensus        85 ~~~   87 (183)
T d1u1qa_          85 RED   87 (183)
T ss_dssp             TTG
T ss_pred             ccc
Confidence            543

>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=99.59  E-value=1.9e-15  Score=97.37  Aligned_cols=74  Identities=19%  Similarity=0.035  Sum_probs=64.7

Q ss_pred             ccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCH-HHHHHHHHHhCCCccCCcEEEEEeec
Q 036791           57 VSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTE-EEAQKALVDMNGKLLDGRVIFVDNVR  135 (157)
Q Consensus        57 ~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~-~~a~~ai~~l~g~~~~g~~l~v~~~~  135 (157)
                      .-.+||||||+.+++++|+++|++||.|..|.++.+      +|||||.|.+. ++|..|+..|++..+.++.+.|.+..
T Consensus        11 ~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~   84 (113)
T d1owxa_          11 CLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   84 (113)
T ss_dssp             CEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEee
Confidence            446899999999999999999999999999999754      68999999985 78999999999999887777777764


Q ss_pred             C
Q 036791          136 P  136 (157)
Q Consensus       136 ~  136 (157)
                      .
T Consensus        85 ~   85 (113)
T d1owxa_          85 L   85 (113)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.56  E-value=3e-15  Score=94.47  Aligned_cols=62  Identities=21%  Similarity=0.290  Sum_probs=55.6

Q ss_pred             ccEEEE--cCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCcc
Q 036791           57 VSFWRC--ISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLL  124 (157)
Q Consensus        57 ~~~l~V--~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~  124 (157)
                      ..+|||  ||||..+++++|+++|++||.|..+.+..+      ++||||.|.+.++|.+|+..|||..+
T Consensus        18 t~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             CSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            456777  559999999999999999999999987654      57999999999999999999999987

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.56  E-value=7.8e-15  Score=92.24  Aligned_cols=82  Identities=20%  Similarity=0.271  Sum_probs=69.1

Q ss_pred             ccccEEEEcCC--CCCCC---------HHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCc
Q 036791           55 VNVSFWRCISV--SFSTT---------KEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKL  123 (157)
Q Consensus        55 ~~~~~l~V~nl--~~~~~---------~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~  123 (157)
                      ...++|+|.||  |.++.         .++|++.|++||.|..+.+..+    ..+|++||.|.+.++|.+|+..|||..
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng~~   81 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDGRW   81 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCCcE
Confidence            45678999998  54321         2678999999999999987654    457999999999999999999999999


Q ss_pred             cCCcEEEEEeecCCCCC
Q 036791          124 LDGRVIFVDNVRPSRRY  140 (157)
Q Consensus       124 ~~g~~l~v~~~~~~~~~  140 (157)
                      ++|++|+|.++.++...
T Consensus        82 ~~gr~i~v~~~~g~~~~   98 (99)
T d2dita1          82 FGGRQITAQAWDGTTDY   98 (99)
T ss_dssp             ETTEECEEEECCSCCCS
T ss_pred             ECCEEEEEEEeCCcCCC
Confidence            99999999999877643

>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=99.55  E-value=1e-14  Score=88.33  Aligned_cols=74  Identities=15%  Similarity=0.275  Sum_probs=62.0

Q ss_pred             cccEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcE-EEEEee
Q 036791           56 NVSFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRV-IFVDNV  134 (157)
Q Consensus        56 ~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~-l~v~~~  134 (157)
                      +.+.|+|+++|++.+++.| +.|++||.|.++.+.      ..+|||||.|.+.++|++|+. +||..++|+. |.|..+
T Consensus         3 ~~~wV~V~G~p~~~~~~il-~~F~~~G~I~~~~~~------~~~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vgV~~~   74 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYIL-LQFAQYGNILKHVMS------NTGNWMHIRYQSKLQARKALS-KDGRIFGESIMIGVKPC   74 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHH-HHHHTTSCEEEEEEC------SSSSEEEEEESSHHHHHHHHT-TTTCEETTTEECEEEEC
T ss_pred             cccEEEEECCChHHHHHHH-HHHHhhhhhheEEec------CCCCEEEEEEcccHHHHHHHh-cCCCeECCcEEEEEEeC
Confidence            4566999999999987666 579999999999764      346899999999999999996 8999999985 568776


Q ss_pred             cCC
Q 036791          135 RPS  137 (157)
Q Consensus       135 ~~~  137 (157)
                      ..+
T Consensus        75 ~~k   77 (81)
T d1wwha1          75 IDK   77 (81)
T ss_dssp             CCH
T ss_pred             CCh
Confidence            543

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.43  E-value=1.4e-13  Score=87.11  Aligned_cols=81  Identities=19%  Similarity=0.233  Sum_probs=67.8

Q ss_pred             cccEEEEcCC--CCCCC--------HHHHHHHHhcCCCeeEEEEeecCCCC--CcceEEEEEeCCHHHHHHHHHHhCCCc
Q 036791           56 NVSFWRCISV--SFSTT--------KEMLADAFSQFGQVTEATIIMDIGKN--RSKGYGYVTSSTEEEAQKALVDMNGKL  123 (157)
Q Consensus        56 ~~~~l~V~nl--~~~~~--------~~~l~~~f~~~G~i~~~~~~~~~~~~--~~~g~afv~f~~~~~a~~ai~~l~g~~  123 (157)
                      +.+.|.+.|+  +..+.        .++|++.|++||.|..+.|+++..+.  ...|++||.|.+.++|.+|+..|||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            3556888998  44432        25689999999999999998765543  356899999999999999999999999


Q ss_pred             cCCcEEEEEeecC
Q 036791          124 LDGRVIFVDNVRP  136 (157)
Q Consensus       124 ~~g~~l~v~~~~~  136 (157)
                      ++||.|.+.+..+
T Consensus        83 f~gR~v~v~f~~~   95 (104)
T d1o0pa_          83 FANRVVVTKYCDP   95 (104)
T ss_dssp             SSSSCCEEEEECH
T ss_pred             ECCeEEEEEEcCH
Confidence            9999999999864

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.77  E-value=4.1e-05  Score=45.49  Aligned_cols=56  Identities=18%  Similarity=0.253  Sum_probs=49.4

Q ss_pred             HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        72 ~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      .+|-+.|..||+|.-++++.+        --+|+|.+-+.|.+|+. ++|..+.|+.|+|....|
T Consensus        39 ~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~-l~g~~v~G~~l~It~~~~   94 (95)
T d1ufwa_          39 TELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLD-VDGMKVKGRAVKISGPSS   94 (95)
T ss_dssp             HHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHH-GGGSEETTEEEEEECCCC
T ss_pred             HHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhc-cCCeEEcceEEEEecCCC
Confidence            467888999999999999877        37999999999999998 799999999999987554

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=0.00011  Score=41.54  Aligned_cols=62  Identities=16%  Similarity=0.222  Sum_probs=52.2

Q ss_pred             HHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEEEEeecC
Q 036791           72 EMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMNGKLLDGRVIFVDNVRP  136 (157)
Q Consensus        72 ~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~g~~~~g~~l~v~~~~~  136 (157)
                      ..|...|.++|.|..+.+...   ....-.|-|...+..+|.-|+..||...|++++|.|.++..
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~---~dg~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~~   72 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPH---TDYQLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLATG   72 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSC---CSTTCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             HHHHHHHHhheeEEEEEEEec---cCCcEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEecC
Confidence            346677889999999988665   22345699999999999999999999999999999999763

>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=97.56  E-value=0.00036  Score=41.65  Aligned_cols=68  Identities=12%  Similarity=0.010  Sum_probs=58.1

Q ss_pred             cEEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCC--cceEEEEEeCCHHHHHHHHHHhCCCccC
Q 036791           58 SFWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNR--SKGYGYVTSSTEEEAQKALVDMNGKLLD  125 (157)
Q Consensus        58 ~~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~--~~g~afv~f~~~~~a~~ai~~l~g~~~~  125 (157)
                      ++|-|+.||+.++++++.+.+...|.+........+.+.+  .-.-|+|.|.+.++...-.+.++|..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            4688999999999999999999989888877777655543  2367999999999999999999999873

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.26  E-value=0.0073  Score=36.07  Aligned_cols=54  Identities=22%  Similarity=0.239  Sum_probs=45.3

Q ss_pred             EEEEcCCCCCCCHHHHHHHHhcCCCeeEEEEeecCCCCCcceEEEEEeCCHHHHHHHHHHhC
Q 036791           59 FWRCISVSFSTTKEMLADAFSQFGQVTEATIIMDIGKNRSKGYGYVTSSTEEEAQKALVDMN  120 (157)
Q Consensus        59 ~l~V~nl~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~afv~f~~~~~a~~ai~~l~  120 (157)
                      .||.-.+|..+...+|.++|+.||.| .|.++-+ .      -|||...+.+++..++..+.
T Consensus        17 HVf~~tFP~~Wk~~dI~~lFSpfG~V-~VswIdd-T------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKTSDLYQLFSAFGNI-QISWIDD-T------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCHHHHHHHHTTTCSC-CCEEEET-T------EEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccchhHHHHHhcCCCce-EEEEecC-c------eEEEEecCHHHHHHHHHHhc
Confidence            48888999999999999999999976 4555554 2      49999999999999987654