Citrus Sinensis ID: 023632

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------28
Protein Sequence
MKELLTEILTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
Secondary Structure (PSIPRED)
cHHHHHHHHHccccccccccEEEEccccccccccHHHHHHHHHccccEEEEEEEccccccccccEEEEEEccHHHHHHHHHcccccEEcccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHccccccccEEEEEEcccccccHHHHHHHHHHcccEEEEEEEEcccccccccEEEEEEccHHHHHHHHHccccEEEcccEEEEEEcccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
MKELLTEILTMFINRQTTtqkmtglsltpvtepalDEFKDFFMqfgdvqehqimrdhstsrsrgfgfitfDTEQAVDDLLAKGNKLELAGAQVevkkaepkkpnlpqpsyrrynnpkpaygsgfgdayggyggggfagggfggsggggggggyrssgaygvrgggyggygvggefggyggygggmgayrgepsslgysgryggfnrgydvtgdygglnesyggyggsgvgggggygggpsgydiglgssyggssggaffgsrggyggaggssryhpygr
Flexible Loop (DISEMBL)
MKELLTEILTMFInrqtttqkmtglsLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGaqvevkkaepkkpnlpqpsyrryNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGgyggaggssryhpygr
Low Complexity Region (SEG)
MKELLTEILTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAygsgfgdayggyggggfagggfggsggggggggyrssgaygvrgggyggygvggefggyggygggmgayrgEPSSLGYSGRYGGFNRGYDVTGDygglnesyggyggsgvgggggygggpsgydiglgssyggssggaffgsrggyggaggssrYHPYGR
Disordered region (IsUnstruct)
****LTEILTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIM********RGFGFITFDTEQAVDDLLAKGNKL*************************************FGDAYGGYGGG************************YGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYG*********************************************************
Disordered Region (DISOPRED)
*********************MTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE*****************************************************************************************************************************************************************************************
Disordered Region (DISEMBL)
MKELLTEILTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
Disordered Region (DISPRO)
MKELLTEILTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP****************KPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRY*PYGR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKELLTEILTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSRYHPYGR
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	279	2.2.26 [Sep-21-2011]
Q8W034	411	Heterogeneous nuclear rib	no	no	0.254	0.172	0.486	9e-12
Q08473	344	RNA-binding protein squid	no	no	0.261	0.212	0.472	3e-10
Q32P51	320	Heterogeneous nuclear rib	no	no	0.229	0.2	0.353	6e-06
Q05966	169	Glycine-rich RNA-binding	N/A	no	0.229	0.378	0.406	6e-06
Q03251	169	Glycine-rich RNA-binding	no	no	0.207	0.343	0.448	7e-06
Q03878	157	Glycine-rich RNA-binding	N/A	no	0.211	0.375	0.423	9e-06
Q99070	168	Glycine-rich RNA-binding	N/A	no	0.211	0.351	0.406	9e-06
Q9PTX2	164	Cold-inducible RNA-bindin	N/A	no	0.254	0.432	0.36	1e-05
Q03250	176	Glycine-rich RNA-binding	no	no	0.207	0.329	0.431	2e-05
Q22037	346	Heterogeneous nuclear rib	yes	no	0.232	0.187	0.378	2e-05

>sp|Q8W034|RNP1_ARATH Heterogeneous nuclear ribonucleoprotein 1 OS=Arabidopsis thaliana GN=RNP1 PE=1 SV=1

 Score = 70.9 bits (172), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 50/74 (67%), Gaps = 3/74 (4%)

Query: 33  PAL--DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG 90
           P L  +EF+ +F  +G V +  IM D +T+R RGFGF++FD+E AVD +L K    +L+G
Sbjct: 119 PTLTDEEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVSFDSEDAVDSVLHKTFH-DLSG 177

Query: 91  AQVEVKKAEPKKPN 104
            QVEVK+A PK  N
Sbjct: 178 KQVEVKRALPKDAN 191

Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection.
Arabidopsis thaliana (taxid: 3702)

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

 Score = 66.2 bits (160), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 50/74 (67%), Gaps = 1/74 (1%)

Query: 31  TEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG 90
           TE + +E K +F QFG++ E ++  D   S+ +GF FITFD+EQ V DLL K  K ++AG
Sbjct: 145 TEISDEEIKTYFGQFGNIVEVEMPFDKQKSQRKGFCFITFDSEQVVTDLL-KTPKQKIAG 203

Query: 91  AQVEVKKAEPKKPN 104
            +V+VK+A PK  N
Sbjct: 204 KEVDVKRATPKPEN 217

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

Drosophila melanogaster (taxid: 7227)

>sp|Q32P51|RA1L2_HUMAN Heterogeneous nuclear ribonucleoprotein A1-like 2 OS=Homo sapiens GN=HNRNPA1L2 PE=2 SV=2

 Score = 51.6 bits (122), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VKGHNCEVRK 179

Query: 98  AEPKK 102
           A PK+
Sbjct: 180 ALPKQ 184

Involved in the packaging of pre-mRNA into hnRNP particles, transport of poly(A) mRNA from the nucleus to the cytoplasm and may modulate splice site selection.

Homo sapiens (taxid: 9606)

>sp|Q05966|GRP10_BRANA Glycine-rich RNA-binding protein 10 OS=Brassica napus GN=GRP10 PE=2 SV=1

 Score = 51.6 bits (122), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 26/64 (40%), Positives = 40/64 (62%)

Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           E +  F QFG+V + +I+ D  T RSRGFGF+TF  E+++ D + + N  EL G  + V 
Sbjct: 21  ELERTFSQFGEVIDSKIINDRETGRSRGFGFVTFKDEKSMKDAIDEMNGKELDGRTITVN 80

Query: 97  KAEP 100
           +A+ 
Sbjct: 81  EAQS 84

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

Brassica napus (taxid: 3708)

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

 Score = 51.6 bits (122), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/58 (44%), Positives = 38/58 (65%)

Query: 42 FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE 99
          F QFGDV + +I+ D  + RSRGFGF+TF  E+A+ D + + N  EL G  + V +A+
Sbjct: 26 FSQFGDVIDSKIINDRESGRSRGFGFVTFKDEKAMRDAIEEMNGKELDGRVITVNEAQ 83

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 51.2 bits (121), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 37/59 (62%)

Query: 42  FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP 100
           F QFGD+ + +I+ D  T RSRGFGF+TF  E+++ D +   N  EL G  + V +A+ 
Sbjct: 26  FSQFGDITDSKIINDRETGRSRGFGFVTFKDEKSMRDAIEGMNGQELDGRNITVNEAQS 84

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

 Score = 51.2 bits (121), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 36/59 (61%)

Query: 42  FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP 100
           F  FG V + +++ D  T RSRGFGF+TF +EQ++ D +   N  EL G  + V +A+ 
Sbjct: 28  FANFGQVIDSKVITDRETGRSRGFGFVTFSSEQSMLDAIENMNGKELDGRNITVNQAQS 86

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

Sorghum bicolor (taxid: 4558)

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

 Score = 50.4 bits (119), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 41/75 (54%), Gaps = 4/75 (5%)

Query: 24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
          GLS     E  L+     F ++G +QE  +++D  T RSRGFGF+TF+  +   D +A  
Sbjct: 12 GLSF-DTDEQCLETV---FSKYGQIQEVVVVKDRETKRSRGFGFVTFENCEDAKDAMAGM 67

Query: 84 NKLELAGAQVEVKKA 98
          N   + G Q+ V +A
Sbjct: 68 NGKTVDGRQIRVDQA 82

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|Q03250|RBG7_ARATH Glycine-rich RNA-binding protein 7 OS=Arabidopsis thaliana GN=RBG7 PE=1 SV=1

 Score = 50.1 bits (118), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 37/58 (63%)

Query: 42 FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE 99
          F Q+GDV + +I+ D  T RSRGFGF+TF  E+A+ D +   N  +L G  + V +A+
Sbjct: 28 FAQYGDVIDSKIINDRETGRSRGFGFVTFKDEKAMKDAIEGMNGQDLDGRSITVNEAQ 85

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q22037|ROA1_CAEEL Heterogeneous nuclear ribonucleoprotein A1 OS=Caenorhabditis elegans GN=hrp-1 PE=1 SV=1

 Score = 49.7 bits (117), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 42/66 (63%), Gaps = 1/66 (1%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D  ++F+ QFG++ +  +MRD +T RSRGFGF+TF  +  VD  + +   + + G  V+ 
Sbjct: 37  DLMREFYSQFGEITDIIVMRDPTTKRSRGFGFVTFSGKTEVDAAMKQRPHI-IDGKTVDP 95

Query: 96  KKAEPK 101
           K+A P+
Sbjct: 96  KRAVPR 101

This protein is a component of ribonucleosomes. Overexpression gradually increases telomere length, leading to increase lifespan.

Caenorhabditis elegans (taxid: 6239)

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	279
388500070	373	unknown [Lotus japonicus] gi|388508218|g	0.813	0.608	0.596	8e-43
359488807	2363	PREDICTED: nuclear pore membrane glycopr	0.627	0.074	0.616	2e-41
356571134	374	PREDICTED: heterogeneous nuclear ribonuc	0.817	0.609	0.555	2e-40
449446702	2257	PREDICTED: LOW QUALITY PROTEIN: nuclear	0.813	0.100	0.547	4e-40
255560914	2256	RNA binding protein, putative [Ricinus c	0.336	0.041	0.772	4e-37
356558851	372	PREDICTED: RNA-binding protein Musashi h	0.523	0.392	0.615	4e-34
356513961	2304	PREDICTED: nuclear pore membrane glycopr	0.806	0.097	0.508	2e-33
242053621	349	hypothetical protein SORBIDRAFT_03g02792	0.544	0.435	0.520	2e-32
296087606	281	unnamed protein product [Vitis vinifera]	0.440	0.437	0.637	3e-32
363807276	377	uncharacterized protein LOC100793209 [Gl	0.623	0.461	0.575	1e-31

>gi|388500070|gb|AFK38101.1| unknown [Lotus japonicus] gi|388508218|gb|AFK42175.1| unknown [Lotus japonicus]

 Score =  180 bits (456), Expect = 8e-43,   Method: Compositional matrix adjust.
 Identities = 151/253 (59%), Positives = 179/253 (70%), Gaps = 26/253 (10%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           VTE   DEF+DFF ++G+V+++QIMRDHST+RSRGFGFITFD+E AVDDLL+ GNK++ A
Sbjct: 144 VTE---DEFRDFFTRYGEVKDNQIMRDHSTNRSRGFGFITFDSEDAVDDLLSMGNKIDFA 200

Query: 90  GAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGG 149
           G QVE+KKAEPKKPN P PS +RYN+ + +Y SG+G+AY             G  G  G 
Sbjct: 201 GTQVEIKKAEPKKPNPPTPSSKRYNDSRSSYSSGYGEAYD------------GFGGSYGA 248

Query: 150 GGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-FNRGY 208
            GGYRSS AY  R G YGGY  G EFGGYGGY G MG YRG+P SLG++GRYGG F+RGY
Sbjct: 249 AGGYRSSAAYAGRSGAYGGY--GSEFGGYGGYAGAMGPYRGDP-SLGFAGRYGGSFSRGY 305

Query: 209 DVTGDYGGLNESYGGYGGSGVGGGGGYGGGPS--GYDIGLGSSYGGSSGGAFFGSRGGYG 266
           D+ G YGG +ESYG YG     GGG    G    GYD  L   YGG+SGG+F+GSRGGYG
Sbjct: 306 DLGG-YGGASESYGAYGAGAAAGGGSSAAGAYQGGYDASLAGGYGGASGGSFYGSRGGYG 364

Query: 267 GAGGSSRYHPYGR 279
                 RYHPYGR
Sbjct: 365 AG----RYHPYGR 373

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359488807|ref|XP_002272790.2| PREDICTED: nuclear pore membrane glycoprotein 210-like [Vitis vinifera]

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 122/198 (61%), Positives = 139/198 (70%), Gaps = 23/198 (11%)

Query: 30   VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
            VTE   +EFKDFF Q+G+V++HQIMRDHSTSRSRGFGF+TFDTEQAVDDLL++GNKLELA
Sbjct: 2127 VTE---EEFKDFFTQYGEVKDHQIMRDHSTSRSRGFGFVTFDTEQAVDDLLSQGNKLELA 2183

Query: 90   GAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGG 149
            GAQVE+KKAEPKKPN P P  RRY++ +P +G GFGDAY             G  G   G
Sbjct: 2184 GAQVEIKKAEPKKPNPPVPPSRRYSDSRPGFGGGFGDAYA------------GFGGSSFG 2231

Query: 150  GGGYRSSGAYGVRGGGYG-------GYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYG 202
             G YRS GAYG R   Y        G   G   GG  G GGG+G YRGEP SLGYSGRYG
Sbjct: 2232 NGPYRSGGAYGSRASAYAGYGGSEFGGYGGYGGGGSSGGGGGIGTYRGEPPSLGYSGRYG 2291

Query: 203  G-FNRGYDVTGDYGGLNE 219
            G FNRGYD+ G +GG +E
Sbjct: 2292 GSFNRGYDLGGSHGGPSE 2309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571134|ref|XP_003553735.1| PREDICTED: heterogeneous nuclear ribonucleoprotein A2 homolog 2-like [Glycine max]

 Score =  171 bits (434), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 140/252 (55%), Positives = 166/252 (65%), Gaps = 24/252 (9%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           VTE   DEF+DFF ++G+V++HQIMRDHST+RSRGFGFIT+D+E+AVDDLL+ GNK+E A
Sbjct: 145 VTE---DEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITYDSEEAVDDLLSVGNKIEFA 201

Query: 90  GAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGG 149
           GAQVE+KKAEPKKPN P PS +RYN+ + +YG G              G G+ G GG  G
Sbjct: 202 GAQVEIKKAEPKKPNPPAPSSKRYNDSRSSYGGG-------------YGDGYDGFGGNFG 248

Query: 150 GGGYRSSGAYGVRG--GGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRG 207
            GGYRS GAYG RG  G YGG+  G EFGGYGGY   MG YRG+PS        GG+ RG
Sbjct: 249 MGGYRSGGAYGGRGSAGAYGGF--GSEFGGYGGYASAMGPYRGDPSLGYAGRYGGGYGRG 306

Query: 208 YDVTGDYGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGG 267
                  G    S G     GVGGG       S YD  LG  YGG +GG+F+G+RGGY G
Sbjct: 307 ---YDLGGYGGPSDGYGAYGGVGGGSSGSAYGSSYDASLGGGYGGPAGGSFYGTRGGYAG 363

Query: 268 AGGSSRYHPYGR 279
           A G+ RYHPYGR
Sbjct: 364 A-GTGRYHPYGR 374

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449446702|ref|XP_004141110.1| PREDICTED: LOW QUALITY PROTEIN: nuclear pore membrane glycoprotein 210-like [Cucumis sativus]

 Score =  171 bits (432), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 138/252 (54%), Positives = 163/252 (64%), Gaps = 25/252 (9%)

Query: 36   DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
            DEF+DFFMQ+G V+EHQIMRDHSTSRSRGFGFITF+TEQAVDDLLA GN+LE+AG+QVE+
Sbjct: 2023 DEFRDFFMQYGVVKEHQIMRDHSTSRSRGFGFITFETEQAVDDLLANGNRLEMAGSQVEI 2082

Query: 96   KKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRS 155
            KKAEPKK N P    +R+++ +P+Y   +GDAY             G  GGGG GG +R+
Sbjct: 2083 KKAEPKKANPPPAPSKRFHDSRPSYSGAYGDAY-------------GEFGGGGYGGSFRA 2129

Query: 156  SGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-FNRGYDVTGDY 214
             G YG RGGGYGGYG     G      GGMGAYR +P S+GYS RYG  F+RGYD  G Y
Sbjct: 2130 GGPYGARGGGYGGYGGNDFSGYGMYGTGGMGAYREDP-SMGYSARYGASFSRGYDFRGGY 2188

Query: 215  GGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGG-------SSGGAFFGSRGGYGG 267
            GG +ESYG Y   G    GGY G    YD+G+G+ Y          S G   G      G
Sbjct: 2189 GGPDESYGAYNSGGAPSTGGYAG---SYDMGMGTGYAAGGRGSFYGSRGGGGGGGYDGAG 2245

Query: 268  AGGSSRYHPYGR 279
            +  S RYHPYGR
Sbjct: 2246 SAPSGRYHPYGR 2257

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255560914|ref|XP_002521470.1| RNA binding protein, putative [Ricinus communis] gi|223539369|gb|EEF40960.1| RNA binding protein, putative [Ricinus communis]

 Score =  160 bits (406), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 78/101 (77%), Positives = 86/101 (85%), Gaps = 7/101 (6%)

Query: 28   TPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE 87
            T VTE    EFK+FFMQ+G+V EHQIMRDHST+RSRGFGFITFDTEQAVDDLLAKGNKLE
Sbjct: 2024 TTVTEV---EFKEFFMQYGEVIEHQIMRDHSTNRSRGFGFITFDTEQAVDDLLAKGNKLE 2080

Query: 88   LAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAY 128
            LAG QVE+KKAEPKKPN P PS +RYN+ +P    GFGDAY
Sbjct: 2081 LAGGQVEIKKAEPKKPNPPLPSSKRYNDSRP----GFGDAY 2117

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558851|ref|XP_003547716.1| PREDICTED: RNA-binding protein Musashi homolog Rbp6-like [Glycine max]

 Score =  151 bits (381), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 101/164 (61%), Positives = 121/164 (73%), Gaps = 18/164 (10%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           VTE   DEF+DFF ++G+V++HQIMRDHST+RSRGFGFIT+D+E+AVDDLL+ GNK+E A
Sbjct: 143 VTE---DEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITYDSEEAVDDLLSVGNKIEFA 199

Query: 90  GAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGG 149
           GAQVE+KKAEPKKPN P PS +RYN+ + +YG G              G  + G GG  G
Sbjct: 200 GAQVEIKKAEPKKPNPPAPSSKRYNDSRSSYGGG-------------YGDAYDGFGGNFG 246

Query: 150 GGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPS 193
            GGYRS GAYG RG  YGG+  G EFGGYGGY G MG YRG+PS
Sbjct: 247 MGGYRSGGAYGGRGSAYGGF--GSEFGGYGGYAGAMGPYRGDPS 288

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356513961|ref|XP_003525676.1| PREDICTED: nuclear pore membrane glycoprotein 210-like [Glycine max]

 Score =  148 bits (374), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 125/246 (50%), Positives = 154/246 (62%), Gaps = 21/246 (8%)

Query: 36   DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
            DEF+DFF ++G+V++HQIMRDHST+RSRGFGFITFD+E+AVDDLL+ GNK++ AG+QVE+
Sbjct: 2078 DEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITFDSEEAVDDLLSMGNKIDFAGSQVEI 2137

Query: 96   KKAEPKKPNLPQPSYRRYNN-PKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYR 154
            KKAEPKKP+   PS +R+N+        G+GD Y G+GG    GGG+   G  GGG G  
Sbjct: 2138 KKAEPKKPSSAPPSSKRHNDSRSSYSSGGYGDTYDGFGGSFGMGGGYRSGGAYGGGRGGA 2197

Query: 155  SSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-FNRGYDVTGD 213
              G     G GYGGY   GE G           YRG+  SLGY+GRYGG F+RGYD+ G 
Sbjct: 2198 YGGFGSEFG-GYGGY--AGEMG----------PYRGD-LSLGYAGRYGGNFSRGYDL-GG 2242

Query: 214  YGGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSSR 273
            YGG +E+YG YG  G   GGG            G   G S G  +  SR GY     + R
Sbjct: 2243 YGGPSENYGAYGAGGGSSGGGGAYQSGYDGNLGGGYGGASGGPFYGSSRAGY----SAGR 2298

Query: 274  YHPYGR 279
            YHPYGR
Sbjct: 2299 YHPYGR 2304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|242053621|ref|XP_002455956.1| hypothetical protein SORBIDRAFT_03g027920 [Sorghum bicolor] gi|241927931|gb|EES01076.1| hypothetical protein SORBIDRAFT_03g027920 [Sorghum bicolor]

 Score =  145 bits (367), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/169 (52%), Positives = 110/169 (65%), Gaps = 17/169 (10%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA-KGNKLELAGAQVE 94
           DEFK+FF +FG V EH+I+RDH+T+RSRGFGFI FD E+ VDDLLA KGN ++L G+QVE
Sbjct: 116 DEFKEFFSKFGKVVEHEIIRDHTTNRSRGFGFIVFDAEKTVDDLLAKKGNMIDLNGSQVE 175

Query: 95  VKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYR 154
           +KKAEPKKP+  QP     + P+   G  + D+Y G+G     GG F         G YR
Sbjct: 176 IKKAEPKKPS-NQPPRSLDSEPR---GRPYADSYDGFGSSYNYGGSF---------GPYR 222

Query: 155 SSGAYGVRGGGYGGYGVGGEFG-GYGGYGGGMGAYRGEPSSLGYSGRYG 202
           S G++G R GGY      G++G GY  YGG +  YRGEPS   YS RYG
Sbjct: 223 SPGSFGARPGGYNSASGPGDYGSGYATYGGALVGYRGEPSL--YSSRYG 269

Source: Sorghum bicolor

Species: Sorghum bicolor

Genus: Sorghum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296087606|emb|CBI34862.3| unnamed protein product [Vitis vinifera]

 Score =  144 bits (364), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 88/138 (63%), Positives = 101/138 (73%), Gaps = 15/138 (10%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           VTE   +EFKDFF Q+G+V++HQIMRDHSTSRSRGFGF+TFDTEQAVDDLL++GNKLELA
Sbjct: 140 VTE---EEFKDFFTQYGEVKDHQIMRDHSTSRSRGFGFVTFDTEQAVDDLLSQGNKLELA 196

Query: 90  GAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGG 149
           GAQVE+KKAEPKKPN P P  RRY++ +P +G GFGDAY             G  G   G
Sbjct: 197 GAQVEIKKAEPKKPNPPVPPSRRYSDSRPGFGGGFGDAYA------------GFGGSSFG 244

Query: 150 GGGYRSSGAYGVRGGGYG 167
            G YRS GAYG R   Y 
Sbjct: 245 NGPYRSGGAYGSRASAYA 262

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|363807276|ref|NP_001242362.1| uncharacterized protein LOC100793209 [Glycine max] gi|255636483|gb|ACU18580.1| unknown [Glycine max]

 Score =  142 bits (359), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 111/193 (57%), Positives = 138/193 (71%), Gaps = 19/193 (9%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           VTE   DEF+DFF ++G+V++HQIMRDHST+RSRGFGFITF++E+AVDDLL+ GNK++ A
Sbjct: 141 VTE---DEFRDFFTRYGEVKDHQIMRDHSTNRSRGFGFITFESEEAVDDLLSMGNKIDFA 197

Query: 90  GAQVEVKKAEPKKPNLPQPSYRRYNN-PKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGG 148
           GAQVE+KKAEPKKPN   PS +RYN+        G+GDAY G+GG    GGG+   G  G
Sbjct: 198 GAQVEIKKAEPKKPNSAPPSSKRYNDSRSSYSSGGYGDAYDGFGGSFGMGGGYRSGGAYG 257

Query: 149 GGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGG-FNRG 207
           GG G  + G +              EFGGYGGY G MG YRG+P SLGY+GRYGG F+RG
Sbjct: 258 GGRGSGAYGGH------------ASEFGGYGGYAGAMGPYRGDP-SLGYAGRYGGSFSRG 304

Query: 208 YDVTGDYGGLNES 220
           YD+ G YGG +E+
Sbjct: 305 YDLGG-YGGPSEN 316

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	279
TAIR|locus:2168848	423	AT5G40490 [Arabidopsis thalian	0.272	0.179	0.714	4e-35
TAIR|locus:504955752	358	AT3G13224 [Arabidopsis thalian	0.297	0.231	0.590	5.2e-29
TAIR|locus:2007903	369	AT1G17640 [Arabidopsis thalian	0.351	0.265	0.475	3.2e-20
TAIR|locus:2077392	495	AT3G07810 [Arabidopsis thalian	0.268	0.151	0.5	1.1e-15
TAIR|locus:2133862	455	AT4G26650 [Arabidopsis thalian	0.258	0.158	0.506	2e-14
TAIR|locus:2173967	460	AT5G55550 [Arabidopsis thalian	0.236	0.143	0.537	5.7e-14
FB|FBgn0263396	344	sqd "squid" [Drosophila melano	0.261	0.212	0.472	8e-14
TAIR|locus:2129590	411	AT4G14300 [Arabidopsis thalian	0.243	0.165	0.492	2.1e-13
TAIR|locus:2050992	404	AT2G33410 [Arabidopsis thalian	0.254	0.175	0.5	4.3e-13
FB|FBgn0004838	421	Hrb27C "Heterogeneous nuclear	0.229	0.152	0.415	1.8e-12

TAIR|locus:2168848 AT5G40490 [Arabidopsis thaliana (taxid:3702)]

 Score = 301 (111.0 bits), Expect = 4.0e-35, Sum P(3) = 4.0e-35
 Identities = 55/77 (71%), Positives = 68/77 (88%)

Query:    36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
             DEFK+FFMQFG+++EHQIMRDHST RSRGFGF+T+++E  VD LLAKGN++EL+G QVE+
Sbjct:   144 DEFKEFFMQFGELKEHQIMRDHSTGRSRGFGFVTYESEDMVDHLLAKGNRIELSGTQVEI 203

Query:    96 KKAEPKKPN-LPQPSYR 111
             KKAEPKKPN +  PS R
Sbjct:   204 KKAEPKKPNSVTTPSKR 220

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:0005829 "cytosol" evidence=IDA

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

 Score = 264 (98.0 bits), Expect = 5.2e-29, Sum P(3) = 5.2e-29
 Identities = 52/88 (59%), Positives = 68/88 (77%)

Query:    24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
             G+  T VTE   DE KDFF ++G+V EHQ++RDH T+RSRGFGF+ FD+E+ VD+LL+KG
Sbjct:   115 GIPST-VTE---DELKDFFAKYGNVVEHQVIRDHETNRSRGFGFVIFDSEEVVDELLSKG 170

Query:    84 NKLELAGAQVEVKKAEPKKP-NLPQPSY 110
             N +++A  QVE+KKAEPKK  N   PSY
Sbjct:   171 NMIDMADTQVEIKKAEPKKSLNRSPPSY 198

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2007903 AT1G17640 [Arabidopsis thaliana (taxid:3702)]

 Score = 223 (83.6 bits), Expect = 3.2e-20, Sum P(2) = 3.2e-20
 Identities = 48/101 (47%), Positives = 63/101 (62%)

Query:    13 INRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT 72
             I   + T+K+    L P+ E   DE K++F  +GD+ EHQIM DH T RSRGFGF+TF T
Sbjct:   150 IKAVSKTRKIFVGGLPPLLEE--DELKNYFCVYGDIIEHQIMYDHHTGRSRGFGFVTFQT 207

Query:    73 EQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRY 113
             E +VD L + G   EL   QVE+K+AEPK+      S+R Y
Sbjct:   208 EDSVDRLFSDGKVHELGDKQVEIKRAEPKRTGRDN-SFRSY 247

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 172 (65.6 bits), Expect = 1.1e-15, Sum P(3) = 1.1e-15
 Identities = 40/80 (50%), Positives = 53/80 (66%)

Query:    30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
             VTE    +FK +F QFG   +  +M DH+T R RGFGFIT+D+E+AV+ +L K    EL 
Sbjct:   119 VTE---SDFKTYFEQFGTTTDVVVMYDHNTQRPRGFGFITYDSEEAVEKVLLKTFH-ELN 174

Query:    90 GAQVEVKKAEPKKPNLPQPS 109
             G  VEVK+A PK+ + P PS
Sbjct:   175 GKMVEVKRAVPKELS-PGPS 193

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005576 "extracellular region" evidence=ISM

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

 Score = 176 (67.0 bits), Expect = 2.0e-14, Sum P(2) = 2.0e-14
 Identities = 37/73 (50%), Positives = 51/73 (69%)

Query:    37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
             EFK++F QFG + +  +M DH+T R RGFGFITFD+E++VD +L K    EL G  VEVK
Sbjct:   137 EFKNYFDQFGTIADVVVMYDHNTQRPRGFGFITFDSEESVDMVLHKTFH-ELNGKMVEVK 195

Query:    97 KAEPKKPNLPQPS 109
             +A PK+ +   P+
Sbjct:   196 RAVPKELSSTTPN 208

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

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

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

 Score = 173 (66.0 bits), Expect = 5.7e-14, Sum P(2) = 5.7e-14
 Identities = 36/67 (53%), Positives = 48/67 (71%)

Query:    36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
             +EFK++F QFG + +  +M DH+T R RGFGFITFD++ AVD +L K    EL G  VEV
Sbjct:   124 EEFKNYFDQFGTIADVVVMYDHNTQRPRGFGFITFDSDDAVDRVLHKTFH-ELNGKLVEV 182

Query:    96 KKAEPKK 102
             K+A PK+
Sbjct:   183 KRAVPKE 189

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

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

 Score = 159 (61.0 bits), Expect = 8.0e-14, Sum P(2) = 8.0e-14
 Identities = 35/74 (47%), Positives = 50/74 (67%)

Query:    31 TEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG 90
             TE + +E K +F QFG++ E ++  D   S+ +GF FITFD+EQ V DLL K  K ++AG
Sbjct:   145 TEISDEEIKTYFGQFGNIVEVEMPFDKQKSQRKGFCFITFDSEQVVTDLL-KTPKQKIAG 203

Query:    91 AQVEVKKAEPKKPN 104
              +V+VK+A PK  N
Sbjct:   204 KEVDVKRATPKPEN 217

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

GO:0005730 "nucleolus" evidence=IDA

GO:0005703 "polytene chromosome puff" evidence=IDA

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

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

GO:0048477 "oogenesis" evidence=IMP;TAS

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

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

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

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

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

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

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

GO:0035062 "omega speckle" evidence=IDA

GO:0000785 "chromatin" evidence=IDA

GO:0005737 "cytoplasm" evidence=TAS

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

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

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

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

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

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

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

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

GO:0071011 "precatalytic spliceosome" evidence=IDA

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

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

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

TAIR|locus:2129590 AT4G14300 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.1e-13, Sum P(2) = 2.1e-13
 Identities = 34/69 (49%), Positives = 48/69 (69%)

Query:    36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
             +EF+ +F  +G V +  IM D +T+R RGFGF++FD+E AVD +L K    +L+G QVEV
Sbjct:   124 EEFRQYFEVYGPVTDVAIMYDQATNRPRGFGFVSFDSEDAVDSVLHKTFH-DLSGKQVEV 182

Query:    96 KKAEPKKPN 104
             K+A PK  N
Sbjct:   183 KRALPKDAN 191

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:0005829 "cytosol" evidence=RCA

TAIR|locus:2050992 AT2G33410 [Arabidopsis thaliana (taxid:3702)]

 Score = 161 (61.7 bits), Expect = 4.3e-13, Sum P(2) = 4.3e-13
 Identities = 37/74 (50%), Positives = 49/74 (66%)

Query:    33 PAL--DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG 90
             PAL  DEF+ +F  +G V +  IM D +T R RGFGF++FD+E +VD +L K    +L G
Sbjct:   119 PALTSDEFRAYFETYGPVSDAVIMIDQTTQRPRGFGFVSFDSEDSVDLVLHKTFH-DLNG 177

Query:    91 AQVEVKKAEPKKPN 104
              QVEVK+A PK  N
Sbjct:   178 KQVEVKRALPKDAN 191

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

FB|FBgn0004838 Hrb27C "Heterogeneous nuclear ribonucleoprotein at 27C" [Drosophila melanogaster (taxid:7227)]

 Score = 135 (52.6 bits), Expect = 1.8e-12, Sum P(3) = 1.8e-12
 Identities = 27/65 (41%), Positives = 42/65 (64%)

Query:    37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
             + + FF ++G V E  IM D    +SRGFGF++F+ E +V+ +  +   + L G QVE+K
Sbjct:   111 DLRTFFNRYGKVTEVVIMYDQEKKKSRGFGFLSFEEESSVEHVTNE-RYINLNGKQVEIK 169

Query:    97 KAEPK 101
             KAEP+
Sbjct:   170 KAEPR 174

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

GO:0005730 "nucleolus" evidence=IDA

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0005654 "nucleoplasm" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006397 "mRNA processing" evidence=ISS

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

GO:0048027 "mRNA 5'-UTR binding" evidence=NAS;TAS

GO:0007319 "negative regulation of oskar mRNA translation" evidence=TAS

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

GO:0007317 "regulation of pole plasm oskar mRNA localization" evidence=IMP

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0048024 "regulation of mRNA splicing, via spliceosome" evidence=IMP

GO:0007298 "border follicle cell migration" evidence=IMP

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

GO:0043234 "protein complex" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0007411 "axon guidance" evidence=IMP

GO:0046331 "lateral inhibition" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	279
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	8e-21
cd12327	80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-21
cd12329	75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	3e-15
cd12323	74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	1e-13
smart00360	73	smart00360, RRM, RNA recognition motif	1e-12
cd12576	75	cd12576, RRM1_MSI, RNA recognition motif 1 in RNA-	1e-12
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	4e-12
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-11
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	2e-11
cd12577	76	cd12577, RRM1_Hrp1p, RNA recognition motif 1 in ye	4e-11
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	5e-11
cd12321	77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	5e-11
cd12759	77	cd12759, RRM1_MSI1, RNA recognition motif 1 in RNA	2e-10
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-10
cd12573	79	cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA	5e-10
cd12760	76	cd12760, RRM1_MSI2, RNA recognition motif 1 in RNA	6e-10
cd12578	78	cd12578, RRM1_hnRNPA_like, RNA recognition motif 1	6e-10
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	9e-10
cd12326	79	cd12326, RRM1_hnRNPA0, RNA recognition motif 1 fou	3e-09
cd12572	74	cd12572, RRM2_MSI1, RNA recognition motif 2 in RNA	4e-09
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	6e-09
cd12582	80	cd12582, RRM2_hnRNPA3, RNA recognition motif 2 in	8e-09
cd12674	79	cd12674, RRM1_Nop4p, RNA recognition motif 1 in ye	1e-08
cd12229	81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	1e-08
cd12412	80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-08
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	2e-08
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	3e-08
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	5e-08
cd12757	75	cd12757, RRM1_hnRNPAB, RNA recognition motif 1 in	6e-08
cd12580	77	cd12580, RRM2_hnRNPA1, RNA recognition motif 2 in	6e-08
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-08
cd12371	77	cd12371, RRM2_PUF60, RNA recognition motif 2 in (U	7e-08
cd12328	73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	9e-08
cd12449	80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	1e-07
cd12574	82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	1e-07
cd12415	82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	2e-07
cd12235	83	cd12235, RRM_PPIL4, RNA recognition motif in pepti	2e-07
cd12579	80	cd12579, RRM2_hnRNPA0, RNA recognition motif 2 in	7e-07
cd12242	73	cd12242, RRM_SLIRP, RNA recognition motif found in	9e-07
cd12763	81	cd12763, RRM1_hnRNPA3, RNA recognition motif 1 in	9e-07
cd12322	71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	1e-06
PLN03134	144	PLN03134, PLN03134, glycine-rich RNA-binding prote	1e-06
cd12316	74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	1e-06
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	1e-06
cd12361	77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	1e-06
cd12384	76	cd12384, RRM_RBM24_RBM38_like, RNA recognition mot	2e-06
cd12552	77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-06
cd12772	84	cd12772, RRM1_HuC, RNA recognition motif 1 in vert	2e-06
cd12363	78	cd12363, RRM_TRA2, RNA recognition motif in transf	2e-06
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	2e-06
cd12237	93	cd12237, RRM_snRNP35, RNA recognition motif found	2e-06
cd12673	81	cd12673, RRM_BOULE, RNA recognition motif in prote	3e-06
cd12761	81	cd12761, RRM1_hnRNPA1, RNA recognition motif 1 in	3e-06
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	3e-06
cd12762	81	cd12762, RRM1_hnRNPA2B1, RNA recognition motif 1 i	4e-06
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	4e-06
cd12408	77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-06
cd12756	74	cd12756, RRM1_hnRNPD, RNA recognition motif 1 in h	5e-06
cd12575	74	cd12575, RRM1_hnRNPD_like, RNA recognition motif 1	6e-06
TIGR01645	612	TIGR01645, half-pint, poly-U binding splicing fact	6e-06
cd12584	80	cd12584, RRM2_hnRNPAB, RNA recognition motif 2 in	9e-06
cd12335	83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	1e-05
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	2e-05
cd12581	80	cd12581, RRM2_hnRNPA2B1, RNA recognition motif 2 i	2e-05
cd12367	74	cd12367, RRM2_RBM45, RNA recognition motif 2 in RN	2e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	2e-05
cd12362	73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	3e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	4e-05
cd12758	76	cd12758, RRM1_hnRPDL, RNA recognition motif 1 in h	4e-05
cd12366	81	cd12366, RRM1_RBM45, RNA recognition motif 1 in RN	5e-05
cd12583	75	cd12583, RRM2_hnRNPD, RNA recognition motif 2 in h	6e-05
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	7e-05
cd12311	73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	8e-05
cd12313	84	cd12313, RRM1_RRM2_RBM5_like, RNA recognition moti	9e-05
cd12769	81	cd12769, RRM1_HuR, RNA recognition motif 1 in vert	9e-05
cd12458	70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	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	1e-04
cd12414	76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	1e-04
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	1e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	2e-04
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-04
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	2e-04
cd12649	81	cd12649, RRM1_SXL, RNA recognition motif 1 in Dros	2e-04
PRK14279	392	PRK14279, PRK14279, chaperone protein DnaJ; Provis	3e-04
cd12376	79	cd12376, RRM2_Hu_like, RNA recognition motif 2 in	3e-04
pfam11456	102	pfam11456, DUF3019, Protein of unknown function (D	3e-04
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	3e-04
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	4e-04
TIGR01642	509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	4e-04
cd12641	89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	4e-04
PLN03138	796	PLN03138, PLN03138, Protein TOC75; Provisional	4e-04
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	5e-04
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	5e-04
PRK07772	186	PRK07772, PRK07772, single-stranded DNA-binding pr	5e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-04
cd12251	72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	7e-04
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-04
PTZ00146	293	PTZ00146, PTZ00146, fibrillarin; Provisional	0.001
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	0.001
cd12652	79	cd12652, RRM2_Hu, RNA recognition motif 2 in the H	0.001
cd12307	74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	0.001
cd12638	92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.001
cd12383	83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	0.001
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.002
pfam07466	280	pfam07466, DUF1517, Protein of unknown function (D	0.002
cd12312	84	cd12312, RRM_SRSF10_SRSF12, RNA recognition motif	0.002
COG4371	334	COG4371, COG4371, Predicted membrane protein [Func	0.002
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	0.002
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	0.003
PRK07772	186	PRK07772, PRK07772, single-stranded DNA-binding pr	0.003
PRK06958	182	PRK06958, PRK06958, single-stranded DNA-binding pr	0.003
cd12753	85	cd12753, RRM1_RBM10, RNA recognition motif 1 in ve	0.003
cd12464	83	cd12464, RRM_G3BP2, RNA recognition motif in ras G	0.003
cd12463	80	cd12463, RRM_G3BP1, RNA recognition motif found in	0.003
cd12651	79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	0.003
cd12585	75	cd12585, RRM2_hnRPDL, RNA recognition motif 2 in h	0.003
cd12566	79	cd12566, RRM2_MRD1, RNA recognition motif 2 in yea	0.003
cd12631	84	cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif	0.003
pfam12810	248	pfam12810, Gly_rich, Glycine rich protein	0.003
cd12676	107	cd12676, RRM3_Nop4p, RNA recognition motif 3 in ye	0.003
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	0.004
pfam05918	543	pfam05918, API5, Apoptosis inhibitory protein 5 (A	0.004
COG4907	595	COG4907, COG4907, Predicted membrane protein [Func	0.004
cd12387	72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	0.004
cd12291	72	cd12291, RRM1_La, RNA recognition motif 1 in La au	0.004

>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 = 83.6 bits (207), Expect = 8e-21
 Identities = 37/63 (58%), Positives = 49/63 (77%), Gaps = 1/63 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          +EFK++F QFG V + Q+M+DH T RSRGFGF+TFD+E AV+ + + G  LEL G QVEV
Sbjct: 14 EEFKEYFSQFGKVVDAQLMQDHDTGRSRGFGFVTFDSESAVERVFSAG-MLELGGKQVEV 72

Query: 96 KKA 98
          K+A
Sbjct: 73 KRA 75

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

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

 Score = 83.6 bits (207), Expect = 8e-21
 Identities = 32/71 (45%), Positives = 46/71 (64%), Gaps = 4/71 (5%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           VTE    + + +F QFG V E  +M DH   R RGFGFITF++E +VD ++ +    ++ 
Sbjct: 14  VTE---TDLRKYFSQFGTVTEVVVMYDHEKKRPRGFGFITFESEDSVDQVVNEHFH-DIN 69

Query: 90  GAQVEVKKAEP 100
           G +VEVK+AEP
Sbjct: 70  GKKVEVKRAEP 80

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

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

 Score = 68.5 bits (168), Expect = 3e-15
 Identities = 28/75 (37%), Positives = 46/75 (61%), Gaps = 5/75 (6%)

Query: 24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
          GLS     E   ++ +++F +FG++ E ++  D  T++ RGF FITFD+E+ V  +L + 
Sbjct: 6  GLS----PETTEEKIREYFGKFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKKIL-ET 60

Query: 84 NKLELAGAQVEVKKA 98
              + G +VEVKKA
Sbjct: 61 QFHVIGGKKVEVKKA 75

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

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

 Score = 64.4 bits (157), Expect = 1e-13
 Identities = 31/74 (41%), Positives = 44/74 (59%), Gaps = 5/74 (6%)

Query: 24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
          GLS    TE   D+ K +F QFG V++  +M D  T+R RGFGF+TF++E  VD  + + 
Sbjct: 6  GLS-ANTTE---DDVKKYFSQFGKVEDAMLMFDKQTNRHRGFGFVTFESEDVVDK-VCEI 60

Query: 84 NKLELAGAQVEVKK 97
          +  E+    VE KK
Sbjct: 61 HFHEINNKMVECKK 74

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

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

 Score = 61.8 bits (151), Expect = 1e-12
 Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 3/66 (4%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           TE   +E ++ F +FG V+  +++RD  T +S+GF F+ F++E+  +  L   N  EL 
Sbjct: 11 TTE---EELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEALNGKELD 67

Query: 90 GAQVEV 95
          G  ++V
Sbjct: 68 GRPLKV 73

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 = 61.7 bits (150), Expect = 1e-12
 Identities = 36/91 (39%), Positives = 50/91 (54%), Gaps = 19/91 (20%)

Query: 11  MFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 70
           MFI          GLS     E      +++F +FG+++E  +MRD +T RSRGFGF+TF
Sbjct: 1   MFIG---------GLSWQTTAE----GLREYFSKFGEIKECMVMRDPTTKRSRGFGFVTF 47

Query: 71  DTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 101
               +VD +LA+G   EL G     KK +PK
Sbjct: 48  SDPASVDKVLAQG-PHELDG-----KKIDPK 72

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

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

 Score = 59.9 bits (146), Expect = 4e-12
 Identities = 23/65 (35%), Positives = 37/65 (56%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++ KD F QFG+V   +++ D  T RSRGFGF+  +T +  +  + K N  +  G  + V
Sbjct: 14  EDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEKLNGTDFGGRTLTV 73

Query: 96  KKAEP 100
            +A P
Sbjct: 74  NEARP 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|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 = 58.8 bits (143), Expect = 1e-11
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 4/76 (5%)

Query: 23 TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 82
          +GLS    TE  L   +  F +FG V+E  +M+D  T  SRGFGF+TF++ +  D  +  
Sbjct: 7  SGLSTR-TTEKEL---EALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIRD 62

Query: 83 GNKLELAGAQVEVKKA 98
           N  EL G  ++V+KA
Sbjct: 63 LNGKELEGRVIKVEKA 78

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

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 23/61 (37%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          +  +++F ++G+V +  IM+D  T RSRGFGF+TF    +VD +LA    + L G +++ 
Sbjct: 13 ESLREYFSKYGEVVDCVIMKDPITGRSRGFGFVTFADPSSVDKVLAAKPHV-LDGREIDP 71

Query: 96 K 96
          K
Sbjct: 72 K 72

This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. . Length = 72

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

 Score = 57.6 bits (139), Expect = 4e-11
 Identities = 26/66 (39%), Positives = 46/66 (69%), Gaps = 2/66 (3%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D  +++F QFG+V +  +MRD +T RSRGFGF+TF   ++V++++ K + L+  G  ++ 
Sbjct: 13  DSLREYFGQFGEVTDCTVMRDSATGRSRGFGFLTFKKPKSVNEVMKKEHILD--GKIIDP 70

Query: 96  KKAEPK 101
           K+A P+
Sbjct: 71  KRAIPR 76

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

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

 Score = 61.9 bits (149), Expect = 5e-11
 Identities = 29/111 (26%), Positives = 54/111 (48%), Gaps = 4/111 (3%)

Query: 14  NRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 73
             +  T  +  L    VTE   ++ ++ F +FG V+  +++RD  T +SRGF F+ F++E
Sbjct: 112 KEENNTLFVGNLPYD-VTE---EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESE 167

Query: 74  QAVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNPKPAYGSGF 124
           ++ +  + + N  EL G  + V+KA+P      + S     +       G 
Sbjct: 168 ESAEKAIEELNGKELEGRPLRVQKAQPASQPRSELSNNLDASFAKKLSRGK 218

Length = 306

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

 Score = 57.4 bits (139), Expect = 5e-11
 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
            + KD+F  FG++   Q+ +D  T +S+GFGF+ F   +    +L++ + ++  G   +V
Sbjct: 14  QDLKDYFSTFGELLMVQVKKDPKTGQSKGFGFVRFADYEDQVKVLSQRHMID--GRWCDV 71

Query: 96  KKAEPK 101
           K    K
Sbjct: 72  KIPNSK 77

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

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

 Score = 55.8 bits (134), Expect = 2e-10
 Identities = 27/61 (44%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 38 FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
           +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+ ++ EL    ++ K 
Sbjct: 17 LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKV 75

Query: 98 A 98
          A
Sbjct: 76 A 76

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

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

 Score = 55.0 bits (133), Expect = 3e-10
 Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 4/67 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           TE   ++ ++ F +FG+++  +I+RD    +S+GF F+ F++ +  +  L   N  EL 
Sbjct: 10 TTE---EDLRELFSKFGEIESVRIVRD-KDGKSKGFAFVEFESPEDAEKALEALNGKELD 65

Query: 90 GAQVEVK 96
          G +++V 
Sbjct: 66 GRKLKVS 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|241017 cd12573, RRM2_MSI2, RNA recognition motif 2 in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins

 Score = 54.7 bits (131), Expect = 5e-10
 Identities = 33/84 (39%), Positives = 49/84 (58%), Gaps = 7/84 (8%)

Query: 17 TTTQKM--TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 74
          T T+K+   GLS   V E    + K +F QFG V++  +M D +T+R RGFGF+TF+ E 
Sbjct: 1  TRTKKIFVGGLSANTVVE----DVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENED 56

Query: 75 AVDDLLAKGNKLELAGAQVEVKKA 98
           V+  + + +  E+    VE KKA
Sbjct: 57 VVEK-VCEIHFHEINNKMVECKKA 79

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

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

 Score = 54.3 bits (130), Expect = 6e-10
 Identities = 23/47 (48%), Positives = 35/47 (74%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 82
          D  +D+F +FG+++E  +MRD +T RSRGFGF+TF    +VD +LA+
Sbjct: 14 DSLRDYFSKFGEIRECMVMRDPTTKRSRGFGFVTFADPASVDKVLAQ 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 = 76

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

 Score = 54.3 bits (131), Expect = 6e-10
 Identities = 27/67 (40%), Positives = 46/67 (68%), Gaps = 3/67 (4%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-AKGNKLELAGAQVE 94
           D  K++F Q+G++ +  +M+D +T RSRGFGF+TF +   VD  + A+ +K++  G +VE
Sbjct: 14  DSLKNYFSQWGEITDCVVMKDPNTKRSRGFGFVTFASASEVDAAMNARPHKVD--GREVE 71

Query: 95  VKKAEPK 101
            K+A P+
Sbjct: 72  PKRAVPR 78

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

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

 Score = 53.8 bits (130), Expect = 9e-10
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 3/68 (4%)

Query: 28 TPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE 87
            +TE   D+ +  F  FG+++  Q+ RD  T RS+G+GFI F   +     L + N  E
Sbjct: 8  FNITE---DDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLNGFE 64

Query: 88 LAGAQVEV 95
          LAG  ++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|240772 cd12326, RRM1_hnRNPA0, RNA recognition motif 1 found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins

 Score = 52.1 bits (125), Expect = 3e-09
 Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-AKGNKLELAGAQVE 94
             +  F ++G + E  +M D +T RSRGFGFITF +    D+ + A+ + ++  G Q+E
Sbjct: 17 SGLRRHFTRYGKLTECVVMVDPNTKRSRGFGFITFSSADEADEAMEAQPHSID--GNQIE 74

Query: 95 VKKA 98
          +K+A
Sbjct: 75 LKRA 78

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

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

 Score = 51.9 bits (124), Expect = 4e-09
 Identities = 28/74 (37%), Positives = 43/74 (58%), Gaps = 5/74 (6%)

Query: 24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
          GLS+    E    + K +F QFG V +  +M D +T+R RGFGF+TF++E  V+  + + 
Sbjct: 6  GLSVNTTVE----DVKQYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60

Query: 84 NKLELAGAQVEVKK 97
          +  E+    VE KK
Sbjct: 61 HFHEINNKMVECKK 74

This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. . Length = 74

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

 Score = 51.0 bits (123), Expect = 6e-09
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 6/73 (8%)

Query: 22 MTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 81
          +  L  + VTE   ++ ++FF  +G V+  +++R+    R RGF F+ F + +  +  L 
Sbjct: 3  VRNLPPS-VTE---EDLREFFSPYGKVEGVRLVRN--KDRPRGFAFVEFASPEDAEAALK 56

Query: 82 KGNKLELAGAQVE 94
          K N L L G  + 
Sbjct: 57 KLNGLVLDGRTLR 69

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

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

 Score = 51.1 bits (122), Expect = 8e-09
 Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F ++G ++  ++M D  + + RGF F+TFD    VD ++ +     + G   EVKK
Sbjct: 17  LRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYH-TINGHNCEVKK 75

Query: 98  AEPKK 102
           A  K+
Sbjct: 76  ALSKQ 80

This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 19/66 (28%), Positives = 33/66 (50%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++  DFF     ++   ++ D  T  SRG+GF+TF   +   + LAK    +L G  + +
Sbjct: 14  EDLTDFFSDVAPIKHAVVVTDPETGESRGYGFVTFAMLEDAQEALAKLKNKKLHGRILRL 73

Query: 96  KKAEPK 101
             AE +
Sbjct: 74  DIAERR 79

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

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

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 20/47 (42%), Positives = 27/47 (57%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 82
          DE K+FF +FG+V E +I       R   FGF+ FD  +AV  +LA 
Sbjct: 18 DELKEFFKEFGNVLEVRINSKGGGGRLPNFGFVVFDDPEAVQKILAN 64

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

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

 Score = 54.9 bits (132), Expect = 1e-08
 Identities = 35/144 (24%), Positives = 51/144 (35%), Gaps = 14/144 (9%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVDDLLAKGNKLELAGAQVE 94
            E +  F  FGD+++ Q+ RD  T RS+GFGFI F D E+A + L    N  ELAG  ++
Sbjct: 201 QELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVM-NGFELAGRPIK 259

Query: 95  VKKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGF---GGSGGGGGGG 151
           V  A+     L         +    +         G                   G GG 
Sbjct: 260 VGYAQDSTYLL---------DAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGL 310

Query: 152 GYRSSGAYGVRGGGYGGYGVGGEF 175
               +G+           G+    
Sbjct: 311 LIPGTGSKIALMQKLQRDGIIDPN 334

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

 Score = 50.0 bits (120), Expect = 2e-08
 Identities = 23/62 (37%), Positives = 40/62 (64%), Gaps = 2/62 (3%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          E +DFF +FG V++ +I+ D     S+G+GF+TF+T++  + +LA GN L   G ++ + 
Sbjct: 18 ELRDFFSRFGSVKDVKIITDR-AGVSKGYGFVTFETQEDAEKILAMGN-LNFRGKKLNIG 75

Query: 97 KA 98
           A
Sbjct: 76 PA 77

This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. . Length = 80

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

 Score = 49.5 bits (119), Expect = 2e-08
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)

Query: 27 LTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 85
          L P  TE   ++ KD F +FG ++  +I+RD  T RS+GF F+ F+ E+  +  L   N 
Sbjct: 6  LPPDTTE---EDLKDLFSKFGPIESIRIVRD-ETGRSKGFAFVEFEDEEDAEKALEALNG 61

Query: 86 LELAGAQVE 94
           EL G ++ 
Sbjct: 62 KELGGRELR 70

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

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

 Score = 49.5 bits (119), Expect = 3e-08
 Identities = 17/66 (25%), Positives = 38/66 (57%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++ ++FF + G ++   +++D  + + RGFG++TF  E+     L +  K +  G ++ V
Sbjct: 14  EQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEEKKKTKFGGRKIHV 73

Query: 96  KKAEPK 101
           + A+ K
Sbjct: 74  EFAKKK 79

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

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

 Score = 48.3 bits (116), Expect = 5e-08
 Identities = 14/61 (22%), Positives = 28/61 (45%), Gaps = 5/61 (8%)

Query: 38 FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
              F  FG+V++ ++++        GF F+ F TE+A +  +   N +   G  + V  
Sbjct: 1  LYKLFSPFGNVEKIKLLKKK-----PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDY 55

Query: 98 A 98
          +
Sbjct: 56 S 56

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

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

 Score = 48.8 bits (116), Expect = 6e-08
 Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 1/62 (1%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          + KD+F +FG+V +  I  D +T RSRGFGFI F    +V+ +L +  +  L G  ++ K
Sbjct: 15 DLKDYFTKFGEVTDCTIKMDPNTGRSRGFGFILFKDASSVEKVLEQ-KEHRLDGRLIDPK 73

Query: 97 KA 98
          KA
Sbjct: 74 KA 75

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

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

 Score = 48.8 bits (116), Expect = 6e-08
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 1/63 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
             +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV
Sbjct: 15 HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEV 73

Query: 96 KKA 98
          +KA
Sbjct: 74 RKA 76

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

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

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 20/70 (28%), Positives = 42/70 (60%), Gaps = 9/70 (12%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDLLAKGNKLELAGA 91
           ++ K+ F ++G +   ++M+D    +S+GFGF+ F+     ++AV++L    N  E+ G 
Sbjct: 16  EKLKELFGKYGKITSAKVMKDDE-GKSKGFGFVNFENHEAAQKAVEEL----NGKEVNGK 70

Query: 92  QVEVKKAEPK 101
           ++ V +A+ K
Sbjct: 71  KLYVGRAQKK 80

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

>gnl|CDD|240817 cd12371, RRM2_PUF60, RNA recognition motif 2 in (U)-binding-splicing factor PUF60 and similar proteins

 Score = 48.4 bits (116), Expect = 7e-08
 Identities = 21/63 (33%), Positives = 34/63 (53%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          D+ K  F  FG ++   +  D  T + +G+GFI ++  Q+  D +A  N  +L G Q+ V
Sbjct: 15 DDIKSVFEAFGKIKSCSLAPDPETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQQLRV 74

Query: 96 KKA 98
           KA
Sbjct: 75 GKA 77

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

 Score = 48.0 bits (115), Expect = 9e-08
 Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          ++ +++F Q+G+V+  +I+ D  T + RGF F+TFD    VD ++ +     + G +VEV
Sbjct: 14 EDLREYFSQYGNVESVEIVTDKETGKKRGFAFVTFDDYDPVDKIVLQKYHT-INGHRVEV 72

Query: 96 K 96
          K
Sbjct: 73 K 73

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

>gnl|CDD|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 = 48.3 bits (115), Expect = 1e-07
 Identities = 20/63 (31%), Positives = 33/63 (52%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
             +  F ++G + E  +++D  T RSRGFGF+TF+      D +   N   + G Q+ V
Sbjct: 15 QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMNGKSVDGRQIRV 74

Query: 96 KKA 98
           +A
Sbjct: 75 DQA 77

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

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

 Score = 48.3 bits (115), Expect = 1e-07
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           +  + +F Q+G+V +  IM+D +T+RSRGFGF+ F     V  +LA G    L G  ++ 
Sbjct: 14  ETLRRYFSQYGEVVDCVIMKDKTTNRSRGFGFVKFKDPNCVGTVLAGGPHT-LDGRTIDP 72

Query: 96  KKAEPK 101
           K   P+
Sbjct: 73  KPCTPR 78

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

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

 Score = 47.6 bits (114), Expect = 2e-07
 Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-----LELAG 90
          +E K+ F QFG+V+  +I++D  T  S+G  F+ F T+++    L   +      L L G
Sbjct: 15 EELKELFSQFGEVKYARIVKDKLTGHSKGTAFVKFKTKESAQKCLEAADNAEDSGLSLDG 74

Query: 91 AQVEVKKA 98
           ++ V  A
Sbjct: 75 RRLIVTLA 82

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 2/49 (4%)

Query: 27 LTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQA 75
          L PVT    ++ +  F +FG ++  +++RD  T  S  + FI F+T++ 
Sbjct: 11 LNPVTTD--EDLEIIFSRFGKIKSCEVIRDKKTGDSLQYAFIEFETKED 57

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

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

 Score = 45.7 bits (108), Expect = 7e-07
 Identities = 24/64 (37%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 40  DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDD-LLAKGNKLELAGAQVEVKKA 98
           + F QFG V++ +++ D  T + RGFGF+ F    + D   + K + +   G +VEVKKA
Sbjct: 18  EHFSQFGPVEKAEVIADKQTGKKRGFGFVYFQNHDSADKAAVVKFHPIN--GHRVEVKKA 75

Query: 99  EPKK 102
            PK+
Sbjct: 76  VPKE 79

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

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

 Score = 45.4 bits (108), Expect = 9e-07
 Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          E K++F QFG V+   +  D  T  S+G+GF++F +   +++ L K  K  L G +++V+
Sbjct: 15 ELKEYFSQFGKVKSCNVPFDKETGLSKGYGFVSFSSRDGLENALQK-QKHILEGNKLQVQ 73

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

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

 Score = 45.5 bits (107), Expect = 9e-07
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 32 EPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVD-DLLAKGNKLELAG 90
          E   D  ++ F ++G + +  +MRD  T RSRGFGF+T+   + VD  + A+ +K++  G
Sbjct: 13 ETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMSARPHKVD--G 70

Query: 91 AQVEVKKA 98
            VE K+A
Sbjct: 71 RVVEPKRA 78

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

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

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 7/64 (10%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          ++ + +F QFG+V +  I +       R F F+TF   +    L   G    + G  V V
Sbjct: 15 EDLRQYFSQFGEVTDVYIPKPF-----RAFAFVTFADPEVAQSLC--GEDHIIKGVSVHV 67

Query: 96 KKAE 99
            AE
Sbjct: 68 SNAE 71

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

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

 Score = 47.0 bits (111), Expect = 1e-06
 Identities = 38/104 (36%), Positives = 54/104 (51%), Gaps = 10/104 (9%)

Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D F  FGDV + +++ D  T RSRGFGF+ F+ E A    +++ +  EL G  + V  
Sbjct: 51  LRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP 110

Query: 98  AEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGF 141
           A   +P+ P+             G G+    GGYGGGG  GGGF
Sbjct: 111 AN-DRPSAPRAYGG---------GGGYSGGGGGYGGGGDGGGGF 144

Length = 144

>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 = 45.0 bits (107), Expect = 1e-06
 Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAV 76
          +E ++ F  FG++ E  +  D  T RS+GF F++F   E AV
Sbjct: 14 EELRELFEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV 55

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

 Score = 44.9 bits (107), Expect = 1e-06
 Identities = 13/40 (32%), Positives = 27/40 (67%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAV 76
          +  +FF + G V++ +I+RD ++ RS+G  ++ F  E++V
Sbjct: 15 DLYEFFSKAGKVRDVRIIRDRNSRRSKGVAYVEFYDEESV 54

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

>gnl|CDD|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 = 44.8 bits (107), Expect = 1e-06
 Identities = 19/64 (29%), Positives = 38/64 (59%), Gaps = 3/64 (4%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKGNKLELAGA--Q 92
          ++ +  F ++G+++E  I+RD  T +S+G  F+ F + E+A   + A   K+ + GA   
Sbjct: 14 EDVRALFEEYGNIEEVTIIRDKDTGQSKGCAFVKFSSREEAQKAIEALHGKVTMPGASRP 73

Query: 93 VEVK 96
          ++VK
Sbjct: 74 LQVK 77

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 18/43 (41%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVD 77
          D  + +F QFG+++E  ++ D  T +SRG+GF+TF D E A  
Sbjct: 15 DSLRKYFSQFGEIEEAVVITDRQTGKSRGYGFVTFKDKESAER 57

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 7/58 (12%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD-------TEQAVDDLLAKGNKLE 87
          E K +F QFG V+  ++ R   T  S+ +GFI F          +++++ L  G  L+
Sbjct: 15 ELKKYFSQFGTVKNVRVARSKKTGNSKHYGFIQFLNPEVAAIAAKSMNNYLLMGKVLQ 72

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

 Score = 44.7 bits (105), Expect = 2e-06
 Identities = 19/65 (29%), Positives = 34/65 (52%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           +EFK  F   G+++  +++RD  T +S G+GF+ +      D  +   N L+L    ++V
Sbjct: 18  EEFKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVDPNDADKAINTLNGLKLQTKTIKV 77

Query: 96  KKAEP 100
             A P
Sbjct: 78  SYARP 82

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

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 9/70 (12%)

Query: 24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
          GLSL   TE    + ++ F ++G +++ Q++ D  T RSRGFGF+ F++   V+D  AK 
Sbjct: 6  GLSLY-TTE---RDLREVFSRYGPIEKVQVVYDQKTGRSRGFGFVYFES---VED--AKE 56

Query: 84 NKLELAGAQV 93
           K  L G ++
Sbjct: 57 AKERLNGMEI 66

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

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 11/65 (16%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNK 85
          V E  L      F+ FGD+++ QI  D+ T + RGF F+ F    D   A+D++    N+
Sbjct: 10 VDEKVL---HAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAIDNM----NE 62

Query: 86 LELAG 90
           EL G
Sbjct: 63 SELFG 67

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 23/87 (26%), Positives = 46/87 (52%), Gaps = 13/87 (14%)

Query: 9  LTMFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFI 68
          LT+F+ R         LSL   TE   +  ++ F ++GD++  +++RD  T  S+G+ F+
Sbjct: 4  LTLFVGR---------LSLQ-TTE---ETLREVFSRYGDIRRLRLVRDIVTGFSKGYAFV 50

Query: 69 TFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++ E+         +KL + G+++ V
Sbjct: 51 EYEHERDALRAYRDAHKLVIDGSEIFV 77

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

 Score = 44.4 bits (105), Expect = 3e-06
 Identities = 18/51 (35%), Positives = 35/51 (68%), Gaps = 1/51 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 86
          ++ + FF Q+G V+E +I+ D +   S+G+GF+TF+T++    +L + N+L
Sbjct: 17 NDLRKFFSQYGTVKEVKIVNDRA-GVSKGYGFVTFETQEDAQKILQEANRL 66

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

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

 Score = 44.3 bits (104), Expect = 3e-06
 Identities = 25/68 (36%), Positives = 42/68 (61%), Gaps = 3/68 (4%)

Query: 32 EPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-AKGNKLELAG 90
          E   +  +  F Q+G + +  +MRD +T RSRGFGF+T+ + + VD  + A+ +K++  G
Sbjct: 13 ETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYSSVEEVDAAMNARPHKVD--G 70

Query: 91 AQVEVKKA 98
            VE K+A
Sbjct: 71 RVVEPKRA 78

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 47.0 bits (112), Expect = 3e-06
 Identities = 29/55 (52%), Positives = 29/55 (52%)

Query: 136 FAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGAYRG 190
             GGGFGG  GGG GGG       G RGGG GG    G  GG GG GGG G   G
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 43.9 bits (103), Expect = 4e-06
 Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 32 EPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA 91
          E   +  ++++ Q+G + +  +MRD ++ RSRGFGF+TF     VD  +A      + G 
Sbjct: 13 ETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSCMNEVDAAMA-ARPHTIDGR 71

Query: 92 QVEVKKA 98
           VE K+A
Sbjct: 72 VVEPKRA 78

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

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

 Score = 43.8 bits (104), Expect = 4e-06
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 2/66 (3%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D+ ++FF + G+V + +I +D    RS+GFG + F TE+     L K  + EL G ++ V
Sbjct: 14  DDLEEFFKECGEVVDVRIAQDDD-GRSKGFGHVEFATEEGAQKALEKSGE-ELLGREIRV 71

Query: 96  KKAEPK 101
             A  +
Sbjct: 72  DLATER 77

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

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

 Score = 43.3 bits (103), Expect = 4e-06
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 4/48 (8%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 79
          D+ ++ F  FG +    + +D  T +SRGF F+TF    D E+A++ L
Sbjct: 14 DDLRELFRPFGPISRVYLAKDKETGQSRGFAFVTFHTREDAERAIEKL 61

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 = 43.1 bits (101), Expect = 5e-06
 Identities = 22/62 (35%), Positives = 39/62 (62%), Gaps = 1/62 (1%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          + KD+F +FG+V +  +  D  T RSRGFGF+ F   ++VD ++ +  + +L G  ++ K
Sbjct: 14 DLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ-KEHKLNGKVIDPK 72

Query: 97 KA 98
          +A
Sbjct: 73 RA 74

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

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

 Score = 42.9 bits (101), Expect = 6e-06
 Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 3/63 (4%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL-AKGNKLELAGAQVEV 95
          + K++F +FG+V +  I  D  T RSRGFGF+ F    +V+ +L  K +KL+  G  ++ 
Sbjct: 14 DLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAASVEKVLDQKEHKLD--GRVIDP 71

Query: 96 KKA 98
          K+A
Sbjct: 72 KRA 74

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

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

 Score = 47.0 bits (111), Expect = 6e-06
 Identities = 20/74 (27%), Positives = 36/74 (48%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
            + K  F  FG++ + Q+ R  +    +G+GFI ++  Q+  + +A  N  +L G  + V
Sbjct: 219 TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRV 278

Query: 96  KKAEPKKPNLPQPS 109
            K       L QP+
Sbjct: 279 GKCVTPPDALLQPA 292

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

 Score = 42.7 bits (100), Expect = 9e-06
 Identities = 21/67 (31%), Positives = 40/67 (59%), Gaps = 1/67 (1%)

Query: 32 EPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA 91
          E   ++ +++F +FG+++  ++  D  T++ RGF FITF  E  V  +L K     ++G+
Sbjct: 15 EATEEKIREYFGEFGEIEAIELPMDPKTNKRRGFVFITFKEEDPVKKVLEKKFH-NVSGS 73

Query: 92 QVEVKKA 98
          + E+K A
Sbjct: 74 KCEIKVA 80

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

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

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 33 PALDE--FKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          P +DE    D F  FG  +Q  +IMRD  T  S+GF FI++D+ +A D  +   N   L 
Sbjct: 11 PEVDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGFAFISYDSFEASDAAIEAMNGQYLC 70

Query: 90 GAQVEVKKA 98
             + V  A
Sbjct: 71 NRPITVSYA 79

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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 44.7 bits (106), Expect = 2e-05
 Identities = 28/55 (50%), Positives = 28/55 (50%)

Query: 133 GGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGGMGA 187
           G G   GG  G G GGGGGG R  G  G   GG  G G GG  GG GG GGG   
Sbjct: 1   GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55

Length = 293

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

 Score = 42.0 bits (98), Expect = 2e-05
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F ++G +   +I+ D  + + RGFGF+TFD    VD ++ +     + G   EV+K
Sbjct: 17  LRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYH-TINGHNAEVRK 75

Query: 98  AEPKK 102
           A  ++
Sbjct: 76  ALSRQ 80

This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. . Length = 80

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 12/35 (34%), Positives = 25/35 (71%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 70
          ++ ++ F +FGD++   I++D +T  S+GFG++ F
Sbjct: 15 EDLREKFKEFGDIEYVSIVKDKNTGESKGFGYVKF 49

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

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 8/67 (11%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
          DE +  F   G+++  +++RD  T +S G+GF+ +    D E+A++ L    N L L   
Sbjct: 16 DEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTL----NGLRLQNK 71

Query: 92 QVEVKKA 98
           ++V  A
Sbjct: 72 TIKVSYA 78

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|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 = 41.1 bits (97), Expect = 3e-05
 Identities = 16/61 (26%), Positives = 31/61 (50%), Gaps = 5/61 (8%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          +    F  FG+V   ++  D +T +S+ FGF+++D  ++     A+     + G QV  K
Sbjct: 14 DLYQLFAPFGNVISAKVFVDKNTGQSKCFGFVSYDNPES-----AQAAIKAMNGFQVGGK 68

Query: 97 K 97
          +
Sbjct: 69 R 69

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

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

 Score = 40.7 bits (96), Expect = 4e-05
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 4/56 (7%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 85
          VTE   D  ++ F   G+V + ++MR     +SR FGF+ F +E+     +   NK
Sbjct: 12 VTE---DRLREHFESKGEVTDVKVMRT-RDGKSRRFGFVGFKSEEDAQQAVKYFNK 63

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

 Score = 40.8 bits (95), Expect = 4e-05
 Identities = 22/66 (33%), Positives = 36/66 (54%), Gaps = 6/66 (9%)

Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           +  ++  +FG+V +  I  D  T RSRGFGF+ F    +VD +      LEL   +++ K
Sbjct: 15  DLTEYLSRFGEVLDCTIKTDPVTGRSRGFGFVLFKDAASVDKV------LELKEHKLDGK 68

Query: 97  KAEPKK 102
             +PK+
Sbjct: 69  LIDPKR 74

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

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

 Score = 40.4 bits (95), Expect = 5e-05
 Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 4/47 (8%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD-TEQA 75
          VTE   D+ ++ F  FG++Q+  +++D  T  S+G  ++ F     A
Sbjct: 14 VTE---DDLREAFAPFGEIQDIWVVKDKQTKESKGVAYVKFAKASSA 57

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

 Score = 40.4 bits (94), Expect = 6e-05
 Identities = 16/47 (34%), Positives = 31/47 (65%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 82
          ++ +++F  FG+V+  ++  D+ T++ RGF FITF  E+ V  ++ K
Sbjct: 14 EKIREYFGAFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60

This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. . Length = 75

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

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 16/63 (25%), Positives = 31/63 (49%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          +E +  F   G ++  +I+RD  T +S G+GF+ +  E      +   N  E+   +++V
Sbjct: 15 EELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAINTLNGFEIRNKRLKV 74

Query: 96 KKA 98
            A
Sbjct: 75 SYA 77

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

 Score = 40.0 bits (94), Expect = 8e-05
 Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDL 79
          D+ +  F ++G+V +  I RD  T  SRGF F+ F    D E A+D +
Sbjct: 13 DDLRRVFEKYGEVGDVYIPRDRYTRESRGFAFVRFYDKRDAEDAMDAM 60

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

 Score = 39.8 bits (94), Expect = 9e-05
 Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 3/49 (6%)

Query: 53 IMRDHSTSRSRGFGFITFDTEQ---AVDDLLAKGNKLELAGAQVEVKKA 98
          ++RD  T  SRGF F+ F + +      D L   +   + G  V V  A
Sbjct: 36 LIRDKLTGTSRGFAFVEFPSLEDATQWMDALNNLDPFVIDGRVVRVSYA 84

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

 Score = 40.1 bits (93), Expect = 9e-05
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L    N L L   
Sbjct: 16  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNAKDAERAINTL----NGLRLQSK 71

Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 72  TIKVSYARP 80

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|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 4/57 (7%)

Query: 40 DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          ++F QFG V + +I       + R FGF+TF+  + V  +L+KGN   + G++V VK
Sbjct: 18 EYFGQFGPVLDVRI----PYQQKRMFGFVTFENAETVKRILSKGNPHFICGSRVRVK 70

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

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

 Score = 39.7 bits (92), Expect = 1e-04
 Identities = 21/69 (30%), Positives = 38/69 (55%), Gaps = 8/69 (11%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           +EF+  F   G+++  +++RD  T +S G+GF+ +    D E+A++ L    N L L   
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL----NGLRLQTK 72

Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 73  TIKVSYARP 81

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 = 43.0 bits (101), Expect = 1e-04
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 8/69 (11%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           +E +  F   G+++  +++RD  T +S G+GF+ +    D E+AV+ L    N L L   
Sbjct: 18  EEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSL----NGLRLQNK 73

Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 74  TIKVSYARP 82

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

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 12/70 (17%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNK 85
           TE  L   K  F  FG V E  I R     + +GF F+ F    D E+A+  +    N 
Sbjct: 11 CTEADL---KKLFSPFGFVWEVTIPRK-PDGKKKGFAFVQFTSKADAEKAIKGV----NG 62

Query: 86 LELAGAQVEV 95
           ++ G  V V
Sbjct: 63 KKIKGRPVAV 72

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

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSR---GFGFITFDTEQAVDDLLAKGNKL 86
          + E   D+ +  F +FG+V+  +I +     + R   GF F+TF    + ++ L      
Sbjct: 12 LDE---DDLRGIFSKFGEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSAENALQLNGT- 67

Query: 87 ELAGAQVEV 95
          EL G ++ 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|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 41.6 bits (98), Expect = 2e-04
 Identities = 27/48 (56%), Positives = 27/48 (56%), Gaps = 2/48 (4%)

Query: 121 GSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGG 168
           G G G   GG GGGG  GGG GG  GGG G G    G  G RGGG GG
Sbjct: 7   GGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRG--RGGGGGGRGGGGGG 52

Length = 293

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 17/57 (29%), Positives = 30/57 (52%)

Query: 42 FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA 98
          F +FG V   +++ D  T RSRGFG++ F++ +     +   +  EL G  + V  +
Sbjct: 20 FEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEAMDGKELDGRPINVDFS 76

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

 Score = 39.3 bits (91), Expect = 2e-04
 Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 8/69 (11%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           +E K  F   G+++  +++RD  T +S G+GF+ +    D E+A++ L    N L L   
Sbjct: 19  EELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL----NGLRLQTK 74

Query: 92  QVEVKKAEP 100
            ++V  A P
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|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila sex-lethal (SXL) and similar proteins

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 20/65 (30%), Positives = 35/65 (53%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           +EF+  F+  G V+  +I+RD  T  S GFGF+ + + +     +   N L+L   +++V
Sbjct: 15  EEFRSLFLAVGPVKNCKIVRDKRTGYSYGFGFVDYQSAEDAQRAIRTLNGLQLQNKRIKV 74

Query: 96  KKAEP 100
             A P
Sbjct: 75  AYARP 79

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

>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 27/59 (45%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 127 AYGGYGGGGFA-GGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGG 184
           A GG+GG  F  GGGFGG G GG G  +  +  +    G  GG G+G  FGG    GGG
Sbjct: 79  AGGGFGGRRFDGGGGFGGFGTGGDGAEFNLNDLFD-AAGRGGGGGIGDLFGGLFNRGGG 136

Length = 392

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

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKGNKLELAGAQ 92
           E +  F Q+G +   +I+RD  T  SRG GFI FD   +A + +     +     ++
Sbjct: 15 KELEQLFSQYGRIITSRILRDQLTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPEGASE 72

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|221115 pfam11456, DUF3019, Protein of unknown function (DUF3019)

 Score = 39.2 bits (92), Expect = 3e-04
 Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 8/50 (16%)

Query: 68  ITFDTEQAVD-DLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRYNNP 116
           + FD+++ +   L+   +   LA A+V+V    PKK        RR  NP
Sbjct: 57  LEFDSDKDIQFVLIDSDSNQPLASAKVKVTWVSPKKR-------RRRRNP 99

This is a bacterial family of uncharacterized proteins. Length = 102

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 13/43 (30%), Positives = 27/43 (62%), Gaps = 4/43 (9%)

Query: 39 KDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVD 77
          +  F  FG++ + ++++D  T +S+G+GF++F    D E A+ 
Sbjct: 17 RAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQ 59

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

 Score = 37.9 bits (88), Expect = 4e-04
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 7/57 (12%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK 82
          VT+  L  F  F   F    + ++M D  + RSRG+GF++F    D E A++++  K
Sbjct: 11 VTDATL--FAAFSA-FPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEMNGK 64

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

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

 Score = 41.0 bits (96), Expect = 4e-04
 Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 7/76 (9%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAK---GNKLEL 88
           D+ K+    FGD++   +++D +T  S+G+ F  +     T+ A+  L  K    NKL +
Sbjct: 310 DQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHV 369

Query: 89  AGAQVEVKKAEPKKPN 104
             A V   +A     N
Sbjct: 370 QRACVGANQATIDTSN 385

These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. Length = 509

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

 Score = 38.5 bits (89), Expect = 4e-04
 Identities = 16/59 (27%), Positives = 32/59 (54%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N +EL G ++ V
Sbjct: 25 DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 83

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|215598 PLN03138, PLN03138, Protein TOC75; Provisional

 Score = 41.4 bits (97), Expect = 4e-04
 Identities = 22/57 (38%), Positives = 25/57 (43%)

Query: 98  AEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYR 154
           A          +    N       +      GG GGGGF G G GG GGGGGGGG+R
Sbjct: 49  ASASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWR 105

Length = 796

>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 = 5e-04
 Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          +E  + F + G + E  ++     + +  F FI F+ EQA    +   N   L    + V
Sbjct: 18 EELNERFSRHGKILEVNLI--KRANHTNAFAFIKFEREQAAARAVESENHSMLKNKTMHV 75

Query: 96 KKAE 99
          +  E
Sbjct: 76 QYKE 79

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

 Score = 40.9 bits (96), Expect = 5e-04
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 15/75 (20%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ----AVD-------DLLAKGN 84
           D+ ++ F +FG++    +M+D S  RSRGF F+ F+  +    AV+        L  +G 
Sbjct: 193 DKLRELFAKFGEITSAAVMKDGS-GRSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGK 251

Query: 85  KLELAGAQVEVKKAE 99
           KL +  AQ   K+AE
Sbjct: 252 KLYVGRAQ---KRAE 263

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|236092 PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 26/57 (45%), Positives = 27/57 (47%), Gaps = 4/57 (7%)

Query: 132 GGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVG----GEFGGYGGYGGG 184
           GGGG  GGGFGG GGG GGGG    G     GGG                 GG+GGG
Sbjct: 124 GGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGG 180

Length = 186

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

 Score = 37.5 bits (88), Expect = 6e-04
 Identities = 21/61 (34%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          +E +  F   GDV+  +I+RD  T   +GFG++ F T+ +V   L   N ++L G ++ V
Sbjct: 14 EELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL-NGIKLKGRKIRV 72

Query: 96 K 96
          K
Sbjct: 73 K 73

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

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

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 18/72 (25%), Positives = 38/72 (52%), Gaps = 13/72 (18%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAVDDLLAKGNKLEL 88
            TE   ++ ++ F ++G+V+  + ++D        + F+ F + + AV   + + N  EL
Sbjct: 13  TTE---EQLRELFSEYGEVERVKKIKD--------YAFVHFEERDDAVK-AMEEMNGKEL 60

Query: 89  AGAQVEVKKAEP 100
            G+ +EV  A+P
Sbjct: 61  EGSPIEVSLAKP 72

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

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

 Score = 37.2 bits (87), Expect = 7e-04
 Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 3/68 (4%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          VTE  L E    F+Q G V    I +D  T   +G+GF+ F +E+  D  +   N ++L 
Sbjct: 10 VTEELLWEL---FIQAGPVVNVHIPKDRVTQAHQGYGFVEFLSEEDADYAIKIMNMIKLY 66

Query: 90 GAQVEVKK 97
          G  + V K
Sbjct: 67 GKPIRVNK 74

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

>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 31/63 (49%), Positives = 31/63 (49%), Gaps = 9/63 (14%)

Query: 121 GSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGG 180
           G GFG   GG  GGG  GG  GG  GGG GGG         RG G GG G G   GG GG
Sbjct: 3   GGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGG---------RGRGRGGGGGGRGGGGGGG 53

Query: 181 YGG 183
            G 
Sbjct: 54  PGK 56

Length = 293

>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 = 36.8 bits (86), Expect = 0.001
 Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 4/48 (8%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD----TEQAVDDL 79
          ++  + F + G V   +++ D  T + +G+GF  F+       A+ +L
Sbjct: 13 EQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

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

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

 Score = 36.9 bits (86), Expect = 0.001
 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 6/66 (9%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQAVDDLLAKGNKLELAGAQ 92
          E +  F  +G +   +I+ D+ T  SRG GFI FD     E+A+  L   G     A   
Sbjct: 16 ELEALFSPYGRIITSRILCDNVTGLSRGVGFIRFDKRIEAERAIKAL--NGTIPPGATEP 73

Query: 93 VEVKKA 98
          + VK A
Sbjct: 74 ITVKFA 79

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 12/38 (31%), Positives = 22/38 (57%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 73
           E + +F QFG V   ++ R   T +S+G+ F+ F++ 
Sbjct: 14 PELRKYFSQFGTVTRLRLSRSKKTGKSKGYAFVEFESP 51

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

 Score = 36.8 bits (86), Expect = 0.001
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQA 75
          +  ++ F  FG +   ++M D    RS+GFGF+ F + E+A
Sbjct: 16 ERLREEFSPFGTITSAKVMTDEKG-RSKGFGFVCFSSPEEA 55

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|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins

 Score = 37.0 bits (85), Expect = 0.001
 Identities = 16/65 (24%), Positives = 33/65 (50%)

Query: 42  FMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK 101
           FM FG+V   ++  D  T+ S+ FGF+++D   +    +   N  ++   +++V+    K
Sbjct: 28  FMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQAMNGFQIGMKRLKVQLKRSK 87

Query: 102 KPNLP 106
             + P
Sbjct: 88  NDSKP 92

This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. . Length = 92

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 10/31 (32%), Positives = 21/31 (67%)

Query: 40 DFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 70
            F ++   Q+ +++RD  T +S+G+GF++F
Sbjct: 25 RAFSKYPSFQKAKVVRDKRTGKSKGYGFVSF 55

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

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 17/66 (25%), Positives = 38/66 (57%), Gaps = 1/66 (1%)

Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           +  +FF + G V++ Q ++D ++ RS+G  ++ F   ++V   LA   ++ L G  + V+
Sbjct: 105 DLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQM-LLGRPIIVQ 163

Query: 97  KAEPKK 102
            ++ +K
Sbjct: 164 SSQAEK 169

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

 Score = 39.0 bits (91), Expect = 0.002
 Identities = 22/97 (22%), Positives = 41/97 (42%), Gaps = 5/97 (5%)

Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           + ++ F + G++   ++M D     SRGFGF+ F   +  +  + + +   L G  + V 
Sbjct: 301 KLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVA 359

Query: 97  KAEPKKPNLP----QPSYRRYNNPKPAYGSGFGDAYG 129
            A+ K+        Q    +    +   GS  G A G
Sbjct: 360 LAQRKEQRRAHLQDQFMQLQPRMRQLPMGSPMGGAMG 396

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|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517)

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 16/52 (30%), Positives = 18/52 (34%)

Query: 133 GGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEFGGYGGYGGG 184
           GG   GG F             S G  G  G   GG+G       +G  GGG
Sbjct: 5   GGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGG 56

This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown. Length = 280

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 16/64 (25%), Positives = 34/64 (53%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          D+ +  F ++G + +  I  D  T R RGF ++ F+  +  +D L   ++    G ++E+
Sbjct: 15 DDLRRLFGKYGPIVDVYIPLDFYTRRPRGFAYVQFEDVRDAEDALYYLDRTRFLGREIEI 74

Query: 96 KKAE 99
          + A+
Sbjct: 75 QFAQ 78

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

>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown]

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 22/58 (37%), Positives = 23/58 (39%), Gaps = 2/58 (3%)

Query: 133 GGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGGEF--GGYGGYGGGMGAY 188
           GG   GG F    G   G         G  GGGY G G G  F   G GG GG  G +
Sbjct: 50  GGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGIF 107

Length = 334

>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 = 35.7 bits (83), Expect = 0.002
 Identities = 10/47 (21%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK 82
          DE +  F + G++ + ++++++   +S+G+ ++ F+ E++V + L  
Sbjct: 14 DELRKLFSKCGEITDVRLVKNYK-GKSKGYAYVEFENEESVQEALKL 59

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

 Score = 38.6 bits (90), Expect = 0.003
 Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 1/64 (1%)

Query: 39  KDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA 98
            D F +FG++   ++  D    +SRG+GF+ F+ E++    + K N + L   +V V + 
Sbjct: 106 FDTFSKFGNILSCKVATD-ENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGRF 164

Query: 99  EPKK 102
             K 
Sbjct: 165 IKKH 168

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|236092 PRK07772, PRK07772, single-stranded DNA-binding protein; Provisional

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 22/58 (37%), Positives = 26/58 (44%)

Query: 215 GGLNESYGGYGGSGVGGGGGYGGGPSGYDIGLGSSYGGSSGGAFFGSRGGYGGAGGSS 272
           GG     GG+GG G G GGG GGG  G   G G +   +     + S    GG GG  
Sbjct: 124 GGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDPWSSAPASGGFGGGD 181

Length = 186

>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein; Provisional

 Score = 37.5 bits (87), Expect = 0.003
 Identities = 28/51 (54%), Positives = 29/51 (56%)

Query: 123 GFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYGVRGGGYGGYGVGG 173
           G G + GG GGG   G G GG GGGGG GG   SG  G R  G GG G GG
Sbjct: 110 GRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGG 160

Length = 182

>gnl|CDD|241197 cd12753, RRM1_RBM10, RNA recognition motif 1 in vertebrate RNA-binding protein 10 (RBM10)

 Score = 35.8 bits (82), Expect = 0.003
 Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 8/64 (12%)

Query: 46  GDVQEH-------QIMRDHSTSRSRGFGFITFDTEQ-AVDDLLAKGNKLELAGAQVEVKK 97
           G +QEH       ++MR+ S+ +SRGF F+ F+  Q A   + A  + L + G +V +  
Sbjct: 21  GQLQEHGIQPREVRLMRNKSSGQSRGFAFVEFNHLQDATRWMEANQHSLMILGQKVSMHY 80

Query: 98  AEPK 101
           ++PK
Sbjct: 81  SDPK 84

This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). 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. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains 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 = 85

>gnl|CDD|240910 cd12464, RRM_G3BP2, RNA recognition motif in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 17/44 (38%), Positives = 24/44 (54%)

Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 80
          E K+FFM FG+V E +I       +   FGF+ FD  + V  +L
Sbjct: 21 ELKEFFMSFGNVVELRINTKGVGGKLPNFGFVVFDDSEPVQRIL 64

This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. Length = 83

>gnl|CDD|240909 cd12463, RRM_G3BP1, RNA recognition motif found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins

 Score = 35.7 bits (82), Expect = 0.003
 Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 5/65 (7%)

Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           E K+FF Q+G+V E   +R +S  +   FGF+ FD  + V  +L   N+  +    V + 
Sbjct: 19  ELKEFFQQYGNVVE---LRINSGGKLPNFGFVVFDDSEPVQKIL--SNRPIMFRGDVRLN 73

Query: 97  KAEPK 101
             E K
Sbjct: 74  VEEKK 78

This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. Length = 80

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 12/36 (33%), Positives = 21/36 (58%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFD 71
          DE +  F  +G++ +  ++RD ST   RG  F+ +D
Sbjct: 15 DELRKIFEAYGNIVQCNLLRDKSTGLPRGVAFVRYD 50

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

 Score = 35.4 bits (81), Expect = 0.003
 Identities = 15/45 (33%), Positives = 28/45 (62%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL 80
          ++ K++F  FG+++  ++  D  T+  RGF F+T+  E+ V  LL
Sbjct: 14 EQIKEYFGAFGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL 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|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF-DTEQAV 76
          D+ +  F +FG++ E  +  D  + +S+GF ++ F D E AV
Sbjct: 17 DDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAV 58

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|241075 cd12631, RRM1_CELF1_2_Bruno, RNA recognition motif 1 in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins

 Score = 35.5 bits (82), Expect = 0.003
 Identities = 14/42 (33%), Positives = 25/42 (59%), Gaps = 2/42 (4%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHST--SRSRGFGFITFDTEQA 75
           + ++ F Q+G V +  ++RD S    +S+G  F+TF T +A
Sbjct: 16 KDLRELFEQYGAVYQINVLRDRSQNPPQSKGCCFVTFYTRKA 57

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

>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 50/146 (34%), Positives = 57/146 (39%), Gaps = 16/146 (10%)

Query: 117 KPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGYRSSGAYG--------VRGGGYGG 168
           K    S      GGY GGG  G     + G G GGG                V GGG G 
Sbjct: 58  KGEDNSSNNMVKGGYNGGGDGGNDNSSNDGSGSGGGATDIRLNENSLKSRIIVAGGGGGS 117

Query: 169 YGVGGEFGGYGGYGGGMGAYRGEPSSLGYSGRYGGFNRGYDVTGDYGGLNESYGGYGGSG 228
              G   GG GG+GGG+    G   +   +   GG           GG      G  G+G
Sbjct: 118 ---GNYNGGSGGFGGGLVGGGG---TSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNG 171

Query: 229 VGGGGGYGGGPSGYDIGLGSSYGGSS 254
            GGGGGY GG  G+  G G   GGSS
Sbjct: 172 GGGGGGYFGGGGGHYAGGGG--GGSS 195

This family of proteins is greatly expanded in Trichomonas vaginalis. The proteins are composed of several glycine rich motifs interspersed through the sequence. Although many proteins have been annotated by similarity in the family these annotations given the biased composition of the sequences these are unlikely to be functionally relevant. Length = 248

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

 Score = 36.1 bits (83), Expect = 0.003
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA 81
          +     F +FG V+    + D ST R++G GF+ F  +   +  L 
Sbjct: 16 ESLAPHFSKFGSVRYALPVIDKSTGRAKGTGFVCFKDQYTYNACLK 61

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

 Score = 35.0 bits (81), Expect = 0.004
 Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          VTE  L E    F+Q G ++  +I +D +  + + F F+TF  E +V   +   N + L 
Sbjct: 13 VTEEILYEL---FLQAGPLEGVKIPKDPNG-KPKSFAFVTFKHEVSVPYAIQLLNGIRLF 68

Query: 90 GAQVEVK 96
          G ++ +K
Sbjct: 69 GRELRIK 75

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

>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5)

 Score = 38.1 bits (88), Expect = 0.004
 Identities = 18/57 (31%), Positives = 23/57 (40%)

Query: 97  KAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGGGGFAGGGFGGSGGGGGGGGY 153
              P K + P    ++Y N      S  G +YGG G     G G GG  G G   G+
Sbjct: 486 NNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRGF 542

This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors. Length = 543

>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown]

 Score = 38.4 bits (89), Expect = 0.004
 Identities = 25/120 (20%), Positives = 41/120 (34%), Gaps = 20/120 (16%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
             FK+F   +  ++E +       S      ++ + T   V D + K  +  L    ++ 
Sbjct: 489 QAFKNFLSDYSQLKEAKP-----ESIHLWEQYLVYATALGVSDKVVKAMRKALDMEIIK- 542

Query: 96  KKAEPKKPNLPQPSYRRYNNPKPAYGSGFGDAYGGYGG---GGFAGGGFGGSGGGGGGGG 152
                            ++N      +    AY           +GGG G SGGG GGGG
Sbjct: 543 -----------DSYSPIFHNNYSRSFNNLNRAYSAIASSRRSSSSGGGGGFSGGGSGGGG 591

Length = 595

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

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 39 KDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          KD F + G+V    +  D+   RS+GFG + F++ +     +   N  +L G ++EV+
Sbjct: 16 KDLFRECGNVLRADVKTDND-GRSKGFGTVLFESPEDAQRAIEMFNGYDLEGRELEVR 72

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|240737 cd12291, RRM1_La, RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 35 LDEFKDFFMQFGDVQEHQI-MRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV 93
          LD+ ++FF +FG V    I MR     + +G  F+ F TE+     L K  KL+    ++
Sbjct: 13 LDDIQEFFEKFGKVN--NIRMRRDLDKKFKGSVFVEFKTEEDAKKFLEK-EKLKYKEKEL 69

Query: 94 EVK 96
           V 
Sbjct: 70 TVM 72

This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. . Length = 72

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	279
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.85
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.76
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.74
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.72
KOG0122	270	consensus Translation initiation factor 3, subunit	99.71
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.7
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.67
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.67
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.67
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.67
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.61
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.61
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.6
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.59
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.59
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.59
PLN03120	260	nucleic acid binding protein; Provisional	99.58
smart00360	71	RRM RNA recognition motif.	99.57
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.56
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.54
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.54
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.54
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.53
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.53
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.53
smart00362	72	RRM_2 RNA recognition motif.	99.53
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	99.52
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.52
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.52
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.52
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.51
PLN03213	759	repressor of silencing 3; Provisional	99.51
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.51
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.49
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.49
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.49
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.49
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.49
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.47
PLN03121	243	nucleic acid binding protein; Provisional	99.47
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.47
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.46
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.45
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.44
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.44
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.43
smart00361	70	RRM_1 RNA recognition motif.	99.43
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.42
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.4
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.38
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.38
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.36
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.36
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	99.35
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.35
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.3
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.28
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	99.26
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.26
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.25
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.24
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.21
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.2
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.15
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.11
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	99.11
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	99.1
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.09
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.08
KOG0533	243	consensus RRM motif-containing protein [RNA proces	99.06
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.05
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.04
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.03
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.02
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	99.0
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	98.98
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.94
KOG1995	351	consensus Conserved Zn-finger protein [General fun	98.9
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.88
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.86
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	98.84
KOG1548	382	consensus Transcription elongation factor TAT-SF1	98.84
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.77
KOG0226	290	consensus RNA-binding proteins [General function p	98.73
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.7
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	98.69
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.69
KOG0151	877	consensus Predicted splicing regulator, contains R	98.52
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	98.44
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	98.38
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	98.33
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	98.32
KOG1855	484	consensus Predicted RNA-binding protein [General f	98.25
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.23
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	98.15
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.14
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.07
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	98.04
COG5175	480	MOT2 Transcriptional repressor [Transcription]	98.0
KOG2314	698	consensus Translation initiation factor 3, subunit	97.98
KOG4210	285	consensus Nuclear localization sequence binding pr	97.97
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.93
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.87
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	97.87
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	97.86
KOG1548	382	consensus Transcription elongation factor TAT-SF1	97.86
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	97.86
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	97.83
KOG1457	284	consensus RNA binding protein (contains RRM repeat	97.77
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.71
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	97.61
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	97.54
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.51
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	97.5
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.46
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	97.36
KOG3152	278	consensus TBP-binding protein, activator of basal	97.3
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.25
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	97.14
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	97.02
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	97.0
KOG2068	327	consensus MOT2 transcription factor [Transcription	96.96
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	96.91
KOG2591	684	consensus c-Mpl binding protein, contains La domai	96.86
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	96.83
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.8
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.77
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	96.72
KOG4660	549	consensus Protein Mei2, essential for commitment t	96.67
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.64
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	96.54
KOG2135	526	consensus Proteins containing the RNA recognition	96.51
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	96.38
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	96.31
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	96.18
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	96.17
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	96.16
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.12
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	95.99
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	95.86
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	95.69
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	95.5
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.83
KOG4210	285	consensus Nuclear localization sequence binding pr	94.15
KOG4019	193	consensus Calcineurin-mediated signaling pathway i	93.73
KOG2318	650	consensus Uncharacterized conserved protein [Funct	93.56
KOG4483	528	consensus Uncharacterized conserved protein [Funct	93.19
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	92.93
PF07530	68	PRE_C2HC: Associated with zinc fingers; InterPro:	92.19
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	91.02
smart00596	69	PRE_C2HC PRE_C2HC domain.	90.67
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	89.37
PF03468	116	XS: XS domain; InterPro: IPR005380 The XS (rice ge	88.71
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	88.49
KOG3262	215	consensus H/ACA small nucleolar RNP component GAR1	88.2
PF02714	325	DUF221: Domain of unknown function DUF221; InterPr	82.08
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	81.62
COG5638	622	Uncharacterized conserved protein [Function unknow	81.22
KOG2187	534	consensus tRNA uracil-5-methyltransferase and rela	80.96
KOG2295	648	consensus C2H2 Zn-finger protein [General function	80.95
COG0724	306	RNA-binding proteins (RRM domain) [General functio	80.2

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

Probab=99.85  E-value=1.4e-20  Score=154.32  Aligned_cols=85  Identities=29%  Similarity=0.529  Sum_probs=79.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++||   ++|+++|++|++|++|+|++|+.|+++++||||+|+++++|++||++||+++|++++|+
T Consensus        31 ~~~~~~lfVgnL~~~~te---~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~  107 (144)
T PLN03134         31 RLMSTKLFIGGLSWGTDD---ASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIR  107 (144)
T ss_pred             cCCCCEEEEeCCCCCCCH---HHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3456778 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |++++++..
T Consensus       108 V~~a~~~~~  116 (144)
T PLN03134        108 VNPANDRPS  116 (144)
T ss_pred             EEeCCcCCC
Confidence            999976543

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.76  E-value=8.6e-18  Score=156.22  Aligned_cols=85  Identities=20%  Similarity=0.413  Sum_probs=77.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC--cee
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQV   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g--~~i   93 (279)
                      ...++| |.|||++|||   ++|+++|++|++|++|+|++|+.|+++|+||||+|+++++|++||++||+++|++  ++|
T Consensus       191 ~~~~~lfV~nLp~~vte---e~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~~~g~~~~l  267 (346)
T TIGR01659       191 IKDTNLYVTNLPRTITD---DQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEAQEAISALNNVIPEGGSQPL  267 (346)
T ss_pred             cccceeEEeCCCCcccH---HHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCccCCCceeE
Confidence            345678 9999999999   9999999999999999999999999999999999999999999999999998876  689


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|++|+++.+.
T Consensus       268 ~V~~a~~~~~~  278 (346)
T TIGR01659       268 TVRLAEEHGKA  278 (346)
T ss_pred             EEEECCccccc
Confidence            99998875443

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).

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.74  E-value=1.1e-17  Score=155.59  Aligned_cols=84  Identities=21%  Similarity=0.385  Sum_probs=78.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.+||+++||   ++|+++|++|++|++|+|++|+.|+++|+||||+|+++++|++||++||+++|.+++|
T Consensus       103 ~~~~~~~LfVgnLp~~~te---~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i  179 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTD---RELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRL  179 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCcee
Confidence            34456788 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|+++++.
T Consensus       180 ~V~~a~p~  187 (346)
T TIGR01659       180 KVSYARPG  187 (346)
T ss_pred             eeeccccc
Confidence            99998764

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).

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.72  E-value=3.8e-17  Score=151.76  Aligned_cols=81  Identities=21%  Similarity=0.274  Sum_probs=77.6

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||++|+|   ++|+++|++||.|++|+|++|+.|+++||||||+|++.++|++||+.||+.+|++++|+|.++
T Consensus       270 ~~lfV~NL~~~~~e---~~L~~~F~~fG~v~~v~i~~d~~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~  346 (352)
T TIGR01661       270 YCIFVYNLSPDTDE---TVLWQLFGPFGAVQNVKIIRDLTTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFK  346 (352)
T ss_pred             cEEEEeCCCCCCCH---HHHHHHHHhCCCeEEEEEeEcCCCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            368 9999999999   999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023632           99 EPKKP  103 (279)
Q Consensus        99 ~~~~~  103 (279)
                      ..+..
T Consensus       347 ~~~~~  351 (352)
T TIGR01661       347 TNKAY  351 (352)
T ss_pred             cCCCC
Confidence            88754

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

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

Probab=99.71  E-value=3.5e-17  Score=141.07  Aligned_cols=82  Identities=22%  Similarity=0.404  Sum_probs=79.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+..+| |.||+++++|   ++|+++|.+|+.|..|.|.+|++|+.+||||||+|++.++|++||+.||++-++.-.|+|
T Consensus       187 ~D~~tvRvtNLsed~~E---~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrv  263 (270)
T KOG0122|consen  187 DDEATVRVTNLSEDMRE---DDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRV  263 (270)
T ss_pred             CccceeEEecCccccCh---hHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEE
Confidence            366789 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCC
Q 023632           96 KKAEPK  101 (279)
Q Consensus        96 ~~a~~~  101 (279)
                      +|++|+
T Consensus       264 EwskP~  269 (270)
T KOG0122|consen  264 EWSKPS  269 (270)
T ss_pred             EecCCC
Confidence            999986

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.70  E-value=6.8e-17  Score=150.09  Aligned_cols=83  Identities=20%  Similarity=0.471  Sum_probs=78.3

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |+|||.+++|   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+++|.+++|+|+
T Consensus         2 ~~~~l~V~nLp~~~~e---~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~   78 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQ---EEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVS   78 (352)
T ss_pred             CCcEEEEeCCCCCCCH---HHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEE
Confidence            35678 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +++++..
T Consensus        79 ~a~~~~~   85 (352)
T TIGR01661        79 YARPSSD   85 (352)
T ss_pred             eeccccc
Confidence            9987653

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

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

Probab=99.67  E-value=1.2e-16  Score=137.29  Aligned_cols=82  Identities=26%  Similarity=0.453  Sum_probs=75.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .|...++| |++|+|+++.   ++|+++|++||+|+++.|++|+.|+++|||+||+|.|.|+|++|++. ..-.|++|+.
T Consensus         8 ~DT~~TKifVggL~w~T~~---~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~d-p~piIdGR~a   83 (247)
T KOG0149|consen    8 GDTTFTKIFVGGLAWETHK---ETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKD-PNPIIDGRKA   83 (247)
T ss_pred             CCceEEEEEEcCcccccch---HHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcC-CCCccccccc
Confidence            35556778 9999999999   99999999999999999999999999999999999999999999998 4578999999


Q ss_pred             EEeeccC
Q 023632           94 EVKKAEP  100 (279)
Q Consensus        94 ~V~~a~~  100 (279)
                      .|++|.-
T Consensus        84 NcnlA~l   90 (247)
T KOG0149|consen   84 NCNLASL   90 (247)
T ss_pred             ccchhhh
Confidence            9998865

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

Probab=99.67  E-value=1.2e-16  Score=142.84  Aligned_cols=83  Identities=22%  Similarity=0.429  Sum_probs=76.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +.....++| |.|||+...|   -||+.+|++||+|++|+||.+  ..-+|||+||+|++.+||++|-++||+.+|.+|+
T Consensus        91 ~s~~~pkRLhVSNIPFrFRd---pDL~aMF~kfG~VldVEIIfN--ERGSKGFGFVTmen~~dadRARa~LHgt~VEGRk  165 (376)
T KOG0125|consen   91 SSKDTPKRLHVSNIPFRFRD---PDLRAMFEKFGKVLDVEIIFN--ERGSKGFGFVTMENPADADRARAELHGTVVEGRK  165 (376)
T ss_pred             CCCCCCceeEeecCCccccC---ccHHHHHHhhCceeeEEEEec--cCCCCccceEEecChhhHHHHHHHhhcceeeceE
Confidence            344556899 9999999999   999999999999999999988  3568999999999999999999999999999999


Q ss_pred             eEEeeccCC
Q 023632           93 VEVKKAEPK  101 (279)
Q Consensus        93 i~V~~a~~~  101 (279)
                      |+|..|..+
T Consensus       166 IEVn~ATar  174 (376)
T KOG0125|consen  166 IEVNNATAR  174 (376)
T ss_pred             EEEeccchh
Confidence            999998765

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

Probab=99.67  E-value=1.3e-16  Score=134.46  Aligned_cols=86  Identities=24%  Similarity=0.415  Sum_probs=79.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +......| |.||...++.   ++|..+|++||.|.+|.|++|+.|.++++||||.|.+..+|++||++|++++|+++.|
T Consensus         9 dv~gm~SLkVdNLTyRTsp---d~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRel   85 (256)
T KOG4207|consen    9 DVEGMTSLKVDNLTYRTSP---DDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGREL   85 (256)
T ss_pred             CcccceeEEecceeccCCH---HHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeecccee
Confidence            33455778 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|++|+--..
T Consensus        86 rVq~arygr~   95 (256)
T KOG4207|consen   86 RVQMARYGRP   95 (256)
T ss_pred             eehhhhcCCC
Confidence            9999975443

>PF00076 RRM_1: RNA recognition motif

Probab=99.67  E-value=2.7e-16  Score=111.67  Aligned_cols=69  Identities=32%  Similarity=0.691  Sum_probs=66.1

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      | |.|||+++|+   ++|+++|++|++|+.++|+.+ .+++++++|||+|+++++|++||+.||+++|++++|+
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 LYVGNLPPDVTE---EELRDFFSQFGKIESIKVMRN-SSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSH---HHHHHHHHTTSTEEEEEEEEE-TTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCH---HHHHHHHHHhhhccccccccc-ccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            5 9999999999   999999999999999999998 6889999999999999999999999999999999885

(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 ....

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

Probab=99.61  E-value=1.7e-15  Score=124.78  Aligned_cols=77  Identities=18%  Similarity=0.400  Sum_probs=70.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |+||+.++++   .||+.+|.+||+|..|+|.+++     .+||||||+++.+|++|+..||+++|++..|+|
T Consensus         8 ~~~~kVYVGnL~~~a~k---~eLE~~F~~yG~lrsvWvArnP-----PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rV   79 (195)
T KOG0107|consen    8 NGNTKVYVGNLGSRATK---RELERAFSKYGPLRSVWVARNP-----PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRV   79 (195)
T ss_pred             CCCceEEeccCCCCcch---HHHHHHHHhcCcceeEEEeecC-----CCceEEeccCcccHHHHHhhcCCccccCceEEE
Confidence            346778 9999999999   9999999999999999998764     789999999999999999999999999999999


Q ss_pred             eeccCC
Q 023632           96 KKAEPK  101 (279)
Q Consensus        96 ~~a~~~  101 (279)
                      ++.+-+
T Consensus        80 E~S~G~   85 (195)
T KOG0107|consen   80 ELSTGR   85 (195)
T ss_pred             EeecCC
Confidence            988654

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

Probab=99.61  E-value=3.3e-15  Score=132.08  Aligned_cols=89  Identities=16%  Similarity=0.367  Sum_probs=82.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+-++| |.-|+.+++|   ++|++.|++||+|+.|.||+|+.|++++|||||+|+++.++.+|.+..++++|+++.|.|
T Consensus        99 DPy~TLFv~RLnydT~E---skLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~V  175 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSE---SKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILV  175 (335)
T ss_pred             CccceeeeeeccccccH---HHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEE
Confidence            456888 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCCCCCCC
Q 023632           96 KKAEPKKPNLPQP  108 (279)
Q Consensus        96 ~~a~~~~~~~~~~  108 (279)
                      .....+....+.+
T Consensus       176 DvERgRTvkgW~P  188 (335)
T KOG0113|consen  176 DVERGRTVKGWLP  188 (335)
T ss_pred             Eeccccccccccc
Confidence            9887766655544

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

Probab=99.60  E-value=4.5e-15  Score=145.75  Aligned_cols=84  Identities=21%  Similarity=0.420  Sum_probs=78.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++++   ++|+++|++||+|++|+|++|+.++++||||||+|+++++|++||+.||+++|+++.|+|.
T Consensus       203 ~~~rLfVgnLp~~vte---edLk~lFs~FG~I~svrl~~D~~tgksKGfGFVeFe~~e~A~kAI~amNg~elgGr~LrV~  279 (612)
T TIGR01645       203 KFNRIYVASVHPDLSE---TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYLRVG  279 (612)
T ss_pred             ccceEEeecCCCCCCH---HHHHHHHhhcCCeeEEEEEecCCCCCcCCeEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            44688 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 023632           97 KAEPKKPN  104 (279)
Q Consensus        97 ~a~~~~~~  104 (279)
                      ++.++...
T Consensus       280 kAi~pP~~  287 (612)
T TIGR01645       280 KCVTPPDA  287 (612)
T ss_pred             ecCCCccc
Confidence            99875443

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=99.59  E-value=1.7e-15  Score=118.91  Aligned_cols=81  Identities=16%  Similarity=0.240  Sum_probs=77.0

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..++++| |+||++.++|   ++|.++|+++|+|+.|.|-.|+.+..+.|||||+|.+.++|+.||+.+|+..|+.++|+
T Consensus        33 ~r~S~tvyVgNlSfyttE---EqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir  109 (153)
T KOG0121|consen   33 LRKSCTVYVGNLSFYTTE---EQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIR  109 (153)
T ss_pred             HhhcceEEEeeeeeeecH---HHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCccccccee
Confidence            3567889 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeecc
Q 023632           95 VKKAE   99 (279)
Q Consensus        95 V~~a~   99 (279)
                      |.+.-
T Consensus       110 ~D~D~  114 (153)
T KOG0121|consen  110 IDWDA  114 (153)
T ss_pred             eeccc
Confidence            99864

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.59  E-value=5.2e-15  Score=105.81  Aligned_cols=69  Identities=26%  Similarity=0.565  Sum_probs=63.9

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      | |.|||+++++   ++|+++|+.++.|++|.++++++ ++++++|||+|.++++|++||+.+++++|++++|+
T Consensus         1 v~i~nlp~~~~~---~~l~~~f~~~g~v~~v~~~~~~~-~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTE---EDLRNFFSRFGPVEKVRLIKNKD-GQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--H---HHHHHHCTTSSBEEEEEEEESTT-SSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCH---HHHHHHHHhcCCcceEEEEeeec-cccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            5 9999999999   99999999999999999999987 89999999999999999999999998999999885

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 ....

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

Probab=99.59  E-value=3.8e-14  Score=138.92  Aligned_cols=75  Identities=25%  Similarity=0.453  Sum_probs=69.1

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcC--CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQF--GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~--G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..++| |.|||++++|   ++|+++|++|  ++|++|+++++        ||||+|+++++|++||++||+++|++++|+
T Consensus       232 ~~k~LfVgNL~~~~te---e~L~~~F~~f~~G~I~rV~~~rg--------fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~  300 (578)
T TIGR01648       232 KVKILYVRNLMTTTTE---EIIEKSFSEFKPGKVERVKKIRD--------YAFVHFEDREDAVKAMDELNGKELEGSEIE  300 (578)
T ss_pred             cccEEEEeCCCCCCCH---HHHHHHHHhcCCCceEEEEeecC--------eEEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            35678 9999999999   9999999999  99999988744        999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |++|+++..
T Consensus       301 V~~Akp~~~  309 (578)
T TIGR01648       301 VTLAKPVDK  309 (578)
T ss_pred             EEEccCCCc
Confidence            999988654

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.

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.58  E-value=1.1e-14  Score=128.60  Aligned_cols=77  Identities=18%  Similarity=0.298  Sum_probs=70.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||++++|   ++|++||+.||+|++|+|++|++   +++||||+|+++++|++||. ||+.+|.++.|+|.
T Consensus         3 ~~rtVfVgNLs~~tTE---~dLrefFS~~G~I~~V~I~~d~~---~~GfAFVtF~d~eaAe~All-LnG~~l~gr~V~Vt   75 (260)
T PLN03120          3 QVRTVKVSNVSLKATE---RDIKEFFSFSGDIEYVEMQSENE---RSQIAYVTFKDPQGAETALL-LSGATIVDQSVTIT   75 (260)
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEeecCC---CCCEEEEEeCcHHHHHHHHH-hcCCeeCCceEEEE
Confidence            35788 9999999999   99999999999999999999864   46899999999999999995 79999999999999


Q ss_pred             eccCC
Q 023632           97 KAEPK  101 (279)
Q Consensus        97 ~a~~~  101 (279)
                      ++..-
T Consensus        76 ~a~~~   80 (260)
T PLN03120         76 PAEDY   80 (260)
T ss_pred             eccCC
Confidence            98743

>smart00360 RRM RNA recognition motif

Probab=99.57  E-value=1.6e-14  Score=101.08  Aligned_cols=71  Identities=34%  Similarity=0.657  Sum_probs=67.4

Q ss_pred             eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           23 TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        23 V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      |.|||+++++   ++|+++|++|+.|++|.|+.++.+.+++++|||+|.+.++|++||+.|++..|.+++|+|+
T Consensus         1 i~~l~~~~~~---~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTE---EELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCH---HHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6799999999   9999999999999999999998889999999999999999999999999999999999874

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

Probab=99.56  E-value=1.2e-14  Score=142.82  Aligned_cols=80  Identities=21%  Similarity=0.400  Sum_probs=75.7

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |+|||++++|   ++|+++|++||+|++|+|++|+.|+++|+||||+|+++++|++||+.||+++|++++|+|
T Consensus       105 ~~~~rLfVGnLp~~~tE---e~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV  181 (612)
T TIGR01645       105 AIMCRVYVGSISFELRE---DTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKV  181 (612)
T ss_pred             cCCCEEEEcCCCCCCCH---HHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeee
Confidence            345788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 023632           96 KKAE   99 (279)
Q Consensus        96 ~~a~   99 (279)
                      .+..
T Consensus       182 ~rp~  185 (612)
T TIGR01645       182 GRPS  185 (612)
T ss_pred             cccc
Confidence            8654

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=99.54  E-value=3.4e-14  Score=136.70  Aligned_cols=80  Identities=36%  Similarity=0.596  Sum_probs=76.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||.++||   ++|+++|++||+|+.|.|++++.++++++||||+|.++++|++||+.||+++|.+++|+|.
T Consensus       185 ~~~~l~v~nl~~~~te---~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~A~~~l~g~~i~g~~i~v~  261 (457)
T TIGR01622       185 NFLKLYVGNLHFNITE---QELRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVG  261 (457)
T ss_pred             CCCEEEEcCCCCCCCH---HHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhcCCcEECCEEEEEE
Confidence            35788 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccC
Q 023632           97 KAEP  100 (279)
Q Consensus        97 ~a~~  100 (279)
                      ++..
T Consensus       262 ~a~~  265 (457)
T TIGR01622       262 YAQD  265 (457)
T ss_pred             EccC
Confidence            9874

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.

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

Probab=99.54  E-value=1.9e-14  Score=142.12  Aligned_cols=85  Identities=21%  Similarity=0.410  Sum_probs=78.9

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.||++++|+   ++|+++|++||+|++|+|+.| .++++++||||+|+++++|++||++||++.|++++|+
T Consensus       282 ~~~~~~l~V~nl~~~~~~---~~L~~~F~~~G~i~~~~i~~d-~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~  357 (562)
T TIGR01628       282 KAQGVNLYVKNLDDTVTD---EKLRELFSECGEITSAKVMLD-EKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLY  357 (562)
T ss_pred             ccCCCEEEEeCCCCccCH---HHHHHHHHhcCCeEEEEEEEC-CCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeE
Confidence            3455678 9999999999   999999999999999999999 6899999999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |.+|+++..+
T Consensus       358 V~~a~~k~~~  367 (562)
T TIGR01628       358 VALAQRKEQR  367 (562)
T ss_pred             EEeccCcHHH
Confidence            9999887644

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

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

Probab=99.54  E-value=9.9e-15  Score=127.60  Aligned_cols=79  Identities=22%  Similarity=0.490  Sum_probs=76.0

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      .| |..|..+++.   ++|++.|.+||+|.+++|++|..|.|+|||+||.|.+.++||+||+.||++.|..|.|+..+|.
T Consensus        64 hvfvgdls~eI~~---e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWlG~R~IRTNWAT  140 (321)
T KOG0148|consen   64 HVFVGDLSPEIDN---EKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWLGRRTIRTNWAT  140 (321)
T ss_pred             eEEehhcchhcch---HHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeeeccceeeccccc
Confidence            35 9999999999   9999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCC
Q 023632          100 PKK  102 (279)
Q Consensus       100 ~~~  102 (279)
                      .|.
T Consensus       141 RKp  143 (321)
T KOG0148|consen  141 RKP  143 (321)
T ss_pred             cCc
Confidence            765

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

Probab=99.53  E-value=6e-15  Score=125.58  Aligned_cols=84  Identities=30%  Similarity=0.517  Sum_probs=79.7

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |++|..+|+|   .-|...|-.||.|++|+|+.|.++.++|+|+||+|+..|+|.+||..||..+|.++.|+|
T Consensus         8 ~~KrtlYVGGladeVte---kvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirV   84 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTE---KVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRV   84 (298)
T ss_pred             ccceeEEeccchHHHHH---HHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEE
Confidence            345778 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      .+|+|.+.
T Consensus        85 N~AkP~ki   92 (298)
T KOG0111|consen   85 NLAKPEKI   92 (298)
T ss_pred             eecCCccc
Confidence            99998654

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

Probab=99.53  E-value=6.1e-14  Score=136.59  Aligned_cols=82  Identities=21%  Similarity=0.388  Sum_probs=77.2

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++++   ++|+++|++||.|+.|.|++++.|+++++||||+|++.++|++||+.||+++|.+++|+|+
T Consensus       294 ~~~~l~v~nlp~~~~~---~~l~~~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~  370 (509)
T TIGR01642       294 SKDRIYIGNLPLYLGE---DQIKELLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQ  370 (509)
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEE
Confidence            34678 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCC
Q 023632           97 KAEPKK  102 (279)
Q Consensus        97 ~a~~~~  102 (279)
                      +|....
T Consensus       371 ~a~~~~  376 (509)
T TIGR01642       371 RACVGA  376 (509)
T ss_pred             ECccCC
Confidence            987543

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

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

Probab=99.53  E-value=3e-14  Score=139.64  Aligned_cols=77  Identities=23%  Similarity=0.373  Sum_probs=69.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-CceeEE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQVEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~~i~V   95 (279)
                      ..++| |.|||++++|   ++|+++|++||+|++|+|++| .++++|+||||+|+++|+|++||+.||+.+|. ++.|.|
T Consensus        57 ~~~~lFVgnLp~~~tE---d~L~~~F~~~G~I~~vrl~~D-~sG~sRGfaFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V  132 (578)
T TIGR01648        57 RGCEVFVGKIPRDLYE---DELVPLFEKAGPIYELRLMMD-FSGQNRGYAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGV  132 (578)
T ss_pred             CCCEEEeCCCCCCCCH---HHHHHHHHhhCCEEEEEEEEC-CCCCccceEEEEeCCHHHHHHHHHHcCCCeecCCccccc
Confidence            35788 9999999999   999999999999999999999 79999999999999999999999999998885 666655


Q ss_pred             eec
Q 023632           96 KKA   98 (279)
Q Consensus        96 ~~a   98 (279)
                      ..+
T Consensus       133 ~~S  135 (578)
T TIGR01648       133 CIS  135 (578)
T ss_pred             ccc
Confidence            433

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.

>smart00362 RRM_2 RNA recognition motif

Probab=99.53  E-value=6.2e-14  Score=98.46  Aligned_cols=71  Identities=28%  Similarity=0.600  Sum_probs=66.2

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +| |.|||.++++   ++|+++|++|++|+++.++.++  ++++++|||+|.+.++|++|++.+++..|.+++|+|+
T Consensus         1 ~v~i~~l~~~~~~---~~l~~~~~~~g~v~~~~~~~~~--~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTE---EDLKELFSKFGPIESVKIPKDT--GKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCH---HHHHHHHHhcCCEEEEEEecCC--CCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            46 9999999999   9999999999999999999886  6788999999999999999999999999999999874

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

Probab=99.52  E-value=3.9e-14  Score=139.88  Aligned_cols=77  Identities=27%  Similarity=0.443  Sum_probs=73.9

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      +| |+|||++|||   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+.||.+.|.++.|+|.++.
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~   78 (562)
T TIGR01628         2 SLYVGDLDPDVTE---AKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALETMNFKRLGGKPIRIMWSQ   78 (562)
T ss_pred             eEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeeEEeeccc
Confidence            67 9999999999   9999999999999999999999999999999999999999999999999999999999999875


Q ss_pred             C
Q 023632          100 P  100 (279)
Q Consensus       100 ~  100 (279)
                      .
T Consensus        79 ~   79 (562)
T TIGR01628        79 R   79 (562)
T ss_pred             c
Confidence            3

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

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

Probab=99.52  E-value=1.1e-14  Score=134.75  Aligned_cols=79  Identities=24%  Similarity=0.432  Sum_probs=72.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..+.| |+||+.+|||   +.|+++|++||+|++|+.++|        ||||.|.+.++|.+||+.+|+++|++..|+|.
T Consensus       258 ~VKvLYVRNL~~~tTe---E~lk~~F~~~G~veRVkk~rD--------YaFVHf~eR~davkAm~~~ngkeldG~~iEvt  326 (506)
T KOG0117|consen  258 KVKVLYVRNLMESTTE---ETLKKLFNEFGKVERVKKPRD--------YAFVHFAEREDAVKAMKETNGKELDGSPIEVT  326 (506)
T ss_pred             heeeeeeeccchhhhH---HHHHHHHHhccceEEeecccc--------eeEEeecchHHHHHHHHHhcCceecCceEEEE
Confidence            45778 9999999999   999999999999999999877        99999999999999999999999999999999


Q ss_pred             eccCCCCCCCC
Q 023632           97 KAEPKKPNLPQ  107 (279)
Q Consensus        97 ~a~~~~~~~~~  107 (279)
                      +|+|..+....
T Consensus       327 LAKP~~k~k~~  337 (506)
T KOG0117|consen  327 LAKPVDKKKKE  337 (506)
T ss_pred             ecCChhhhccc
Confidence            99997655433

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

Probab=99.52  E-value=4.6e-14  Score=135.73  Aligned_cols=83  Identities=22%  Similarity=0.368  Sum_probs=76.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      +...++| |.|||+++++   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+ ||++.|.+++|.
T Consensus        86 ~~~~~~l~V~nlp~~~~~---~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~-l~g~~~~g~~i~  161 (457)
T TIGR01622        86 ERDDRTVFVLQLALKARE---RDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALA-LTGQMLLGRPII  161 (457)
T ss_pred             ccCCcEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHH-hCCCEECCeeeE
Confidence            4456789 9999999999   9999999999999999999999999999999999999999999997 699999999999


Q ss_pred             EeeccCCC
Q 023632           95 VKKAEPKK  102 (279)
Q Consensus        95 V~~a~~~~  102 (279)
                      |+.+..++
T Consensus       162 v~~~~~~~  169 (457)
T TIGR01622       162 VQSSQAEK  169 (457)
T ss_pred             Eeecchhh
Confidence            98876543

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.

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

Probab=99.52  E-value=6.1e-14  Score=116.64  Aligned_cols=78  Identities=17%  Similarity=0.424  Sum_probs=69.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..+++| |.|||.+|.|   ++|+++|.||+.|.+|+|...   -....||||+|+++.+|+.||..-|+..+++..|+|
T Consensus         4 r~~~~iyvGNLP~diRe---keieDlFyKyg~i~~ieLK~r---~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRV   77 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIRE---KEIEDLFYKYGRIREIELKNR---PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRV   77 (241)
T ss_pred             cccceEEecCCCcchhh---ccHHHHHhhhcceEEEEeccC---CCCCCeeEEEecCccchhhhhhcccccccCcceEEE
Confidence            356889 9999999999   999999999999999988543   244679999999999999999999999999999999


Q ss_pred             eeccC
Q 023632           96 KKAEP  100 (279)
Q Consensus        96 ~~a~~  100 (279)
                      +++..
T Consensus        78 Efprg   82 (241)
T KOG0105|consen   78 EFPRG   82 (241)
T ss_pred             EeccC
Confidence            99754

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

Probab=99.51  E-value=3.9e-14  Score=133.90  Aligned_cols=83  Identities=23%  Similarity=0.285  Sum_probs=75.8

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      ..+| |+||||.|.+   .+|+.+|++||.|.+|.|++.+++.. +|||||+|....+|++||+.+|+++|++++|-|.|
T Consensus       117 k~rLIIRNLPf~~k~---~dLk~vFs~~G~V~Ei~IP~k~dgkl-cGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDW  192 (678)
T KOG0127|consen  117 KWRLIIRNLPFKCKK---PDLKNVFSNFGKVVEIVIPRKKDGKL-CGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDW  192 (678)
T ss_pred             cceEEeecCCcccCc---HHHHHHHhhcceEEEEEcccCCCCCc-cceEEEEEeeHHHHHHHHHhccCceecCceeEEee
Confidence            5667 9999999999   99999999999999999998875555 49999999999999999999999999999999999


Q ss_pred             ccCCCCCC
Q 023632           98 AEPKKPNL  105 (279)
Q Consensus        98 a~~~~~~~  105 (279)
                      |.++..-.
T Consensus       193 AV~Kd~ye  200 (678)
T KOG0127|consen  193 AVDKDTYE  200 (678)
T ss_pred             eccccccc
Confidence            99876543

>PLN03213 repressor of silencing 3; Provisional

Probab=99.51  E-value=5.1e-14  Score=131.75  Aligned_cols=79  Identities=19%  Similarity=0.363  Sum_probs=71.8

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCH--HHHHHHHHHcCCCccCCce
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE--QAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~--e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....+| |+||+++|++   ++|+++|..||.|++|.|+  ++|+  |+||||+|.+.  +++++||+.||+.+|+++.
T Consensus         7 ~~~gMRIYVGNLSydVTE---DDLravFSeFGsVkdVEIp--RETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~   79 (759)
T PLN03213          7 GGGGVRLHVGGLGESVGR---DDLLKIFSPMGTVDAVEFV--RTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGR   79 (759)
T ss_pred             CCcceEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEe--cccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCce
Confidence            3456788 9999999999   9999999999999999999  4466  99999999977  7899999999999999999


Q ss_pred             eEEeeccCC
Q 023632           93 VEVKKAEPK  101 (279)
Q Consensus        93 i~V~~a~~~  101 (279)
                      |+|.+|++.
T Consensus        80 LKVNKAKP~   88 (759)
T PLN03213         80 LRLEKAKEH   88 (759)
T ss_pred             eEEeeccHH
Confidence            999998754

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

Probab=99.51  E-value=4.4e-14  Score=111.94  Aligned_cols=84  Identities=20%  Similarity=0.325  Sum_probs=78.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..-..| |.++.+++||   ++|.+.|..||+|+.|.|..|+.|+..|+||+|+|++.++|++||..||+.+|.+++|.|
T Consensus        70 VEGwIi~VtgvHeEatE---edi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~V  146 (170)
T KOG0130|consen   70 VEGWIIFVTGVHEEATE---EDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSV  146 (170)
T ss_pred             eeeEEEEEeccCcchhH---HHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeE
Confidence            344567 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      .|+..+.+
T Consensus       147 Dw~Fv~gp  154 (170)
T KOG0130|consen  147 DWCFVKGP  154 (170)
T ss_pred             EEEEecCC
Confidence            99876554

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

Probab=99.49  E-value=2.4e-14  Score=132.08  Aligned_cols=88  Identities=25%  Similarity=0.423  Sum_probs=78.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC-cc--CCce
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL-EL--AGAQ   92 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~-~l--~g~~   92 (279)
                      .+.++| |+-|+..+||   +||+++|++||.|++|.|++|. .+.+||||||+|++.|.|..||+.||+. ++  +..+
T Consensus       122 ~~e~KLFvg~lsK~~te---~evr~iFs~fG~Ied~~ilrd~-~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~P  197 (510)
T KOG0144|consen  122 VEERKLFVGMLSKQCTE---NEVREIFSRFGHIEDCYILRDP-DGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQP  197 (510)
T ss_pred             ccchhhhhhhccccccH---HHHHHHHHhhCccchhhheecc-cccccceeEEEEehHHHHHHHHHhhccceeeccCCCc
Confidence            446788 9999999999   9999999999999999999995 7899999999999999999999999984 33  3678


Q ss_pred             eEEeeccCCCCCCCCC
Q 023632           93 VEVKKAEPKKPNLPQP  108 (279)
Q Consensus        93 i~V~~a~~~~~~~~~~  108 (279)
                      |.|+||++++++..++
T Consensus       198 LVVkFADtqkdk~~~~  213 (510)
T KOG0144|consen  198 LVVKFADTQKDKDGKR  213 (510)
T ss_pred             eEEEecccCCCchHHH
Confidence            9999999998876543

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

Probab=99.49  E-value=4.5e-14  Score=130.22  Aligned_cols=87  Identities=23%  Similarity=0.449  Sum_probs=77.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC-ccC--C
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL-ELA--G   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~-~l~--g   90 (279)
                      .|.+..+| |+-||..|+|   +||+++|++|+.|.+|.|++||.|+.+++||||+|.+.++|++||.+||++ +|-  .
T Consensus        30 ~d~~~vKlfVgqIprt~sE---~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~  106 (510)
T KOG0144|consen   30 PDGSAVKLFVGQIPRTASE---KDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMH  106 (510)
T ss_pred             CCchhhhheeccCCccccH---HHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCC
Confidence            34566677 9999999999   999999999999999999999999999999999999999999999999774 444  5


Q ss_pred             ceeEEeeccCCCCC
Q 023632           91 AQVEVKKAEPKKPN  104 (279)
Q Consensus        91 ~~i~V~~a~~~~~~  104 (279)
                      ++|.|++|+.++++
T Consensus       107 ~pvqvk~Ad~E~er  120 (510)
T KOG0144|consen  107 HPVQVKYADGERER  120 (510)
T ss_pred             cceeecccchhhhc
Confidence            78999999876665

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

Probab=99.49  E-value=1.3e-13  Score=120.52  Aligned_cols=79  Identities=33%  Similarity=0.660  Sum_probs=75.8

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |.|||+++++   ++|+++|.+|+.|..|.|+.|+.++++++||||+|.++++|++||+.+++..|.+++|+|.+
T Consensus       115 ~~~l~v~nL~~~~~~---~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~  191 (306)
T COG0724         115 NNTLFVGNLPYDVTE---EDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQK  191 (306)
T ss_pred             CceEEEeCCCCCCCH---HHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeec
Confidence            4888 9999999999   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 023632           98 AEP  100 (279)
Q Consensus        98 a~~  100 (279)
                      +.+
T Consensus       192 ~~~  194 (306)
T COG0724         192 AQP  194 (306)
T ss_pred             ccc
Confidence            653

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

Probab=99.49  E-value=7.4e-14  Score=121.63  Aligned_cols=83  Identities=22%  Similarity=0.468  Sum_probs=78.2

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..+.| |.-||.++|+   |||+.+|...|+|++|++++||.|+++-||+||.|.+++||++||..||+..|..+.|+|.
T Consensus        40 skTNLIvNYLPQ~MTq---dE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVS  116 (360)
T KOG0145|consen   40 SKTNLIVNYLPQNMTQ---DELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVS  116 (360)
T ss_pred             ccceeeeeecccccCH---HHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEE
Confidence            34456 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +|+|...
T Consensus       117 yARPSs~  123 (360)
T KOG0145|consen  117 YARPSSD  123 (360)
T ss_pred             eccCChh
Confidence            9998654

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

Probab=99.49  E-value=1.2e-13  Score=128.00  Aligned_cols=80  Identities=25%  Similarity=0.400  Sum_probs=74.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-CceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~~i~   94 (279)
                      ..-+.| |+.||.++.|   ++|.-+|++.|+|-+++||+|+.++.+||||||+|.+.++|++||+.||+++|. ++.|.
T Consensus        81 ~~G~EVfvGkIPrD~~E---deLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK~ig  157 (506)
T KOG0117|consen   81 PRGCEVFVGKIPRDVFE---DELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGKLLG  157 (506)
T ss_pred             CCCceEEecCCCccccc---hhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCCEeE
Confidence            345788 9999999999   999999999999999999999999999999999999999999999999999997 88888


Q ss_pred             Eeecc
Q 023632           95 VKKAE   99 (279)
Q Consensus        95 V~~a~   99 (279)
                      |+.+.
T Consensus       158 vc~Sv  162 (506)
T KOG0117|consen  158 VCVSV  162 (506)
T ss_pred             EEEee
Confidence            87654

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

Probab=99.47  E-value=1.7e-13  Score=119.93  Aligned_cols=87  Identities=22%  Similarity=0.457  Sum_probs=78.3

Q ss_pred             hhhcCCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc
Q 023632           10 TMFINRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL   88 (279)
Q Consensus        10 ~~~~~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l   88 (279)
                      +...+..+++++| |+||+.-++|   ++|++.|+.||+|.+|+|.++      ++||||.|+++|+|.+||.++|+.+|
T Consensus       155 eV~NQssp~NtsVY~G~I~~~lte---~~mr~~Fs~fG~I~EVRvFk~------qGYaFVrF~tkEaAahAIv~mNntei  225 (321)
T KOG0148|consen  155 EVYNQSSPDNTSVYVGNIASGLTE---DLMRQTFSPFGPIQEVRVFKD------QGYAFVRFETKEAAAHAIVQMNNTEI  225 (321)
T ss_pred             HHhccCCCCCceEEeCCcCccccH---HHHHHhcccCCcceEEEEecc------cceEEEEecchhhHHHHHHHhcCcee
Confidence            3444567788999 9999999999   999999999999999999988      68999999999999999999999999


Q ss_pred             CCceeEEeeccCCCCCC
Q 023632           89 AGAQVEVKKAEPKKPNL  105 (279)
Q Consensus        89 ~g~~i~V~~a~~~~~~~  105 (279)
                      .++.|++.+-+......
T Consensus       226 ~G~~VkCsWGKe~~~~~  242 (321)
T KOG0148|consen  226 GGQLVRCSWGKEGDDGI  242 (321)
T ss_pred             CceEEEEeccccCCCCC
Confidence            99999999987765443

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.47  E-value=2.8e-13  Score=118.09  Aligned_cols=76  Identities=16%  Similarity=0.218  Sum_probs=68.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ...+| |.||++.+||   ++|++||+.||+|++|+|++|.+   .++||||+|+++++|+.|| .||+.+|.+++|.|.
T Consensus         4 ~g~TV~V~NLS~~tTE---~dLrefFS~~G~I~~V~I~~D~e---t~gfAfVtF~d~~aaetAl-lLnGa~l~d~~I~It   76 (243)
T PLN03121          4 GGYTAEVTNLSPKATE---KDVYDFFSHCGAIEHVEIIRSGE---YACTAYVTFKDAYALETAV-LLSGATIVDQRVCIT   76 (243)
T ss_pred             CceEEEEecCCCCCCH---HHHHHHHHhcCCeEEEEEecCCC---cceEEEEEECCHHHHHHHH-hcCCCeeCCceEEEE
Confidence            44688 9999999999   99999999999999999999854   4579999999999999999 569999999999998


Q ss_pred             eccC
Q 023632           97 KAEP  100 (279)
Q Consensus        97 ~a~~  100 (279)
                      .+..
T Consensus        77 ~~~~   80 (243)
T PLN03121         77 RWGQ   80 (243)
T ss_pred             eCcc
Confidence            8653

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

Probab=99.47  E-value=7.1e-14  Score=115.95  Aligned_cols=80  Identities=29%  Similarity=0.451  Sum_probs=76.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ....+| |.||+..+++   +.|.++|-+.++|++|.|++|+.|.+.++||||+|.++|+|+-||+.||.+.|-+++|+|
T Consensus         7 nqd~tiyvgnld~kvs~---~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv   83 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSE---ELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRV   83 (203)
T ss_pred             CCCceEEEecCCHHHHH---HHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEE
Confidence            345778 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 023632           96 KKAE   99 (279)
Q Consensus        96 ~~a~   99 (279)
                      .++.
T Consensus        84 ~kas   87 (203)
T KOG0131|consen   84 NKAS   87 (203)
T ss_pred             Eecc
Confidence            9987

>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=99.46  E-value=5.2e-13  Score=94.18  Aligned_cols=73  Identities=33%  Similarity=0.622  Sum_probs=67.7

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      +| |.+||+++++   ++|+++|+.++.|+.+.++.++.+ +++++|||+|.+.++|++|++.++...+++++|+|++
T Consensus         1 ~i~i~~l~~~~~~---~~i~~~~~~~g~i~~~~~~~~~~~-~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTE---EDLRELFSKFGKVESVRIVRDKDT-KSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCH---HHHHHHHHhcCCEEEEEEeeCCCC-CcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            46 9999999999   999999999999999999988765 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).

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

Probab=99.45  E-value=1.4e-14  Score=120.01  Aligned_cols=80  Identities=20%  Similarity=0.424  Sum_probs=75.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .++..| |++||+++||   .||..+|++||+|++|.+++|+.|++++||||+.|++..+...||..||++.|.+|.|+|
T Consensus        33 kdsA~Iyiggl~~~LtE---gDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirV  109 (219)
T KOG0126|consen   33 KDSAYIYIGGLPYELTE---GDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRV  109 (219)
T ss_pred             ccceEEEECCCcccccC---CcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEe
Confidence            345678 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 023632           96 KKAE   99 (279)
Q Consensus        96 ~~a~   99 (279)
                      ....
T Consensus       110 DHv~  113 (219)
T KOG0126|consen  110 DHVS  113 (219)
T ss_pred             eecc
Confidence            8653

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

Probab=99.44  E-value=2.1e-13  Score=129.26  Aligned_cols=82  Identities=23%  Similarity=0.413  Sum_probs=78.2

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +.| |+|||++++|   ++|.++|+..+.|.+++++.|++|+++|+|+||+|.++++|++||+.||+.++.+++|+|.++
T Consensus        19 ~~v~vgnip~~~se---~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~   95 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSE---EQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYA   95 (435)
T ss_pred             cceEecCCCCcccH---HHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeecc
Confidence            778 9999999999   999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cCCCCC
Q 023632           99 EPKKPN  104 (279)
Q Consensus        99 ~~~~~~  104 (279)
                      ...+.+
T Consensus        96 ~~~~~~  101 (435)
T KOG0108|consen   96 SNRKNA  101 (435)
T ss_pred             cccchh
Confidence            765543

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

Probab=99.44  E-value=4e-13  Score=101.94  Aligned_cols=80  Identities=15%  Similarity=0.248  Sum_probs=71.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ...++.| |.|||+++|.   +++.++|.+||.|..|+|-..++|   +|.|||+|++..+|++|++.|++..++++.|.
T Consensus        15 pevnriLyirNLp~~ITs---eemydlFGkyg~IrQIRiG~~k~T---rGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~   88 (124)
T KOG0114|consen   15 PEVNRILYIRNLPFKITS---EEMYDLFGKYGTIRQIRIGNTKET---RGTAFVVYEDIFDAKKACDHLSGYNVDNRYLV   88 (124)
T ss_pred             hhhheeEEEecCCccccH---HHHHHHhhcccceEEEEecCccCc---CceEEEEehHhhhHHHHHHHhcccccCCceEE
Confidence            3445666 9999999999   999999999999999999876654   79999999999999999999999999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |-.-.+.
T Consensus        89 vlyyq~~   95 (124)
T KOG0114|consen   89 VLYYQPE   95 (124)
T ss_pred             EEecCHH
Confidence            9876654

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

Probab=99.43  E-value=7e-13  Score=128.81  Aligned_cols=78  Identities=15%  Similarity=0.238  Sum_probs=71.7

Q ss_pred             CCCcee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ...++| |.|||+ ++|+   ++|+++|++||.|++|+|++++     ++||||+|+++++|++||+.||+++|.+++|+
T Consensus       273 ~~~~~l~v~nL~~~~vt~---~~L~~lF~~yG~V~~vki~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~  344 (481)
T TIGR01649       273 GPGSVLMVSGLHQEKVNC---DRLFNLFCVYGNVERVKFMKNK-----KETALIEMADPYQAQLALTHLNGVKLFGKPLR  344 (481)
T ss_pred             CCCCEEEEeCCCCCCCCH---HHHHHHHHhcCCeEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEE
Confidence            456788 999998 6999   9999999999999999999874     68999999999999999999999999999999


Q ss_pred             EeeccCCC
Q 023632           95 VKKAEPKK  102 (279)
Q Consensus        95 V~~a~~~~  102 (279)
                      |++++.+.
T Consensus       345 v~~s~~~~  352 (481)
T TIGR01649       345 VCPSKQQN  352 (481)
T ss_pred             EEEccccc
Confidence            99987654

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=99.43  E-value=6.7e-13  Score=95.49  Aligned_cols=61  Identities=25%  Similarity=0.410  Sum_probs=55.2

Q ss_pred             HHHHHHHh----cCCCeEEEE-EeecCCC--CCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           36 DEFKDFFM----QFGDVQEHQ-IMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        36 ~~L~~~F~----~~G~V~~v~-i~~d~~t--g~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ++|+++|+    +||+|.+|. |+.++.+  +++++|+||+|+++++|++||+.||+..|++++|+++
T Consensus         3 ~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        3 EDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             hhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            67778887    999999995 7777766  8999999999999999999999999999999999873

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

Probab=99.42  E-value=2.4e-13  Score=123.84  Aligned_cols=90  Identities=43%  Similarity=0.667  Sum_probs=82.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..+++| |+.||.+++|   ++|+++|++|+.|.++.|+.|+++.++++|+||+|++++++++++.+ .-++|++++|+|
T Consensus        95 ~~tkkiFvGG~~~~~~e---~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdkv~~~-~f~~~~gk~vev  170 (311)
T KOG4205|consen   95 LRTKKIFVGGLPPDTTE---EDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDKVTLQ-KFHDFNGKKVEV  170 (311)
T ss_pred             cceeEEEecCcCCCCch---HHHhhhhhccceeEeeEEeecccccccccceeeEeccccccceeccc-ceeeecCceeeE
Confidence            346789 9999999999   99999999999999999999999999999999999999999999988 789999999999


Q ss_pred             eeccCCCCCCCCCCC
Q 023632           96 KKAEPKKPNLPQPSY  110 (279)
Q Consensus        96 ~~a~~~~~~~~~~~~  110 (279)
                      ++|.|+....+....
T Consensus       171 krA~pk~~~~~~~~~  185 (311)
T KOG4205|consen  171 KRAIPKEVMQSTKSS  185 (311)
T ss_pred             eeccchhhccccccc
Confidence            999999887765543

>PF13893 RRM_5: RNA recognition motif

Probab=99.40  E-value=1.2e-12  Score=89.85  Aligned_cols=56  Identities=25%  Similarity=0.559  Sum_probs=51.1

Q ss_pred             HHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           38 FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        38 L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      |+++|++||+|++|.|..++     +++|||+|++.++|++|++.||+..|++++|+|++|
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            68999999999999997664     579999999999999999999999999999999985

(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 ....

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

Probab=99.38  E-value=1.5e-12  Score=126.43  Aligned_cols=75  Identities=11%  Similarity=0.201  Sum_probs=68.3

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc--CCCccCCceeEE
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGAQVEV   95 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l--ng~~l~g~~i~V   95 (279)
                      +++| |+|||++++|   ++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.|  +.+.|.+++|.|
T Consensus         2 s~vv~V~nLp~~~te---~~L~~~f~~fG~V~~v~i~~~------k~~afVef~~~e~A~~Ai~~~~~~~~~l~g~~l~v   72 (481)
T TIGR01649         2 SPVVHVRNLPQDVVE---ADLVEALIPFGPVSYVMMLPG------KRQALVEFEDEESAKACVNFATSVPIYIRGQPAFF   72 (481)
T ss_pred             ccEEEEcCCCCCCCH---HHHHHHHHhcCCeeEEEEECC------CCEEEEEeCchHHHHHHHHHhhcCCceEcCeEEEE
Confidence            5788 9999999999   999999999999999999864      579999999999999999974  778999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      +++..++
T Consensus        73 ~~s~~~~   79 (481)
T TIGR01649        73 NYSTSQE   79 (481)
T ss_pred             EecCCcc
Confidence            9987653

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).

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

Probab=99.38  E-value=1.1e-12  Score=121.35  Aligned_cols=78  Identities=22%  Similarity=0.351  Sum_probs=71.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHH-hcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFF-MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F-~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      .+.+ |.|||+++.|   ++||++| ++-++|+.|+|+.|. ++|+|+||.|||+++|.++||++.||.++|++++|+|+
T Consensus        44 ~R~vfItNIpyd~rW---qdLKdLvrekvGev~yveLl~D~-~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vK  119 (608)
T KOG4212|consen   44 DRSVFITNIPYDYRW---QDLKDLVREKVGEVEYVELLFDE-SGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVK  119 (608)
T ss_pred             cceEEEecCcchhhh---HhHHHHHHHhcCceEeeeeeccc-CCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEe
Confidence            3447 9999999999   9999999 578999999999995 89999999999999999999999999999999999998


Q ss_pred             eccC
Q 023632           97 KAEP  100 (279)
Q Consensus        97 ~a~~  100 (279)
                      ....
T Consensus       120 Ed~d  123 (608)
T KOG4212|consen  120 EDHD  123 (608)
T ss_pred             ccCc
Confidence            7543

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

Probab=99.36  E-value=1.1e-12  Score=116.00  Aligned_cols=73  Identities=26%  Similarity=0.520  Sum_probs=68.6

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      .+| |+|||.++++   .+|+.+|++|++|++|+|+++        |+||..++++.++.||..||+.+|++..|+|+.+
T Consensus         3 ~KLFIGNLp~~~~~---~elr~lFe~ygkVlECDIvKN--------YgFVHiEdktaaedairNLhgYtLhg~nInVeaS   71 (346)
T KOG0109|consen    3 VKLFIGNLPREATE---QELRSLFEQYGKVLECDIVKN--------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEAS   71 (346)
T ss_pred             cchhccCCCcccch---HHHHHHHHhhCceEeeeeecc--------cceEEeecccccHHHHhhcccceecceEEEEEec
Confidence            456 9999999999   999999999999999999977        9999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023632           99 EPKKP  103 (279)
Q Consensus        99 ~~~~~  103 (279)
                      +.|.+
T Consensus        72 ksKsk   76 (346)
T KOG0109|consen   72 KSKSK   76 (346)
T ss_pred             cccCC
Confidence            88733

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

Probab=99.36  E-value=9.2e-13  Score=115.23  Aligned_cols=88  Identities=19%  Similarity=0.383  Sum_probs=82.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +-++-++| |-.||.+..+   .||..+|..||.|++.+|..|+.|..+|+|+||.|+++.+++.||..||++.|.-++|
T Consensus       281 eGPeGCNlFIYHLPQEFgD---aEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRL  357 (371)
T KOG0146|consen  281 EGPEGCNLFIYHLPQEFGD---AELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRL  357 (371)
T ss_pred             cCCCcceEEEEeCchhhcc---HHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhh
Confidence            45677899 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|...+||...+
T Consensus       358 KVQLKRPkdanR  369 (371)
T KOG0146|consen  358 KVQLKRPKDANR  369 (371)
T ss_pred             hhhhcCccccCC
Confidence            999988876544

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

Probab=99.35  E-value=1.2e-12  Score=118.39  Aligned_cols=83  Identities=16%  Similarity=0.346  Sum_probs=78.0

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .++.++| |..|.+.+|+   ++|+-||+.||+|+.|.|++|+.|+.+-.||||+|++.+++++|.-+|++..|+++.|.
T Consensus       236 ~PPeNVLFVCKLNPVTtD---eDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIH  312 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTD---EDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIH  312 (479)
T ss_pred             CCCcceEEEEecCCcccc---cchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEE
Confidence            4566788 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |.++++-
T Consensus       313 VDFSQSV  319 (479)
T KOG0415|consen  313 VDFSQSV  319 (479)
T ss_pred             eehhhhh
Confidence            9987653

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

Probab=99.35  E-value=2.2e-12  Score=122.22  Aligned_cols=83  Identities=27%  Similarity=0.430  Sum_probs=75.8

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc-----CC-CccCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-----NK-LELAG   90 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l-----ng-~~l~g   90 (279)
                      ..++| |+|||+++||   ++|+++|++||+|+.+.|+.++.|++++|+|||.|.+.++|++||+..     .+ ..|++
T Consensus       291 ~~~tVFvRNL~fD~tE---Eel~~~fskFG~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~G  367 (678)
T KOG0127|consen  291 EGKTVFVRNLPFDTTE---EELKEHFSKFGEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDG  367 (678)
T ss_pred             ccceEEEecCCccccH---HHHHHHHHhhccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEec
Confidence            34788 9999999999   999999999999999999999999999999999999999999999986     22 67889


Q ss_pred             ceeEEeeccCCCC
Q 023632           91 AQVEVKKAEPKKP  103 (279)
Q Consensus        91 ~~i~V~~a~~~~~  103 (279)
                      +.|+|..|.++++
T Consensus       368 R~Lkv~~Av~Rke  380 (678)
T KOG0127|consen  368 RLLKVTLAVTRKE  380 (678)
T ss_pred             cEEeeeeccchHH
Confidence            9999999987654

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

Probab=99.30  E-value=2.4e-12  Score=117.33  Aligned_cols=85  Identities=39%  Similarity=0.635  Sum_probs=78.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |.+|+|+++|   +.|++.|.+|++|.+|.|++|+.|+++++|.||+|++++.+.++|.. ..++|+++.|+++
T Consensus         5 ~~~KlfiGgisw~tte---e~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~-~~h~~dgr~ve~k   80 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTE---ESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNA-RTHKLDGRSVEPK   80 (311)
T ss_pred             CCcceeecCcCccccH---HHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecc-cccccCCccccce
Confidence            67888 9999999999   99999999999999999999999999999999999999999999888 5789999999999


Q ss_pred             eccCCCCCCC
Q 023632           97 KAEPKKPNLP  106 (279)
Q Consensus        97 ~a~~~~~~~~  106 (279)
                      .|.++.....
T Consensus        81 ~av~r~~~~~   90 (311)
T KOG4205|consen   81 RAVSREDQTK   90 (311)
T ss_pred             eccCcccccc
Confidence            9998776543

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

Probab=99.28  E-value=1.4e-11  Score=107.48  Aligned_cols=79  Identities=23%  Similarity=0.316  Sum_probs=75.0

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ..| |-||.++++|   ..|.++|.+||.|..|+|++|..|.++|||+||++.+-++|..||..||+..|.++.|.|.+.
T Consensus       279 ~ciFvYNLspd~de---~~LWQlFgpFGAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~lg~rvLQVsFK  355 (360)
T KOG0145|consen  279 WCIFVYNLSPDADE---SILWQLFGPFGAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYRLGDRVLQVSFK  355 (360)
T ss_pred             eEEEEEecCCCchH---hHHHHHhCcccceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCccccceEEEEEEe
Confidence            456 9999999999   999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             cCC
Q 023632           99 EPK  101 (279)
Q Consensus        99 ~~~  101 (279)
                      ..+
T Consensus       356 tnk  358 (360)
T KOG0145|consen  356 TNK  358 (360)
T ss_pred             cCC
Confidence            654

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

Probab=99.26  E-value=4.4e-11  Score=112.98  Aligned_cols=79  Identities=24%  Similarity=0.440  Sum_probs=68.4

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ..| |.|||.++++   ++|+++|++||+|++..|.......+..+|+||+|++.++++.||++ +...|++++|.|+..
T Consensus       289 ~~i~V~nlP~da~~---~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~A-sp~~ig~~kl~Veek  364 (419)
T KOG0116|consen  289 LGIFVKNLPPDATP---AELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEA-SPLEIGGRKLNVEEK  364 (419)
T ss_pred             cceEeecCCCCCCH---HHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhc-CccccCCeeEEEEec
Confidence            448 9999999999   99999999999999988876543344459999999999999999999 689999999999987


Q ss_pred             cCCC
Q 023632           99 EPKK  102 (279)
Q Consensus        99 ~~~~  102 (279)
                      ++..
T Consensus       365 ~~~~  368 (419)
T KOG0116|consen  365 RPGF  368 (419)
T ss_pred             cccc
Confidence            6543

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

Probab=99.26  E-value=6.9e-12  Score=104.22  Aligned_cols=85  Identities=28%  Similarity=0.379  Sum_probs=76.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~-v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....+| |+||.++++|   ..|.++|+.||+|.. -+|++|..|+.+++|+||.|++.|.+++||+.+|++.++.++|+
T Consensus        94 ~vganlfvgNLd~~vDe---~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfeasd~ai~s~ngq~l~nr~it  170 (203)
T KOG0131|consen   94 DVGANLFVGNLDPEVDE---KLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEASDAAIGSMNGQYLCNRPIT  170 (203)
T ss_pred             cccccccccccCcchhH---HHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHHHHHHHHHhccchhcCCceE
Confidence            345678 9999999999   999999999999865 48999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |..+..+...
T Consensus       171 v~ya~k~~~k  180 (203)
T KOG0131|consen  171 VSYAFKKDTK  180 (203)
T ss_pred             EEEEEecCCC
Confidence            9998765443

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

Probab=99.25  E-value=1e-11  Score=109.78  Aligned_cols=79  Identities=20%  Similarity=0.423  Sum_probs=72.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +...+++| |.||.+.|+.   +||++.|++|++|.+|+|++|        ++||.|+-.++|..||+.||+.+|.++++
T Consensus        74 Ksk~stkl~vgNis~tctn---~ElRa~fe~ygpviecdivkd--------y~fvh~d~~eda~~air~l~~~~~~gk~m  142 (346)
T KOG0109|consen   74 KSKASTKLHVGNISPTCTN---QELRAKFEKYGPVIECDIVKD--------YAFVHFDRAEDAVEAIRGLDNTEFQGKRM  142 (346)
T ss_pred             cCCCccccccCCCCccccC---HHHhhhhcccCCceeeeeecc--------eeEEEEeeccchHHHHhccccccccccee
Confidence            45567889 9999999999   999999999999999999977        99999999999999999999999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|+.+.++...
T Consensus       143 ~vq~stsrlrt  153 (346)
T KOG0109|consen  143 HVQLSTSRLRT  153 (346)
T ss_pred             eeeeecccccc
Confidence            99998776543

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

Probab=99.24  E-value=1.1e-11  Score=117.72  Aligned_cols=80  Identities=33%  Similarity=0.547  Sum_probs=75.0

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      | |+||.++++|   ++|+.+|+.|+.|+.|.+++|.+|+++|+|+||+|.+.++|.+|+++||+.+|.++.|+|.....
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 LYVGNLHFNITE---DMLRGIFEPFGKIENVQLTKDSETGRSKGFGFITFVNKEDARKALEQLNGFELAGRLIKVSVVTE  357 (549)
T ss_pred             hhhcccccCchH---HHHhhhccCcccceeeeeccccccccccCcceEEEecHHHHHHHHHHhccceecCceEEEEEeee
Confidence            7 9999999999   99999999999999999999999999999999999999999999999999999999999987665


Q ss_pred             CCCC
Q 023632          101 KKPN  104 (279)
Q Consensus       101 ~~~~  104 (279)
                      +...
T Consensus       358 r~~~  361 (549)
T KOG0147|consen  358 RVDT  361 (549)
T ss_pred             eccc
Confidence            4433

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

Probab=99.21  E-value=9.7e-12  Score=112.92  Aligned_cols=76  Identities=22%  Similarity=0.419  Sum_probs=73.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      -++| |+.|.+++.|   +.|+..|..||+|++|.+.+|+.|.++|+||||||+-+|.|+.|++.||+.+|.+|.|+|..
T Consensus       113 McRvYVGSIsfEl~E---DtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgr  189 (544)
T KOG0124|consen  113 MCRVYVGSISFELRE---DTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGR  189 (544)
T ss_pred             hHheeeeeeEEEech---HHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccC
Confidence            4788 9999999999   99999999999999999999999999999999999999999999999999999999999973

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

Probab=99.20  E-value=5.3e-11  Score=111.65  Aligned_cols=81  Identities=21%  Similarity=0.382  Sum_probs=74.1

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ..| |.||+++++.   ++|.++|+.||+|++|+|++|++ + +++| ||+|+++++|++||++||+..+.+++|.|...
T Consensus        77 ~~~~i~nl~~~~~~---~~~~d~f~~~g~ilS~kv~~~~~-g-~kg~-FV~f~~e~~a~~ai~~~ng~ll~~kki~vg~~  150 (369)
T KOG0123|consen   77 SLVFIKNLDESIDN---KSLYDTFSEFGNILSCKVATDEN-G-SKGY-FVQFESEESAKKAIEKLNGMLLNGKKIYVGLF  150 (369)
T ss_pred             ceeeecCCCcccCc---HHHHHHHHhhcCeeEEEEEEcCC-C-ceee-EEEeCCHHHHHHHHHHhcCcccCCCeeEEeec
Confidence            338 9999999999   99999999999999999999964 3 9999 99999999999999999999999999999988


Q ss_pred             cCCCCCCC
Q 023632           99 EPKKPNLP  106 (279)
Q Consensus        99 ~~~~~~~~  106 (279)
                      ..++++..
T Consensus       151 ~~~~er~~  158 (369)
T KOG0123|consen  151 ERKEEREA  158 (369)
T ss_pred             cchhhhcc
Confidence            87766553

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

Probab=99.15  E-value=5.4e-11  Score=104.26  Aligned_cols=87  Identities=21%  Similarity=0.410  Sum_probs=76.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC---C
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA---G   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~---g   90 (279)
                      +.-+.++| |+-|...-+|   ||++.+|..||+|++|.+++.. .+.+||||||.|.+..+|+.||..||+....   .
T Consensus        15 rg~~drklfvgml~kqq~e---~dvrrlf~pfG~~~e~tvlrg~-dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGAS   90 (371)
T KOG0146|consen   15 RGGDDRKLFVGMLNKQQSE---DDVRRLFQPFGNIEECTVLRGP-DGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGAS   90 (371)
T ss_pred             CCccchhhhhhhhcccccH---HHHHHHhcccCCcceeEEecCC-CCCCCCceEEEeccchHHHHHHHHhcccccCCCCc
Confidence            34467888 9999999999   9999999999999999999886 6889999999999999999999999985443   5


Q ss_pred             ceeEEeeccCCCCCC
Q 023632           91 AQVEVKKAEPKKPNL  105 (279)
Q Consensus        91 ~~i~V~~a~~~~~~~  105 (279)
                      ..|.|++|+..+++.
T Consensus        91 SSLVVK~ADTdkER~  105 (371)
T KOG0146|consen   91 SSLVVKFADTDKERT  105 (371)
T ss_pred             cceEEEeccchHHHH
Confidence            679999999877754

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

Probab=99.11  E-value=2.1e-10  Score=111.86  Aligned_cols=84  Identities=14%  Similarity=0.172  Sum_probs=68.2

Q ss_pred             CCCcee-eeCCCCC--C-C----cccHHHHHHHHhcCCCeEEEEEeecC---CCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           17 TTTQKM-TGLSLTP--V-T----EPALDEFKDFFMQFGDVQEHQIMRDH---STSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        17 ~~~~~l-V~nLp~~--~-t----e~~~~~L~~~F~~~G~V~~v~i~~d~---~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      ..+++| |.||...  + +    ++.+++|+++|++||.|++|+|+++.   .+...+|++||+|+++++|++||+.||+
T Consensus       407 ~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~G~v~~v~i~~~~~~~~~~~~~G~~fV~F~~~e~A~~A~~~lnG  486 (509)
T TIGR01642       407 KPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTPGVGKVFLEYADVRSAEKAMEGMNG  486 (509)
T ss_pred             CCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhcCCeeEEEeeccCcCCCcCCCcceEEEEECCHHHHHHHHHHcCC
Confidence            356777 8888532  1 1    11236899999999999999998753   3456689999999999999999999999


Q ss_pred             CccCCceeEEeeccC
Q 023632           86 LELAGAQVEVKKAEP  100 (279)
Q Consensus        86 ~~l~g~~i~V~~a~~  100 (279)
                      .+|++++|.|.+...
T Consensus       487 r~~~gr~v~~~~~~~  501 (509)
T TIGR01642       487 RKFNDRVVVAAFYGE  501 (509)
T ss_pred             CEECCeEEEEEEeCH
Confidence            999999999998754

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

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

Probab=99.11  E-value=1.5e-10  Score=110.33  Aligned_cols=81  Identities=20%  Similarity=0.401  Sum_probs=75.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |..|...+..   .+|+.||++||+|+-.+|+++..+--.++|+||++.+.++|.+||+.||..+|.++.|.|
T Consensus       403 ~~gRNlWVSGLSstTRA---tDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISV  479 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRA---TDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISV  479 (940)
T ss_pred             ccccceeeeccccchhh---hHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeee
Confidence            345788 9999999988   999999999999999999999888888999999999999999999999999999999999


Q ss_pred             eeccC
Q 023632           96 KKAEP  100 (279)
Q Consensus        96 ~~a~~  100 (279)
                      ++++.
T Consensus       480 EkaKN  484 (940)
T KOG4661|consen  480 EKAKN  484 (940)
T ss_pred             eeccc
Confidence            98764

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

Probab=99.10  E-value=2.9e-10  Score=96.39  Aligned_cols=81  Identities=22%  Similarity=0.367  Sum_probs=72.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcC-CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQF-GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~-G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ....+ |..||.-+.|   .+|..+|.+| +.|..+++-+++.|+.+|+||||+|+++|.|+-|.+.||+..|.++.|+|
T Consensus        48 ~~g~~~~~~~p~g~~e---~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c  124 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFE---TEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLEC  124 (214)
T ss_pred             CccceeecccccchhH---HHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeee
Confidence            33445 8899999999   9999999888 77888888899999999999999999999999999999999999999999


Q ss_pred             eeccCC
Q 023632           96 KKAEPK  101 (279)
Q Consensus        96 ~~a~~~  101 (279)
                      .+-.|.
T Consensus       125 ~vmppe  130 (214)
T KOG4208|consen  125 HVMPPE  130 (214)
T ss_pred             EEeCch
Confidence            876654

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

Probab=99.09  E-value=2.6e-10  Score=107.26  Aligned_cols=81  Identities=23%  Similarity=0.332  Sum_probs=69.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +......| +..|||++|+   +||.+||+.+ .|++++|+++  ++++.+-|||||+++|++++||++ |..++..+-|
T Consensus         6 e~~~~~~vr~rGLPwsat~---~ei~~Ff~~~-~I~~~~~~r~--~Gr~sGeA~Ve~~seedv~~Alkk-dR~~mg~RYI   78 (510)
T KOG4211|consen    6 EGSTAFEVRLRGLPWSATE---KEILDFFSNC-GIENLEIPRR--NGRPSGEAYVEFTSEEDVEKALKK-DRESMGHRYI   78 (510)
T ss_pred             CCCcceEEEecCCCccccH---HHHHHHHhcC-ceeEEEEecc--CCCcCcceEEEeechHHHHHHHHh-hHHHhCCceE
Confidence            34455677 9999999999   9999999998 5777666554  899999999999999999999999 8889999999


Q ss_pred             EEeeccCCC
Q 023632           94 EVKKAEPKK  102 (279)
Q Consensus        94 ~V~~a~~~~  102 (279)
                      +|..+..++
T Consensus        79 EVf~~~~~e   87 (510)
T KOG4211|consen   79 EVFTAGGAE   87 (510)
T ss_pred             EEEccCCcc
Confidence            998885543

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

Probab=99.08  E-value=3.8e-10  Score=96.90  Aligned_cols=80  Identities=20%  Similarity=0.361  Sum_probs=71.0

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHH----HHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKD----FFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~----~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ..+| |.||++.+..   ++|++    +|++||+|.+|.+.+   |.+.||-|||+|++.+.|..|+.+|++..+-++++
T Consensus         9 n~TlYInnLnekI~~---~elkrsL~~LFsqfG~ildI~a~k---t~KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~m   82 (221)
T KOG4206|consen    9 NGTLYINNLNEKIKK---DELKRSLYLLFSQFGKILDISAFK---TPKMRGQAFVVFKETEAASAALRALQGFPFYGKPM   82 (221)
T ss_pred             CceEeehhccccccH---HHHHHHHHHHHHhhCCeEEEEecC---CCCccCceEEEecChhHHHHHHHHhcCCcccCchh
Confidence            3488 9999999999   66666    999999999997763   67889999999999999999999999999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|++|+.+...
T Consensus        83 riqyA~s~sdi   93 (221)
T KOG4206|consen   83 RIQYAKSDSDI   93 (221)
T ss_pred             heecccCccch
Confidence            99999876543

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

Probab=99.06  E-value=7.5e-10  Score=97.56  Aligned_cols=84  Identities=19%  Similarity=0.356  Sum_probs=75.7

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      +....+| |.|||..|++   +||+++|++|++++.+.|..|+ ++++.++|-|+|+..++|++||+.+|++.|+++.|+
T Consensus        80 ~~~~~~v~v~NL~~~V~~---~Dl~eLF~~~~~~~r~~vhy~~-~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk  155 (243)
T KOG0533|consen   80 ETRSTKVNVSNLPYGVID---ADLKELFAEFGELKRVAVHYDR-AGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMK  155 (243)
T ss_pred             CCCcceeeeecCCcCcch---HHHHHHHHHhccceEEeeccCC-CCCCCccceeeecchHhHHHHHHHhcCcccCCceee
Confidence            3444677 9999999999   9999999999999999999986 899999999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |+...+...
T Consensus       156 ~~~i~~~~~  164 (243)
T KOG0533|consen  156 IEIISSPSQ  164 (243)
T ss_pred             eEEecCccc
Confidence            988766543

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

Probab=99.05  E-value=3e-10  Score=105.42  Aligned_cols=75  Identities=20%  Similarity=0.227  Sum_probs=67.8

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |+|||+++||   +.|++-|..|+.|+.++|+.   .+++++  .|.|.++++|+.|+..||+..|+++.|+
T Consensus       533 arKa~qIiirNlP~dfTW---qmlrDKfre~G~v~yadime---~GkskG--VVrF~s~edAEra~a~Mngs~l~Gr~I~  604 (608)
T KOG4212|consen  533 ARKACQIIIRNLPFDFTW---QMLRDKFREIGHVLYADIME---NGKSKG--VVRFFSPEDAERACALMNGSRLDGRNIK  604 (608)
T ss_pred             cccccEEEEecCCccccH---HHHHHHHHhccceehhhhhc---cCCccc--eEEecCHHHHHHHHHHhccCcccCceee
Confidence            4566788 9999999999   99999999999999999953   567777  8999999999999999999999999999


Q ss_pred             Eeec
Q 023632           95 VKKA   98 (279)
Q Consensus        95 V~~a   98 (279)
                      |.++
T Consensus       605 V~y~  608 (608)
T KOG4212|consen  605 VTYF  608 (608)
T ss_pred             eeeC
Confidence            9763

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

Probab=99.04  E-value=5e-10  Score=101.31  Aligned_cols=79  Identities=29%  Similarity=0.551  Sum_probs=70.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc-CCCccCCc
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGA   91 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l-ng~~l~g~   91 (279)
                      +++...++| |.+|...++|   .+|+++|.+||+|+.|.|+..      +++|||+|.+.++|++|.+++ |...|+++
T Consensus       223 PeD~~I~tLyIg~l~d~v~e---~dIrdhFyqyGeirsi~~~~~------~~CAFv~ftTR~aAE~Aae~~~n~lvI~G~  293 (377)
T KOG0153|consen  223 PEDTSIKTLYIGGLNDEVLE---QDIRDHFYQYGEIRSIRILPR------KGCAFVTFTTREAAEKAAEKSFNKLVINGF  293 (377)
T ss_pred             CcccceeEEEecccccchhH---HHHHHHHhhcCCeeeEEeecc------cccceeeehhhHHHHHHHHhhcceeeecce
Confidence            356667888 9999999999   999999999999999999866      359999999999999999874 77889999


Q ss_pred             eeEEeeccCC
Q 023632           92 QVEVKKAEPK  101 (279)
Q Consensus        92 ~i~V~~a~~~  101 (279)
                      +|+|.|..++
T Consensus       294 Rl~i~Wg~~~  303 (377)
T KOG0153|consen  294 RLKIKWGRPK  303 (377)
T ss_pred             EEEEEeCCCc
Confidence            9999999883

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

Probab=99.03  E-value=3.7e-10  Score=102.80  Aligned_cols=86  Identities=21%  Similarity=0.413  Sum_probs=78.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +..+..+| |..+.++++|   +||+.+|+.||+|+.|++.+++.+..+|||+||||.+..+.+.||..||-+.|.++.|
T Consensus       206 eAk~fnRiYVaSvHpDLSe---~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~n~qs~~eAiasMNlFDLGGQyL  282 (544)
T KOG0124|consen  206 EAKKFNRIYVASVHPDLSE---TDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYNNLQSQSEAIASMNLFDLGGQYL  282 (544)
T ss_pred             HHHhhheEEeeecCCCccH---HHHHHHHHhhcceeeEEeeccCCCCCccceeeEEeccccchHHHhhhcchhhcccceE
Confidence            33456788 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|-++..+..
T Consensus       283 RVGk~vTPP~  292 (544)
T KOG0124|consen  283 RVGKCVTPPD  292 (544)
T ss_pred             ecccccCCCc
Confidence            9988765443

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

Probab=99.02  E-value=1.9e-10  Score=112.03  Aligned_cols=82  Identities=20%  Similarity=0.347  Sum_probs=75.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+..+.   .+|+++|..||.|++|+|+.......++|||||+|.++++|.+|+++|....|-++.|.++
T Consensus       612 ~~tKIlVRNipFeAt~---rEVr~LF~aFGqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyGRrLVLE  688 (725)
T KOG0110|consen  612 KGTKILVRNIPFEATK---REVRKLFTAFGQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYGRRLVLE  688 (725)
T ss_pred             ccceeeeeccchHHHH---HHHHHHHhcccceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceechhhhee
Confidence            34677 9999999999   9999999999999999999886677889999999999999999999999999999999999


Q ss_pred             eccCCC
Q 023632           97 KAEPKK  102 (279)
Q Consensus        97 ~a~~~~  102 (279)
                      ||+...
T Consensus       689 wA~~d~  694 (725)
T KOG0110|consen  689 WAKSDN  694 (725)
T ss_pred             hhccch
Confidence            998654

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

Probab=99.00  E-value=7.1e-10  Score=108.97  Aligned_cols=79  Identities=24%  Similarity=0.422  Sum_probs=71.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..+++| |+.|+.+|+|   .||+.+|+.||+|++|.|+-.      ++||||++.+.++|++||.+|+...|..+.|+|
T Consensus       419 V~SrTLwvG~i~k~v~e---~dL~~~feefGeiqSi~li~~------R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki  489 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTE---QDLANLFEEFGEIQSIILIPP------RGCAFIKMVRRQDAEKALQKLSNVKVADKTIKI  489 (894)
T ss_pred             EeeeeeeeccccchhhH---HHHHHHHHhcccceeEeeccC------CceeEEEEeehhHHHHHHHHHhcccccceeeEE
Confidence            345789 9999999999   999999999999999988755      789999999999999999999999999999999


Q ss_pred             eeccCCCCC
Q 023632           96 KKAEPKKPN  104 (279)
Q Consensus        96 ~~a~~~~~~  104 (279)
                      .||..+-.+
T Consensus       490 ~Wa~g~G~k  498 (894)
T KOG0132|consen  490 AWAVGKGPK  498 (894)
T ss_pred             eeeccCCcc
Confidence            999876543

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

Probab=98.98  E-value=1.4e-09  Score=106.20  Aligned_cols=75  Identities=24%  Similarity=0.369  Sum_probs=68.7

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg---~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      | |.||++++|.   ++|+.+|.+.+.|+.|.|.+.++..   .+.||+||+|.++++|++|++.|+++.|+++.|+|++
T Consensus       518 lfvkNlnf~Tt~---e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~  594 (725)
T KOG0110|consen  518 LFVKNLNFDTTL---EDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKI  594 (725)
T ss_pred             hhhhcCCcccch---hHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEe
Confidence            8 9999999999   9999999999999999988766432   2459999999999999999999999999999999999


Q ss_pred             cc
Q 023632           98 AE   99 (279)
Q Consensus        98 a~   99 (279)
                      +.
T Consensus       595 S~  596 (725)
T KOG0110|consen  595 SE  596 (725)
T ss_pred             cc
Confidence            88

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.94  E-value=2.3e-09  Score=94.38  Aligned_cols=84  Identities=17%  Similarity=0.319  Sum_probs=77.7

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+.+.+.+ |+|+.+.+|.   ++|+.+|+.|+.|..|.|++|+.++++|+|+||+|++.+.+++||+ ||..+|.++.
T Consensus        96 ~~~~d~~sv~v~nvd~~~t~---~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~-l~gs~i~~~~  171 (231)
T KOG4209|consen   96 QKEVDAPSVWVGNVDFLVTL---TKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYK-LDGSEIPGPA  171 (231)
T ss_pred             hhccCCceEEEecccccccc---chhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhh-cCCccccccc
Confidence            345677888 9999999999   8899999999999999999999999999999999999999999999 7999999999


Q ss_pred             eEEeeccCC
Q 023632           93 VEVKKAEPK  101 (279)
Q Consensus        93 i~V~~a~~~  101 (279)
                      |+|...+..
T Consensus       172 i~vt~~r~~  180 (231)
T KOG4209|consen  172 IEVTLKRTN  180 (231)
T ss_pred             ceeeeeeee
Confidence            999887665

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=98.90  E-value=3.6e-09  Score=96.33  Aligned_cols=85  Identities=19%  Similarity=0.317  Sum_probs=77.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL   86 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~--------~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~   86 (279)
                      .....+| |-+||..+++   ++|.++|.+++.|+        +|+|.+|++|.++|+-|.|+|+|..+|+.||+.++.+
T Consensus        63 ~s~~~ti~v~g~~d~~~~---~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agk  139 (351)
T KOG1995|consen   63 KSDNETIFVWGCPDSVCE---NDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGK  139 (351)
T ss_pred             ccccccceeeccCccchH---HHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccc
Confidence            4455677 9999999999   99999999999985        4788899999999999999999999999999999999


Q ss_pred             ccCCceeEEeeccCCCC
Q 023632           87 ELAGAQVEVKKAEPKKP  103 (279)
Q Consensus        87 ~l~g~~i~V~~a~~~~~  103 (279)
                      .|.+.+|+|.+|+.+..
T Consensus       140 df~gn~ikvs~a~~r~~  156 (351)
T KOG1995|consen  140 DFCGNTIKVSLAERRTG  156 (351)
T ss_pred             cccCCCchhhhhhhccC
Confidence            99999999999987654

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

Probab=98.88  E-value=9.6e-09  Score=88.19  Aligned_cols=86  Identities=13%  Similarity=0.193  Sum_probs=69.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC---Cc
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIM-RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA---GA   91 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~-~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~---g~   91 (279)
                      ...++| |.+||.+|..   .||..+|..|--.+.+.|. +++....++-++||+|.+..+|++|+++||++.|+   ..
T Consensus        32 ~~VRTLFVSGLP~DvKp---REiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~s  108 (284)
T KOG1457|consen   32 GAVRTLFVSGLPNDVKP---REIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGS  108 (284)
T ss_pred             cccceeeeccCCcccCH---HHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCc
Confidence            346888 9999999999   9999999999766665543 34444455689999999999999999999999887   67


Q ss_pred             eeEEeeccCCCCCC
Q 023632           92 QVEVKKAEPKKPNL  105 (279)
Q Consensus        92 ~i~V~~a~~~~~~~  105 (279)
                      .|+|++|++..++.
T Consensus       109 tLhiElAKSNtK~k  122 (284)
T KOG1457|consen  109 TLHIELAKSNTKRK  122 (284)
T ss_pred             eeEeeehhcCcccc
Confidence            89999888654443

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

Probab=98.86  E-value=1.2e-09  Score=93.30  Aligned_cols=78  Identities=17%  Similarity=0.233  Sum_probs=69.6

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .+..++| |.||...|+|   +.|.|+|-+-|+|.+|.|+.+++ .+.| ||||+|+++.++.-||+.+|+..|.+++|.
T Consensus         6 ae~drtl~v~n~~~~v~e---elL~ElfiqaGPV~kv~ip~~~d-~~~k-Fa~v~f~~E~sv~~a~~L~ng~~l~~~e~q   80 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSE---ELLSELFIQAGPVYKVGIPSGQD-QEQK-FAYVFFPNENSVQLAGQLENGDDLEEDEEQ   80 (267)
T ss_pred             cchhhHHHHHhhhhhhhH---HHHHHHhhccCceEEEeCCCCcc-CCCc-eeeeecccccchhhhhhhcccchhccchhh
Confidence            3456788 9999999999   99999999999999999998874 4455 999999999999999999999999999888


Q ss_pred             Eeec
Q 023632           95 VKKA   98 (279)
Q Consensus        95 V~~a   98 (279)
                      |++-
T Consensus        81 ~~~r   84 (267)
T KOG4454|consen   81 RTLR   84 (267)
T ss_pred             cccc
Confidence            8754

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

Probab=98.84  E-value=5.2e-09  Score=98.30  Aligned_cols=86  Identities=19%  Similarity=0.412  Sum_probs=78.2

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ......| |.||+..+++   +.|+++|+.+++|..++|+.+. .+++++|+||+|++.++|.+|+..+|+..|..+.|.
T Consensus       267 ~~~~~nl~vknld~~~~~---e~L~~~f~~~GeI~s~kv~~~~-~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~  342 (369)
T KOG0123|consen  267 SLQGANLYVKNLDETLSD---EKLRKIFSSFGEITSAKVMVDE-NGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLY  342 (369)
T ss_pred             cccccccccccCccccch---hHHHHHHhcccceeeEEEEecc-CCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchh
Confidence            5566788 9999999999   9999999999999999999985 789999999999999999999999999999999999


Q ss_pred             EeeccCCCCCC
Q 023632           95 VKKAEPKKPNL  105 (279)
Q Consensus        95 V~~a~~~~~~~  105 (279)
                      |.+++.+..+.
T Consensus       343 vav~qr~~~r~  353 (369)
T KOG0123|consen  343 VAVAQRKEDRR  353 (369)
T ss_pred             hhHHhhhccch
Confidence            99988555443

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

Probab=98.84  E-value=8e-09  Score=93.58  Aligned_cols=81  Identities=17%  Similarity=0.273  Sum_probs=72.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE   87 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~--------~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~   87 (279)
                      ..++.| |.+||.++|.   +++.++|++||.|.        .|+|.++. .++.||=|.|+|...|+++.||+.|+..+
T Consensus       132 ~~Nt~VYVsgLP~DiT~---dE~~~~~sKcGiI~~d~~t~epk~KlYrd~-~G~lKGDaLc~y~K~ESVeLA~~ilDe~~  207 (382)
T KOG1548|consen  132 KVNTSVYVSGLPLDITV---DEFAEVMSKCGIIMRDPQTGEPKVKLYRDN-QGKLKGDALCCYIKRESVELAIKILDEDE  207 (382)
T ss_pred             ccCceEEecCCCCcccH---HHHHHHHHhcceEeccCCCCCeeEEEEecC-CCCccCceEEEeecccHHHHHHHHhCccc
Confidence            345668 9999999999   99999999999885        47888886 59999999999999999999999999999


Q ss_pred             cCCceeEEeeccCC
Q 023632           88 LAGAQVEVKKAEPK  101 (279)
Q Consensus        88 l~g~~i~V~~a~~~  101 (279)
                      |.+++|+|+.|+-+
T Consensus       208 ~rg~~~rVerAkfq  221 (382)
T KOG1548|consen  208 LRGKKLRVERAKFQ  221 (382)
T ss_pred             ccCcEEEEehhhhh
Confidence            99999999998743

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.77  E-value=4.6e-08  Score=74.61  Aligned_cols=79  Identities=14%  Similarity=0.140  Sum_probs=66.9

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcC--CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC----Cce
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQF--GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA----GAQ   92 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~--G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~----g~~   92 (279)
                      ++| |+|||...|.   ++|.+++...  ++..-+.++.|..+..+.|||||.|.++++|.+-.+.++++.+.    .+.
T Consensus         2 TTvMirNIPn~~t~---~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kv   78 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQ---EMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKV   78 (97)
T ss_pred             eeEEEecCCCCCCH---HHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcE
Confidence            578 9999999999   7777777543  56677889999999999999999999999999999999998775    566


Q ss_pred             eEEeeccCC
Q 023632           93 VEVKKAEPK  101 (279)
Q Consensus        93 i~V~~a~~~  101 (279)
                      ++|.+|+-+
T Consensus        79 c~i~yAriQ   87 (97)
T PF04059_consen   79 CEISYARIQ   87 (97)
T ss_pred             EEEehhHhh
Confidence            788887643

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.73  E-value=6.9e-09  Score=90.55  Aligned_cols=86  Identities=21%  Similarity=0.374  Sum_probs=78.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +.+.+..+| .+.|..++++   +.|...|.+|-.....++++|+.|+++++|.||.|.+.+++..|+++||++.++.+.
T Consensus       185 ew~~~DfRIfcgdlgNevnd---~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~~pad~~rAmrem~gkyVgsrp  261 (290)
T KOG0226|consen  185 EWDEDDFRIFCGDLGNEVND---DVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVRAMREMNGKYVGSRP  261 (290)
T ss_pred             cCccccceeecccccccccH---HHHHHHHHhccchhhccccccccccccccceeeeecCHHHHHHHHHhhcccccccch
Confidence            445666788 9999999999   999999999998889999999999999999999999999999999999999999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+++....++
T Consensus       262 iklRkS~wke  271 (290)
T KOG0226|consen  262 IKLRKSEWKE  271 (290)
T ss_pred             hHhhhhhHHh
Confidence            9998776554

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

Probab=98.70  E-value=9.3e-09  Score=98.19  Aligned_cols=72  Identities=19%  Similarity=0.340  Sum_probs=65.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++..+.+| |-|||..|++   ++|+++|+.||+|++|+...     ..++.+||+|-|..+|++|+++||..+|.++.|
T Consensus        71 ~~~~~~~L~v~nl~~~Vsn---~~L~~~f~~yGeir~ir~t~-----~~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~  142 (549)
T KOG4660|consen   71 KDMNQGTLVVFNLPRSVSN---DTLLRIFGAYGEIREIRETP-----NKRGIVFVEFYDVRDAERALKALNRREIAGKRI  142 (549)
T ss_pred             ccCccceEEEEecCCcCCH---HHHHHHHHhhcchhhhhccc-----ccCceEEEEEeehHhHHHHHHHHHHHHhhhhhh
Confidence            46678889 9999999999   99999999999999976543     447899999999999999999999999999988


Q ss_pred             E
Q 023632           94 E   94 (279)
Q Consensus        94 ~   94 (279)
                      +
T Consensus       143 k  143 (549)
T KOG4660|consen  143 K  143 (549)
T ss_pred             c
Confidence            7

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

Probab=98.69  E-value=3.2e-08  Score=93.33  Aligned_cols=77  Identities=17%  Similarity=0.295  Sum_probs=65.2

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~-v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...+| ++.||+.|||   +||.+||+-.-.|.+ |.++.|+ ..++.+.|||.|++.|+|++||.. |...|..+-|+|
T Consensus       102 ~d~vVRLRGLPfscte---~dI~~FFaGL~Iv~~gi~l~~d~-rgR~tGEAfVqF~sqe~ae~Al~r-hre~iGhRYIEv  176 (510)
T KOG4211|consen  102 NDGVVRLRGLPFSCTE---EDIVEFFAGLEIVPDGILLPMDQ-RGRPTGEAFVQFESQESAEIALGR-HRENIGHRYIEV  176 (510)
T ss_pred             CCceEEecCCCccCcH---HHHHHHhcCCcccccceeeeccC-CCCcccceEEEecCHHHHHHHHHH-HHHhhccceEEe
Confidence            45678 9999999999   999999998755544 4455564 567999999999999999999999 888999999999


Q ss_pred             eecc
Q 023632           96 KKAE   99 (279)
Q Consensus        96 ~~a~   99 (279)
                      .++.
T Consensus       177 F~Ss  180 (510)
T KOG4211|consen  177 FRSS  180 (510)
T ss_pred             ehhH
Confidence            8765

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

Probab=98.69  E-value=1.3e-08  Score=87.98  Aligned_cols=71  Identities=25%  Similarity=0.513  Sum_probs=64.6

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      .+| |++||+.+.+   .+|++||..|++|.+|.|.        .+|+||+|+++.+|+.||..||.++|.+.+|.|+++
T Consensus         2 ~rv~vg~~~~~~~~---~d~E~~f~~yg~~~d~~mk--------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~   70 (216)
T KOG0106|consen    2 PRVYIGRLPYRARE---RDVERFFKGYGKIPDADMK--------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHA   70 (216)
T ss_pred             CceeecccCCccch---hHHHHHHhhccccccceee--------cccceeccCchhhhhcccchhcCceecceeeeeecc
Confidence            357 9999999999   9999999999999999875        358999999999999999999999999998999888


Q ss_pred             cCC
Q 023632           99 EPK  101 (279)
Q Consensus        99 ~~~  101 (279)
                      +.+
T Consensus        71 r~~   73 (216)
T KOG0106|consen   71 RGK   73 (216)
T ss_pred             ccc
Confidence            754

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

Probab=98.52  E-value=1.8e-07  Score=91.50  Aligned_cols=82  Identities=18%  Similarity=0.287  Sum_probs=74.1

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHS---TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~---tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      ++.+++| |.||++.|+|   +.|...|..||+|..|+|+..+.   ..+.+-|+||.|.+..+|++|++.|+++.|...
T Consensus       171 DP~TTNlyv~Nlnpsv~E---~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~  247 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDE---NFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEY  247 (877)
T ss_pred             CCcccceeeecCCccccH---HHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeee
Confidence            6678889 9999999999   99999999999999999997653   455667999999999999999999999999999


Q ss_pred             eeEEeeccC
Q 023632           92 QVEVKKAEP  100 (279)
Q Consensus        92 ~i~V~~a~~  100 (279)
                      .|++-|+++
T Consensus       248 e~K~gWgk~  256 (877)
T KOG0151|consen  248 EMKLGWGKA  256 (877)
T ss_pred             eeeeccccc
Confidence            999998854

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

Probab=98.44  E-value=1.9e-07  Score=80.91  Aligned_cols=74  Identities=23%  Similarity=0.337  Sum_probs=63.7

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.+|+..+.|   .+|+++|.+++++..+.++        +.++||+|+++++|.+||+.|++.+|+++.|+
T Consensus        96 ~~s~~r~~~~~~~~r~~~---qdl~d~~~~~g~~~~~~~~--------~~~~~v~Fs~~~da~ra~~~l~~~~~~~~~l~  164 (216)
T KOG0106|consen   96 SRTHFRLIVRNLSLRVSW---QDLKDHFRPAGEVTYVDAR--------RNFAFVEFSEQEDAKRALEKLDGKKLNGRRIS  164 (216)
T ss_pred             ccccceeeeccchhhhhH---HHHhhhhcccCCCchhhhh--------ccccceeehhhhhhhhcchhccchhhcCceee
Confidence            4455677 9999999999   9999999999999655542        45999999999999999999999999999999


Q ss_pred             EeeccC
Q 023632           95 VKKAEP  100 (279)
Q Consensus        95 V~~a~~  100 (279)
                      |..+..
T Consensus       165 ~~~~~~  170 (216)
T KOG0106|consen  165 VEKNSR  170 (216)
T ss_pred             ecccCc
Confidence            955443

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

Probab=98.38  E-value=1.6e-06  Score=80.46  Aligned_cols=78  Identities=18%  Similarity=0.212  Sum_probs=68.1

Q ss_pred             Ccee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           19 TQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        19 ~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.+| |.||.+ .||.   +.|..+|..||+|.+|+|+.++.     --|.|.+.+...|+-|++.|+++.|.+++|+|.
T Consensus       297 n~vllvsnln~~~VT~---d~LftlFgvYGdVqRVkil~nkk-----d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt  368 (492)
T KOG1190|consen  297 NVVLLVSNLNEEAVTP---DVLFTLFGVYGDVQRVKILYNKK-----DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVT  368 (492)
T ss_pred             ceEEEEecCchhccch---hHHHHHHhhhcceEEEEeeecCC-----cceeeeecchhHHHHHHHHhhcceecCceEEEe
Confidence            4666 888865 5888   99999999999999999998863     479999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 023632           97 KAEPKKPN  104 (279)
Q Consensus        97 ~a~~~~~~  104 (279)
                      +++-....
T Consensus       369 ~SKH~~vq  376 (492)
T KOG1190|consen  369 LSKHTNVQ  376 (492)
T ss_pred             eccCcccc
Confidence            88755433

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

Probab=98.33  E-value=4.5e-07  Score=87.20  Aligned_cols=84  Identities=24%  Similarity=0.415  Sum_probs=77.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ....+| |.+||..+++   ++++|+++.|+.++...++.|..++.+++|||.+|.+....++||+.||++.+.+++|.|
T Consensus       287 ~~~~ki~v~~lp~~l~~---~q~~Ell~~fg~lk~f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvv  363 (500)
T KOG0120|consen  287 DSPNKIFVGGLPLYLTE---DQVKELLDSFGPLKAFRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVV  363 (500)
T ss_pred             cccchhhhccCcCccCH---HHHHHHHHhcccchhheeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEe
Confidence            344677 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ..|.....
T Consensus       364 q~A~~g~~  371 (500)
T KOG0120|consen  364 QRAIVGAS  371 (500)
T ss_pred             ehhhccch
Confidence            98876543

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

Probab=98.32  E-value=1.8e-07  Score=89.43  Aligned_cols=86  Identities=23%  Similarity=0.367  Sum_probs=75.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++.+.++| +--|+..+++   .+|.+||+.+++|.+|.||.|+.+.++|+.|+|+|.+.+++..||. |.++.+.+.+|
T Consensus       175 eERd~Rtvf~~qla~r~~p---RdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aia-LsGqrllg~pv  250 (549)
T KOG0147|consen  175 EERDQRTVFCMQLARRNPP---RDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIA-LSGQRLLGVPV  250 (549)
T ss_pred             hHHhHHHHHHHHHhhcCCc---hhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhh-hcCCcccCcee
Confidence            34455677 7788888888   9999999999999999999999999999999999999999999995 59999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      .|+..+..+.+
T Consensus       251 ~vq~sEaeknr  261 (549)
T KOG0147|consen  251 IVQLSEAEKNR  261 (549)
T ss_pred             EecccHHHHHH
Confidence            99876654443

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=98.25  E-value=8.2e-07  Score=82.71  Aligned_cols=70  Identities=7%  Similarity=0.123  Sum_probs=57.8

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeec---CCCC--C--------cccEEEEEEcCHHHHHHH
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRD---HSTS--R--------SRGFGFITFDTEQAVDDL   79 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d---~~tg--~--------~rG~aFV~F~s~e~a~~A   79 (279)
                      .+++..++| +.|||.+-.-   +.|.+||..+|.|+.|+|...   +.+.  .        .+=+|||+|+..+.|.+|
T Consensus       226 ~eel~srtivaenLP~Dh~~---enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA  302 (484)
T KOG1855|consen  226 EEELPSRTIVAENLPLDHSY---ENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA  302 (484)
T ss_pred             ccccccceEEEecCCcchHH---HHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH
Confidence            345678889 9999999888   999999999999999999866   3221  1        246899999999999999


Q ss_pred             HHHcCCC
Q 023632           80 LAKGNKL   86 (279)
Q Consensus        80 i~~lng~   86 (279)
                      .+.||..
T Consensus       303 ~e~~~~e  309 (484)
T KOG1855|consen  303 RELLNPE  309 (484)
T ss_pred             HHhhchh
Confidence            9998653

>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=98.23  E-value=4.4e-06  Score=61.48  Aligned_cols=73  Identities=10%  Similarity=0.171  Sum_probs=47.6

Q ss_pred             cee-eeCCCCCCCcccH-HHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           20 QKM-TGLSLTPVTEPAL-DEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~-~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..| |.|||.+.+..-+ ..|+.++..+| +|.+|.          .+.|+|.|.++|.|++|.+.|++..+-+++|.|+
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            356 9999999886111 45677888885 566651          2489999999999999999999999999999999


Q ss_pred             eccCCC
Q 023632           97 KAEPKK  102 (279)
Q Consensus        97 ~a~~~~  102 (279)
                      +....+
T Consensus        73 ~~~~~r   78 (90)
T PF11608_consen   73 FSPKNR   78 (90)
T ss_dssp             SS--S-
T ss_pred             EcCCcc
Confidence            875443

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=98.15  E-value=3.6e-06  Score=65.31  Aligned_cols=68  Identities=26%  Similarity=0.438  Sum_probs=42.7

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC-----CCccCCceeE
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN-----KLELAGAQVE   94 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln-----g~~l~g~~i~   94 (279)
                      .| |.+++..|+.   ++|+++|++|++|..|.+.....      .|+|.|.++++|++||+++.     ...|.+..++
T Consensus         3 il~~~g~~~~~~r---e~iK~~f~~~g~V~yVD~~~G~~------~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~   73 (105)
T PF08777_consen    3 ILKFSGLGEPTSR---EDIKEAFSQFGEVAYVDFSRGDT------EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVT   73 (105)
T ss_dssp             EEEEEE--SS--H---HHHHHHT-SS--EEEEE--TT-S------EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEE
T ss_pred             EEEEecCCCCcCH---HHHHHHHHhcCCcceEEecCCCC------EEEEEECCcchHHHHHHHHHhccCCceEEcCceEE
Confidence            56 8889999999   99999999999999998876532      79999999999999998763     3456666666


Q ss_pred             Eee
Q 023632           95 VKK   97 (279)
Q Consensus        95 V~~   97 (279)
                      ++.
T Consensus        74 ~~v   76 (105)
T PF08777_consen   74 LEV   76 (105)
T ss_dssp             EE-
T ss_pred             EEE
Confidence            553

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

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.14  E-value=5.9e-06  Score=81.08  Aligned_cols=78  Identities=10%  Similarity=0.161  Sum_probs=66.5

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      +-.++| |.|+|++|+-   +||.+||..|-.+-.-.+++-.+.+++.|.|.|.|++.|+|.+|...|+++.|..++|.|
T Consensus       865 pGp~V~~~~n~Pf~v~l---~dI~~FF~dY~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l  941 (944)
T KOG4307|consen  865 PGPRVLSCNNFPFDVTL---EDIVEFFNDYEPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSL  941 (944)
T ss_pred             CCCeEEEecCCCccccH---HHHHHHhcccccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEE
Confidence            344577 9999999999   999999999976644334444468999999999999999999999999999999999988


Q ss_pred             ee
Q 023632           96 KK   97 (279)
Q Consensus        96 ~~   97 (279)
                      .+
T Consensus       942 ~i  943 (944)
T KOG4307|consen  942 RI  943 (944)
T ss_pred             Ee
Confidence            64

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

Probab=98.07  E-value=1.2e-05  Score=69.34  Aligned_cols=76  Identities=12%  Similarity=0.241  Sum_probs=65.1

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-Ccee
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQV   93 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~~i   93 (279)
                      .+.+..| +.|||.+++.   +.|..+|++|.-.++|+++..+     +..|||+|+++..+..|...|++..|- ..++
T Consensus       143 ~ppn~ilf~~niP~es~~---e~l~~lf~qf~g~keir~i~~~-----~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m  214 (221)
T KOG4206|consen  143 APPNNILFLTNIPSESES---EMLSDLFEQFPGFKEIRLIPPR-----SGIAFVEFLSDRQASAAQQALQGFKITKKNTM  214 (221)
T ss_pred             CCCceEEEEecCCcchhH---HHHHHHHhhCcccceeEeccCC-----CceeEEecchhhhhHHHhhhhccceeccCceE
Confidence            3455666 9999999999   9999999999999999988764     569999999999999999999887776 7788


Q ss_pred             EEeecc
Q 023632           94 EVKKAE   99 (279)
Q Consensus        94 ~V~~a~   99 (279)
                      +|.+++
T Consensus       215 ~i~~a~  220 (221)
T KOG4206|consen  215 QITFAK  220 (221)
T ss_pred             EecccC
Confidence            887764

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

Probab=98.04  E-value=1e-05  Score=54.90  Aligned_cols=51  Identities=12%  Similarity=0.311  Sum_probs=41.8

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHH
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLL   80 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai   80 (279)
                      +.| |.+++.+..+    +|.++|++||+|+++.+...      +-+.+|+|+++.+|++||
T Consensus         2 ~wI~V~Gf~~~~~~----~vl~~F~~fGeI~~~~~~~~------~~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAE----EVLEHFASFGEIVDIYVPES------TNWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHH----HHHHHHHhcCCEEEEEcCCC------CcEEEEEECCHHHHHhhC
Confidence            567 9999877764    56668999999999988732      338999999999999986

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=98.00  E-value=1.1e-05  Score=73.23  Aligned_cols=77  Identities=14%  Similarity=0.257  Sum_probs=58.2

Q ss_pred             eeCCCCCCCcccH-HHH--HHHHhcCCCeEEEEEeecCCCC-CcccEE--EEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           23 TGLSLTPVTEPAL-DEF--KDFFMQFGDVQEHQIMRDHSTS-RSRGFG--FITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        23 V~nLp~~~te~~~-~~L--~~~F~~~G~V~~v~i~~d~~tg-~~rG~a--FV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      |-.||+.+..++. ..|  .++|.+||+|++|.|-+...+- .....+  +|+|.+.|+|.+||.++++..++++.|+..
T Consensus       119 Vigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkat  198 (480)
T COG5175         119 VIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKAT  198 (480)
T ss_pred             EecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCceEeee
Confidence            7888888887221 123  4799999999999876554211 112234  999999999999999999999999999987


Q ss_pred             ecc
Q 023632           97 KAE   99 (279)
Q Consensus        97 ~a~   99 (279)
                      .-.
T Consensus       199 YGT  201 (480)
T COG5175         199 YGT  201 (480)
T ss_pred             cCc
Confidence            644

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.98  E-value=2.4e-05  Score=75.36  Aligned_cols=79  Identities=11%  Similarity=0.129  Sum_probs=63.4

Q ss_pred             CCCcee-eeCCCCCCCcccH----HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-C
Q 023632           17 TTTQKM-TGLSLTPVTEPAL----DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-G   90 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~----~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g   90 (279)
                      -....| |.++|.--.. .|    .-|.++|+++|+|+.+.++.+.+++ ++|+.|++|.+..+|++|++.||++.|+ .
T Consensus        56 g~D~vVvv~g~PvV~~~-rl~klk~vl~kvfsk~gk~vn~~~P~~e~gg-tkG~lf~E~~~~~~A~~aVK~l~G~~ldkn  133 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPA-RLEKLKKVLTKVFSKAGKIVNMYYPIDEEGG-TKGYLFVEYASMRDAKKAVKSLNGKRLDKN  133 (698)
T ss_pred             CcceEEEECCCcccChh-HHHHHHHHHHHHHHhhccccceeeccCccCC-eeeEEEEEecChhhHHHHHHhcccceeccc
Confidence            334555 9999864332 12    3467799999999999999887655 9999999999999999999999999887 6


Q ss_pred             ceeEEee
Q 023632           91 AQVEVKK   97 (279)
Q Consensus        91 ~~i~V~~   97 (279)
                      +++.|..
T Consensus       134 Htf~v~~  140 (698)
T KOG2314|consen  134 HTFFVRL  140 (698)
T ss_pred             ceEEeeh
Confidence            7777764

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=97.97  E-value=5.5e-06  Score=75.35  Aligned_cols=81  Identities=19%  Similarity=0.422  Sum_probs=73.4

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +.+ |.+|++++++   ++|+++|..++.|..|+++.++.+..+++|++|+|.+.+++.+++.. +...|.+++|.|.+.
T Consensus       186 ~~~~~~~~~f~~~~---d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~  261 (285)
T KOG4210|consen  186 TIFFVGELDFSLTR---DDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDFSAGNSKKLALND-QTRSIGGRPLRLEED  261 (285)
T ss_pred             cceeecccccccch---HHHhhhccCcCcceeeccCCCCCccchhhhhhhhhhhchhHHHHhhc-ccCcccCcccccccC
Confidence            344 9999999999   99999999999999999999999999999999999999999999988 788999999999988


Q ss_pred             cCCCCC
Q 023632           99 EPKKPN  104 (279)
Q Consensus        99 ~~~~~~  104 (279)
                      .+....
T Consensus       262 ~~~~~~  267 (285)
T KOG4210|consen  262 EPRPKS  267 (285)
T ss_pred             CCCccc
Confidence            765443

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

Probab=97.93  E-value=4.5e-05  Score=70.25  Aligned_cols=74  Identities=18%  Similarity=0.203  Sum_probs=61.9

Q ss_pred             eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC--CceeEEeeccC
Q 023632           23 TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--GAQVEVKKAEP  100 (279)
Q Consensus        23 V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~--g~~i~V~~a~~  100 (279)
                      |-|--..+|.   +-|..++...|+|..|.|++.  ++   --|.|||++.+.|++|.+.||+..|-  =.+|+|++|+|
T Consensus       127 IlNp~YpItv---DVly~Icnp~GkVlRIvIfkk--ng---VQAmVEFdsv~~AqrAk~alNGADIYsGCCTLKIeyAkP  198 (494)
T KOG1456|consen  127 ILNPQYPITV---DVLYTICNPQGKVLRIVIFKK--NG---VQAMVEFDSVEVAQRAKAALNGADIYSGCCTLKIEYAKP  198 (494)
T ss_pred             eecCccccch---hhhhhhcCCCCceEEEEEEec--cc---eeeEEeechhHHHHHHHhhcccccccccceeEEEEecCc
Confidence            4455566787   889999999999999998865  33   36999999999999999999998886  46899999998


Q ss_pred             CCCC
Q 023632          101 KKPN  104 (279)
Q Consensus       101 ~~~~  104 (279)
                      .+-+
T Consensus       199 ~rln  202 (494)
T KOG1456|consen  199 TRLN  202 (494)
T ss_pred             ceee
Confidence            7543

>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=97.87  E-value=4.3e-05  Score=58.66  Aligned_cols=78  Identities=22%  Similarity=0.325  Sum_probs=51.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEE-EeecC------CCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQ-IMRDH------STSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~-i~~d~------~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      ..+.| |-++|+..+    ..|.++|++||+|++.. +.++.      ..-....+..|+|+++.+|++||.+ |+..|.
T Consensus         5 ~~~wVtVFGfp~~~~----~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~-NG~i~~   79 (100)
T PF05172_consen    5 SETWVTVFGFPPSAS----NQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQK-NGTIFS   79 (100)
T ss_dssp             GCCEEEEE---GGGH----HHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTT-TTEEET
T ss_pred             CCeEEEEEccCHHHH----HHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHh-CCeEEc
Confidence            44567 999998865    67889999999998874 11110      0011234899999999999999999 999998


Q ss_pred             Cce-eEEeeccC
Q 023632           90 GAQ-VEVKKAEP  100 (279)
Q Consensus        90 g~~-i~V~~a~~  100 (279)
                      +.. |-|.+.++
T Consensus        80 g~~mvGV~~~~~   91 (100)
T PF05172_consen   80 GSLMVGVKPCDP   91 (100)
T ss_dssp             TCEEEEEEE-HH
T ss_pred             CcEEEEEEEcHH
Confidence            754 45666643

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.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=97.87  E-value=1.3e-05  Score=73.06  Aligned_cols=71  Identities=14%  Similarity=0.287  Sum_probs=63.0

Q ss_pred             eeCCCCCCCcccHHHHHHHHhcCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           23 TGLSLTPVTEPALDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        23 V~nLp~~~te~~~~~L~~~F~~~G--~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      |+||-|++|+   +||.+.+...|  .|.++++..++.++++|+||+|...++.++++.|+.|..++|.++.-.|.
T Consensus        85 vGNL~W~TTD---~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   85 VGNLLWYTTD---ADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             ecceeEEecc---HHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            9999999999   88888777665  56788889999999999999999999999999999999999998766554

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

Probab=97.86  E-value=8.6e-05  Score=68.44  Aligned_cols=79  Identities=16%  Similarity=0.219  Sum_probs=67.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+..++ |-+|.......  +.|..+|..||.|++|++|+.+     .+.|.||+-|+.++++||..||+..|-+.+|.|
T Consensus       285 ~~g~VmMVyGLdh~k~N~--drlFNl~ClYGNV~rvkFmkTk-----~gtamVemgd~~aver~v~hLnn~~lfG~kl~v  357 (494)
T KOG1456|consen  285 APGCVMMVYGLDHGKMNC--DRLFNLFCLYGNVERVKFMKTK-----PGTAMVEMGDAYAVERAVTHLNNIPLFGGKLNV  357 (494)
T ss_pred             CCCcEEEEEeccccccch--hhhhhhhhhcCceeeEEEeecc-----cceeEEEcCcHHHHHHHHHHhccCccccceEEE
Confidence            345677 88997654432  7799999999999999999876     568999999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      .+++...
T Consensus       358 ~~SkQ~~  364 (494)
T KOG1456|consen  358 CVSKQNF  364 (494)
T ss_pred             eeccccc
Confidence            9876543

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

Probab=97.86  E-value=3.7e-05  Score=70.11  Aligned_cols=62  Identities=15%  Similarity=0.269  Sum_probs=53.6

Q ss_pred             HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccCC
Q 023632           36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  101 (279)
Q Consensus        36 ~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~~  101 (279)
                      ++|.+-+++||.|.+|.|.-    ..+.|.+-|.|.+.++|+.||+.|++..|++|+|..+...-+
T Consensus       291 edl~eec~K~G~v~~vvv~d----~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG~  352 (382)
T KOG1548|consen  291 EDLTEECEKFGQVRKVVVYD----RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDGK  352 (382)
T ss_pred             HHHHHHHHHhCCcceEEEec----cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCCc
Confidence            67778899999999997753    356889999999999999999999999999999998865543

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

Probab=97.86  E-value=0.00013  Score=61.50  Aligned_cols=63  Identities=16%  Similarity=0.239  Sum_probs=55.7

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ...+| |..||...+|   ++||+++.+-|.|...++.+|       +.+.|+|...|+++-||.+|+.+++..
T Consensus       114 Se~RVvVsGLp~SgSW---QDLKDHmReaGdvCfadv~rD-------g~GvV~~~r~eDMkYAvr~ld~~~~~s  177 (241)
T KOG0105|consen  114 SEYRVVVSGLPPSGSW---QDLKDHMREAGDVCFADVQRD-------GVGVVEYLRKEDMKYAVRKLDDQKFRS  177 (241)
T ss_pred             cceeEEEecCCCCCch---HHHHHHHHhhCCeeeeeeecc-------cceeeeeeehhhHHHHHHhhccccccC
Confidence            34556 9999999999   999999999999999998887       388999999999999999998776654

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

Probab=97.83  E-value=1.8e-05  Score=76.36  Aligned_cols=65  Identities=15%  Similarity=0.221  Sum_probs=54.7

Q ss_pred             HHHHHHHhcCCCeEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           36 DEFKDFFMQFGDVQEHQIMRDHS---TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        36 ~~L~~~F~~~G~V~~v~i~~d~~---tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      ++|+..+.+|+.|..|+|+++-.   ..-..+..||+|.+.+++++|+++|++.+|++++|.+.+-.+
T Consensus       424 Edvr~ec~k~g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~GrKF~nRtVvtsYyde  491 (500)
T KOG0120|consen  424 EDVRTECAKFGAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTGRKFANRTVVASYYDE  491 (500)
T ss_pred             HHHHHHhcccCceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccCceeCCcEEEEEecCH
Confidence            66777888999999999998722   223356789999999999999999999999999998887654

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

Probab=97.77  E-value=3.2e-05  Score=66.82  Aligned_cols=63  Identities=16%  Similarity=0.168  Sum_probs=50.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL   88 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l   88 (279)
                      ..+| |.||..+|+|   ++|+.+|+.|--...++|...  .+  -..|||+|++.|.|..||..|.+..|
T Consensus       210 cstlfianl~~~~~e---d~l~~~~~~~~gf~~l~~~~~--~g--~~vaf~~~~~~~~at~am~~lqg~~~  273 (284)
T KOG1457|consen  210 CSTLFIANLGPNCTE---DELKQLLSRYPGFHILKIRAR--GG--MPVAFADFEEIEQATDAMNHLQGNLL  273 (284)
T ss_pred             hhhHhhhccCCCCCH---HHHHHHHHhCCCceEEEEecC--CC--cceEeecHHHHHHHHHHHHHhhccee
Confidence            4567 9999999999   999999999976666655322  22  35899999999999999999877554

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.71  E-value=0.0001  Score=60.06  Aligned_cols=77  Identities=17%  Similarity=0.337  Sum_probs=53.6

Q ss_pred             CCCCcee-eeCCCC------CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc
Q 023632           16 QTTTQKM-TGLSLT------PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL   88 (279)
Q Consensus        16 ~~~~~~l-V~nLp~------~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l   88 (279)
                      -++..+| |.-+.+      ...++.+++|.+.|..||+|.-|+++.+        .-+|+|.+-++|.+|++. ++++|
T Consensus        24 GPpDaTVvVsv~~~~~~e~~~Fdd~l~~~ll~~~~~~GevvLvRfv~~--------~mwVTF~dg~sALaals~-dg~~v   94 (146)
T PF08952_consen   24 GPPDATVVVSVDSPSEDEDSSFDDNLMDELLQKFAQYGEVVLVRFVGD--------TMWVTFRDGQSALAALSL-DGIQV   94 (146)
T ss_dssp             --TT-EEEEEECS-SCCCCHS--HHHHHHHHHHHHCCS-ECEEEEETT--------CEEEEESSCHHHHHHHHG-CCSEE
T ss_pred             CCCCceEEEEecCCCccccCcCCHHHHHHHHHHHHhCCceEEEEEeCC--------eEEEEECccHHHHHHHcc-CCcEE
Confidence            3445556 654441      2333334688889999999998888866        468999999999999988 99999


Q ss_pred             CCceeEEeeccCC
Q 023632           89 AGAQVEVKKAEPK  101 (279)
Q Consensus        89 ~g~~i~V~~a~~~  101 (279)
                      +++.|+|+...|.
T Consensus        95 ~g~~l~i~LKtpd  107 (146)
T PF08952_consen   95 NGRTLKIRLKTPD  107 (146)
T ss_dssp             TTEEEEEEE----
T ss_pred             CCEEEEEEeCCcc
Confidence            9999999876654

; PDB: 1UFW_A 2DNR_A.

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

Probab=97.61  E-value=0.00014  Score=67.80  Aligned_cols=78  Identities=12%  Similarity=0.149  Sum_probs=63.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC-cee
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG-AQV   93 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g-~~i   93 (279)
                      .+++.+| +.|||.+|+|   ++|+++|..-+-+++......+    .+-+|.+.+++.|+|..|+..++.+.+.. ..|
T Consensus       411 ~PpsatlHlsnip~svse---e~lk~~f~~~g~~vkafkff~k----d~kmal~q~~sveeA~~ali~~hnh~lgen~hl  483 (492)
T KOG1190|consen  411 FPPSATLHLSNIPPSVSE---EDLKNLFQEPGGQVKAFKFFQK----DRKMALPQLESVEEAIQALIDLHNHYLGENHHL  483 (492)
T ss_pred             CCchhheeeccCCcccch---hHHHHhhhcCCceEEeeeecCC----CcceeecccCChhHhhhhccccccccCCCCceE
Confidence            3566789 9999999999   9999999888776554433222    23499999999999999999999998884 589


Q ss_pred             EEeeccC
Q 023632           94 EVKKAEP  100 (279)
Q Consensus        94 ~V~~a~~  100 (279)
                      +|.+++.
T Consensus       484 RvSFSks  490 (492)
T KOG1190|consen  484 RVSFSKS  490 (492)
T ss_pred             EEEeecc
Confidence            9999875

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=97.54  E-value=3.5e-05  Score=67.75  Aligned_cols=65  Identities=12%  Similarity=0.246  Sum_probs=52.5

Q ss_pred             HHHHHHHh-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccCC
Q 023632           36 DEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  101 (279)
Q Consensus        36 ~~L~~~F~-~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~~  101 (279)
                      ++|...|+ +|++|+++.|-.+ ..-..++-++|.|..+|+|++|++.||+-.+.+++|..++..-.
T Consensus        83 Ed~f~E~~~kygEiee~~Vc~N-l~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~pvT  148 (260)
T KOG2202|consen   83 EDVFTELEDKYGEIEELNVCDN-LGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSPVT  148 (260)
T ss_pred             HHHHHHHHHHhhhhhhhhhhcc-cchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecCcC
Confidence            34444555 9999999866554 34566789999999999999999999999999999998876543

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

Probab=97.51  E-value=5e-05  Score=70.15  Aligned_cols=75  Identities=15%  Similarity=0.147  Sum_probs=58.6

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCC----eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGD----VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~----V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      -.| +++||+++++   .++.+||..--.    ++.|.+++. .+++..|-|||.|..+++|++||.+ |...|.-|-|+
T Consensus       162 vivRmRGLPfdat~---~dVv~FF~~~cpv~~g~egvLFV~r-pdgrpTGdAFvlfa~ee~aq~aL~k-hrq~iGqRYIE  236 (508)
T KOG1365|consen  162 VIVRMRGLPFDATA---LDVVEFFGPPCPVTGGTEGVLFVTR-PDGRPTGDAFVLFACEEDAQFALRK-HRQNIGQRYIE  236 (508)
T ss_pred             eEEEecCCCCCcch---HHHHHhcCCCCcccCCccceEEEEC-CCCCcccceEEEecCHHHHHHHHHH-HHHHHhHHHHH
Confidence            344 8899999999   999999964333    345555544 3789999999999999999999998 77777777777


Q ss_pred             Eeecc
Q 023632           95 VKKAE   99 (279)
Q Consensus        95 V~~a~   99 (279)
                      |.++.
T Consensus       237 lFRST  241 (508)
T KOG1365|consen  237 LFRST  241 (508)
T ss_pred             HHHHh
Confidence            65443

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

Probab=97.50  E-value=0.00011  Score=67.91  Aligned_cols=78  Identities=15%  Similarity=0.165  Sum_probs=64.5

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCC-eEE--EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGD-VQE--HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~-V~~--v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      +..| +++||++.+.   ++|.+||..|-. |..  |.|+.+. .+++.|-|||+|.++|+|..|+.+.+++..+.+-|+
T Consensus       280 kdcvRLRGLPy~Atv---EdIL~FlgdFa~~i~f~gVHmv~N~-qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiE  355 (508)
T KOG1365|consen  280 KDCVRLRGLPYEATV---EDILDFLGDFATDIRFQGVHMVLNG-QGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIE  355 (508)
T ss_pred             CCeeEecCCChhhhH---HHHHHHHHHHhhhcccceeEEEEcC-CCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEE
Confidence            4456 9999999999   888888888754 333  6777764 789999999999999999999999888888899999


Q ss_pred             EeeccC
Q 023632           95 VKKAEP  100 (279)
Q Consensus        95 V~~a~~  100 (279)
                      |..+..
T Consensus       356 vfp~S~  361 (508)
T KOG1365|consen  356 VFPCSV  361 (508)
T ss_pred             EeeccH
Confidence            976643

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

Probab=97.46  E-value=0.0004  Score=66.47  Aligned_cols=79  Identities=23%  Similarity=0.294  Sum_probs=66.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHh-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHH----cCCCccCC
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK----GNKLELAG   90 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~-~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~----lng~~l~g   90 (279)
                      .+.+|| |+.||..++.   ++|..||+ .||.|+-+-|-+|++-+-+||-+-|+|.+..+-.+||++    |+..+| .
T Consensus       368 DprrTVFVGgvprpl~A---~eLA~imd~lyGgV~yaGIDtD~k~KYPkGaGRVtFsnqqsYi~AIsarFvql~h~d~-~  443 (520)
T KOG0129|consen  368 DPRRTVFVGGLPRPLTA---EELAMIMEDLFGGVLYVGIDTDPKLKYPKGAGRVTFSNQQAYIKAISARFVQLDHTDI-D  443 (520)
T ss_pred             CccceEEecCCCCcchH---HHHHHHHHHhcCceEEEEeccCcccCCCCCcceeeecccHHHHHHHhhheEEEecccc-c
Confidence            456778 9999999999   99999998 799999999999988999999999999999999999986    233333 3


Q ss_pred             ceeEEeecc
Q 023632           91 AQVEVKKAE   99 (279)
Q Consensus        91 ~~i~V~~a~   99 (279)
                      ++|+|+.-.
T Consensus       444 KRVEIkPYv  452 (520)
T KOG0129|consen  444 KRVEIKPYV  452 (520)
T ss_pred             eeeeeccee
Confidence            467776544

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=97.36  E-value=0.0001  Score=74.04  Aligned_cols=78  Identities=15%  Similarity=0.199  Sum_probs=70.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      ...| |.|+|+..|.   ++|+.+|++++.++++.+++.+ .+++++.|||.|.++.++.+++..++...++.+.++|..
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~v  811 (881)
T KOG0128|consen  736 KISVAISGPPFQGTK---EELKSLASKTGNVTSLRLVTVR-AGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQV  811 (881)
T ss_pred             hhhhheeCCCCCCch---HHHHhhccccCCccccchhhhh-ccccccceeccCCCcchhhhhcccchhhhhhhcCccccc
Confidence            4556 9999999999   9999999999999999988876 789999999999999999999999888888888888887


Q ss_pred             ccC
Q 023632           98 AEP  100 (279)
Q Consensus        98 a~~  100 (279)
                      ..|
T Consensus       812 snp  814 (881)
T KOG0128|consen  812 SNP  814 (881)
T ss_pred             cCC
Confidence            665

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=97.30  E-value=0.00012  Score=64.32  Aligned_cols=72  Identities=11%  Similarity=0.211  Sum_probs=59.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCC--------CCcc----cEEEEEEcCHHHHHHHHHHcC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHST--------SRSR----GFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~t--------g~~r----G~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      .+-+| +++||+.++-   ..|++||+.||+|-.|.|.....+        +.++    --++|+|.+...|+++.+.||
T Consensus        73 k~GVvylS~IPp~m~~---~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Ln  149 (278)
T KOG3152|consen   73 KTGVVYLSNIPPYMDP---VRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLN  149 (278)
T ss_pred             cceEEEeccCCCccCH---HHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhC
Confidence            45677 9999999999   999999999999999988765444        2222    236799999999999999999


Q ss_pred             CCccCCce
Q 023632           85 KLELAGAQ   92 (279)
Q Consensus        85 g~~l~g~~   92 (279)
                      +..|.+++
T Consensus       150 n~~Iggkk  157 (278)
T KOG3152|consen  150 NTPIGGKK  157 (278)
T ss_pred             CCccCCCC
Confidence            99998764

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.25  E-value=0.00083  Score=60.28  Aligned_cols=73  Identities=19%  Similarity=0.121  Sum_probs=57.0

Q ss_pred             CCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcc-cEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           28 TPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSR-GFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        28 ~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~r-G~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      -.++++.-+++++.+++|++|..|.|..++..-... ---||+|+..++|.+|+..||+..|.++.+...+...
T Consensus       293 gevd~elede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn~  366 (378)
T KOG1996|consen  293 GEVDEELEDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYNL  366 (378)
T ss_pred             ccccHHHHHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheeccH
Confidence            345543336889999999999999888775322221 2469999999999999999999999999998887654

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

Probab=97.14  E-value=0.0012  Score=63.25  Aligned_cols=62  Identities=26%  Similarity=0.412  Sum_probs=47.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecC---CCCCccc---EEEEEEcCHHHHHHHHHHc
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDH---STSRSRG---FGFITFDTEQAVDDLLAKG   83 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~---~tg~~rG---~aFV~F~s~e~a~~Ai~~l   83 (279)
                      -.++| |+.||++++|   ++|.+.|..||.|+ |+.+...   .--.++|   |+|+.|+++.++++.|.++
T Consensus       258 ~S~KVFvGGlp~dise---~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC  326 (520)
T KOG0129|consen  258 YSRKVFVGGLPWDITE---AQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSAC  326 (520)
T ss_pred             cccceeecCCCccccH---HHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHH
Confidence            34677 9999999999   99999999999864 3333211   1223567   9999999999999888774

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=97.02  E-value=0.0038  Score=50.60  Aligned_cols=77  Identities=9%  Similarity=0.124  Sum_probs=57.1

Q ss_pred             CCCCCcee-eeCCCCCCCc-ccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTE-PALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te-~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .+++..+| |.=|..++.. +|++.+...++.||+|++|.+.-       +-.|.|+|+|..+|-+|+.+++. ..-+..
T Consensus        82 kepPMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cG-------rqsavVvF~d~~SAC~Av~Af~s-~~pgtm  153 (166)
T PF15023_consen   82 KEPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCG-------RQSAVVVFKDITSACKAVSAFQS-RAPGTM  153 (166)
T ss_pred             CCCCceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecC-------CceEEEEehhhHHHHHHHHhhcC-CCCCce
Confidence            35566677 8877777664 34455666778999999997642       22799999999999999999865 566777


Q ss_pred             eEEeecc
Q 023632           93 VEVKKAE   99 (279)
Q Consensus        93 i~V~~a~   99 (279)
                      +.+.+..
T Consensus       154 ~qCsWqq  160 (166)
T PF15023_consen  154 FQCSWQQ  160 (166)
T ss_pred             EEeeccc
Confidence            7777653

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=97.00  E-value=0.0032  Score=43.94  Aligned_cols=55  Identities=13%  Similarity=0.181  Sum_probs=43.1

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcC---CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQF---GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG   83 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~---G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l   83 (279)
                      ...+| |.+|.. ++.   ++|+++|..|   -....|+.+-|.       -|-|.|.+++.|.+||.+|
T Consensus         4 rpeavhirGvd~-lsT---~dI~~y~~~y~~~~~~~~IEWIdDt-------ScNvvf~d~~~A~~AL~~L   62 (62)
T PF10309_consen    4 RPEAVHIRGVDE-LST---DDIKAYFSEYFDEEGPFRIEWIDDT-------SCNVVFKDEETAARALVAL   62 (62)
T ss_pred             eeceEEEEcCCC-CCH---HHHHHHHHHhcccCCCceEEEecCC-------cEEEEECCHHHHHHHHHcC
Confidence            34567 888854 555   7899999888   235678888885       5889999999999999875

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=96.96  E-value=0.00026  Score=64.60  Aligned_cols=77  Identities=16%  Similarity=0.228  Sum_probs=58.5

Q ss_pred             eeCCCCCCCcccHHHH--HHHHhcCCCeEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           23 TGLSLTPVTEPALDEF--KDFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        23 V~nLp~~~te~~~~~L--~~~F~~~G~V~~v~i~~d~~tg---~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      |-.|+..+.++  ..|  .+.|.+|+.|.+|.+-.++.+.   -...-++|+|+.+|+|+.||...+++.++++.|++.+
T Consensus        82 vvgl~~~~ade--~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lka~~  159 (327)
T KOG2068|consen   82 VVGLPLDLADE--SVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALKASL  159 (327)
T ss_pred             hhCCCccccch--hhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhHHhh
Confidence            67788777662  233  3688999999999888776311   1123489999999999999999999999999877776


Q ss_pred             ccCC
Q 023632           98 AEPK  101 (279)
Q Consensus        98 a~~~  101 (279)
                      ..++
T Consensus       160 gttk  163 (327)
T KOG2068|consen  160 GTTK  163 (327)
T ss_pred             CCCc
Confidence            6554

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=96.91  E-value=5.7e-05  Score=75.85  Aligned_cols=68  Identities=16%  Similarity=0.231  Sum_probs=58.2

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      ..++ |.||+..+.+   .+|.+.|..++.|+.|+|.-.+.+++.||.|+|+|.+++++.+||...+.+.+.
T Consensus       667 ~~~~fvsnl~~~~~~---~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~~~~~~~aaV~f~d~~~~g  735 (881)
T KOG0128|consen  667 LIKIFVSNLSPKMSE---EDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFLKPEHAGAAVAFRDSCFFG  735 (881)
T ss_pred             HHHHHHhhcchhhcC---chhhhhcCccchhhhHHHHHHhhccccccceeeEeecCCchhhhhhhhhhhhhh
Confidence            3456 9999999999   999999999999988887766678999999999999999999999875554444

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=96.86  E-value=0.0011  Score=64.11  Aligned_cols=68  Identities=10%  Similarity=0.084  Sum_probs=52.2

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhc--CCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC--CCccCCce
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQ--FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQ   92 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~--~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln--g~~l~g~~   92 (279)
                      +.+.| |+-||+++-+   |++|.||+.  +-++.+|++-.+.       -=||+|++++||++|.+.|.  -++|.+++
T Consensus       174 kRcIvilREIpettp~---e~Vk~lf~~encPk~iscefa~N~-------nWyITfesd~DAQqAykylreevk~fqgKp  243 (684)
T KOG2591|consen  174 KRCIVILREIPETTPI---EVVKALFKGENCPKVISCEFAHND-------NWYITFESDTDAQQAYKYLREEVKTFQGKP  243 (684)
T ss_pred             ceeEEEEeecCCCChH---HHHHHHhccCCCCCceeeeeeecC-------ceEEEeecchhHHHHHHHHHHHHHhhcCcc
Confidence            34556 9999999999   999999964  6678888776542       24899999999999988763  36677776


Q ss_pred             eEE
Q 023632           93 VEV   95 (279)
Q Consensus        93 i~V   95 (279)
                      |..
T Consensus       244 ImA  246 (684)
T KOG2591|consen  244 IMA  246 (684)
T ss_pred             hhh
Confidence            644

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=96.83  E-value=0.0032  Score=56.78  Aligned_cols=69  Identities=16%  Similarity=0.176  Sum_probs=53.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce-eEE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ-VEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~-i~V   95 (279)
                      ....| |-++|..-.    ..|..+|++||+|+++....+      --|-.|.|.+..+|+|||.+ |++.|++.. |-|
T Consensus       196 ~D~WVTVfGFppg~~----s~vL~~F~~cG~Vvkhv~~~n------gNwMhirYssr~~A~KALsk-ng~ii~g~vmiGV  264 (350)
T KOG4285|consen  196 ADTWVTVFGFPPGQV----SIVLNLFSRCGEVVKHVTPSN------GNWMHIRYSSRTHAQKALSK-NGTIIDGDVMIGV  264 (350)
T ss_pred             ccceEEEeccCccch----hHHHHHHHhhCeeeeeecCCC------CceEEEEecchhHHHHhhhh-cCeeeccceEEee
Confidence            35667 888887665    467889999999998865522      23889999999999999999 888888654 455


Q ss_pred             ee
Q 023632           96 KK   97 (279)
Q Consensus        96 ~~   97 (279)
                      +.
T Consensus       265 kp  266 (350)
T KOG4285|consen  265 KP  266 (350)
T ss_pred             ee
Confidence            54

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.80  E-value=0.0013  Score=61.10  Aligned_cols=75  Identities=12%  Similarity=0.154  Sum_probs=57.8

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCC---CCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHST---SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~t---g~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..| |.||.+.+|.   ++++.||.-.|+|.++.|+.....   ....-.|||.|.|.+++..|-.. .++.|-++.|.|
T Consensus         8 ~vIqvanispsat~---dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhL-tntvfvdraliv   83 (479)
T KOG4676|consen    8 GVIQVANISPSATK---DQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHL-TNTVFVDRALIV   83 (479)
T ss_pred             ceeeecccCchhhH---HHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhh-ccceeeeeeEEE
Confidence            478 9999999999   999999999999999988764321   22345899999999988877554 556666666666


Q ss_pred             eec
Q 023632           96 KKA   98 (279)
Q Consensus        96 ~~a   98 (279)
                      ..+
T Consensus        84 ~p~   86 (479)
T KOG4676|consen   84 RPY   86 (479)
T ss_pred             Eec
Confidence            544

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.77  E-value=0.0044  Score=45.71  Aligned_cols=56  Identities=11%  Similarity=0.207  Sum_probs=42.4

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      ..+.+ |. +|.++..   .||.++|+.||.|. |..+.|.       -|||...+.+.|+.|+..++.
T Consensus         8 RdHVFhlt-FPkeWK~---~DI~qlFspfG~I~-VsWi~dT-------SAfV~l~~r~~~~~v~~~~~~   64 (87)
T PF08675_consen    8 RDHVFHLT-FPKEWKT---SDIYQLFSPFGQIY-VSWINDT-------SAFVALHNRDQAKVVMNTLKK   64 (87)
T ss_dssp             GCCEEEEE---TT--H---HHHHHHCCCCCCEE-EEEECTT-------EEEEEECCCHHHHHHHHHHTT
T ss_pred             cceEEEEe-CchHhhh---hhHHHHhccCCcEE-EEEEcCC-------cEEEEeecHHHHHHHHHHhcc
Confidence            34566 77 9999999   99999999999975 4455553       799999999999999998753

; 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.

>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=96.72  E-value=0.013  Score=45.79  Aligned_cols=68  Identities=18%  Similarity=0.226  Sum_probs=51.3

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      .+..+ +...|..++.   ++|..+.+.+- .|+.++|++|.  ..++-.+.++|.+.++|++-.+++|++.++.
T Consensus        12 ~~~~~~l~vp~~~~~~---d~l~~f~~~~~~~i~~~riird~--~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fns   81 (110)
T PF07576_consen   12 RSTLCCLAVPPYMTPS---DFLLFFGAPFREDIEHIRIIRDG--TPNRYMVLIKFRDQESADEFYEEFNGKPFNS   81 (110)
T ss_pred             CceEEEEEeCcccccH---HHHHHhhhcccccEEEEEEeeCC--CCceEEEEEEECCHHHHHHHHHHhCCCccCC
Confidence            34444 6666666666   67776666664 46778898874  3466789999999999999999999988774

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=96.67  E-value=0.0035  Score=60.66  Aligned_cols=84  Identities=11%  Similarity=0.033  Sum_probs=59.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHh-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC----
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA----   89 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~-~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~----   89 (279)
                      +...+++ |.|+|...|.   ..|.+.-+ ..+.-.-+.++.|-.+..+.|||||.|.+++++..+.+++|++.++    
T Consensus       385 e~~rtt~~iknipNK~T~---~ml~~~d~~~~gtYDFlYLPiDF~nkcNvGYAFINm~sp~ai~~F~kAFnGk~W~~FnS  461 (549)
T KOG4660|consen  385 ECPRTTLMIKNIPNKYTS---KMLLAADEKNKGTYDFLYLPIDFKNKCNVGYAFINMTSPEAIIRFYKAFNGKKWEKFNS  461 (549)
T ss_pred             cCchhhhHhhccCchhhH---HhhhhhhccccCccceEEeccccccccccceeEEeecCHHHHHHHHHHHcCCchhhhcc
Confidence            3344455 7777766665   54444332 3455566778888888999999999999999999999999997654    


Q ss_pred             CceeEEeeccCCC
Q 023632           90 GAQVEVKKAEPKK  102 (279)
Q Consensus        90 g~~i~V~~a~~~~  102 (279)
                      .+.++|.+|+-+.
T Consensus       462 ~Kia~itYArIQG  474 (549)
T KOG4660|consen  462 EKIASITYARIQG  474 (549)
T ss_pred             eeeeeeehhhhhc
Confidence            3455666666443

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.64  E-value=0.0014  Score=63.89  Aligned_cols=76  Identities=9%  Similarity=0.179  Sum_probs=59.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHh-cCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc---C
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFM-QFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL---A   89 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~-~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l---~   89 (279)
                      ....+++| |.||-.-+|.   -+|++++. ..+.|++.+|-+-      |-.|||.|.+.++|.+.+.+||+..|   +
T Consensus       440 R~~~SnvlhI~nLvRPFTl---gQLkelL~rtgg~Vee~WmDkI------KShCyV~yss~eEA~atr~AlhnV~WP~sN  510 (718)
T KOG2416|consen  440 RKEPSNVLHIDNLVRPFTL---GQLKELLGRTGGNVEEFWMDKI------KSHCYVSYSSVEEAAATREALHNVQWPPSN  510 (718)
T ss_pred             CCCccceEeeecccccchH---HHHHHHHhhccCchHHHHHHHh------hcceeEecccHHHHHHHHHHHhccccCCCC
Confidence            44567788 9999999999   99999997 5667777744222      44899999999999999999999766   3


Q ss_pred             CceeEEeecc
Q 023632           90 GAQVEVKKAE   99 (279)
Q Consensus        90 g~~i~V~~a~   99 (279)
                      .+.|.|.++.
T Consensus       511 PK~L~adf~~  520 (718)
T KOG2416|consen  511 PKHLIADFVR  520 (718)
T ss_pred             CceeEeeecc
Confidence            5667777654

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=96.54  E-value=0.0018  Score=64.18  Aligned_cols=77  Identities=14%  Similarity=0.004  Sum_probs=63.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~-v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .....| |..||..+++   .++.++|++.-.|++ |.|..-+ +.+.+..|||+|..++++.+|+...+.+.+..+.|+
T Consensus       432 ~ag~~lyv~~lP~~t~~---~~~v~~f~~~~~Ved~I~lt~~P-~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~ir  507 (944)
T KOG4307|consen  432 GAGGALYVFQLPVMTPI---VPPVNKFMGAAAVEDFIELTRLP-TDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIR  507 (944)
T ss_pred             CccceEEeccCCccccc---cchhhhhhhhhhhhheeEeccCC-cccccchhhheeccccccchhhhcccccccCceEEE
Confidence            345678 9999999999   999999988878887 5555543 778889999999999988888887777777788888


Q ss_pred             Eee
Q 023632           95 VKK   97 (279)
Q Consensus        95 V~~   97 (279)
                      |..
T Consensus       508 v~s  510 (944)
T KOG4307|consen  508 VDS  510 (944)
T ss_pred             eec
Confidence            863

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=96.51  E-value=0.0014  Score=62.20  Aligned_cols=73  Identities=16%  Similarity=0.251  Sum_probs=58.0

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .+.| |.-+|+.+..  |++|..+|.+||+|+.|.|-...      -.|.|+|.+..+|-+|... +...|+++.|+|.|
T Consensus       372 hs~l~lek~~~glnt--~a~ln~hfA~fG~i~n~qv~~~~------~~a~vTF~t~aeag~a~~s-~~avlnnr~iKl~w  442 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNT--IADLNPHFAQFGEIENIQVDYSS------LHAVVTFKTRAEAGEAYAS-HGAVLNNRFIKLFW  442 (526)
T ss_pred             cchhhhhccCCCCch--HhhhhhhhhhcCccccccccCch------hhheeeeeccccccchhcc-ccceecCceeEEEE
Confidence            3445 5566666554  48999999999999999886552      2689999999999777665 78999999999999


Q ss_pred             ccC
Q 023632           98 AEP  100 (279)
Q Consensus        98 a~~  100 (279)
                      -++
T Consensus       443 hnp  445 (526)
T KOG2135|consen  443 HNP  445 (526)
T ss_pred             ecC
Confidence            876

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=96.38  E-value=0.0044  Score=63.04  Aligned_cols=79  Identities=15%  Similarity=0.228  Sum_probs=66.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC--Cc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--GA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~--g~   91 (279)
                      +...++.+ |..|+.++..   ..|..+|..||.|..|.+-..      .-||+|.+++...++.|++.|.+..|.  .+
T Consensus       451 kst~ttr~~sgglg~w~p~---~~l~r~fd~fGpir~Idy~hg------q~yayi~yes~~~aq~a~~~~rgap~G~P~~  521 (975)
T KOG0112|consen  451 KSTPTTRLQSGGLGPWSPV---SRLNREFDRFGPIRIIDYRHG------QPYAYIQYESPPAAQAATHDMRGAPLGGPPR  521 (975)
T ss_pred             ccccceeeccCCCCCCChH---HHHHHHhhccCcceeeecccC------CcceeeecccCccchhhHHHHhcCcCCCCCc
Confidence            34556778 9999999998   999999999999999876422      349999999999999999999998887  47


Q ss_pred             eeEEeeccCCC
Q 023632           92 QVEVKKAEPKK  102 (279)
Q Consensus        92 ~i~V~~a~~~~  102 (279)
                      .|.|.+|.+.-
T Consensus       522 r~rvdla~~~~  532 (975)
T KOG0112|consen  522 RLRVDLASPPG  532 (975)
T ss_pred             ccccccccCCC
Confidence            79999887643

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=96.31  E-value=0.003  Score=63.81  Aligned_cols=76  Identities=17%  Similarity=0.207  Sum_probs=63.2

Q ss_pred             eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC--CceeEEeeccC
Q 023632           23 TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--GAQVEVKKAEP  100 (279)
Q Consensus        23 V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~--g~~i~V~~a~~  100 (279)
                      +.|.+.+.+.   ..|..+|++|+.|++++.+++-.      .|.|+|.+.|.|..|+++|+++++-  +-+.+|.+|++
T Consensus       303 ~~nn~v~~tS---ssL~~l~s~yg~v~s~wtlr~~N------~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~  373 (1007)
T KOG4574|consen  303 LENNAVNLTS---SSLATLCSDYGSVASAWTLRDLN------MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKT  373 (1007)
T ss_pred             hhcccccchH---HHHHHHHHhhcchhhheeccccc------chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEeccc
Confidence            5555666676   88999999999999999988843      7999999999999999999998765  78899999987


Q ss_pred             CCCCCCC
Q 023632          101 KKPNLPQ  107 (279)
Q Consensus       101 ~~~~~~~  107 (279)
                      -..-+++
T Consensus       374 ~~~~ep~  380 (1007)
T KOG4574|consen  374 LPMYEPP  380 (1007)
T ss_pred             cccccCC
Confidence            6655544

>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=96.18  E-value=0.0036  Score=53.00  Aligned_cols=81  Identities=16%  Similarity=0.094  Sum_probs=47.3

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhc-CCCe---EEEEEeecC-CCC-CcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQ-FGDV---QEHQIMRDH-STS-RSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~-~G~V---~~v~i~~d~-~tg-~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      ..+| |++||+++||   +++.+.++. +...   ..+.-.... ... ....-|+|.|.+.+++...++.++++.|.+.
T Consensus         7 ~~KvVIR~LPP~Lte---eeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~   83 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTE---EEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDS   83 (176)
T ss_dssp             --EEEEEEE-TTS-H---HHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-T
T ss_pred             CceEEEeCCCCCCCH---HHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECC
Confidence            3466 9999999999   888876655 4443   233211111 111 1234699999999999999999999766542


Q ss_pred             -----eeEEeeccCCC
Q 023632           92 -----QVEVKKAEPKK  102 (279)
Q Consensus        92 -----~i~V~~a~~~~  102 (279)
                           ...|++|.-++
T Consensus        84 kg~~~~~~VE~Apyqk   99 (176)
T PF03467_consen   84 KGNEYPAVVEFAPYQK   99 (176)
T ss_dssp             TS-EEEEEEEE-SS--
T ss_pred             CCCCcceeEEEcchhc
Confidence                 44666665533

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.

>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=96.17  E-value=0.013  Score=49.89  Aligned_cols=62  Identities=11%  Similarity=0.220  Sum_probs=45.7

Q ss_pred             cHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC--CCccCCceeEEeeccCC
Q 023632           34 ALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGAQVEVKKAEPK  101 (279)
Q Consensus        34 ~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln--g~~l~g~~i~V~~a~~~  101 (279)
                      .++.|+++|.++..+..+.+++.-      .=..|.|.+.++|++|...|+  ...|.+..|+|.++++.
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sF------rRi~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~   71 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSF------RRIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPT   71 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTT------TEEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----S
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCC------CEEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEcccc
Confidence            348899999999999888777542      257899999999999999999  88999999999988544

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=96.16  E-value=0.0049  Score=54.47  Aligned_cols=75  Identities=13%  Similarity=0.218  Sum_probs=59.7

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC----ccCCceeE
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL----ELAGAQVE   94 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~----~l~g~~i~   94 (279)
                      +.| |.||+.-++.   +.|.+.|+.|++|+...|+.| ...++.+-.+|+|.+.-.+.+|+..++..    ++..+++-
T Consensus        32 a~l~V~nl~~~~sn---dll~~~f~~fg~~e~av~~vD-~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~  107 (275)
T KOG0115|consen   32 AELYVVNLMQGASN---DLLEQAFRRFGPIERAVAKVD-DRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVG  107 (275)
T ss_pred             ceEEEEecchhhhh---HHHHHhhhhcCccchheeeec-ccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccC
Confidence            667 9999999999   999999999999988777766 36778889999999999999999887432    33344555


Q ss_pred             Eeec
Q 023632           95 VKKA   98 (279)
Q Consensus        95 V~~a   98 (279)
                      |...
T Consensus       108 VeP~  111 (275)
T KOG0115|consen  108 VEPM  111 (275)
T ss_pred             CChh
Confidence            5443

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.12  E-value=0.0043  Score=58.35  Aligned_cols=76  Identities=22%  Similarity=0.328  Sum_probs=58.1

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC-CccCCceeEEee
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-LELAGAQVEVKK   97 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng-~~l~g~~i~V~~   97 (279)
                      .++ +.||.+.++.   ++|+.+|...-.-..-.++.      ..+++||.+.+...|.+||+.+++ .++.+++++|+.
T Consensus         2 nklyignL~p~~~p---sdl~svfg~ak~~~~g~fl~------k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~   72 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTP---SDLESVFGDAKIPGSGQFLV------KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEH   72 (584)
T ss_pred             CcccccccCCCCCh---HHHHHHhccccCCCCcceee------ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccc
Confidence            457 9999999999   99999996541111111111      146999999999999999999987 578899999998


Q ss_pred             ccCCCCC
Q 023632           98 AEPKKPN  104 (279)
Q Consensus        98 a~~~~~~  104 (279)
                      ..+++.+
T Consensus        73 sv~kkqr   79 (584)
T KOG2193|consen   73 SVPKKQR   79 (584)
T ss_pred             hhhHHHH
Confidence            8877654

>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=95.99  E-value=0.023  Score=41.01  Aligned_cols=58  Identities=17%  Similarity=0.324  Sum_probs=34.7

Q ss_pred             CCCcccHHHHHHHHhcCCC-----eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           29 PVTEPALDEFKDFFMQFGD-----VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        29 ~~te~~~~~L~~~F~~~G~-----V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      .++.   .+|..++.....     |-+|+|..+        |+||+-.. +.|+++|+.|+...+.+++|+|+.|
T Consensus        12 g~~~---~~iv~~i~~~~gi~~~~IG~I~I~~~--------~S~vev~~-~~a~~v~~~l~~~~~~gk~v~ve~A   74 (74)
T PF03880_consen   12 GLTP---RDIVGAICNEAGIPGRDIGRIDIFDN--------FSFVEVPE-EVAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--H---HHHHHHHHTCTTB-GGGEEEEEE-SS---------EEEEE-T-T-HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCH---HHHHHHHHhccCCCHHhEEEEEEeee--------EEEEEECH-HHHHHHHHHhcCCCCCCeeEEEEEC
Confidence            4555   777777766543     457777655        88998875 4789999999999999999999876

; PDB: 2G0C_A 3MOJ_B.

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=95.86  E-value=0.0023  Score=64.98  Aligned_cols=81  Identities=15%  Similarity=0.199  Sum_probs=65.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +...+.+| ++||+..+++   .+|+..|..++.|.+|.|.+.+. +.-.-++||.|.+.+.+-+|+..+....|..-.+
T Consensus       368 D~~atrTLf~Gnl~~kl~e---seiR~af~e~gkve~VDiKtP~~-~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~  443 (975)
T KOG0112|consen  368 DFRATRTLFLGNLDSKLTE---SEIRPAFDESGKVEEVDIKTPHI-KTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTH  443 (975)
T ss_pred             chhhhhhhhhcCcccchhh---hhhhhhhhhhccccccccccCCC-CcccchhhhhhhccccCcccchhhcCCccccCcc
Confidence            45667888 9999999999   99999999999999999876642 2223489999999999999999888877766566


Q ss_pred             EEeecc
Q 023632           94 EVKKAE   99 (279)
Q Consensus        94 ~V~~a~   99 (279)
                      ++.+-.
T Consensus       444 r~glG~  449 (975)
T KOG0112|consen  444 RIGLGQ  449 (975)
T ss_pred             cccccc
Confidence            665554

>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=95.69  E-value=0.052  Score=38.44  Aligned_cols=51  Identities=16%  Similarity=0.371  Sum_probs=39.9

Q ss_pred             HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        36 ~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ++|+..+.+|.- ++  |+.|+     .|| ||.|.+.++|++|.+..|+..+....|.+
T Consensus        15 ~d~K~~Lr~y~~-~~--I~~d~-----tGf-YIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   15 EDFKKRLRKYRW-DR--IRDDR-----TGF-YIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             HHHHHHHhcCCc-ce--EEecC-----CEE-EEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            889999999843 33  34453     234 89999999999999999998887777665

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=95.50  E-value=0.0071  Score=59.74  Aligned_cols=72  Identities=14%  Similarity=0.097  Sum_probs=60.2

Q ss_pred             CCCCCceeeeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           15 RQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        15 ~~~~~~~lV~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+..++||.||...|.+   +-++.++..+|.|..++++.         |+|++|.+++....|+..|+-..+++..|.
T Consensus        37 ~~~~~~vfv~~~~~~~s~---~~~~~il~~~g~v~s~kr~~---------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~  104 (668)
T KOG2253|consen   37 LPPRDTVFVGNISYLVSQ---EFWKSILAKSGFVPSWKRDK---------FGFCEFLKHIGDLRASRLLTELNIDDQKLI  104 (668)
T ss_pred             CCCCceeEecchhhhhhH---HHHHHHHhhCCcchhhhhhh---------hcccchhhHHHHHHHHHHhcccCCCcchhh
Confidence            334444449999999999   99999999999998876543         999999999999999999999999988887


Q ss_pred             Eeec
Q 023632           95 VKKA   98 (279)
Q Consensus        95 V~~a   98 (279)
                      +...
T Consensus       105 ~~~d  108 (668)
T KOG2253|consen  105 ENVD  108 (668)
T ss_pred             ccch
Confidence            7653

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.83  E-value=0.12  Score=49.28  Aligned_cols=67  Identities=16%  Similarity=0.224  Sum_probs=55.8

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ...| |--+|..++-   .||..|+..+- .|++|+|++|..  -++=.+.|+|.+.++|+.-.+.+|++.|+.
T Consensus        74 ~~mLcilaVP~~mt~---~Dll~F~~~~~~~I~~irivRd~~--pnrymvLIkFr~q~da~~Fy~efNGk~Fn~  142 (493)
T KOG0804|consen   74 STMLCILAVPAYMTS---HDLLRFCASFIKQISDIRIVRDGM--PNRYMVLIKFRDQADADTFYEEFNGKQFNS  142 (493)
T ss_pred             CcEEEEEeccccccH---HHHHHHHHHHhhhhheeEEeecCC--CceEEEEEEeccchhHHHHHHHcCCCcCCC
Confidence            6677 9999999999   88888887654 588999999753  334468999999999999999999988875

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=94.15  E-value=0.044  Score=49.93  Aligned_cols=80  Identities=15%  Similarity=0.099  Sum_probs=64.2

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .+++ |+++.+++.+   .++..++.+.+.+..+.+.....+-.+++++.|.|...+.+..||+......+..+.+...+
T Consensus        88 ~~~~f~g~~s~~~e~---~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl  164 (285)
T KOG4210|consen   88 SSTFFVGELSENIEE---SEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDL  164 (285)
T ss_pred             cccccccccccchhh---ccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcc
Confidence            5666 9999999988   88889999999888888777777888999999999999999999998544566666665555


Q ss_pred             ccCC
Q 023632           98 AEPK  101 (279)
Q Consensus        98 a~~~  101 (279)
                      ....
T Consensus       165 ~~~~  168 (285)
T KOG4210|consen  165 NTRR  168 (285)
T ss_pred             cccc
Confidence            4443

>KOG4019 consensus Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms; General function prediction only]

Probab=93.73  E-value=0.054  Score=45.65  Aligned_cols=81  Identities=19%  Similarity=0.176  Sum_probs=56.6

Q ss_pred             CCCCceeeeCCCCCCCc--ccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc-e
Q 023632           16 QTTTQKMTGLSLTPVTE--PALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA-Q   92 (279)
Q Consensus        16 ~~~~~~lV~nLp~~~te--~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~-~   92 (279)
                      ++.+..|+.+|+.+|-.  ++....+.+|.+|-+.+..++++.      ..+.-|.|.+++.|.+|..+++...|.++ .
T Consensus         8 dlp~~~~~c~i~~~VF~~~~~k~~~~~lFrq~n~~~~fq~lrs------frrvRi~f~~p~~a~~a~i~~~~~~f~~~~~   81 (193)
T KOG4019|consen    8 DLPTAIIACDIHEEVFVNREDKALFENLFRQINEDATFQLLRS------FRRVRINFSNPEAAADARIKLHSTSFNGKNE   81 (193)
T ss_pred             cccceeeeecccHHhhccHHHHHHHHhHHhhhCcchHHHHHHh------hceeEEeccChhHHHHHHHHhhhcccCCCce
Confidence            34444447788776553  223455667777766655555533      34567899999999999999999999988 8


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+.-+|.+..
T Consensus        82 ~k~yfaQ~~~   91 (193)
T KOG4019|consen   82 LKLYFAQPGH   91 (193)
T ss_pred             EEEEEccCCC
Confidence            8887777543

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.56  E-value=0.31  Score=47.90  Aligned_cols=78  Identities=10%  Similarity=0.185  Sum_probs=57.3

Q ss_pred             CCCCcee-eeCCCCC-CCcccHHHHHHHHhcC----CCeEEEEEeecC----------CCCC------------------
Q 023632           16 QTTTQKM-TGLSLTP-VTEPALDEFKDFFMQF----GDVQEHQIMRDH----------STSR------------------   61 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~----G~V~~v~i~~d~----------~tg~------------------   61 (279)
                      ...+++| |.||.|+ |..   ++|..+|..|    |.|..|.|....          .++.                  
T Consensus       171 ~~~T~RLAVvNMDWd~v~A---kDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~  247 (650)
T KOG2318|consen  171 GEETKRLAVVNMDWDRVKA---KDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDD  247 (650)
T ss_pred             ccccceeeEeccccccccH---HHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccch
Confidence            5678999 9999997 445   7888888776    578888775311          0111                  


Q ss_pred             ------------------cc-cEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           62 ------------------SR-GFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        62 ------------------~r-G~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                                        .+ =||.|+|++.++|.++.+.++++++...-+.+.
T Consensus       248 ee~~~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~D  301 (650)
T KOG2318|consen  248 EEEEDVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLD  301 (650)
T ss_pred             hhhhhHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceee
Confidence                              11 379999999999999999999999986544443

>KOG4483 consensus Uncharacterized conserved protein [Function unknown]

Probab=93.19  E-value=0.17  Score=47.63  Aligned_cols=58  Identities=7%  Similarity=0.089  Sum_probs=47.6

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCe-EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDV-QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG   83 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V-~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l   83 (279)
                      ....++| |-++|.....   +||..+|+.|..- .+|+++.|.       .||.+|++...|..||..-
T Consensus       388 ~dlpHVlEIydfp~efkt---eDll~~f~~yq~kgfdIkWvDdt-------halaVFss~~~AaeaLt~k  447 (528)
T KOG4483|consen  388 SDLPHVLEIYDFPDEFKT---EDLLKAFETYQNKGFDIKWVDDT-------HALAVFSSVNRAAEALTLK  447 (528)
T ss_pred             ccccceeEeccCchhhcc---HHHHHHHHHhhcCCceeEEeecc-------eeEEeecchHHHHHHhhcc
Confidence            3446788 9999999998   9999999999653 567777775       7999999999999998763

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=92.93  E-value=0.0056  Score=57.59  Aligned_cols=76  Identities=16%  Similarity=0.205  Sum_probs=62.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEE-eecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQI-MRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i-~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..++++ |.|||....|   +.|..++.+|+.|+.|.+ ++|.+|-    ..-|++.+.+.++.||.+||+..|....++
T Consensus        78 qrsrk~Qirnippql~w---evld~Ll~qyg~ve~~eqvnt~~eta----vvnvty~~~~~~~~ai~kl~g~Q~en~~~k  150 (584)
T KOG2193|consen   78 QRSRKIQIRNIPPQLQW---EVLDSLLAQYGTVENCEQVNTDSETA----VVNVTYSAQQQHRQAIHKLNGPQLENQHLK  150 (584)
T ss_pred             HHhhhhhHhcCCHHHHH---HHHHHHHhccCCHhHhhhhccchHHH----HHHHHHHHHHHHHHHHHhhcchHhhhhhhh
Confidence            445678 9999999999   999999999999998854 3444332    234788999999999999999999999999


Q ss_pred             Eeecc
Q 023632           95 VKKAE   99 (279)
Q Consensus        95 V~~a~   99 (279)
                      |.+-.
T Consensus       151 ~~YiP  155 (584)
T KOG2193|consen  151 VGYIP  155 (584)
T ss_pred             cccCc
Confidence            97654

>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth

Probab=92.19  E-value=0.27  Score=34.98  Aligned_cols=63  Identities=17%  Similarity=0.305  Sum_probs=45.3

Q ss_pred             HHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccCC
Q 023632           36 DEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPK  101 (279)
Q Consensus        36 ~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~~  101 (279)
                      ++|++.|...| +|.+|.-+..+.+.++--.-||+++...+..+   .++-+.|.+..|+|+....+
T Consensus         2 ~~I~~~L~~~G~~v~~i~~~~~~~~k~pl~mf~veL~p~~~~k~---i~~Ik~l~~~~V~vE~~~k~   65 (68)
T PF07530_consen    2 EEIKEELKDQGHPVRNIHNMHSRNTKKPLNMFFVELEPKPNNKE---IYKIKTLCGQRVKVERPRKR   65 (68)
T ss_pred             HHHHHHHHHcCCceEEEEccccCCCCCCceEEEEeeccCccccc---eeehHhhCCeEEEEecCCCC
Confidence            45777776666 68888888887777777788888887655333   34447888899999876543

These proteins are possibly involved in RNA binding or single strand DNA binding.

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=91.02  E-value=4.2  Score=41.26  Aligned_cols=61  Identities=8%  Similarity=0.113  Sum_probs=44.1

Q ss_pred             CCCCcccHHHHHHHHhcCCCe-----EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           28 TPVTEPALDEFKDFFMQFGDV-----QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        28 ~~~te~~~~~L~~~F~~~G~V-----~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      ..++.   .+|..++..-..|     -.|+|..+        |.||+... +.+++.++.|+...+.+++|.|+.+..
T Consensus       497 ~~~~~---~~~~~~i~~~~~~~~~~ig~i~i~~~--------~s~v~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (629)
T PRK11634        497 DGVEV---RHIVGAIANEGDISSRYIGNIKLFAS--------HSTIELPK-GMPGEVLQHFTRTRILNKPMNMQLLGD  562 (629)
T ss_pred             cCCCH---HHHHHHHHhhcCCChhhCCcEEEeCC--------ceEEEcCh-hhHHHHHHHhccccccCCceEEEECCC
Confidence            34555   6676666554444     35666544        78998764 568889999999999999999998753

>smart00596 PRE_C2HC PRE_C2HC domain

Probab=90.67  E-value=0.5  Score=33.60  Aligned_cols=62  Identities=15%  Similarity=0.153  Sum_probs=46.6

Q ss_pred             HHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           36 DEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        36 ~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      ++|++.|++.| +|+.|..|..+++..+--.-||+.....+...   .|+=+.|.+++|+|+....
T Consensus         2 ~~I~~~L~~~G~~v~~i~~m~~~~~r~P~nmf~vel~~~~~~~~---Il~ik~Lg~~~V~VEr~~k   64 (69)
T smart00596        2 SQIEEALKDIGFPVLFIHNMLNRDTKNPQNMFEVELVPAANGKE---ILNIKTLGGQRVTVERPHK   64 (69)
T ss_pred             HHHHHHHHHcCCceeEEEcccccCCCCcceeEEEEeeecCCCcc---eEeehhhCCeeEEEecCcc
Confidence            46778888777 68889888888878777788898887654444   4455788899999986543

>PF10567 Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IPR018885 This conserved domain is found in fungal proteins and appears to be involved in RNA-processing

Probab=89.37  E-value=0.91  Score=41.19  Aligned_cols=82  Identities=12%  Similarity=0.229  Sum_probs=59.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecC-------CCCCcccEEEEEEcCHHHHHH----HHHH
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDH-------STSRSRGFGFITFDTEQAVDD----LLAK   82 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~-------~tg~~rG~aFV~F~s~e~a~~----Ai~~   82 (279)
                      +.-.++.| +.||..+++-   .++...|.+|++|+.|.++.+.       +..+......+.|-+.+.|..    .|+.
T Consensus        11 D~YrTRSLLfeNv~~sidL---h~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQr   87 (309)
T PF10567_consen   11 DEYRTRSLLFENVNNSIDL---HSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQR   87 (309)
T ss_pred             ccceeHHHHHhhccccccH---HHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHH
Confidence            45567888 9999988776   8888999999999999999775       123344577889988877654    3333


Q ss_pred             cC--CCccCCceeEEeecc
Q 023632           83 GN--KLELAGAQVEVKKAE   99 (279)
Q Consensus        83 ln--g~~l~g~~i~V~~a~   99 (279)
                      |+  .+.|....|+|.+..
T Consensus        88 LsEfK~~L~S~~L~lsFV~  106 (309)
T PF10567_consen   88 LSEFKTKLKSESLTLSFVS  106 (309)
T ss_pred             HHHHHHhcCCcceeEEEEE
Confidence            32  256777788887765

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

>PF03468 XS: XS domain; InterPro: IPR005380 The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X Q9SBW2 from SWISSPROT and SGS3 Q9LDX1 from SWISSPROT

Probab=88.71  E-value=1.1  Score=35.32  Aligned_cols=56  Identities=13%  Similarity=0.207  Sum_probs=29.5

Q ss_pred             eeCCCCCCCccc------HHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcC-HHHHHHHHH
Q 023632           23 TGLSLTPVTEPA------LDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLA   81 (279)
Q Consensus        23 V~nLp~~~te~~------~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s-~e~a~~Ai~   81 (279)
                      |.|++.+.+++.      .++|++.|+.|..++ |+.+.++.  -++++++|+|.+ -.-...|++
T Consensus        13 i~N~~~~~~~~g~~~g~~~~~l~~~l~~f~p~k-v~~l~~~~--gh~g~aiv~F~~~w~Gf~~A~~   75 (116)
T PF03468_consen   13 IVNIPTEKDDDGRWVGMSNEELLDKLAEFNPLK-VKPLYGKQ--GHTGFAIVEFNKDWSGFKNAMR   75 (116)
T ss_dssp             EE----EE-TTS-EE---SHHHHHHHHH---SE-EEEEEETT--EEEEEEEEE--SSHHHHHHHHH
T ss_pred             EEcCccccCCCCceeccCHHHHHHHHHhcCCce-eEECcCCC--CCcEEEEEEECCChHHHHHHHH
Confidence            667765543211      178999999998875 55666643  568899999974 444555554

SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain containing proteins contain coiled-coils, which suggests that they will oligomerise. Most coiled-coil proteins form either a dimeric or a trimeric structure. It is possible that different members of the XS domain family could oligomerise via their coiled-coils forming a variety of complexes [].; PDB: 4E8U_C.

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=88.49  E-value=0.074  Score=49.81  Aligned_cols=63  Identities=11%  Similarity=0.050  Sum_probs=47.8

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      .+| |.+|+..|..   .+|.++|..+|+|....+...    ...-+|-|+|....+...|+.. ++.++.-
T Consensus       152 Rt~~v~sl~~~~~l---~e~~e~f~r~Gev~ya~~ask----~~s~~c~~sf~~qts~~halr~-~gre~k~  215 (479)
T KOG4676|consen  152 RTREVQSLISAAIL---PESGESFERKGEVSYAHTASK----SRSSSCSHSFRKQTSSKHALRS-HGRERKR  215 (479)
T ss_pred             hhhhhhcchhhhcc---hhhhhhhhhcchhhhhhhhcc----CCCcchhhhHhhhhhHHHHHHh-cchhhhh
Confidence            567 9999999998   999999999999877655432    2233667999988888888877 5655553

>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]

Probab=88.20  E-value=2.5  Score=35.85  Aligned_cols=17  Identities=12%  Similarity=0.298  Sum_probs=8.5

Q ss_pred             HHHHHHHhcCCCeEEEE
Q 023632           36 DEFKDFFMQFGDVQEHQ   52 (279)
Q Consensus        36 ~~L~~~F~~~G~V~~v~   52 (279)
                      ++|-++=+-|++|.++.
T Consensus        89 ~qIGKVDEIfG~i~d~~  105 (215)
T KOG3262|consen   89 EQIGKVDEIFGPINDVH  105 (215)
T ss_pred             hhhcchhhhcccccccE
Confidence            44444445555665543

>PF02714 DUF221: Domain of unknown function DUF221; InterPro: IPR003864 This domain is found in a family of hypothetical transmembrane proteins none of which have any known function, the aligned region is at 538 residues at maximum length

Probab=82.08  E-value=1.6  Score=40.07  Aligned_cols=38  Identities=16%  Similarity=0.146  Sum_probs=28.5

Q ss_pred             EEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccCCCCCC
Q 023632           66 GFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL  105 (279)
Q Consensus        66 aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~~~~~~  105 (279)
                      |||+|+++++|+.|++.+..++  .+.++|+.|.++++-.
T Consensus         1 aFVtF~~~~~a~~~~q~~~~~~--~~~~~v~~APeP~DI~   38 (325)
T PF02714_consen    1 AFVTFNSQKSAQIALQLLLSKR--PNSWRVSPAPEPDDII   38 (325)
T ss_pred             CEEEECCHHHHHHHHHHHhcCC--CCCceEeeCCCccccc
Confidence            7999999999999999764433  3566888776665543

; GO: 0016020 membrane

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

Probab=81.62  E-value=0.36  Score=42.07  Aligned_cols=75  Identities=29%  Similarity=0.383  Sum_probs=56.6

Q ss_pred             CCCcee-eeC----CCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           17 TTTQKM-TGL----SLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        17 ~~~~~l-V~n----Lp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      +...++ .++    |...+++   +.+.++|++-++|+.++|.++.+ ++++-+.||++....++-.++......++--+
T Consensus        78 e~q~~~r~G~shapld~r~~~---ei~~~v~s~a~p~~~~R~~~~~d-~rnrn~~~~~~qr~~~~P~~~~~y~~l~~~~~  153 (267)
T KOG4454|consen   78 EEQRTLRCGNSHAPLDERVTE---EILYEVFSQAGPIEGVRIPTDND-GRNRNFGFVTYQRLCAVPFALDLYQGLELFQK  153 (267)
T ss_pred             hhhcccccCCCcchhhhhcch---hhheeeecccCCCCCcccccccc-CCccCccchhhhhhhcCcHHhhhhcccCcCCC
Confidence            334455 666    7777888   88889999999999999998864 78888999999888777778777666554444


Q ss_pred             eeEE
Q 023632           92 QVEV   95 (279)
Q Consensus        92 ~i~V   95 (279)
                      ++.+
T Consensus       154 ~~~~  157 (267)
T KOG4454|consen  154 KVTI  157 (267)
T ss_pred             Cccc
Confidence            4433

>COG5638 Uncharacterized conserved protein [Function unknown]

Probab=81.22  E-value=4.5  Score=38.51  Aligned_cols=27  Identities=4%  Similarity=0.266  Sum_probs=23.0

Q ss_pred             EEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           65 FGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        65 ~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      ||.|+|++.+.++.+...+++.++...
T Consensus       260 yAvvec~d~~tsK~iY~~CDG~Eye~s  286 (622)
T COG5638         260 YAVVECEDIETSKNIYSACDGVEYENS  286 (622)
T ss_pred             EEEEEeccchhhHHHHhccCccccccc
Confidence            789999999999999999888877643

>KOG2187 consensus tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis]

Probab=80.96  E-value=1.3  Score=43.35  Aligned_cols=40  Identities=15%  Similarity=0.267  Sum_probs=33.3

Q ss_pred             ccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccCCC
Q 023632           63 RGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK  102 (279)
Q Consensus        63 rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~~~  102 (279)
                      ..+++++|++++.+.+|+..+++.......+.|..+....
T Consensus        63 ~~~~~~~~et~~~~~ka~~~v~g~~~k~~~~~~~~~~~~~  102 (534)
T KOG2187|consen   63 PKYAYVTFETPSDAGKAINLVDGLLYKGFILRVQLGATEV  102 (534)
T ss_pred             CCceEEEEeccchhhhHHHHHhhhhhhcchhhhhhccccc
Confidence            4599999999999999999999988888777777665443

>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]

Probab=80.95  E-value=0.28  Score=47.90  Aligned_cols=72  Identities=8%  Similarity=0.067  Sum_probs=55.0

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      .+++.| |.||+++++-   ++|..+++.+--+..+.+..+....+..-+.+|+|+--..++.|+.+||++.+...
T Consensus       229 hke~sll~rni~Pnis~---aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aLn~irl~s~  301 (648)
T KOG2295|consen  229 HKECSLLVRNILPNISV---AEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWALNGIRLRSN  301 (648)
T ss_pred             hHHHHHHHhccCCcccH---HHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHhhhcccccc
Confidence            345677 9999999999   99999999887666666554444455566889999988888888888887766543

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

Probab=80.20  E-value=1.8  Score=36.99  Aligned_cols=61  Identities=13%  Similarity=0.229  Sum_probs=41.2

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHH
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDL   79 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~A   79 (279)
                      ......+ +.+++..+++   .++..+|..++.+..+.+...........+.++.+.....+..+
T Consensus       222 ~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  283 (306)
T COG0724         222 LEKSDNLYVGNLPLKTAE---EELADLFKSRGDIVRASLPPSKDGKIPKSRSFVGNEASKDALES  283 (306)
T ss_pred             ccccceeeccccccccch---hHHHHhccccccceeeeccCCCCCcccccccccchhHHHhhhhh
Confidence            3445666 9999999999   99999999999998777766654444444444444433333333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	279
2cjk_A	167	Structure Of The Rna Binding Domain Of Hrp1 In Comp		9e-10
2rs2_A	109	1h, 13c, And 15n Chemical Shift Assignments For Mus		2e-08
2dgs_A	99	Solution Structure Of The Second Rna Binding Domain		2e-08
1uaw_A	77	Solution Structure Of The N-Terminal Rna-Binding Do		4e-07
2mss_A	75	Musashi1 Rbd2, Nmr Length = 75		6e-07
1l3k_A	196	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		4e-06
1pgz_A	195	Crystal Structure Of Up1 Complexed With D(Ttagggtta		5e-06
2lyv_A	197	Solution Structure Of The Two Rrm Domains Of Hnrnp		5e-06
1x5s_A	102	Solution Structure Of Rrm Domain In A18 Hnrnp Lengt		6e-06
1x4b_A	116	Solution Structure Of Rrm Domain In Heterogeneous N		7e-06
2jrs_A	108	Solution Nmr Structure Of Caper Rrm2 Domain. Northe		8e-06
1d8z_A	89	Solution Structure Of The First Rna-Binding Domain		8e-06
1up1_A	182	Up1, The Two Rna-Recognition Motif Domain Of Hnrnp		1e-05
1ha1_A	184	Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184		1e-05
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		1e-05
2up1_A	183	Structure Of Up1-Telomeric Dna Complex Length = 183		1e-05
2dh8_A	105	Solution Structure Of The N-Terminal Rna Binding Do		2e-05
3uwt_A	200	Crystal Structure Of A Rna Binding Domain Of Poly-U		2e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-05
3s7r_A	87	Crystal Structure Of A Heterogeneous Nuclear Ribonu		3e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		4e-05
2dnz_A	95	Solution Structure Of The Second Rna Binding Domain		4e-05
2ki2_A	90	Solution Structure Of Ss-Dna Binding Protein 12rnp2		5e-05
1x5u_A	105	Solution Structure Of Rrm Domain In Splicing Factor		7e-05
1hd0_A	75	Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D		7e-05
2dgo_A	115	Solution Structure Of The Rna Binding Domain In Cyt		2e-04
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		2e-04
2cqb_A	102	Solution Structure Of The Rna Recognition Motif In		2e-04
3hi9_A	84	The X-Ray Crystal Structure Of The First Rna Recogn		2e-04
2dh7_A	105	Solution Structure Of The Second Rna Binding Domain		2e-04
2rrb_A	96	Refinement Of Rna Binding Domain In Human Tra2 Beta		3e-04
2rra_A	99	Solution Structure Of Rna Binding Domain In Human T		3e-04
2kxn_B	129	Nmr Structure Of Human Tra2beta1 Rrm In Complex Wit		3e-04
4fxv_A	99	Crystal Structure Of An Elav-Like Protein 1 (Elavl1		4e-04
1wf0_A	88	Solution Structure Of Rrm Domain In Tar Dna-Binding		5e-04
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		6e-04
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		6e-04

>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex With Rna Length = 167

Iteration: 1
 Score = 60.8 bits (146), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 31/88 (35%), Positives = 53/88 (60%), Gaps = 3/88 (3%)
Query: 14  NRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 73
           + Q  T K+    + P   P   EF++FF Q+G + + Q+M D  T +SRGFGF+T+D+ 
Sbjct: 82  DEQDKTGKIFVGGIGPDVRPK--EFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA 139
Query: 74  QAVDDLLAKGNKLELAGAQVEVKKAEPK 101
            AV D + +   ++    ++E+K+AEP+
Sbjct: 140 DAV-DRVCQNKFIDFKDRKIEIKRAEPR 166

>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1 Rbd1:r(Guagu) Complex Length = 109

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 44/65 (67%), Gaps = 1/65 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+ ++ EL    ++ K 
Sbjct: 42  LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKV 100
Query: 98  AEPKK 102
           A P++
Sbjct: 101 AFPRR 105

>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In Daz- Associated Protein 1 Length = 99

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 30/73 (41%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           E +++F +FG V E  ++ D    R RGFGFITF+ EQ+VD  +   +  ++ G +VEVK
Sbjct: 26  ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM-HFHDIMGKKVEVK 84
Query: 97  KAEPKKPNLPQPS 109
           +AEP+      PS
Sbjct: 85  RAEPRDSKSSGPS 97

>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of Mouse Musashi1 Length = 77

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 38 FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
           +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+ ++ EL    ++ K 
Sbjct: 17 LREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKV 75
Query: 98 A 98
          A
Sbjct: 76 A 76

>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr Length = 75

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/75 (38%), Positives = 44/75 (58%), Gaps = 5/75 (6%)
Query: 24 GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
          GLS+    E    + K +F QFG V +  +M D +T+R RGFGF+TF++E  V+  + + 
Sbjct: 6  GLSVNTTVE----DVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEK-VCEI 60
Query: 84 NKLELAGAQVEVKKA 98
          +  E+    VE KKA
Sbjct: 61 HFHEINNKMVECKKA 75

>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 196

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRK 179
Query: 98  AEPKKPNLPQPSYRR 112
           A  K+      S +R
Sbjct: 180 ALSKQEMASASSSQR 194

>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 = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 120 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRK 178
Query: 98  AEPKKPNLPQPSYRR 112
           A  K+      S +R
Sbjct: 179 ALSKQEMASASSSQR 193

>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 = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 1/75 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 122 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRK 180
Query: 98  AEPKKPNLPQPSYRR 112
           A  K+      S +R
Sbjct: 181 ALSKQEMASASSSQR 195

>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp Length = 102

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 24  GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG 83
           GLS     E +L++    F ++G + E  +++D  T RSRGFGF+TF+      D +   
Sbjct: 19  GLSF-DTNEQSLEQV---FSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 84  NKLELAGAQVEVKKAEPKKPNLPQPS 109
           N   + G Q+ V +A     N   PS
Sbjct: 75  NGKSVDGRQIRVDQAGKSSDNRSGPS 100

>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear Ribonucleaoproteins A2B1 Length = 116

Iteration: 1
 Score = 47.8 bits (112), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 32  EPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA 91
           E   +  ++++ Q+G + +  +MRD ++ RSRGFGF+TF +   VD  +A      + G 
Sbjct: 38  ETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGR 96
Query: 92  QVEVKKAEPKKPNLPQPS 109
            VE K+A  ++ +   PS
Sbjct: 97  VVEPKRAVAREESGSGPS 114

>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast Structural Genomics Target Hr4730a Length = 108

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D  +  F  FG ++  Q+M D  T RS+G+GFITF   +     L + N  ELAG  ++V
Sbjct: 41  DMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1) Of Hu Antigen C (Huc) Length = 89

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           DEFK  F   GD++  +++RD  T +S G+GF+ +      D  +   N L+L    ++V
Sbjct: 19  DEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKV 78
Query: 96  KKAEPKKPNL 105
             A P   ++
Sbjct: 79  SYARPSSASI 88

>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1 Length = 182

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 119 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRK 177
Query: 98  AEPKK 102
           A  K+
Sbjct: 178 ALSKQ 182

>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens Length = 184

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 121 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRK 179
Query: 98  AEPKK 102
           A  K+
Sbjct: 180 ALSKQ 184

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           DEFK  F   GD++  +++RD  T +S G+GF+ +      D  +   N L+L    ++V
Sbjct: 19  DEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKV 78
Query: 96  KKAEPKKPNL 105
             A P   ++
Sbjct: 79  SYARPSSASI 88

>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex Length = 183

Iteration: 1
 Score = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 38  FKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK 97
            +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + G   EV+K
Sbjct: 114 LRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHT-VNGHNCEVRK 172
Query: 98  AEPKK 102
           A  K+
Sbjct: 173 ALSKQ 177

>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In Daz-Associated Protein 1 Length = 105

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 37/66 (56%), Gaps = 1/66 (1%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           +  + +F Q+G+V +  IM+D +T++SRGFGF+ F     V  +LA      L G  ++ 
Sbjct: 31  ETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRNIDP 89
Query: 96  KKAEPK 101
           K   P+
Sbjct: 90  KPCTPR 95

>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U Binding Splicing Factor 60kda (Puf60) From Homo Sapiens At 2.50 A Resolution Length = 200

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D+ K  F  FG ++   + RD +T + +G+GFI ++  Q+  D ++  N  +L G  + V
Sbjct: 124 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Query: 96  KKA 98
            KA
Sbjct: 184 GKA 186

>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To Ssdna From A Portion Of Fuse Length = 216

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D+ K  F  FG ++   + RD +T + +G+GFI ++  Q+  D ++  N  +L G  + V
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Query: 96  KKA 98
            KA
Sbjct: 200 GKA 202

>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 = 45.4 bits (106), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/62 (40%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          + KD+F +FG+V +  I  D +T RSRGFGFI F    +V+ +L +  +  L G  ++ K
Sbjct: 27 DLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRVIDPK 85
Query: 97 KA 98
          KA
Sbjct: 86 KA 87

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D+ K  F  FG ++   + RD +T + +G+GFI ++  Q+  D ++  N  +L G  + V
Sbjct: 125 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Query: 96  KKA 98
            KA
Sbjct: 185 GKA 187

>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna Binding Motif Protein 23 Length = 95

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 34/74 (45%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           D  +  F  FG +    +M+D  T RS+G+GFITF   +     L + N  ELAG  + V
Sbjct: 20  DMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV 79
Query: 96  KKAEPKKPNLPQPS 109
                +      PS
Sbjct: 80  GHVTERLDGGSGPS 93

>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 = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++ K+ F QFG V   +++ D  T + +GFGF+    E++V + +AK +  +  G  + V
Sbjct: 16  EQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKLDNTDFMGRTIRV 74
Query: 96  KKAEPKK 102
            +A PKK
Sbjct: 75  TEANPKK 81

>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b Length = 105

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 3/80 (3%)
Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           V+EP L E    F+Q G V    + +D  T + +G+GF+ F +E+  D  +   + ++L 
Sbjct: 27  VSEPLLWEL---FLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLY 83
Query: 90  GAQVEVKKAEPKKPNLPQPS 109
           G  + V KA     NL  PS
Sbjct: 84  GKPIRVNKASAHNKNLSGPS 103

>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0 Rbd1), Nmr Length = 75

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 39/62 (62%), Gaps = 1/62 (1%)
Query: 37 EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
          + KD+F +FG+V +  +  D  T RSRGFGF+ F   ++VD ++ +  + +L G  ++ K
Sbjct: 15 DLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ-KEHKLNGKVIDPK 73
Query: 97 KA 98
          +A
Sbjct: 74 RA 75

>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 = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/84 (26%), Positives = 46/84 (54%), Gaps = 3/84 (3%)
Query: 27  LTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 86
           L+P  E   ++ K  F  FG + + ++++D +T +S+G+GF++F  +   ++ + +    
Sbjct: 23  LSP--EITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQ 80
Query: 87  ELAGAQVEVKKAEPKKPNLPQPSY 110
            L G Q+    A  +KP  P+ +Y
Sbjct: 81  WLGGRQIRTNWAT-RKPPAPKSTY 103

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 8/74 (10%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           +EF+  F   G+++  +++RD  T +S G+GF+ +    D E+A++ L    N L L   
Sbjct: 17  EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTL----NGLRLQTK 72
Query: 92  QVEVKKAEPKKPNL 105
            ++V  A P   ++
Sbjct: 73  TIKVSYARPSSASI 86

>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In Peptidyl- Prolyl Cis-Trans Isomerase E Length = 102

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 8/72 (11%)
Query: 42  FMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGAQVEVKK 97
           F+ FGD+ + QI  D+ T + RGF F+ F    D   A+D++    N+ EL G  + V  
Sbjct: 33  FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM----NESELFGRTIRVNL 88
Query: 98  AEPKKPNLPQPS 109
           A+P +     PS
Sbjct: 89  AKPMRIKESGPS 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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L    N L L   
Sbjct: 19  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL----NGLRLQSK 74
Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 75  TIKVSYARP 83

>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In Nucleolysin Tiar Length = 105

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 2/83 (2%)
Query: 27  LTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 86
           L+P  E   ++ K  F  FG + + ++++D +T +S+G+GF++F  +   ++ +      
Sbjct: 23  LSP--EITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQ 80
Query: 87  ELAGAQVEVKKAEPKKPNLPQPS 109
            L G Q+    A  K P    PS
Sbjct: 81  WLGGRQIRTNWATRKPPAPSGPS 103

>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta Protein Length = 96

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 37/68 (54%)
Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N +EL G ++ V 
Sbjct: 28  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 87
Query: 97  KAEPKKPN 104
            +  K+P+
Sbjct: 88  FSITKRPH 95

>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2 Beta Protein In Complex With Rna (Gaagaa) Length = 99

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 37/68 (54%)
Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N +EL G ++ V 
Sbjct: 31  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 90
Query: 97  KAEPKKPN 104
            +  K+P+
Sbjct: 91  FSITKRPH 98

>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With Aagaac Rna Length = 129

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/68 (26%), Positives = 37/68 (54%)
Query: 37  EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
           + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N +EL G ++ V 
Sbjct: 62  DLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD 121
Query: 97  KAEPKKPN 104
            +  K+P+
Sbjct: 122 FSITKRPH 129

>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 = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L    N L L   
Sbjct: 34  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL----NGLRLQSK 89
Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 90  TIKVSYARP 98

>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding Protein- 43 Length = 88

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/74 (35%), Positives = 36/74 (48%), Gaps = 7/74 (9%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           DE ++FF Q+GDV +  I +       R F F+TF  +Q    L   G  L + G  V +
Sbjct: 20  DELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQSLC--GEDLIIKGISVHI 72
Query: 96  KKAEPKKPNLPQPS 109
             AEPK  +   PS
Sbjct: 73  SNAEPKHNSNSGPS 86

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L    N L L   
Sbjct: 17  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL----NGLRLQSK 72
Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 73  TIKVSYARP 81

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 8/69 (11%)
Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF----DTEQAVDDLLAKGNKLELAGA 91
           DE +  F   G+V+  +++RD     S G+GF+ +    D E+A++ L    N L L   
Sbjct: 17  DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL----NGLRLQSK 72
Query: 92  QVEVKKAEP 100
            ++V  A P
Sbjct: 73  TIKVSYARP 81

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	279
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.88
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.87
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.86
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.86
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.86
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.86
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.86
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.85
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.85
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.85
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.85
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.85
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.85
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.85
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.85
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.85
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.85
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.84
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.84
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.84
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.84
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.84
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.84
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.84
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.84
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.84
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.84
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.84
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.84
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.84
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.84
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.83
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.83
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.83
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.83
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.83
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.83
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.83
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.83
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.83
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.83
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.82
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.82
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.82
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.82
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.82
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.82
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.82
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.82
2div_A	99	TRNA selenocysteine associated protein; structural	99.82
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.82
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.82
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.81
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.81
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.81
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.81
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.81
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.81
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.81
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.81
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.81
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.81
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.81
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.81
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.81
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.81
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.8
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.8
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.8
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.8
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.8
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.8
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.8
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.8
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.8
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.8
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.8
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.8
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.8
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.8
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.8
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.79
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.79
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.79
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.79
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.79
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.79
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.79
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.79
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.79
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.78
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.78
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.78
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.78
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.78
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.78
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.78
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.78
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.77
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.77
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.77
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.77
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.77
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.77
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.77
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.77
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.77
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.77
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.77
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.77
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.76
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.76
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.76
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.76
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.76
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.76
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.76
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.76
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.62
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.76
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.75
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.75
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.75
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.75
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.75
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.75
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.75
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.75
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.74
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.74
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.74
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.74
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.74
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.74
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.74
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.73
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.73
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.73
1x5p_A	97	Negative elongation factor E; structure genomics,	99.73
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.73
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.73
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.73
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.73
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.73
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.73
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.72
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.72
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.72
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.72
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.72
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.72
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.71
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.71
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.71
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.7
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.7
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.7
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.7
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.69
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.69
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.69
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.68
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.68
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.67
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.67
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.67
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.67
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.67
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.67
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.67
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.66
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.66
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.65
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.65
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.65
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.64
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.64
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.62
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.62
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.62
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.6
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.6
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.6
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.6
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.59
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.59
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.59
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.57
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.57
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.57
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.56
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.55
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.54
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.53
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.52
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.51
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.5
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.5
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.49
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.47
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.44
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.39
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.32
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	99.24
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.21
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	99.19
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.79
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.47
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	98.3
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	98.19
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.85
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.8
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	97.59
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	97.34
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	97.28
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	96.95
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	96.49
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	96.34
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	93.81
2g0c_A	76	ATP-dependent RNA helicase DBPA; RNA recognition m	88.58
4eyt_A	129	Telomerase associated protein P65; RNA, LA protein	86.52

>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=99.88  E-value=2.4e-22  Score=164.98  Aligned_cols=84  Identities=15%  Similarity=0.213  Sum_probs=79.8

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+.++| |.|||++|||   ++|+++|++|++|++|+|++++.|+++++||||+|+++++|++||+.||+++|++++|+|
T Consensus        37 ~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  113 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTE---EQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT  113 (156)
T ss_dssp             TTCCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            456888 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ++|+++..
T Consensus       114 ~~a~~~~~  121 (156)
T 1h2v_Z          114 DWDAGFKE  121 (156)
T ss_dssp             EEESCCCT
T ss_pred             EECCCCCC
Confidence            99987554

>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=99.87  E-value=4.5e-22  Score=151.84  Aligned_cols=81  Identities=23%  Similarity=0.478  Sum_probs=77.5

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||+++|++++|+|
T Consensus        17 ~~gt~lfV~nLp~~~te---~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V   93 (99)
T 4fxv_A           17 FQGTNLIVNYLPQNMTQ---DELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKV   93 (99)
T ss_dssp             CCCSEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            345778 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccC
Q 023632           96 KKAEP  100 (279)
Q Consensus        96 ~~a~~  100 (279)
                      ++|+|
T Consensus        94 ~~AkP   98 (99)
T 4fxv_A           94 SYARP   98 (99)
T ss_dssp             EECCB
T ss_pred             EEeeC
Confidence            99976

>2dgs_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=3.5e-21  Score=146.01  Aligned_cols=90  Identities=34%  Similarity=0.593  Sum_probs=82.8

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ....+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+ ||+++|++++
T Consensus         5 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~   80 (99)
T 2dgs_A            5 SSGSKSNKIFVGGIPHNCGE---TELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKK   80 (99)
T ss_dssp             CCCSSCCEEEEESCCSSCCH---HHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHH-HCCCBSSSCB
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHH-hCCCEECCeE
Confidence            345677889 9999999999   9999999999999999999999999999999999999999999999 8999999999


Q ss_pred             eEEeeccCCCCCCCC
Q 023632           93 VEVKKAEPKKPNLPQ  107 (279)
Q Consensus        93 i~V~~a~~~~~~~~~  107 (279)
                      |+|++++++....+.
T Consensus        81 l~V~~a~~~~~~~~~   95 (99)
T 2dgs_A           81 VEVKRAEPRDSKSSG   95 (99)
T ss_dssp             CEEEECCCCCCCCCC
T ss_pred             EEEEECCCCcccCCC
Confidence            999999987665543

>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=99.86  E-value=1.7e-21  Score=151.84  Aligned_cols=91  Identities=18%  Similarity=0.351  Sum_probs=83.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        21 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   97 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGD---QDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRL   97 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCH---HHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            44566888 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCCCC
Q 023632           94 EVKKAEPKKPNLPQP  108 (279)
Q Consensus        94 ~V~~a~~~~~~~~~~  108 (279)
                      +|++++++..+.+.+
T Consensus        98 ~V~~a~~~~~~~~~~  112 (115)
T 2cpz_A           98 KVQLKRSKNDSKSGP  112 (115)
T ss_dssp             EEECCCCSCCCCCCC
T ss_pred             EEEEcCCCCcCCCCC
Confidence            999999877655443

>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=99.86  E-value=3.6e-21  Score=145.87  Aligned_cols=88  Identities=18%  Similarity=0.275  Sum_probs=82.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   80 (99)
T 1whw_A            4 GSSGSGRLFVRNLSYTSSE---EDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRML   80 (99)
T ss_dssp             CCCSCEEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34567889 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|+++++++...
T Consensus        81 ~V~~a~~~~~~~   92 (99)
T 1whw_A           81 HVLPSTIKKEAS   92 (99)
T ss_dssp             EEEECCCCSTTC
T ss_pred             EEEEcCCCcccc
Confidence            999999876654

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.86  E-value=2.2e-21  Score=150.92  Aligned_cols=83  Identities=14%  Similarity=0.228  Sum_probs=79.0

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ++.++| |.|||++++|   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||+++|++++|+|
T Consensus         4 ~p~~~lfV~nL~~~~te---~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V   80 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRE---TFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHA   80 (110)
T ss_dssp             SCCCEEEEESCCTTCCH---HHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCcEEEEECCCCCCCH---HHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            466889 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      ++|..++
T Consensus        81 ~~a~~~~   87 (110)
T 3s8s_A           81 QLDIKGQ   87 (110)
T ss_dssp             EECSTTH
T ss_pred             EECCCCc
Confidence            9997654

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.86  E-value=5.3e-21  Score=143.70  Aligned_cols=86  Identities=29%  Similarity=0.498  Sum_probs=80.7

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++|++|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+|
T Consensus         3 ~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   79 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITE---DMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRV   79 (95)
T ss_dssp             SCCCEEEEESCCTTCCH---HHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCcEEEEeCCCCCCCH---HHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            456788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCCCC
Q 023632           96 KKAEPKKPNL  105 (279)
Q Consensus        96 ~~a~~~~~~~  105 (279)
                      ++++++....
T Consensus        80 ~~a~~~~~~~   89 (95)
T 2dnz_A           80 GHVTERLDGG   89 (95)
T ss_dssp             EESSCCCCCC
T ss_pred             EEcccccCCC
Confidence            9998866544

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.85  E-value=1.1e-20  Score=147.03  Aligned_cols=90  Identities=21%  Similarity=0.416  Sum_probs=83.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .+..+.++| |.|||+++++   ++|+++|++||.|++|+|++++.++++++||||+|+++++|++||+.||+++|++++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITT---EDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQ   86 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            345667889 9999999999   999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeeccCCCCCCC
Q 023632           93 VEVKKAEPKKPNLP  106 (279)
Q Consensus        93 i~V~~a~~~~~~~~  106 (279)
                      |+|++++++.....
T Consensus        87 l~V~~a~~~~~~~~  100 (115)
T 2dgo_A           87 IRTNWATRKPPAPK  100 (115)
T ss_dssp             CEEEESSCCCCCSC
T ss_pred             EEEEEccCCCCCCc
Confidence            99999988765543

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.2e-21  Score=147.26  Aligned_cols=89  Identities=20%  Similarity=0.383  Sum_probs=82.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +..+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRE---TDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLIL   87 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCH---HHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            45567888 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCC
Q 023632           94 EVKKAEPKKPNLP  106 (279)
Q Consensus        94 ~V~~a~~~~~~~~  106 (279)
                      +|++++++....+
T Consensus        88 ~v~~a~~~~~~~~  100 (103)
T 2cq0_A           88 NVEWAKPSTNSGP  100 (103)
T ss_dssp             EEEESSCCCCSCC
T ss_pred             EEEECCCCCCCCC
Confidence            9999988765543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.85  E-value=2.6e-21  Score=147.80  Aligned_cols=89  Identities=22%  Similarity=0.351  Sum_probs=82.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +....++| |.|||+++++   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++||+.||+++|++++|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSP---DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGREL   85 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCH---HHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCC
T ss_pred             CCCCCeEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEE
Confidence            44567889 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCC
Q 023632           94 EVKKAEPKKPNLP  106 (279)
Q Consensus        94 ~V~~a~~~~~~~~  106 (279)
                      +|++|++++....
T Consensus        86 ~V~~a~~~~~~~~   98 (103)
T 2dnm_A           86 RVQVARYGRRDLS   98 (103)
T ss_dssp             EEEECSSCCSCCC
T ss_pred             EEEECCcCCCCCC
Confidence            9999988665544

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3.7e-21  Score=146.54  Aligned_cols=88  Identities=27%  Similarity=0.473  Sum_probs=82.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++|++|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus         8 ~~~~~~~l~v~nLp~~~t~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 1x5s_A            8 MASDEGKLFVGGLSFDTNE---QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQI   84 (102)
T ss_dssp             CCCCCSEEEEESCCTTCCH---HHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCC
T ss_pred             CCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            34567889 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++++++....
T Consensus        85 ~v~~a~~~~~~~   96 (102)
T 1x5s_A           85 RVDQAGKSSDNR   96 (102)
T ss_dssp             EEEEEECCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998876544

>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=99.85  E-value=6.8e-21  Score=145.83  Aligned_cols=89  Identities=25%  Similarity=0.418  Sum_probs=82.7

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .+....++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (105)
T 1x5u_A           10 SERNQDATVYVGGLDEKVSE---PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKP   86 (105)
T ss_dssp             CCCCTTTEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCB
T ss_pred             ccCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            345667889 9999999999   999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|+++++++...
T Consensus        87 l~v~~a~~~~~~~   99 (105)
T 1x5u_A           87 IRVNKASAHNKNL   99 (105)
T ss_dssp             CEEEETTTTSCCC
T ss_pred             EEEEECCCCCcCC
Confidence            9999998876543

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=3e-21  Score=147.04  Aligned_cols=90  Identities=27%  Similarity=0.423  Sum_probs=83.2

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus         8 ~~~~~~~l~V~nLp~~~t~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   84 (102)
T 2cqb_A            8 MATTKRVLYVGGLAEEVDD---KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTI   84 (102)
T ss_dssp             SCCCCSCEEEESCCSSCCH---HHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEE
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34567888 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCCC
Q 023632           94 EVKKAEPKKPNLPQ  107 (279)
Q Consensus        94 ~V~~a~~~~~~~~~  107 (279)
                      +|+++++++...+.
T Consensus        85 ~V~~a~~~~~~~~~   98 (102)
T 2cqb_A           85 RVNLAKPMRIKESG   98 (102)
T ss_dssp             EEEECCCCCCCCCC
T ss_pred             EEEeCCCCCCCCCC
Confidence            99999987665543

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.85  E-value=8.1e-21  Score=145.77  Aligned_cols=90  Identities=21%  Similarity=0.372  Sum_probs=83.4

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHHc-CCCccCC
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRD-HSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAG   90 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d-~~tg~~rG~aFV~F~s~e~a~~Ai~~l-ng~~l~g   90 (279)
                      .++...++| |.|||+++++   ++|+++|++||+|++|+|+++ +.++++++||||+|+++++|++||+.| |+++|++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g   86 (107)
T 2cph_A           10 PKKQTTSKILVRNIPFQANQ---REIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG   86 (107)
T ss_dssp             CCSSCCCCEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSS
T ss_pred             ccCCCCCEEEEeCCCCcCCH---HHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECC
Confidence            355677888 9999999999   999999999999999999999 789999999999999999999999999 9999999


Q ss_pred             ceeEEeeccCCCCCCC
Q 023632           91 AQVEVKKAEPKKPNLP  106 (279)
Q Consensus        91 ~~i~V~~a~~~~~~~~  106 (279)
                      ++|+|++++++.....
T Consensus        87 ~~l~v~~a~~~~~~~~  102 (107)
T 2cph_A           87 RRLVLEWADSEVTVQS  102 (107)
T ss_dssp             CBCEEEECCCCCCCCC
T ss_pred             CEEEEEeCCCCCCCCC
Confidence            9999999998766554

>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=99.85  E-value=7.6e-21  Score=146.87  Aligned_cols=91  Identities=23%  Similarity=0.324  Sum_probs=83.5

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC------CC
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN------KL   86 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln------g~   86 (279)
                      .+....++| |.|||+++++   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||      ++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~   86 (111)
T 1x4h_A           10 SDVTEGKTVFIRNLSFDSEE---EALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGL   86 (111)
T ss_dssp             CCCCCCCCEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCE
T ss_pred             CcCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCc
Confidence            345567888 9999999999   9999999999999999999999999999999999999999999999999      99


Q ss_pred             ccCCceeEEeeccCCCCCCCC
Q 023632           87 ELAGAQVEVKKAEPKKPNLPQ  107 (279)
Q Consensus        87 ~l~g~~i~V~~a~~~~~~~~~  107 (279)
                      +|++++|+|++++++......
T Consensus        87 ~~~g~~l~v~~a~~~~~~~~~  107 (111)
T 1x4h_A           87 KLDGRQLKVDLAVTRDEAASG  107 (111)
T ss_dssp             ESSSCEEEEECCCCCCCCCCC
T ss_pred             EEcCEEEEEEECCCCccCCCC
Confidence            999999999999987665543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.85  E-value=6.4e-21  Score=146.23  Aligned_cols=86  Identities=17%  Similarity=0.319  Sum_probs=80.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++||+.||+++|++++|
T Consensus        19 ~~~~~~~l~V~nlp~~~t~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   95 (106)
T 1p27_B           19 RSVEGWILFVTGVHEEATE---EDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPI   95 (106)
T ss_dssp             CBTTBEEEEEECCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEE
Confidence            44566789 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|++|+++.+
T Consensus        96 ~V~~a~~~~~  105 (106)
T 1p27_B           96 SVDWCFVRGP  105 (106)
T ss_dssp             EEEESEESSC
T ss_pred             EEEeecCCCC
Confidence            9999988654

>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=99.85  E-value=4.5e-21  Score=151.68  Aligned_cols=90  Identities=17%  Similarity=0.287  Sum_probs=83.1

Q ss_pred             cCCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           13 INRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        13 ~~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      .....+.++| |.|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|+++
T Consensus        16 ~~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~   92 (126)
T 3ex7_B           16 PQRSVEGWILFVTGVHEEATE---EDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQ   92 (126)
T ss_dssp             BCCCSSSEEEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             CCCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCe
Confidence            3455667889 9999999999   99999999999999999999999999999999999999999999999999999999


Q ss_pred             eeEEeeccCCCCCC
Q 023632           92 QVEVKKAEPKKPNL  105 (279)
Q Consensus        92 ~i~V~~a~~~~~~~  105 (279)
                      +|+|++|+++....
T Consensus        93 ~l~v~~a~~~~~~~  106 (126)
T 3ex7_B           93 PISVDWCFVRGPPK  106 (126)
T ss_dssp             BCEEEESEESSSCC
T ss_pred             EEEEEEecCCCCCC
Confidence            99999998765543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.84  E-value=6.8e-21  Score=144.04  Aligned_cols=87  Identities=18%  Similarity=0.315  Sum_probs=80.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCC---CCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHS---TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~---tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .+.++| |.|||+++++   ++|+++|++||+|++|+|++++.   |+++++||||+|+++++|++||+.||+++|++++
T Consensus         3 ~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   79 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTE---ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHK   79 (98)
T ss_dssp             CCCCCEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeE
Confidence            456788 9999999999   99999999999999999999887   6689999999999999999999999999999999


Q ss_pred             eEEeeccCCCCCCC
Q 023632           93 VEVKKAEPKKPNLP  106 (279)
Q Consensus        93 i~V~~a~~~~~~~~  106 (279)
                      |+|++++++....+
T Consensus        80 l~V~~a~~~~~~~~   93 (98)
T 2cpf_A           80 LEVRISERATKPAS   93 (98)
T ss_dssp             CEEECSSCSSCCCC
T ss_pred             EEEEEccCCCCCCC
Confidence            99999988765544

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.84  E-value=1e-21  Score=147.44  Aligned_cols=83  Identities=24%  Similarity=0.467  Sum_probs=76.6

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc-CCCccCCceeEE
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQVEV   95 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l-ng~~l~g~~i~V   95 (279)
                      +++| |.|||+++||   ++|+++|++|| +|++|+|++|+.|+++|+||||+|+++++|++||+.+ |.++|++++|+|
T Consensus         1 S~~i~v~nLp~~~te---~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V   77 (91)
T 2lxi_A            1 SNIVMLRMLPQAATE---DDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSM   77 (91)
T ss_dssp             CCEEEEETCCSSCCH---HHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEE
T ss_pred             CCEEEEeCCCCCCCH---HHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEE
Confidence            4678 9999999999   99999999999 8999999999999999999999999999999999987 457899999999


Q ss_pred             eeccCCCCC
Q 023632           96 KKAEPKKPN  104 (279)
Q Consensus        96 ~~a~~~~~~  104 (279)
                      ++|++++..
T Consensus        78 ~~a~~~~~~   86 (91)
T 2lxi_A           78 HYSDPKPKI   86 (91)
T ss_dssp             ECCCSCCCC
T ss_pred             EEcCCCCCC
Confidence            999886543

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=1.8e-20  Score=146.18  Aligned_cols=88  Identities=26%  Similarity=0.432  Sum_probs=81.0

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .++.+.++| |.|||++++|   ++|+++|++|++|++|+|++++.|+++++||||+|+++++|++||+.||. +|++++
T Consensus        12 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~   87 (116)
T 2cqd_A           12 QKDTTFTKIFVGGLPYHTTD---ASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   87 (116)
T ss_dssp             CCSCSSSEEEEECCCSSCCH---HHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             cCCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEE
Confidence            456677889 9999999999   99999999999999999999999999999999999999999999999997 899999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|++|+++....
T Consensus        88 l~V~~a~~~~~~~  100 (116)
T 2cqd_A           88 ANVNLAYLGAKPR  100 (116)
T ss_dssp             CEEEESTTTCCCC
T ss_pred             EEEEEcccCCCcc
Confidence            9999998764433

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=6.4e-21  Score=143.51  Aligned_cols=86  Identities=27%  Similarity=0.351  Sum_probs=80.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEH-QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v-~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++| +|++|+.++++++||||+|+++++|++||+.||++.|++++|+
T Consensus         3 ~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   79 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDE---KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPIT   79 (96)
T ss_dssp             SCCCEEEEECCCTTCCH---HHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            456788 9999999999   9999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCCCC
Q 023632           95 VKKAEPKKPNL  105 (279)
Q Consensus        95 V~~a~~~~~~~  105 (279)
                      |++++++..+.
T Consensus        80 v~~a~~~~~~~   90 (96)
T 1x5t_A           80 VSYAFKKDSKG   90 (96)
T ss_dssp             EEESCCCCCCC
T ss_pred             EEEecccCCCC
Confidence            99998876544

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=1.3e-20  Score=143.96  Aligned_cols=89  Identities=19%  Similarity=0.355  Sum_probs=81.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .+.+.++| |.|||+++++   ++|+++|++||+|++|+|+++  ++++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~--~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   85 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDD---ERLRKAFSPFGTITSAKVMME--GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPL   85 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCH---HHHHHTTTTTSCEEEEEEEEC--SSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEcC--CCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            45577888 9999999999   999999999999999999998  88999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCCCC
Q 023632           94 EVKKAEPKKPNLPQP  108 (279)
Q Consensus        94 ~V~~a~~~~~~~~~~  108 (279)
                      +|++++++.++...+
T Consensus        86 ~V~~a~~~~~~~~~~  100 (103)
T 2d9p_A           86 YVALAQRKEERQSGP  100 (103)
T ss_dssp             EEEECSSCCCCCCCC
T ss_pred             EEEEecccccCCCCC
Confidence            999999877665443

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.84  E-value=6.3e-21  Score=146.13  Aligned_cols=89  Identities=28%  Similarity=0.523  Sum_probs=82.8

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+.+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+. |+++|++++
T Consensus        11 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~-~~~~~~g~~   86 (105)
T 2dh8_A           11 SGADEIGKLFVGGLDWSTTQ---ETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLDGRN   86 (105)
T ss_dssp             CCSSSSSEECCBSCCTTCCH---HHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHH-CSEEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHh-CCCeECCEE
Confidence            356677899 9999999999   99999999999999999999999999999999999999999999999 999999999


Q ss_pred             eEEeeccCCCCCCC
Q 023632           93 VEVKKAEPKKPNLP  106 (279)
Q Consensus        93 i~V~~a~~~~~~~~  106 (279)
                      |+|++++++.....
T Consensus        87 l~V~~a~~~~~~~~  100 (105)
T 2dh8_A           87 IDPKPCTPRGMQPS  100 (105)
T ss_dssp             EBCCCSCCSSCCTT
T ss_pred             EEEEEccCCCCCCC
Confidence            99999988766543

>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=99.84  E-value=7.9e-21  Score=145.70  Aligned_cols=89  Identities=18%  Similarity=0.319  Sum_probs=82.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc---C
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL---A   89 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l---~   89 (279)
                      ..+.+.++| |.|||++++|   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||+++|   .
T Consensus         8 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   84 (106)
T 2dgp_A            8 MKDHDAIKLFIGQIPRNLDE---KDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGM   84 (106)
T ss_dssp             CCCTTCEEEEEESCCTTCCH---HHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTC
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCC
Confidence            345677889 9999999999   99999999999999999999999999999999999999999999999999888   8


Q ss_pred             CceeEEeeccCCCCCC
Q 023632           90 GAQVEVKKAEPKKPNL  105 (279)
Q Consensus        90 g~~i~V~~a~~~~~~~  105 (279)
                      +++|+|++++++....
T Consensus        85 g~~l~v~~a~~~~~~~  100 (106)
T 2dgp_A           85 NRPIQVKPADSESRGG  100 (106)
T ss_dssp             SSCCEEEECCCCSCCC
T ss_pred             CceEEEEECCcccccC
Confidence            9999999998876544

>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=99.84  E-value=2.1e-21  Score=145.03  Aligned_cols=84  Identities=18%  Similarity=0.282  Sum_probs=71.9

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G--~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      .+| |+|||+++||   ++|+++|++||  +|++|+|++|+.|+++++||||+|+++++|++||+.||+++|++++|+|+
T Consensus         2 ~~l~V~nL~~~~t~---~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~   78 (90)
T 3p5t_L            2 IALYIGNLTWWTTD---EDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVT   78 (90)
T ss_dssp             --CEEESCCTTCCH---HHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEEC
T ss_pred             eEEEEeCCCCCCCH---HHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEE
Confidence            467 9999999999   99999999999  99999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCCCC
Q 023632           97 KAEPKKPNLP  106 (279)
Q Consensus        97 ~a~~~~~~~~  106 (279)
                      ++.++.+..+
T Consensus        79 ~~~~~~~~~~   88 (90)
T 3p5t_L           79 PSNKLEHHHH   88 (90)
T ss_dssp             CC--------
T ss_pred             ECCCCccccC
Confidence            9988765543

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.84  E-value=1.5e-20  Score=151.07  Aligned_cols=88  Identities=20%  Similarity=0.416  Sum_probs=81.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++...++| |.|||++++|   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++||+.||+++|++++|
T Consensus        38 ~~~~~~~l~V~nLp~~~~~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  114 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDE---VQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRL  114 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCH---HHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEE
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEE
Confidence            44566889 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++|+++..+.
T Consensus       115 ~v~~a~~~~~~~  126 (139)
T 1u6f_A          115 KVALAASGHQRP  126 (139)
T ss_dssp             EEEESSCCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998875543

>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=99.84  E-value=1.6e-20  Score=137.52  Aligned_cols=81  Identities=21%  Similarity=0.403  Sum_probs=77.6

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      +.+| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+|++
T Consensus         1 t~~l~V~nlp~~~t~---~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~   77 (83)
T 3md1_A            1 TFNLFVGDLNVNVDD---ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINW   77 (83)
T ss_dssp             CEEEEEECCCTTCCH---HHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CeEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEe
Confidence            4678 9999999999   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCC
Q 023632           98 AEPKK  102 (279)
Q Consensus        98 a~~~~  102 (279)
                      |++++
T Consensus        78 a~~~~   82 (83)
T 3md1_A           78 AAKLE   82 (83)
T ss_dssp             CCCCC
T ss_pred             cCcCC
Confidence            98764

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.84  E-value=1.6e-20  Score=142.58  Aligned_cols=86  Identities=10%  Similarity=0.303  Sum_probs=80.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ....+.++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|++++
T Consensus        12 ~~~~~~~~l~v~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   87 (100)
T 2do4_A           12 STSLEKHKLFISGLPFSCTK---EELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKMDGMTIKENI   87 (100)
T ss_dssp             SSCCCCSCEEEESCCTTCCH---HHHHHHHTTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCE
T ss_pred             ccCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCeEEEEEEECC-CCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            345667889 9999999999   9999999999999999999998 9999999999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++++++..
T Consensus        88 l~v~~a~~~~~   98 (100)
T 2do4_A           88 IKVAISNSGPS   98 (100)
T ss_dssp             EEEEECCCCSC
T ss_pred             EEEEECCCCCC
Confidence            99999987654

>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=99.84  E-value=2.5e-20  Score=142.61  Aligned_cols=88  Identities=20%  Similarity=0.365  Sum_probs=81.2

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC---
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG---   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g---   90 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|.+   
T Consensus        11 ~~~~~~~l~v~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~   86 (105)
T 2dnh_A           11 RGGRDRKLFVGMLNKQQSE---EDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGAS   86 (105)
T ss_dssp             SCCCCCEEEEESCCTTCCH---HHHHHHHTTTSCEEEEEEEECS-SSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCS
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEECC-CCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCC
Confidence            44567889 9999999999   9999999999999999999998 79999999999999999999999999999998   


Q ss_pred             ceeEEeeccCCCCCCC
Q 023632           91 AQVEVKKAEPKKPNLP  106 (279)
Q Consensus        91 ~~i~V~~a~~~~~~~~  106 (279)
                      ++|+|++|+++.++.+
T Consensus        87 ~~l~V~~a~~~~~~~~  102 (105)
T 2dnh_A           87 SSLVVKFADTDKESGP  102 (105)
T ss_dssp             SCCEEEESCSSCCCSC
T ss_pred             ccEEEEECccCcccCC
Confidence            9999999998776544

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.84  E-value=9.5e-21  Score=147.03  Aligned_cols=89  Identities=20%  Similarity=0.300  Sum_probs=82.6

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~--------~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      .++.+.++| |.|||+++++   ++|+++|++|++|+        +|+|++++.++++++||||+|+++++|++||+.||
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~   86 (113)
T 2cpe_A           10 DEDSDNSAIYVQGLNDSVTL---DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD   86 (113)
T ss_dssp             CCCCCCCEEEEECCCTTCCH---HHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT
T ss_pred             ccCCCCCEEEEcCCCCCCCH---HHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcC
Confidence            355677889 9999999999   99999999999999        69999999999999999999999999999999999


Q ss_pred             CCccCCceeEEeeccCCCCCC
Q 023632           85 KLELAGAQVEVKKAEPKKPNL  105 (279)
Q Consensus        85 g~~l~g~~i~V~~a~~~~~~~  105 (279)
                      +++|++++|+|++++++....
T Consensus        87 g~~~~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           87 GKDFQGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             TCEETTEECEEECSSCCCCST
T ss_pred             CCccCCCEEEEEECCCCCCCC
Confidence            999999999999998876554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.84  E-value=2.1e-20  Score=142.77  Aligned_cols=86  Identities=17%  Similarity=0.328  Sum_probs=79.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++|+ |++|+|++++.|+++++||||+|+++++|++|| +||+++|++++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l   85 (103)
T 2dng_A           11 PTEPPYTAYVGNLPFNTVQ---GDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL-TYDGALLGDRSL   85 (103)
T ss_dssp             CSSSCEEEEEESCCTTCCH---HHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHG-GGTTCEETTEEC
T ss_pred             CCCCCeEEEEeCCCCCCCH---HHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHH-hhCCCeECCeEE
Confidence            45567888 9999999999   99999999995 999999999999999999999999999999999 899999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++++++....
T Consensus        86 ~V~~a~~~~~~~   97 (103)
T 2dng_A           86 RVDIAEGRKQDK   97 (103)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEEecCCCCCC
Confidence            999998866544

>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=99.83  E-value=1.4e-20  Score=138.92  Aligned_cols=82  Identities=21%  Similarity=0.395  Sum_probs=76.0

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+|
T Consensus         4 ~~~~~l~v~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   80 (87)
T 3bs9_A            4 GSHFHVFVGDLSPEITT---AAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   80 (87)
T ss_dssp             --CEEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCceEEEEeCCCCCCCH---HHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEE
Confidence            356788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCC
Q 023632           96 KKAEPK  101 (279)
Q Consensus        96 ~~a~~~  101 (279)
                      ++|+++
T Consensus        81 ~~a~~k   86 (87)
T 3bs9_A           81 NWATRK   86 (87)
T ss_dssp             EEEC--
T ss_pred             EecCCC
Confidence            999875

>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=99.83  E-value=3.4e-20  Score=141.53  Aligned_cols=90  Identities=22%  Similarity=0.428  Sum_probs=81.0

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+.+.++| |.|||+++++   ++|+++|++||+|++|+|++++.  .+++||||+|+++++|++||+.||+++|++++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~---~~l~~~f~~~G~v~~v~i~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   84 (103)
T 2cq3_A           10 ESKSTPKRLHVSNIPFRFRD---PDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRK   84 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCH---HHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCC--CCcEEEEEEECCHHHHHHHHHHhCCCEECCEE
Confidence            345677889 9999999999   99999999999999999999864  38999999999999999999999999999999


Q ss_pred             eEEeeccCCCCCCCCC
Q 023632           93 VEVKKAEPKKPNLPQP  108 (279)
Q Consensus        93 i~V~~a~~~~~~~~~~  108 (279)
                      |+|++++++....+.+
T Consensus        85 l~v~~a~~~~~~~~~~  100 (103)
T 2cq3_A           85 IEVNNATARVMTNSGP  100 (103)
T ss_dssp             CEEEECCSSCCCCCSS
T ss_pred             EEEEEcccCCCCCCCC
Confidence            9999999877655433

>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=99.83  E-value=1.1e-20  Score=145.88  Aligned_cols=87  Identities=20%  Similarity=0.320  Sum_probs=81.4

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ....+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||++.|++++
T Consensus        21 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   97 (110)
T 1oo0_B           21 QRSVEGWILFVTSIHEEAQE---DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQT   97 (110)
T ss_dssp             CCBTTBEEEEEESCCTTCCH---HHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            345667889 9999999999   999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++++++.+
T Consensus        98 l~V~~a~~~~~  108 (110)
T 1oo0_B           98 IQVDWCFVKGP  108 (110)
T ss_dssp             CEEEESEESSC
T ss_pred             EEEEEcccCCC
Confidence            99999988654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=7.4e-20  Score=142.04  Aligned_cols=87  Identities=22%  Similarity=0.214  Sum_probs=79.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~V~nlp~~~~~---~~l~~~f~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (114)
T 2do0_A           11 AGRLGSTVFVANLDYKVGW---KKLKEVFSMAGVVVRADILEDK-DGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPM   86 (114)
T ss_dssp             CCCCCSCEEEESCCTTCCH---HHHHHHHTTTSCEEEEEEEECT-TCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEECC-CCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEE
Confidence            44567888 9999999999   9999999999999999999997 68999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|+++++..++.
T Consensus        87 ~v~~a~~~~~~~   98 (114)
T 2do0_A           87 HVKMDERALPKG   98 (114)
T ss_dssp             EEEECSCCCCCS
T ss_pred             EEEEcccCCCCC
Confidence            999998655443

>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=99.83  E-value=1.9e-20  Score=149.51  Aligned_cols=86  Identities=23%  Similarity=0.434  Sum_probs=80.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        42 ~~~~~~~l~V~nLp~~~te---~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l  118 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTE---RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI  118 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCH---HHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34566788 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|++++++++
T Consensus       119 ~V~~a~~~~p  128 (129)
T 2kxn_B          119 RVDFSITKRP  128 (129)
T ss_dssp             EESCCSSSSC
T ss_pred             EEEEecCCCC
Confidence            9999988764

>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=99.83  E-value=4.4e-20  Score=144.59  Aligned_cols=85  Identities=27%  Similarity=0.406  Sum_probs=79.2

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|++++|+
T Consensus         4 ~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~   79 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNE---KMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIK   79 (116)
T ss_dssp             TCSCCEEEEECCTTTCCH---HHHHHHHHTSSCCSEEEEECST-TTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4556788 9999999999   9999999999999999999998 999999999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |++|+++...
T Consensus        80 V~~a~~~~~~   89 (116)
T 2fy1_A           80 VEQAKKPSFQ   89 (116)
T ss_dssp             EEECCCSSCS
T ss_pred             EEECCCCCCC
Confidence            9999876543

>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=99.83  E-value=2.4e-20  Score=142.71  Aligned_cols=86  Identities=22%  Similarity=0.359  Sum_probs=79.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCC-CCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~t-g~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....++| |.|||+++++   ++|+++|++|+ |++|+|++++.| +++++||||+|+++++|++|| .||+++|++++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~   85 (104)
T 1wi8_A           11 PKSPPYTAFLGNLPYDVTE---ESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKR   85 (104)
T ss_dssp             CSSSCEEEEEESCCSSCCH---HHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEE
T ss_pred             CCCCCCEEEEeCCCCcCCH---HHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHH-hcCCCEeCCcE
Confidence            34566888 9999999999   99999999999 999999999988 999999999999999999999 99999999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|+++++++...
T Consensus        86 l~V~~a~~~~~~~   98 (104)
T 1wi8_A           86 IRVDVADQAQDKD   98 (104)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEEccCCCCCC
Confidence            9999998876544

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.83  E-value=4.6e-20  Score=140.90  Aligned_cols=87  Identities=21%  Similarity=0.376  Sum_probs=80.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhc-CCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc-cCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQ-FGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE-LAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~-~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~-l~g~   91 (279)
                      +....++| |.|||+++++   ++|+++|++ |++|++|+|++++ ++++++||||+|+++++|++||+.||++. |+++
T Consensus         5 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~   80 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDD---GMLYEFFVKVYPSCRGGKVVLDQ-TGVSKGYGFVKFTDELEQKRALTECQGAVGLGSK   80 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCH---HHHHHHHHHHCTTEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSS
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHHHccCCcccCCE
Confidence            34566888 9999999999   999999999 9999999999998 99999999999999999999999999999 9999


Q ss_pred             eeEEeeccCCCCCC
Q 023632           92 QVEVKKAEPKKPNL  105 (279)
Q Consensus        92 ~i~V~~a~~~~~~~  105 (279)
                      +|+|++++++..+.
T Consensus        81 ~l~v~~a~~~~~~~   94 (104)
T 2dhg_A           81 PVRLSVAIPKASRV   94 (104)
T ss_dssp             CCCCCBCCCCCSCC
T ss_pred             eEEEEEccCCCcCC
Confidence            99999998766544

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.83  E-value=2.5e-20  Score=139.86  Aligned_cols=83  Identities=22%  Similarity=0.412  Sum_probs=78.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +..+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   87 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTE---RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI   87 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCH---HHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            45567888 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccC
Q 023632           94 EVKKAEP  100 (279)
Q Consensus        94 ~V~~a~~  100 (279)
                      +|++|++
T Consensus        88 ~v~~a~~   94 (95)
T 2cqc_A           88 RVSGPSS   94 (95)
T ss_dssp             EEECCSC
T ss_pred             EEEecCC
Confidence            9999864

>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=99.83  E-value=2.2e-20  Score=137.34  Aligned_cols=81  Identities=28%  Similarity=0.461  Sum_probs=77.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+
T Consensus         4 ~~~~~~l~V~nl~~~~~~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   80 (85)
T 3mdf_A            4 ATTKRVLYVGGLAEEVDD---KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR   80 (85)
T ss_dssp             CCCSSEEEEECCCTTCCH---HHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEE
Confidence            4567888 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeecc
Q 023632           95 VKKAE   99 (279)
Q Consensus        95 V~~a~   99 (279)
                      |++|+
T Consensus        81 v~~ak   85 (85)
T 3mdf_A           81 VNLAK   85 (85)
T ss_dssp             EEECC
T ss_pred             EEEcC
Confidence            99985

>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=99.82  E-value=5.4e-20  Score=140.40  Aligned_cols=87  Identities=20%  Similarity=0.303  Sum_probs=78.8

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .++...++| |.|||+++++   ++|+++|++||+|++|+|++++.+  +++||||+|+++++|++||+.||+++|++++
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~--~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   84 (103)
T 2cqi_A           10 EDDGQPRTLYVGNLSRDVTE---VLILQLFSQIGPCKSCKMITEHTS--NDPYCFVEFYEHRDAAAALAAMNGRKILGKE   84 (103)
T ss_dssp             CCSCCCCEEEEESCCTTCCH---HHHHHHHHHHSCEEEEEEECCCCS--SCCEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCEEEEeCCCccCCH---HHHHHHHHhcCCEeEEEEEecCCC--CCCEEEEEECCHHHHHHHHHHhCCCCcCCCe
Confidence            345667888 9999999999   999999999999999999998654  6899999999999999999999999999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|++++++..+.
T Consensus        85 l~V~~a~~~~~~~   97 (103)
T 2cqi_A           85 VKVNWATTPSSQK   97 (103)
T ss_dssp             EEEEECCCTTCCC
T ss_pred             EEEEECCCCcccc
Confidence            9999998866544

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.82  E-value=2.6e-20  Score=139.61  Aligned_cols=82  Identities=21%  Similarity=0.329  Sum_probs=77.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        12 ~~~~~~~l~V~nlp~~~t~---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   88 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTN---NDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVI   88 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCH---HHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEE
Confidence            45567888 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecc
Q 023632           94 EVKKAE   99 (279)
Q Consensus        94 ~V~~a~   99 (279)
                      +|++|+
T Consensus        89 ~v~~ak   94 (94)
T 2e5h_A           89 KASIAI   94 (94)
T ss_dssp             EEEECC
T ss_pred             EEEecC
Confidence            999985

>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=99.82  E-value=2.6e-20  Score=145.58  Aligned_cols=84  Identities=21%  Similarity=0.394  Sum_probs=75.0

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      .+.+| |+|||+++||   ++|+++|++||+|++|+|++|+  ..+|+||||+|+++++|++||++||+++|++++|+|+
T Consensus         4 ~~~~lfV~nLp~~~te---~~L~~~F~~~G~v~~v~i~~d~--~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~   78 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDN---KALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG   78 (115)
T ss_dssp             -CCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEECCCCCCCCH---HHHHHHHhccCCEEEEEEeecC--CCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            35678 9999999999   9999999999999999999986  4479999999999999999999999999999999999


Q ss_pred             eccCCCCCCC
Q 023632           97 KAEPKKPNLP  106 (279)
Q Consensus        97 ~a~~~~~~~~  106 (279)
                      ++++++++..
T Consensus        79 ~a~~~~~~~~   88 (115)
T 4f25_A           79 RFKSRKEREA   88 (115)
T ss_dssp             ESSCCCC---
T ss_pred             ECCCcccccc
Confidence            9988765543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.82  E-value=8.4e-21  Score=143.89  Aligned_cols=83  Identities=17%  Similarity=0.325  Sum_probs=75.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCC--eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC----c
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGD--VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL----E   87 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~--V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~----~   87 (279)
                      ....-.+| |+|||+++||   ++|+++|++||.  |++|+|++|+.|+++||||||+|+++++|++||+.||+.    .
T Consensus         5 ~~~~m~tlfV~nL~~~~te---e~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~   81 (95)
T 2lkz_A            5 HHHHMDTIILRNIAPHTVV---DSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLK   81 (95)
T ss_dssp             SSCCCCEEEEESCCTTCCH---HHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEE
T ss_pred             cCCccCEEEEeCCCCcCCH---HHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCce
Confidence            34456778 9999999999   999999999995  679999999999999999999999999999999999886    4


Q ss_pred             cCCceeEEeeccC
Q 023632           88 LAGAQVEVKKAEP  100 (279)
Q Consensus        88 l~g~~i~V~~a~~  100 (279)
                      |++++|+|++|++
T Consensus        82 i~Gr~i~V~~Aks   94 (95)
T 2lkz_A           82 IDGKTIGVDFAKS   94 (95)
T ss_dssp             ETTEEEEEEECCC
T ss_pred             ECCEEEEEEEccC
Confidence            8999999999975

>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=99.82  E-value=2.7e-20  Score=137.57  Aligned_cols=84  Identities=15%  Similarity=0.360  Sum_probs=78.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCC-cccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSR-SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~-~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|+.++.+.. +++||||+|+++++|++||+.||+.+|++++|+
T Consensus         2 ~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   78 (88)
T 4a8x_A            2 MKPTKVHIGRLTRNVTK---DHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEIT   78 (88)
T ss_dssp             CCCCEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEE
Confidence            356788 9999999999   99999999999999999999987766 899999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |+++.++++
T Consensus        79 v~~a~~~~~   87 (88)
T 4a8x_A           79 ATAVLAPWP   87 (88)
T ss_dssp             EEEECCCCC
T ss_pred             EEECCCCCC
Confidence            999987654

>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=99.82  E-value=3.4e-20  Score=143.44  Aligned_cols=86  Identities=30%  Similarity=0.530  Sum_probs=81.0

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+...++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|++++
T Consensus        21 ~~~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~   97 (108)
T 2jrs_A           21 KGSAGPMRLYVGSLHFNITE---DMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRP   97 (108)
T ss_dssp             CSCSSCEEEEEECCCSSCCH---HHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSC
T ss_pred             cCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            345667889 9999999999   999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+|++++++.
T Consensus        98 l~V~~a~~k~  107 (108)
T 2jrs_A           98 MKVGHVTERT  107 (108)
T ss_dssp             CEEECSCSSC
T ss_pred             EEEEEcccCC
Confidence            9999998764

>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=99.82  E-value=5.2e-20  Score=138.83  Aligned_cols=83  Identities=20%  Similarity=0.287  Sum_probs=79.0

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      +++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+|++
T Consensus         2 ~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   78 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTE---EQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGY   78 (96)
T ss_dssp             CSEEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CcEEEEECCCCCCCH---HHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEE
Confidence            5788 9999999999   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCCC
Q 023632           98 AEPKKPN  104 (279)
Q Consensus        98 a~~~~~~  104 (279)
                      |+++...
T Consensus        79 a~~~~~~   85 (96)
T 2x1f_A           79 SSNSDIS   85 (96)
T ss_dssp             CSCSSGG
T ss_pred             cCCCCCC
Confidence            9887643

>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=99.82  E-value=8.4e-20  Score=140.61  Aligned_cols=88  Identities=18%  Similarity=0.257  Sum_probs=80.7

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCC-eEEEEEe-ecCCCCCcccEEEEEEcCHHHHHHHHHHcC--CCccCC
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGD-VQEHQIM-RDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAG   90 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~-V~~v~i~-~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln--g~~l~g   90 (279)
                      ..+.++| |.|||+++++   ++|+++|++||+ |++|.|+ .++.++++++||||+|+++++|++||+.||  .++|++
T Consensus         5 s~~~~~l~V~nLp~~~t~---~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g   81 (109)
T 2dis_A            5 SSGNCRLFIGGIPKMKKR---EEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWG   81 (109)
T ss_dssp             CCCSEEEEEECCCTTSCH---HHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTT
T ss_pred             ccCCCEEEEeCCCCcCCH---HHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecC
Confidence            4567889 9999999999   999999999998 9999998 888899999999999999999999999996  599999


Q ss_pred             ceeEEeeccCCCCCCC
Q 023632           91 AQVEVKKAEPKKPNLP  106 (279)
Q Consensus        91 ~~i~V~~a~~~~~~~~  106 (279)
                      ++|+|++|+++.....
T Consensus        82 ~~l~V~~a~~~~~~~~   97 (109)
T 2dis_A           82 HQIAVDWAEPEIDVDE   97 (109)
T ss_dssp             BCCEEEESCSSCSTTT
T ss_pred             CeEEEEEcCCCCCcCH
Confidence            9999999998776544

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.82  E-value=4.3e-20  Score=139.83  Aligned_cols=85  Identities=20%  Similarity=0.262  Sum_probs=79.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeE-EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQ-EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~-~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....++| |.|||++++|   ++|+++|++|++|+ +|+|++|+.++++++||||+|+++++|++||+.||+++|+++.
T Consensus         5 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   81 (99)
T 2div_A            5 SSGMAASLWMGDLEPYMDE---NFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGAT   81 (99)
T ss_dssp             CCSSSSEEEECSCCTTCCH---HHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCS
T ss_pred             CCCCccEEEEeCCCCCCCH---HHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCC
Confidence            34567889 9999999999   99999999999999 9999999999999999999999999999999999999999999


Q ss_pred             ----eEEeeccCCC
Q 023632           93 ----VEVKKAEPKK  102 (279)
Q Consensus        93 ----i~V~~a~~~~  102 (279)
                          |+|++|++..
T Consensus        82 ~~~~l~v~~a~~~~   95 (99)
T 2div_A           82 PAKRFKLNYATYSG   95 (99)
T ss_dssp             SCEECCEEETTCCS
T ss_pred             cceeEEEeecCCCC
Confidence                9999997754

>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=99.82  E-value=1.1e-19  Score=138.72  Aligned_cols=87  Identities=23%  Similarity=0.383  Sum_probs=79.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.  .++|++++|
T Consensus        11 ~~~~~~~l~v~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~l   85 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTE---QDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ--RHMIDGRWC   85 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCH---HHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHS--CEEETTEEE
T ss_pred             ccCCCCEEEEEcCCCcCCH---HHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHHc--CCeeCCeEE
Confidence            45567888 9999999999   99999999999999999999999999999999999999999999995  579999999


Q ss_pred             EEeeccCCCCCCC
Q 023632           94 EVKKAEPKKPNLP  106 (279)
Q Consensus        94 ~V~~a~~~~~~~~  106 (279)
                      +|++++++.....
T Consensus        86 ~v~~a~~~~~~~~   98 (103)
T 2cqg_A           86 DCKLPNSKQSQDS   98 (103)
T ss_dssp             EEECCCTTCCCCC
T ss_pred             EEEecCCCCcCCC
Confidence            9999998766543

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.82  E-value=6.8e-20  Score=138.95  Aligned_cols=83  Identities=18%  Similarity=0.277  Sum_probs=78.5

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE--------HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~--------v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      ......++| |.|||+++++   ++|+++|++||.|++        |+|++++.|+++++||||+|+++++|++||+.||
T Consensus         8 ~~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~   84 (99)
T 2la6_A            8 HSHSDNNTIFVQGLGENVTI---ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFD   84 (99)
T ss_dssp             CSCCCCSEEEEECCCSSCCH---HHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhC
Confidence            455677889 9999999999   999999999999999        9999999999999999999999999999999999


Q ss_pred             CCccCCceeEEeecc
Q 023632           85 KLELAGAQVEVKKAE   99 (279)
Q Consensus        85 g~~l~g~~i~V~~a~   99 (279)
                      +++|++++|+|++|+
T Consensus        85 g~~~~g~~l~V~~A~   99 (99)
T 2la6_A           85 GKEFSGNPIKVSFAT   99 (99)
T ss_dssp             TCBSSSSBCEEEECC
T ss_pred             CCEeCCcEEEEEecC
Confidence            999999999999874

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.81  E-value=1.4e-20  Score=146.90  Aligned_cols=85  Identities=31%  Similarity=0.538  Sum_probs=79.5

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++||+. |+++|++++|+|
T Consensus        25 ~~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~-~~~~~~g~~l~V  100 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTE---ESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA-RPHSIDGRVVEP  100 (116)
T ss_dssp             HHHTEEEEECCTTCCCH---HHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTS-CSEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHh-CCcEECCEEEEE
Confidence            345788 9999999999   99999999999999999999999999999999999999999999999 999999999999


Q ss_pred             eeccCCCCCC
Q 023632           96 KKAEPKKPNL  105 (279)
Q Consensus        96 ~~a~~~~~~~  105 (279)
                      ++++++....
T Consensus       101 ~~a~~~~~~~  110 (116)
T 1x4b_A          101 KRAVAREESG  110 (116)
T ss_dssp             ECCSSCCCCC
T ss_pred             EECCCCccCC
Confidence            9998876544

>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=99.81  E-value=1.6e-19  Score=139.29  Aligned_cols=80  Identities=20%  Similarity=0.327  Sum_probs=73.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC----
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG----   90 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g----   90 (279)
                      ....++| |.|||+++||   ++|+++|++||+|++|+|+++       +||||+|+++++|++||+.||+++|++    
T Consensus        12 ~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~   81 (108)
T 1x4c_A           12 RRSENRVVVSGLPPSGSW---QDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGE   81 (108)
T ss_dssp             CSCCCEEEEESCCSSCCH---HHHHHHHGGGSCEEEEEEETT-------TEEEEEESSHHHHHHHHHHSSSEEEECTTSC
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEeEEEEecC-------CEEEEEECCHHHHHHHHHHHCcCCccCCcCc
Confidence            4456788 9999999999   999999999999999999876       799999999999999999999999999    


Q ss_pred             -ceeEEeeccCCCCCC
Q 023632           91 -AQVEVKKAEPKKPNL  105 (279)
Q Consensus        91 -~~i~V~~a~~~~~~~  105 (279)
                       ++|+|++|+++....
T Consensus        82 ~~~i~V~~a~~~~~~~   97 (108)
T 1x4c_A           82 TAYIRVKVDGPRSPSY   97 (108)
T ss_dssp             EEEEEEEESSCCSCCC
T ss_pred             ceEEEEEeCCCCCCCC
Confidence             999999998865543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.81  E-value=7.4e-20  Score=141.70  Aligned_cols=87  Identities=37%  Similarity=0.594  Sum_probs=76.7

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +...+.++| |.|||+++++   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++||+.++ ++|++++
T Consensus        20 ~~~~~~~~lfV~nLp~~~te---~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~-~~l~g~~   95 (109)
T 2rs2_A           20 HMGSSGCKMFIGGLSWQTTQ---EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKT   95 (109)
T ss_dssp             ------CCEEEESCCTTCCH---HHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSC-EEETTEE
T ss_pred             ccCCCCCEEEEeCCCCCCCH---HHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCC-CcCCCEE
Confidence            345567888 9999999999   9999999999999999999999999999999999999999999999975 9999999


Q ss_pred             eEEeeccCCCCC
Q 023632           93 VEVKKAEPKKPN  104 (279)
Q Consensus        93 i~V~~a~~~~~~  104 (279)
                      |+|+++.++..+
T Consensus        96 l~V~~a~~~~~~  107 (109)
T 2rs2_A           96 IDPKVAFPRRAQ  107 (109)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEEccCCCCC
Confidence            999999876543

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.81  E-value=1.4e-20  Score=143.45  Aligned_cols=82  Identities=15%  Similarity=0.236  Sum_probs=77.6

Q ss_pred             CCcee-eeCCCC------CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           18 TTQKM-TGLSLT------PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        18 ~~~~l-V~nLp~------~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ..++| |.|||+      ++++   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||+++|++
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~---~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g   81 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLK---KALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDL   81 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHH---HHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHH---HHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCC
Confidence            45778 999999      9999   9999999999999999999999999999999999999999999999999999999


Q ss_pred             -ceeEEeeccCCC
Q 023632           91 -AQVEVKKAEPKK  102 (279)
Q Consensus        91 -~~i~V~~a~~~~  102 (279)
                       ++|+|++|++++
T Consensus        82 ~r~l~V~~a~~~~   94 (100)
T 3ns6_A           82 KHRLFLYTMKDVE   94 (100)
T ss_dssp             SCBCEEEESHHHH
T ss_pred             CeEEEEEECchhh
Confidence             999999998753

>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=99.81  E-value=1.2e-19  Score=139.94  Aligned_cols=84  Identities=12%  Similarity=0.334  Sum_probs=76.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .+.+.++| |.|||+++++   ++|+++|++|++|++|+|+.+   .++++||||+|+++++|++||+.||+++|++++|
T Consensus        18 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~v~~~~i~~~---~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   91 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRT---KDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRL   91 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEEC---CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            45567889 9999999999   999999999999999999654   4579999999999999999999999999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|+++++++..
T Consensus        92 ~V~~a~~~~~~  102 (109)
T 1x4a_A           92 RVEFPRSGRGT  102 (109)
T ss_dssp             EEECCCCCCCC
T ss_pred             EEEEcccCCCC
Confidence            99999876543

>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=99.81  E-value=9.9e-20  Score=134.93  Aligned_cols=81  Identities=21%  Similarity=0.370  Sum_probs=76.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++|| .||+++|++++|+|+
T Consensus         5 ~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~-~~~g~~~~g~~l~V~   80 (89)
T 3ucg_A            5 DARSIYVGNVDYGATA---EELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQIKVI   80 (89)
T ss_dssp             HHTEEEEESCCTTCCH---HHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHG-GGTTCEETTEECEEE
T ss_pred             cCCEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHH-hcCCCEECCcEEEEE
Confidence            35788 9999999999   999999999999999999999999999999999999999999999 899999999999999


Q ss_pred             eccCCC
Q 023632           97 KAEPKK  102 (279)
Q Consensus        97 ~a~~~~  102 (279)
                      +++++.
T Consensus        81 ~a~~~~   86 (89)
T 3ucg_A           81 PKRTNR   86 (89)
T ss_dssp             ETTTTS
T ss_pred             EccCCC
Confidence            997743

>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=99.81  E-value=8.7e-20  Score=137.00  Aligned_cols=83  Identities=22%  Similarity=0.417  Sum_probs=76.8

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+...++| |.|||+++++   ++|+++|++||+|++|+|++++. +++++||||+|+++++|++||+.||+++|++++
T Consensus        11 ~~~~~~~~l~v~nlp~~~~~---~~l~~~F~~~G~i~~v~i~~~~~-g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   86 (95)
T 2ywk_A           11 AQEEADRTVFVGNLEARVRE---EILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALLNGIRLYGRP   86 (95)
T ss_dssp             -CTTGGGEEEEECCCTTCCH---HHHHHHHGGGSCEEEEEEEECTT-SCEEEEEEEEESSTHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCEEEEEEEECCC-CCCceEEEEEECCHHHHHHHHHHhCCCEECCCE
Confidence            345567889 9999999999   99999999999999999999985 899999999999999999999999999999999


Q ss_pred             eEEeeccC
Q 023632           93 VEVKKAEP  100 (279)
Q Consensus        93 i~V~~a~~  100 (279)
                      |+|++|+.
T Consensus        87 l~V~~a~~   94 (95)
T 2ywk_A           87 INVSGPSS   94 (95)
T ss_dssp             CEEECCCC
T ss_pred             EEEEEcCC
Confidence            99999864

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.81  E-value=1.6e-19  Score=134.80  Aligned_cols=85  Identities=18%  Similarity=0.261  Sum_probs=78.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++|+|+++  ++++++||||+|+++++|++||+.||+++|++++|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~---~~l~~~f~~~G~v~~~~i~~~--~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l   78 (92)
T 2dgv_A            4 GSSGACQIFVRNLPFDFTW---KMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESPEVAERACRMMNGMKLSGREI   78 (92)
T ss_dssp             SSSSCCEEEECSCCTTCCH---HHHHHHHHTTSCEEEEEEEES--SSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCC
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEcc--CCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34567888 9999999999   999999999999999999985  78999999999999999999999999999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|++++++...
T Consensus        79 ~v~~a~~~~~~   89 (92)
T 2dgv_A           79 DVRIDRNASGP   89 (92)
T ss_dssp             CCEECSCCSSC
T ss_pred             EEEEcCCCCCC
Confidence            99999876543

>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=99.81  E-value=1.1e-19  Score=137.29  Aligned_cols=82  Identities=9%  Similarity=0.101  Sum_probs=75.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHH----HHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~----~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ..+.++| |.|||+++++   ++|+    ++|++||+|++|+|++|+.+   ++||||+|+++++|++||+.||+++|++
T Consensus         6 ~~~~~~l~V~nL~~~~~~---~~l~~~l~~~F~~~G~v~~v~i~~~~~~---rg~afV~f~~~~~A~~Ai~~l~g~~~~g   79 (96)
T 2dgx_A            6 SGNGADVQVSNIDYRLSR---KELQQLLQEAFARHGKVKSVELSPHTDY---QLKAVVQMENLQDAIGAVNSLHRYKIGS   79 (96)
T ss_dssp             CSSCEEEEEESCCTTSCH---HHHHHHHHHHHHHHSCEEEEEECSCCST---TCCEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHHHHhccccCcEEEEEEEeCCCC---CeEEEEEECCHHHHHHHHHHhCCCEECC
Confidence            3456788 9999999999   8888    99999999999999999876   7899999999999999999999999999


Q ss_pred             ceeEEeeccCCCC
Q 023632           91 AQVEVKKAEPKKP  103 (279)
Q Consensus        91 ~~i~V~~a~~~~~  103 (279)
                      ++|+|++|+++..
T Consensus        80 r~l~V~~a~~~~~   92 (96)
T 2dgx_A           80 KKILVSLATGASG   92 (96)
T ss_dssp             EEEEEEECCCSSC
T ss_pred             eEEEEEEcCCCCC
Confidence            9999999977544

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.81  E-value=4e-20  Score=147.64  Aligned_cols=88  Identities=19%  Similarity=0.301  Sum_probs=80.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE--EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC----c
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE--HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL----E   87 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~--v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~----~   87 (279)
                      .+...++| |.|||+++||   ++|+++|++||+|+.  |+|++|+.|+++|+||||+|+++ +|++||+.||++    +
T Consensus        19 ~~~~~~~lfV~nL~~~~te---~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~   94 (131)
T 2m2b_A           19 SENANDTIILRNLNPHSTM---DSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLT   94 (131)
T ss_dssp             CSCCCCEEEECSCCTTCCS---HHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCcc
Confidence            44567889 9999999999   999999999999976  99999999999999999999999 999999999999    9


Q ss_pred             cCCceeEEeeccCCCCCCC
Q 023632           88 LAGAQVEVKKAEPKKPNLP  106 (279)
Q Consensus        88 l~g~~i~V~~a~~~~~~~~  106 (279)
                      |++++|+|++|++++....
T Consensus        95 ~~gr~l~V~~a~~~~~~~~  113 (131)
T 2m2b_A           95 IDGKTINVEFAKGSKRDMA  113 (131)
T ss_dssp             GGGCCCCCEECCCSCCCCC
T ss_pred             CCCEEEEEEECCCCCCCCC
Confidence            9999999999988765443

>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=99.81  E-value=7.6e-20  Score=149.99  Aligned_cols=88  Identities=23%  Similarity=0.371  Sum_probs=81.7

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+++|++++|+
T Consensus        67 ~~~~~~l~v~nl~~~~~~---~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  143 (158)
T 2kn4_A           67 VEGMTSLKVDNLTYRTSP---DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELR  143 (158)
T ss_dssp             CCBCCEEEEESCCTTCCH---HHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEE
Confidence            3456888 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCCCCC
Q 023632           95 VKKAEPKKPNLP  106 (279)
Q Consensus        95 V~~a~~~~~~~~  106 (279)
                      |++|+++.++.+
T Consensus       144 v~~a~~~~~~~~  155 (158)
T 2kn4_A          144 VQMARYGRPPDS  155 (158)
T ss_dssp             EEEECCSSCCCC
T ss_pred             EEECCCCCCCCC
Confidence            999988765543

>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=99.81  E-value=4.2e-20  Score=139.65  Aligned_cols=84  Identities=12%  Similarity=0.179  Sum_probs=78.3

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++|++|++++|+.++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~v~nLp~~~t~---~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   87 (98)
T 2cqp_A           11 GKPGPTIIKVQNMPFTVSI---DEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKV   87 (98)
T ss_dssp             CCCSSEEEEEESCCTTCCH---HHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEE
Confidence            34556788 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|++++.+
T Consensus        88 ~V~~a~~~   95 (98)
T 2cqp_A           88 KLVLGSGP   95 (98)
T ss_dssp             EEEESSCS
T ss_pred             EEEEcCCC
Confidence            99998754

>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=99.81  E-value=1.6e-19  Score=138.63  Aligned_cols=81  Identities=17%  Similarity=0.301  Sum_probs=76.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|++++|
T Consensus        25 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  100 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSD---ADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPM  100 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEE
Confidence            44567888 9999999999   9999999999999999999998 99999999999999999999999999999999999


Q ss_pred             EEeecc
Q 023632           94 EVKKAE   99 (279)
Q Consensus        94 ~V~~a~   99 (279)
                      +|++|.
T Consensus       101 ~V~~a~  106 (107)
T 3ulh_A          101 NIQLVT  106 (107)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999985

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.81  E-value=6e-20  Score=143.54  Aligned_cols=82  Identities=20%  Similarity=0.353  Sum_probs=77.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++.+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        36 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l  112 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTD---TDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRL  112 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCH---HHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34566889 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeecc
Q 023632           94 EVKKAE   99 (279)
Q Consensus        94 ~V~~a~   99 (279)
                      +|++++
T Consensus       113 ~V~~ak  118 (118)
T 2khc_A          113 KVQLKK  118 (118)
T ss_dssp             CEEEC-
T ss_pred             EEEecC
Confidence            999874

>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=99.81  E-value=1.2e-19  Score=150.56  Aligned_cols=90  Identities=19%  Similarity=0.300  Sum_probs=79.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++||+|+.|.|++++.|+++++||||+|.++++|++||+.||+++|.+++|
T Consensus        68 ~~~~~~~l~V~nLp~~~t~---~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l  144 (165)
T 1rk8_A           68 RSVEGWILFVTSIHEEAQE---DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI  144 (165)
T ss_dssp             CCC-CEEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34556778 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCCC
Q 023632           94 EVKKAEPKKPNLPQ  107 (279)
Q Consensus        94 ~V~~a~~~~~~~~~  107 (279)
                      +|++|+++..+...
T Consensus       145 ~V~~a~~~~~~~~~  158 (165)
T 1rk8_A          145 QVDWCFVKGPKRVK  158 (165)
T ss_dssp             EEEESEECC-----
T ss_pred             EEEEecCCCCCCCC
Confidence            99999887665543

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.80  E-value=4.1e-20  Score=148.69  Aligned_cols=89  Identities=22%  Similarity=0.366  Sum_probs=82.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +....++| |.|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|
T Consensus        43 ~~~~~~~l~V~nLp~~~te---~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l  119 (135)
T 2lea_A           43 DVEGMTSLKVDNLTYRTSP---DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGREL  119 (135)
T ss_dssp             SGGGCCCEEEECCCSSCHH---HHHHHHHGGGSCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34556788 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCCC
Q 023632           94 EVKKAEPKKPNLP  106 (279)
Q Consensus        94 ~V~~a~~~~~~~~  106 (279)
                      +|+++++++++..
T Consensus       120 ~V~~a~~~~~~~~  132 (135)
T 2lea_A          120 RVQMARYGRPPDS  132 (135)
T ss_dssp             EEEECCCCCCCTT
T ss_pred             EEEECCCCCCCcc
Confidence            9999988665543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=1.8e-19  Score=134.45  Aligned_cols=82  Identities=22%  Similarity=0.334  Sum_probs=76.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++| .|++|+|+++ .++++++||||+|+++++|++||+ ||+++|++++|
T Consensus         6 ~~~~~~~l~v~nLp~~~t~---~~l~~~F~~~-~i~~v~i~~~-~~g~~~g~afV~f~~~~~a~~A~~-~~g~~~~gr~i   79 (91)
T 2dgw_A            6 SGTTCHTVKLRGAPFNVTE---KNVMEFLAPL-KPVAIRIVRN-AHGNKTGYIFVDFSNEEEVKQALK-CNREYMGGRYI   79 (91)
T ss_dssp             CCCCCCEEEEECCCSSCCH---HHHHHHHTTS-CCSEEEEEEC-TTSCEEEEEEEECSSHHHHHHHHH-SCSEEETTEEE
T ss_pred             CCCCccEEEEECCCCCCCH---HHHHHHHhhC-CceEEEEEEC-CCCCCceEEEEEECCHHHHHHHHH-hCCceeCCcEE
Confidence            44567888 9999999999   9999999999 9999999999 789999999999999999999999 99999999999


Q ss_pred             EEeeccCCC
Q 023632           94 EVKKAEPKK  102 (279)
Q Consensus        94 ~V~~a~~~~  102 (279)
                      +|++|+++.
T Consensus        80 ~v~~a~~~~   88 (91)
T 2dgw_A           80 EVFREKSGP   88 (91)
T ss_dssp             EEEEESSCC
T ss_pred             EEEECCcCC
Confidence            999998764

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A

Probab=99.80  E-value=1.8e-19  Score=133.26  Aligned_cols=81  Identities=35%  Similarity=0.599  Sum_probs=75.1

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +.+.+.++| |.|||+++++   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++||+. ++++|++++
T Consensus         6 ~~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~-~~~~~~g~~   81 (87)
T 3s7r_A            6 KNEEDAGKMFVGGLSWDTSK---KDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQ-KEHRLDGRV   81 (87)
T ss_dssp             -CCSCTTEEEEECCCTTCCH---HHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHS-SCEEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHh-CCCEECCEE
Confidence            345677889 9999999999   99999999999999999999999999999999999999999999976 788999999


Q ss_pred             eEEeec
Q 023632           93 VEVKKA   98 (279)
Q Consensus        93 i~V~~a   98 (279)
                      |+|++|
T Consensus        82 i~v~~A   87 (87)
T 3s7r_A           82 IDPKKA   87 (87)
T ss_dssp             EEEEEC
T ss_pred             EEEEeC
Confidence            999976

>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=99.80  E-value=1.1e-20  Score=165.21  Aligned_cols=82  Identities=18%  Similarity=0.293  Sum_probs=76.8

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G--~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..++| |.|||++|||   ++|+++|++||  +|++|+|++|+.|+++|+||||+|+++++|++||++||+++|++++|+
T Consensus        67 ~~~~lfVgnL~~~~te---~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~  143 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTD---EDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPV  143 (229)
T ss_dssp             --CEEEEESCCTTCCH---HHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCE
T ss_pred             CccEEEEeCCCCCCCH---HHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeE
Confidence            45678 9999999999   99999999999  999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCC
Q 023632           95 VKKAEPKK  102 (279)
Q Consensus        95 V~~a~~~~  102 (279)
                      |++|+++.
T Consensus       144 V~~a~~~~  151 (229)
T 3q2s_C          144 VTPVNKQF  151 (229)
T ss_dssp             EEECCHHH
T ss_pred             EEECCCCc
Confidence            99997643

>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=99.80  E-value=1.2e-19  Score=140.80  Aligned_cols=86  Identities=13%  Similarity=0.168  Sum_probs=77.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHH---HHHhcCCCeEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHHcCCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFK---DFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLE   87 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~---~~F~~~G~V~~v~i~~d~~tg---~~rG~aFV~F~s~e~a~~Ai~~lng~~   87 (279)
                      +....++| |.|||++++|   ++|+   ++|++||+|++|+|++++.+.   ++++||||+|+++++|++||+.||+++
T Consensus        11 r~~~~~~l~V~nLp~~~~~---~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~   87 (111)
T 2cpi_A           11 RVVQKNLVFVVGLSQRLAD---PEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVV   87 (111)
T ss_dssp             CCCCSSCEEEEEECTTTCC---HHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEE
T ss_pred             cccCCCEEEEECCCCCCCH---HHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCE
Confidence            44566788 9999999999   9999   999999999999999988744   566999999999999999999999999


Q ss_pred             cCCceeEEeeccCCCC
Q 023632           88 LAGAQVEVKKAEPKKP  103 (279)
Q Consensus        88 l~g~~i~V~~a~~~~~  103 (279)
                      |++++|+|++|+++..
T Consensus        88 ~~gr~l~V~~a~~k~~  103 (111)
T 2cpi_A           88 VDGRTLKASLGTTKYC  103 (111)
T ss_dssp             ETTEEEEEESCCCCSC
T ss_pred             ECCEEEEEEecccccc
Confidence            9999999999988753

>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=99.80  E-value=5.1e-20  Score=140.54  Aligned_cols=85  Identities=22%  Similarity=0.434  Sum_probs=79.8

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||++.|++++|+|
T Consensus         6 ~~~~~l~V~nlp~~~~~---~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v   82 (104)
T 1p1t_A            6 RSLRSVFVGNIPYEATE---EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRV   82 (104)
T ss_dssp             HHHSCEEEESCCTTSCH---HHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEE
T ss_pred             CCccEEEEeCCCCcCCH---HHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEE
Confidence            345788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCCC
Q 023632           96 KKAEPKKPN  104 (279)
Q Consensus        96 ~~a~~~~~~  104 (279)
                      ++|+++...
T Consensus        83 ~~a~~~~~~   91 (104)
T 1p1t_A           83 DNAASEKNK   91 (104)
T ss_dssp             EETTCTTHH
T ss_pred             EeCCCccch
Confidence            999876543

>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=99.80  E-value=5.7e-20  Score=139.94  Aligned_cols=84  Identities=21%  Similarity=0.364  Sum_probs=74.6

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~-~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      ......++| |.|||+++++   ++|+++|++|| |++|+|++++ .++++++||||+|+++++|++|| .||+++|+++
T Consensus        14 ~~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai-~l~g~~~~g~   88 (100)
T 2j76_E           14 LPKSPPYTAFLGNLPYDVTE---ESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNR   88 (100)
T ss_dssp             ------CEEEESCCSSCCSS---SHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHH-HTTTCCBTTB
T ss_pred             CCCCCCcEEEEeCCCCCCCH---HHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHH-hcCCCEECCe
Confidence            345667889 9999999999   99999999999 9999999998 69999999999999999999999 8999999999


Q ss_pred             eeEEeeccCCC
Q 023632           92 QVEVKKAEPKK  102 (279)
Q Consensus        92 ~i~V~~a~~~~  102 (279)
                      +|+|++++++.
T Consensus        89 ~l~V~~a~~~~   99 (100)
T 2j76_E           89 RIRVDVADQAQ   99 (100)
T ss_dssp             CCCCEECCCSC
T ss_pred             EEEEEeccCCC
Confidence            99999998754

>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=99.80  E-value=4.3e-20  Score=138.68  Aligned_cols=82  Identities=12%  Similarity=0.210  Sum_probs=75.2

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .+..++| |.|||+++++   ++|+++|++|++|++++|+.++.++++++||||+|+++++|++||+.||+++|++++|+
T Consensus        12 ~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~   88 (95)
T 2ek1_A           12 KPGPTVIKVQNMPFTVSI---DEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   88 (95)
T ss_dssp             ---CEEEEEECCCTTCCH---HHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEE
Confidence            3456888 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccC
Q 023632           95 VKKAEP  100 (279)
Q Consensus        95 V~~a~~  100 (279)
                      |+++.+
T Consensus        89 v~~a~s   94 (95)
T 2ek1_A           89 LSGPSS   94 (95)
T ss_dssp             EECCC-
T ss_pred             EEeccC
Confidence            998764

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=7.4e-21  Score=147.99  Aligned_cols=84  Identities=20%  Similarity=0.368  Sum_probs=78.5

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.|+++++||||+|+++++|++|| .||+++|+++.|+|
T Consensus        23 ~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V   98 (114)
T 2cq4_A           23 RDARTVFCMQLAARIRP---RDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAI-GLTGQRLLGVPIIV   98 (114)
T ss_dssp             HHHTEEEEESCCTTCCH---HHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHH-HHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHH-HcCCCEeCCeEEEE
Confidence            345788 9999999999   999999999999999999999999999999999999999999999 89999999999999


Q ss_pred             eeccCCCCC
Q 023632           96 KKAEPKKPN  104 (279)
Q Consensus        96 ~~a~~~~~~  104 (279)
                      ++++++..+
T Consensus        99 ~~a~~~~~~  107 (114)
T 2cq4_A           99 QASQAEKNR  107 (114)
T ss_dssp             EEHHHHHHH
T ss_pred             EecCCCccC
Confidence            999876543

>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=99.80  E-value=1.3e-19  Score=138.77  Aligned_cols=82  Identities=18%  Similarity=0.168  Sum_probs=74.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++||   ++|+++|++|+.| +|+|++|+ ++++++||||+|+++++|++||+ +|+++|+++.|
T Consensus        11 ~~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~~-~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~-~~~~~~~gr~i   84 (102)
T 1wez_A           11 QSTTGHCVHMRGLPYRATE---NDIYNFFSPLNPM-RVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYV   84 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCH---HHHHHSSCSCCCS-EEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHcCce-EEEEEECC-CCCEeeEEEEEECCHHHHHHHHH-hCCCeECCcEE
Confidence            34566788 9999999999   9999999999955 99999998 89999999999999999999995 69999999999


Q ss_pred             EEeeccCCC
Q 023632           94 EVKKAEPKK  102 (279)
Q Consensus        94 ~V~~a~~~~  102 (279)
                      +|.++.++.
T Consensus        85 ~V~~~~~~~   93 (102)
T 1wez_A           85 ELFLNSTAG   93 (102)
T ss_dssp             EEEEECCCC
T ss_pred             EEEECCCCC
Confidence            999987654

>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=99.80  E-value=2.3e-19  Score=137.62  Aligned_cols=85  Identities=18%  Similarity=0.220  Sum_probs=77.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE-EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE-HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~-v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +....++| |.|||+++||   ++|+++|++|+.|++ |+|+++ .++++++||||+|+++++|++||+. |+++|+++.
T Consensus        11 ~~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~v~~~v~i~~~-~~g~~~G~afV~F~~~~~a~~A~~~-~~~~~~gr~   85 (104)
T 1wg5_A           11 DTANDGFVRLRGLPFGCSK---EEIVQFFSGLEIVPNGMTLPVD-FQGRSTGEAFVQFASQEIAEKALKK-HKERIGHRY   85 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCH---HHHHHHTTTCCEEEEEEECCBC-SSSCBCSEEEEEESSHHHHHHHHTT-TTCCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCcceeEEEEEC-CCCCcceEEEEEECCHHHHHHHHHh-CcchhCCcE
Confidence            44567888 9999999999   999999999999998 888888 7999999999999999999999998 999999999


Q ss_pred             eEEeeccCCCCC
Q 023632           93 VEVKKAEPKKPN  104 (279)
Q Consensus        93 i~V~~a~~~~~~  104 (279)
                      |+|.++.+++..
T Consensus        86 i~v~~~~~~~~~   97 (104)
T 1wg5_A           86 IEIFKSSRAEVR   97 (104)
T ss_dssp             CEEEEECTTTSC
T ss_pred             EEEEECCHHHHH
Confidence            999998765543

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.80  E-value=1.6e-19  Score=139.23  Aligned_cols=83  Identities=18%  Similarity=0.256  Sum_probs=74.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC--CCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln--g~~l~g~   91 (279)
                      .+.+.++| |+|||+++||   ++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.|+  +.+|+++
T Consensus        12 ~~~~~~~LfV~nLp~~vte---~dL~~lF~~fG~V~~v~i~~~------kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr   82 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTE---GEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   82 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCH---HHHHHHHHHHCCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTSCCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            34567888 9999999999   999999999999999999976      6899999999999999999876  4789999


Q ss_pred             eeEEeeccCCCCCCC
Q 023632           92 QVEVKKAEPKKPNLP  106 (279)
Q Consensus        92 ~i~V~~a~~~~~~~~  106 (279)
                      +|+|++|+++.....
T Consensus        83 ~l~V~~A~~~~~~~~   97 (105)
T 1sjq_A           83 PIYIQFSNHKELKTD   97 (105)
T ss_dssp             ECCBCCCSSSSCCCT
T ss_pred             EEEEEEcCCCCCCcc
Confidence            999999988765543

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.80  E-value=3.7e-19  Score=140.44  Aligned_cols=88  Identities=15%  Similarity=0.245  Sum_probs=81.2

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|++++|+
T Consensus        32 ~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~v~~v~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~  107 (124)
T 2kt5_A           32 VETGAKLLVSNLDFGVSD---ADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD  107 (124)
T ss_dssp             CSSCEEEEEESCCSSCCH---HHHHHHHHTTSCCSEEEEECCS-SSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEEECC-CCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEE
Confidence            4556788 9999999999   9999999999999999999998 999999999999999999999999999999999999


Q ss_pred             EeeccCCCCCCCC
Q 023632           95 VKKAEPKKPNLPQ  107 (279)
Q Consensus        95 V~~a~~~~~~~~~  107 (279)
                      |++|.++....+.
T Consensus       108 V~~a~~~~~~~~~  120 (124)
T 2kt5_A          108 IQLVASQIDLEHH  120 (124)
T ss_dssp             EEEECCTTCCCCC
T ss_pred             EEEeCCCCCCCCC
Confidence            9999887665543

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.80  E-value=5.8e-19  Score=131.48  Aligned_cols=80  Identities=24%  Similarity=0.459  Sum_probs=73.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++|+|+        ++||||+|+++++|++||+.||+++|++++|
T Consensus         4 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   72 (90)
T 2dnq_A            4 GSSGMVKLFIGNLPREATE---QEIRSLFEQYGKVLECDII--------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNI   72 (90)
T ss_dssp             CSSCCEEEEEESCCSSCCH---HHHHHHHHTSSCEEEEEEE--------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBC
T ss_pred             CCCCCeEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHhcCCccCCcEE
Confidence            45667889 9999999999   9999999999999999997        5799999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++++++....
T Consensus        73 ~v~~a~~~~~~~   84 (90)
T 2dnq_A           73 NVEASKNKSKAS   84 (90)
T ss_dssp             EEECSSCCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998876544

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.80  E-value=1.6e-19  Score=148.81  Aligned_cols=81  Identities=21%  Similarity=0.304  Sum_probs=76.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCC--CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFG--DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G--~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..++| |.|||++++|   ++|+++|++||  +|++|+|++|+.|++++|||||+|+++++|++||+.||+++|++++|+
T Consensus        54 ~~~~lfVgnLp~~~te---~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~  130 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTD---QQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVD  130 (156)
T ss_dssp             --CEEEEECCCTTCCH---HHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeE
Confidence            45788 9999999999   99999999999  999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |++|.++
T Consensus       131 V~~a~~~  137 (156)
T 3n9u_C          131 VRPATRQ  137 (156)
T ss_dssp             EEECCHH
T ss_pred             EEEcCCC
Confidence            9999764

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3e-19  Score=135.86  Aligned_cols=85  Identities=25%  Similarity=0.384  Sum_probs=77.1

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ......++| |.|||+++++   ++|+++|++|   .+|+|++++.++++++||||+|+++++|++||+.||+++|++++
T Consensus        10 ~~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~---~~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   83 (102)
T 2fc8_A           10 ARSQPSKTLFVKGLSEDTTE---ETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNK   83 (102)
T ss_dssp             SSSCCCSSEEEECCCTTCCH---HHHHHTSTTC---SEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEeCCCCccCH---HHHHHHhcCC---eEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            345677888 9999999999   9999999977   47888999899999999999999999999999999999999999


Q ss_pred             eEEeeccCCCCC
Q 023632           93 VEVKKAEPKKPN  104 (279)
Q Consensus        93 i~V~~a~~~~~~  104 (279)
                      |+|++|+++.+.
T Consensus        84 l~V~~a~~~~~~   95 (102)
T 2fc8_A           84 VTLDWAKPKGEG   95 (102)
T ss_dssp             CEEEECCCCCSS
T ss_pred             EEEEEecCCCCC
Confidence            999999886553

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=2.3e-19  Score=137.84  Aligned_cols=81  Identities=15%  Similarity=0.196  Sum_probs=75.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++.+.++| |.|||+++|+   ++|+++|++||+|++|+|++|+. ++++|||||+|+++++|++||+ +|+++|++++|
T Consensus         7 ~~~~~~~lfV~~Lp~~~te---~~L~~~F~~~G~v~~v~i~~d~~-g~~rG~aFV~F~~~e~a~~Ai~-~~~~~~~gr~l   81 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATL---DDIKEWLEDKGQVLNIQMRRTLH-KAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDL   81 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCH---HHHHHHHHTSSCEEEEEEECCCT-TSCCCEEEEEESSHHHHHHHHT-SSCCCCTTTTC
T ss_pred             ccCCCCEEEEECCCCCCCH---HHHHHHHhhcCCEEEEEEEECCC-CCCccEEEEEECCHHHHHHHHH-cCCCEECCEEE
Confidence            45667889 9999999999   99999999999999999999987 9999999999999999999999 79999999999


Q ss_pred             EEeeccC
Q 023632           94 EVKKAEP  100 (279)
Q Consensus        94 ~V~~a~~  100 (279)
                      +|+++..
T Consensus        82 ~V~~~~~   88 (103)
T 1s79_A           82 LILFKDD   88 (103)
T ss_dssp             EEEEHHH
T ss_pred             EEEEchH
Confidence            9998764

>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=99.79  E-value=7.2e-19  Score=134.33  Aligned_cols=82  Identities=21%  Similarity=0.373  Sum_probs=73.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++|+   ++|+++|++||+|++|+|++        +||||+|+++++|++||+.||+++|++++|
T Consensus         7 ~~~~~~~l~V~nl~~~~t~---~~l~~~F~~~G~i~~v~~~~--------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l   75 (103)
T 2dgu_A            7 GMAKVKVLFVRNLANTVTE---EILEKAFSQFGKLERVKKLK--------DYAFIHFDERDGAVKAMEEMNGKDLEGENI   75 (103)
T ss_dssp             CCCCCCCEEEECCCTTCCH---HHHHHHHHHHSCEEEEEECS--------SCEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEC--------CEEEEEeCCHHHHHHHHHHHCCCccCCCEE
Confidence            34566888 9999999999   99999999999999999873        499999999999999999999999999999


Q ss_pred             EEeeccCCCCCCCC
Q 023632           94 EVKKAEPKKPNLPQ  107 (279)
Q Consensus        94 ~V~~a~~~~~~~~~  107 (279)
                      +|++++++......
T Consensus        76 ~v~~a~~~~~~~~~   89 (103)
T 2dgu_A           76 EIVFAKPPDQKRKE   89 (103)
T ss_dssp             EEEECCCCCCCCCC
T ss_pred             EEEEcCCCcccchh
Confidence            99999887665543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.79  E-value=4.2e-19  Score=139.92  Aligned_cols=82  Identities=17%  Similarity=0.356  Sum_probs=77.1

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++|| .||+++|++++|+|+
T Consensus        35 ~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~-~l~g~~~~g~~l~V~  110 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTA---QDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAV-AMDETVFRGRTIKVL  110 (124)
T ss_dssp             HHTEEEEEEECTTCCH---HHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHH-TTTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHH-hcCCCeECCeEEEEE
Confidence            35788 9999999999   999999999999999999999999999999999999999999999 799999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      ++++...
T Consensus       111 ~a~~~~~  117 (124)
T 2jwn_A          111 PKRTNMP  117 (124)
T ss_dssp             ESSCCCS
T ss_pred             ECCCCCC
Confidence            9986544

>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=99.79  E-value=5.3e-20  Score=143.07  Aligned_cols=89  Identities=22%  Similarity=0.238  Sum_probs=76.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |.|||+++|+   ++|+++|++||.|++|.|..+..++++++||||+|+++++|++||+.||+++|++++|+
T Consensus        22 ~~~~~~l~V~nLp~~~t~---~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           22 GEPNKVLYLKNLSPRVTE---RDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             CSCCSEEEEECCCTTCCH---HHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCccceEEEEEcCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3456889 9999999999   99999999999995443333333788999999999999999999999999999999999


Q ss_pred             EeeccCCCCCCCC
Q 023632           95 VKKAEPKKPNLPQ  107 (279)
Q Consensus        95 V~~a~~~~~~~~~  107 (279)
                      |++|+++..+.+.
T Consensus        99 v~~a~~~~~~~~~  111 (115)
T 2cpx_A           99 IEFGKNKKQRSSG  111 (115)
T ss_dssp             EEECCCCSCCCCC
T ss_pred             EEEccCCCCCCCC
Confidence            9999987665543

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.79  E-value=3.9e-19  Score=135.14  Aligned_cols=84  Identities=17%  Similarity=0.334  Sum_probs=75.3

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .+.+.++| |.|||+++++   ++|+++|++|++|   +|+++ .++++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~g~v---~~~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   83 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATE---ETLQEVFEKATFI---KVPQN-QNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAI   83 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCH---HHHHHHCSSCSEE---ECCBC-SSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEE
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCEE---EEEEC-CCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEE
Confidence            45667889 9999999999   9999999999977   56666 688999999999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++++++....
T Consensus        84 ~v~~a~~~~~~~   95 (101)
T 2fc9_A           84 RLELQGPRGSPN   95 (101)
T ss_dssp             EEEECSSCCCCC
T ss_pred             EEEEcCCCCCCC
Confidence            999998875443

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.79  E-value=6.4e-20  Score=135.06  Aligned_cols=80  Identities=13%  Similarity=0.301  Sum_probs=75.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|+++.|+|
T Consensus         3 ~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~   79 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTD---QDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQ   79 (85)
T ss_dssp             CCCCEEEEESCCTTCCH---HHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCS
T ss_pred             CCCcEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEee
Confidence            456888 9999999999   999999999999999999999999999999999999999999999999999999999988


Q ss_pred             eecc
Q 023632           96 KKAE   99 (279)
Q Consensus        96 ~~a~   99 (279)
                      +++.
T Consensus        80 ~~~~   83 (85)
T 1x4e_A           80 SGPS   83 (85)
T ss_dssp             SCCC
T ss_pred             cCCC
Confidence            7653

>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=99.79  E-value=5.4e-19  Score=136.38  Aligned_cols=84  Identities=15%  Similarity=0.318  Sum_probs=76.6

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +.+...++| |.|||+++++   ++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||+++|++++
T Consensus        20 ~~~~~~~~l~V~nl~~~~t~---~~l~~~F~~~G~i~~v~i~~~------~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   90 (109)
T 1x4g_A           20 QSSPKNCTVYCGGIASGLTD---QLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHV   90 (109)
T ss_dssp             HSCSSCCEEEEECCSSCCCH---HHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHcCCCEECCcE
Confidence            355677889 9999999999   999999999999999999876      689999999999999999999999999999


Q ss_pred             eEEeeccCCCCCCC
Q 023632           93 VEVKKAEPKKPNLP  106 (279)
Q Consensus        93 i~V~~a~~~~~~~~  106 (279)
                      |+|++++++.....
T Consensus        91 l~v~~a~~~~~~~~  104 (109)
T 1x4g_A           91 VKCYWGKESPDMTS  104 (109)
T ss_dssp             CEEECCCCCCSSCC
T ss_pred             EEEEecCCCCCCCC
Confidence            99999988765443

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.79  E-value=1.7e-19  Score=129.68  Aligned_cols=74  Identities=38%  Similarity=0.608  Sum_probs=71.1

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+ ||+++|++++|+|++|
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 KIFVGGLSVNTTV---EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCH---HHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHS-SSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCH---HHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHH-CCCCEECCEEEEEEeC
Confidence            47 9999999999   9999999999999999999999999999999999999999999998 8999999999999875

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.78  E-value=1.7e-19  Score=140.51  Aligned_cols=85  Identities=13%  Similarity=0.203  Sum_probs=71.7

Q ss_pred             hhhcCCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc
Q 023632           10 TMFINRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE   87 (279)
Q Consensus        10 ~~~~~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~   87 (279)
                      .++.......++| |.|||++++|   ++|+++|++|| +|+.|+|+.+    ++++||||+|+++++|++||+.||+.+
T Consensus        19 ~~~~~~p~~~~~l~VgnLp~~~te---~dL~~~F~~~G~~v~~v~i~~~----~~rGfaFV~F~~~e~A~~Ai~~lng~~   91 (111)
T 2jvr_A           19 SHMSKLPAKRYRITMKNLPEGCSW---QDLKDLARENSLETTFSSVNTR----DFDGTGALEFPSEEILVEALERLNNIE   91 (111)
T ss_dssp             ------CCCCEEEEEECSSCCCCH---HHHHHHHHHHTCCCSEEECSSC----SSSCCEEEEESSHHHHHHHHHHTTTEE
T ss_pred             hhcCCCCCCCCEEEEECCCCCCCH---HHHHHHHHHhCCeeEEEEEEcC----CCCCEEEEEECCHHHHHHHHHHcCCCE
Confidence            3344455567788 9999999999   99999999999 8999988643    478999999999999999999999999


Q ss_pred             cCCceeEEeeccCC
Q 023632           88 LAGAQVEVKKAEPK  101 (279)
Q Consensus        88 l~g~~i~V~~a~~~  101 (279)
                      |++++|+|++++.+
T Consensus        92 l~Gr~i~V~~a~~~  105 (111)
T 2jvr_A           92 FRGSVITVERDDNP  105 (111)
T ss_dssp             ETTEEEEEEESCC-
T ss_pred             ECCeEEEEEECCCC
Confidence            99999999998754

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.78  E-value=1.8e-19  Score=129.92  Aligned_cols=76  Identities=41%  Similarity=0.617  Sum_probs=72.7

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.+| ++|++++|+|++|
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 CKMFIGGLSWQTTQ---EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCS---HHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            467 9999999999   9999999999999999999999999999999999999999999999999 9999999999987


Q ss_pred             c
Q 023632           99 E   99 (279)
Q Consensus        99 ~   99 (279)
                      .
T Consensus        77 ~   77 (77)
T 1uaw_A           77 F   77 (77)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.78  E-value=7.1e-19  Score=134.72  Aligned_cols=83  Identities=16%  Similarity=0.199  Sum_probs=73.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc--CCCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l--ng~~l~g~   91 (279)
                      ...++++| |.|||++++|   ++|+++|++||+|++|.|+++      |+||||+|+++++|++||+.|  +..+|.++
T Consensus        11 ~~~p~~~l~V~nLp~~~te---~~L~~~F~~fG~v~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   81 (101)
T 2cq1_A           11 DGAPSRVLHIRKLPGEVTE---TEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   81 (101)
T ss_dssp             CSSCCSEEEEESCCTTCCH---HHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCc
Confidence            44567889 9999999999   999999999999999998865      789999999999999999976  56789999


Q ss_pred             eeEEeeccCCCCCCC
Q 023632           92 QVEVKKAEPKKPNLP  106 (279)
Q Consensus        92 ~i~V~~a~~~~~~~~  106 (279)
                      +|+|++|+++.....
T Consensus        82 ~l~V~~a~~~~~~~~   96 (101)
T 2cq1_A           82 PIYIQYSNHKELKTS   96 (101)
T ss_dssp             ECEEEECSCSSCCCC
T ss_pred             EEEEEEcCcccCcCC
Confidence            999999988765543

>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=99.78  E-value=5.5e-19  Score=137.22  Aligned_cols=83  Identities=19%  Similarity=0.371  Sum_probs=77.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc-----
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL-----   88 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l-----   88 (279)
                      ++.+.++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|     
T Consensus        21 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~~~i~~~~-~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~   96 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDE---QELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   96 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCH---HHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEEECC-CCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCcc
Confidence            45567889 9999999999   9999999999999999999998 999999999999999999999999999999     


Q ss_pred             ---CCceeEEeeccCC
Q 023632           89 ---AGAQVEVKKAEPK  101 (279)
Q Consensus        89 ---~g~~i~V~~a~~~  101 (279)
                         .+++|+|++|+++
T Consensus        97 ~~~~~~~l~v~~a~p~  112 (114)
T 1x5o_A           97 VSAPTEPLLCKFSGPS  112 (114)
T ss_dssp             SCCCSSCBEEEECCCS
T ss_pred             ccCCCCceeEEccCCC
Confidence               5788999999864

>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=99.78  E-value=7.1e-20  Score=136.25  Aligned_cols=83  Identities=29%  Similarity=0.560  Sum_probs=73.2

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|++++ |++||+.||+++|++++|+|++|
T Consensus         2 ~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a   77 (90)
T 2ki2_A            2 RNIYVGNLVYSATS---EQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEA   77 (90)
T ss_dssp             EEEEEEEECTTSSH---HHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC
T ss_pred             cEEEECCCCCCCCH---HHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEc
Confidence            578 9999999999   999999999999999999999999999999999999999 99999999999999999999999


Q ss_pred             cCCCCCCC
Q 023632           99 EPKKPNLP  106 (279)
Q Consensus        99 ~~~~~~~~  106 (279)
                      .++....+
T Consensus        78 ~~~~~~~~   85 (90)
T 2ki2_A           78 NPKKSLEH   85 (90)
T ss_dssp             --------
T ss_pred             CCCCCCCC
Confidence            88655443

>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=99.78  E-value=2.5e-19  Score=137.49  Aligned_cols=81  Identities=15%  Similarity=0.097  Sum_probs=72.0

Q ss_pred             CCCCcee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC--CccCCc
Q 023632           16 QTTTQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK--LELAGA   91 (279)
Q Consensus        16 ~~~~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng--~~l~g~   91 (279)
                      ..+.++| |.|||+ ++||   ++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||.  .+|+++
T Consensus        12 ~~p~~~l~V~nLp~~~~te---~dL~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr   82 (102)
T 1x4d_A           12 VETRRVVHIMDFQRGKNLR---YQLLQLVEPFGVISNHLILNK------INEAFIEMATTEDAQAAVDYYTTTPALVFGK   82 (102)
T ss_dssp             CCCCCEEEEESCCCSSSHH---HHHHTTTGGGSCEEEEEECSS------SSCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCEEEEeCCCCCcCCH---HHHHHHHHhcCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHHcCCCceECCc
Confidence            4467889 999999 9999   999999999999999999876      47999999999999999998875  469999


Q ss_pred             eeEEeeccCCCCCC
Q 023632           92 QVEVKKAEPKKPNL  105 (279)
Q Consensus        92 ~i~V~~a~~~~~~~  105 (279)
                      +|+|++|++++...
T Consensus        83 ~l~V~~a~~~~~~~   96 (102)
T 1x4d_A           83 PVRVHLSQKYKRIK   96 (102)
T ss_dssp             ECEEEEECCCTTSS
T ss_pred             EEEEEECCCCCCCC
Confidence            99999998765544

>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=99.78  E-value=8.9e-19  Score=138.01  Aligned_cols=83  Identities=18%  Similarity=0.254  Sum_probs=74.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC--CCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln--g~~l~g~   91 (279)
                      ...+.++| |+|||+++||   ++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.|+  ..+|.++
T Consensus        27 ~~~ps~~LfVgNLp~~vte---~dL~~lF~~fG~V~~v~i~~~------kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr   97 (119)
T 2ad9_A           27 AGVPSRVIHIRKLPIDVTE---GEVISLGLPFGKVTNLLMLKG------KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQ   97 (119)
T ss_dssp             CSSCCSEEEEESCCTTCCH---HHHHHHHTTTSCCCEEEEEGG------GTEEEEECSCHHHHHHHHHHHHHHCCCBTTB
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEeCC------CCEEEEEECCHHHHHHHHHHhccCCceECCe
Confidence            44567889 9999999999   999999999999999999976      6899999999999999999886  4789999


Q ss_pred             eeEEeeccCCCCCCC
Q 023632           92 QVEVKKAEPKKPNLP  106 (279)
Q Consensus        92 ~i~V~~a~~~~~~~~  106 (279)
                      +|+|++|++++....
T Consensus        98 ~l~V~~a~~k~~~~~  112 (119)
T 2ad9_A           98 PIYIQFSNHKELKTD  112 (119)
T ss_dssp             CCEEEECSSSSCCCC
T ss_pred             EEEEEEccCCCCCcc
Confidence            999999988766543

>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=99.78  E-value=1.1e-18  Score=131.68  Aligned_cols=80  Identities=16%  Similarity=0.273  Sum_probs=73.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC--Cc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--GA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~--g~   91 (279)
                      ...+.++| |.|||+++++   ++|+++|++|++|++|+|+++      ++||||+|+++++|++||+.||+++|+  ++
T Consensus        13 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~v~~v~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~   83 (97)
T 1why_A           13 KANPTTRLWVGGLGPNTSL---AALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCH---HHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEeCC------CCEEEEEECCHHHHHHHHHHHCCCEeCCCCc
Confidence            44566888 9999999999   999999999999999999865      679999999999999999999999999  99


Q ss_pred             eeEEeeccCCCC
Q 023632           92 QVEVKKAEPKKP  103 (279)
Q Consensus        92 ~i~V~~a~~~~~  103 (279)
                      +|+|++++++..
T Consensus        84 ~l~V~~a~~~~~   95 (97)
T 1why_A           84 RLRVDFAKSGPS   95 (97)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEECCCCCC
Confidence            999999988643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=129.92  Aligned_cols=81  Identities=17%  Similarity=0.366  Sum_probs=73.6

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ......++| |.|||+++++   ++|+++|++||+|++|+|+++        ||||+|+++++|++||+.||+++|++++
T Consensus         5 ~~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~v~~v~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~   73 (92)
T 2dgt_A            5 SSGKASTKLHVGNISPTCTN---QELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGLDNTEFQGKR   73 (92)
T ss_dssp             CCCCSSEEEEEESCCSSCCH---HHHHHHHHTTSCCCEEEECSS--------EEEEEESCHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCeeCCcE
Confidence            345677889 9999999999   999999999999999999844        9999999999999999999999999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|++++++....
T Consensus        74 l~V~~a~~~~~~~   86 (92)
T 2dgt_A           74 MHVQLSTSRLRTA   86 (92)
T ss_dssp             EEEEESSCCCSCC
T ss_pred             EEEEEccCCCCCC
Confidence            9999998866544

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=5.4e-19  Score=136.75  Aligned_cols=84  Identities=21%  Similarity=0.442  Sum_probs=77.2

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+...++| |.|||+++++   ++|+++|++||+|++|+|++++.  ++++||||+|+++++|++||+.||+++|++++
T Consensus        24 ~~~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~   98 (109)
T 2err_A           24 ENKSQPKRLHVSNIPFRFRD---PDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRK   98 (109)
T ss_dssp             SCTTCCCEEEEESCCTTCCH---HHHHHHGGGTCCCSCEEECCBTT--BCTTEEEEECCCSHHHHHHHHHHTTCEETTEE
T ss_pred             cCCCCCCEEEEECCCCcCCH---HHHHHHHHhcCCEEEEEEEECCC--CCceEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            355677889 9999999999   99999999999999999999853  48999999999999999999999999999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+|++|+++.
T Consensus        99 l~V~~a~~~~  108 (109)
T 2err_A           99 IEVNNATARV  108 (109)
T ss_dssp             CEEEECCCSC
T ss_pred             EEEEECCCCc
Confidence            9999998753

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.77  E-value=1.3e-18  Score=132.25  Aligned_cols=77  Identities=21%  Similarity=0.342  Sum_probs=72.0

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||+++|+   ++|+++|++||+|++|+|+++     +++||||+|+++++|++||+.||+++|++++|+|+++
T Consensus         1 ~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   72 (101)
T 2hvz_A            1 MKVYVGNLGTGAGK---GELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS   72 (101)
T ss_dssp             CEEEEECCCSSCSH---HHHHHHHHHHCCCSEEEEESS-----SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEES
T ss_pred             CEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEeeC-----CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEc
Confidence            468 9999999999   999999999999999999987     6899999999999999999999999999999999999


Q ss_pred             cCCCCC
Q 023632           99 EPKKPN  104 (279)
Q Consensus        99 ~~~~~~  104 (279)
                      +++...
T Consensus        73 ~~~~~~   78 (101)
T 2hvz_A           73 TGMPRR   78 (101)
T ss_dssp             SSCCCS
T ss_pred             cCCCCc
Confidence            887644

>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=99.77  E-value=2.1e-19  Score=140.10  Aligned_cols=83  Identities=11%  Similarity=0.112  Sum_probs=77.3

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCe-EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDV-QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V-~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .+.+.++| |.|||+++||   ++|+++|++|+.| ++|+|++|+ ++++++||||+|+++++|++||+. |+++|++++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~g~v~~~v~i~~d~-~g~~~G~afV~F~~~~~a~~Al~~-~~~~~~gr~   85 (114)
T 2cpy_A           11 VNSAKVCAHITNIPFSITK---MDVLQFLEGIPVDENAVHVLVDN-NGQGLGQALVQFKNEDDARKSERL-HRKKLNGRE   85 (114)
T ss_dssp             CCSCCCEEEEESCCTTSCH---HHHHHHTTTSCCCSTTEEECCCT-TSSCSSCEEEECSSHHHHHHHGGG-CSEEETTEE
T ss_pred             CCCCccEEEEeCcCCcCCH---HHHHHHHHhCCCcCCeEEEEECC-CCCcceEEEEEECCHHHHHHHHHh-CCCccCCeE
Confidence            34556788 9999999999   9999999999999 899999998 999999999999999999999998 999999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+|++|.++.
T Consensus        86 i~v~~a~~~~   95 (114)
T 2cpy_A           86 AFVHVVTLED   95 (114)
T ss_dssp             EEEEEECHHH
T ss_pred             EEEEECCHHH
Confidence            9999998765

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=1.6e-18  Score=129.12  Aligned_cols=80  Identities=21%  Similarity=0.377  Sum_probs=72.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++.+.++| |.|||+++|+   ++|+++|++||+|++|+|+++        ||||+|+++++|++||+.||+++|++++|
T Consensus         5 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~v~~~~~~~~--------~afV~f~~~~~a~~A~~~l~g~~~~g~~l   73 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTS---QELRSLFERRGRVIECDVVKD--------YAFVHMEKEADAKAAIAQLNGKEVKGKRI   73 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCH---HHHHHHHHHHSCEEEEEECSS--------CEEEEESCHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHcCCCEEEEEEECC--------EEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            45667888 9999999999   999999999999999999844        99999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++++++.+..
T Consensus        74 ~v~~a~~~~~~~   85 (90)
T 2dnp_A           74 NVELSTKGQKKS   85 (90)
T ss_dssp             EEEESCCCCCCC
T ss_pred             EEEECCCCCCCC
Confidence            999998865433

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.77  E-value=2e-18  Score=129.67  Aligned_cols=83  Identities=18%  Similarity=0.336  Sum_probs=72.9

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++||+|++|  +.++.+++   ||||+|+++++|++||+ ||+++|++++|+
T Consensus         5 ~~~~~~l~V~nl~~~~t~---~~l~~~F~~~G~v~~v--~~~~~~g~---~afV~f~~~~~a~~ai~-l~g~~~~g~~l~   75 (94)
T 2e5g_A            5 SSGLRSVFVSGFPRGVDS---AQLSEYFLAFGPVASV--VMDKDKGV---FAIVEMGDVGAREAVLS-QSQHSLGGHRLR   75 (94)
T ss_dssp             CTTCCEEEEECCCTTCCH---HHHHHHGGGTSCEEEE--EECSSSCC---EEEEEESSHHHHHHHHT-CSCCEETTEECC
T ss_pred             cCCCCEEEEECCCCCCCH---HHHHHHHHhcCCeEEE--EEcCCCCc---EEEEEECCHHHHHHHHh-cCCeEECCEEEE
Confidence            3456789 9999999999   9999999999999987  66666665   99999999999999999 999999999999


Q ss_pred             EeeccCCCCCCCC
Q 023632           95 VKKAEPKKPNLPQ  107 (279)
Q Consensus        95 V~~a~~~~~~~~~  107 (279)
                      |+++.+++...+.
T Consensus        76 V~~a~~~~~~~~~   88 (94)
T 2e5g_A           76 VRPREQKEFQSPA   88 (94)
T ss_dssp             CBCSCCSCCCCCC
T ss_pred             EEECCcCCCCCCC
Confidence            9999876655443

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.77  E-value=1e-18  Score=140.04  Aligned_cols=80  Identities=29%  Similarity=0.462  Sum_probs=75.7

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+
T Consensus        60 ~~~~~~l~v~nlp~~~~~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  136 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDD---KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIR  136 (140)
T ss_dssp             CSSCCEEEEECCCTTCCH---HHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEE
T ss_pred             CCCCcEEEEEeCCCCCCH---HHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            4567889 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             Eeec
Q 023632           95 VKKA   98 (279)
Q Consensus        95 V~~a   98 (279)
                      |++|
T Consensus       137 v~~A  140 (140)
T 2ku7_A          137 VNLA  140 (140)
T ss_dssp             EEC-
T ss_pred             EEeC
Confidence            9976

>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=99.77  E-value=2.2e-18  Score=163.95  Aligned_cols=85  Identities=14%  Similarity=0.318  Sum_probs=79.8

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||++||+   ++|+++|++||+|+.|.|++++.|+++++||||+|+++++|++||++||+++|++++|+|+
T Consensus       101 ~~~~lfV~nL~~~~te---~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~  177 (437)
T 3pgw_S          101 AFKTLFVARVNYDTTE---SKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVD  177 (437)
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34688 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCCC
Q 023632           97 KAEPKKPNL  105 (279)
Q Consensus        97 ~a~~~~~~~  105 (279)
                      +|+++....
T Consensus       178 ~a~~~~~~~  186 (437)
T 3pgw_S          178 VERGRTVKG  186 (437)
T ss_pred             EeCCCCCCC
Confidence            998765543

>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=99.77  E-value=1.7e-18  Score=133.27  Aligned_cols=82  Identities=12%  Similarity=0.180  Sum_probs=72.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC--CccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK--LELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng--~~l~g~   91 (279)
                      ...++++| |.|||++++|   ++|+++|++||+|++|.|+++      |+||||+|+++++|++||+.||.  .+|+++
T Consensus        11 ~~~p~~~l~V~nLp~~~te---~~L~~~F~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr   81 (104)
T 1wex_A           11 KVSVSPVVHVRGLCESVVE---ADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCH---HHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEECC------CCEEEEEECCHHHHHHHHHHhccCCceECCE
Confidence            34567889 9999999999   999999999999999998864      68999999999999999998854  569999


Q ss_pred             eeEEeeccCCCCCC
Q 023632           92 QVEVKKAEPKKPNL  105 (279)
Q Consensus        92 ~i~V~~a~~~~~~~  105 (279)
                      +|+|++++++....
T Consensus        82 ~l~V~~a~~~~~~~   95 (104)
T 1wex_A           82 QAFFNYSTSKRITR   95 (104)
T ss_dssp             BCEEEECSSSSCCC
T ss_pred             EEEEEEccCccccC
Confidence            99999998866543

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.77  E-value=3.3e-19  Score=140.02  Aligned_cols=83  Identities=13%  Similarity=0.161  Sum_probs=76.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCC---eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGD---VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~---V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ...+.++| |.|||+++||   ++|+++|++|++   |++|+|++++. +++++||||+|+++++|++||+ ||+++|++
T Consensus        13 ~~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~g~~~~g   87 (118)
T 2db1_A           13 EGGEGYVVKLRGLPWSCSI---EDVQNFLSDCTIHDGVAGVHFIYTRE-GRQSGEAFVELESEDDVKLALK-KDRESMGH   87 (118)
T ss_dssp             CBCCCCEEEEESCCTTCCH---HHHHHHTTTSCBTTGGGGEEEEECSS-SCEEEEEEEEBSSHHHHHHHGG-GTTEEETT
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHHcCCccCceeEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCeECC
Confidence            34566788 9999999999   999999999999   89999999986 9999999999999999999999 89999999


Q ss_pred             ceeEEeeccCCC
Q 023632           91 AQVEVKKAEPKK  102 (279)
Q Consensus        91 ~~i~V~~a~~~~  102 (279)
                      +.|+|.++.+++
T Consensus        88 r~i~V~~a~~~~   99 (118)
T 2db1_A           88 RYIEVFKSHRTE   99 (118)
T ss_dssp             EEEEEEEECHHH
T ss_pred             eEEEEEECCHHH
Confidence            999999987654

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.77  E-value=1.4e-18  Score=132.68  Aligned_cols=79  Identities=13%  Similarity=0.216  Sum_probs=71.3

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc--cCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE--LAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~--l~g~   91 (279)
                      ...++++| |+|||+++||   ++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.||+..  |.++
T Consensus        17 ~~~ps~~l~V~NLp~~~te---~~L~~lF~~fG~V~~v~i~~~------kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr   87 (100)
T 3r27_A           17 KTPASPVVHIRGLIDGVVE---ADLVEALQEFGPISYVVVMPK------KRQALVEFEDVLGACNAVNYAADNQIYIAGH   87 (100)
T ss_dssp             CCCCCSEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCEEETTE
T ss_pred             cCCCCcEEEEeCCCCCCCH---HHHHHHHhccCCEEEEEEEcC------CCEEEEEECCHHHHHHHHHHhcCCCceeCCc
Confidence            34567889 9999999999   999999999999999999853      6899999999999999999998765  7899


Q ss_pred             eeEEeeccCCC
Q 023632           92 QVEVKKAEPKK  102 (279)
Q Consensus        92 ~i~V~~a~~~~  102 (279)
                      +|.|+++++++
T Consensus        88 ~i~V~~S~~k~   98 (100)
T 3r27_A           88 PAFVNYSTSQK   98 (100)
T ss_dssp             EEEEEECSCSC
T ss_pred             EEEEEeccccc
Confidence            99999998764

>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=1.3e-18  Score=135.88  Aligned_cols=76  Identities=18%  Similarity=0.302  Sum_probs=65.2

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce---
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ---   92 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~---   92 (279)
                      ...++| |.|||++++|   ++|+++|++||+|++|+|+++       +||||+|+++++|++||++||+++|++++   
T Consensus        14 r~~~~l~V~nLp~~~t~---~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~   83 (115)
T 3beg_B           14 RSENRVVVSGLPPSGSW---QDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGET   83 (115)
T ss_dssp             ---CCEEEEECCSSCCT---THHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCC
T ss_pred             CCCcEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEecC-------CEEEEEECCHHHHHHHHHHhCCCEECCcEeee
Confidence            345788 9999999999   999999999999999999866       79999999999999999999999999998   


Q ss_pred             --eEEeeccCCC
Q 023632           93 --VEVKKAEPKK  102 (279)
Q Consensus        93 --i~V~~a~~~~  102 (279)
                        |+|+.+.++.
T Consensus        84 ~~i~v~~~~~~~   95 (115)
T 3beg_B           84 AYIRVKVDGPRS   95 (115)
T ss_dssp             CBCEEEECC---
T ss_pred             EEEEeccCCCCC
Confidence              6666665543

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A

Probab=99.76  E-value=3.8e-19  Score=143.43  Aligned_cols=83  Identities=12%  Similarity=0.141  Sum_probs=76.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCC---eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGD---VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~---V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      +..+.++| |+|||+++||   ++|+++|++|++   |++|+|++|+. ++++|||||+|+++++|++||+ ||+++|++
T Consensus        40 ~~~~~~~lfVgnLp~~~te---~dL~~~F~~~G~v~~v~~v~i~~d~~-g~srG~aFV~F~~~e~a~~Al~-~~g~~l~g  114 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSV---EDVQNFLSDCTIHDGAAGVHFIYTRE-GRQSGEAFVELGSEDDVKMALK-KDRESMGH  114 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCH---HHHHHHTTTCCCSSSSTTEEEEECSS-SCEEEEEEEECSSHHHHHHHHT-TTEEESSS
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCcCceeEEEEEECCC-CCCCeEEEEEECCHHHHHHHHh-cCCCEECC
Confidence            34556788 9999999999   999999999999   89999999987 9999999999999999999999 89999999


Q ss_pred             ceeEEeeccCCC
Q 023632           91 AQVEVKKAEPKK  102 (279)
Q Consensus        91 ~~i~V~~a~~~~  102 (279)
                      ++|+|.++.+++
T Consensus       115 r~i~V~~a~~~e  126 (136)
T 2hgl_A          115 RYIEVFKSHRTE  126 (136)
T ss_dssp             SEEEEEECCHHH
T ss_pred             EEEEEEECChHH
Confidence            999999987543

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.76  E-value=9.6e-20  Score=138.52  Aligned_cols=84  Identities=18%  Similarity=0.293  Sum_probs=76.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++|++|++ .|+.++.++++++||||+|+++++|++||+ ||+++|++++|+
T Consensus        14 ~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l~   88 (101)
T 1fj7_A           14 STTPFNLFIGNLNPNKSV---AELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK   88 (101)
T ss_dssp             CSCSEEEEEECCCTTSCH---HHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGCCBTTBCCE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHh-cCCcEECCcEEE
Confidence            3456788 9999999999   999999999999988 677787889999999999999999999999 999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |++|++++.+
T Consensus        89 V~~a~~~~~~   98 (101)
T 1fj7_A           89 LEKPKGRDGT   98 (101)
T ss_dssp             EECCSCCCCS
T ss_pred             EEEcCCCCCC
Confidence            9999876544

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.76  E-value=1.6e-18  Score=128.68  Aligned_cols=73  Identities=11%  Similarity=0.156  Sum_probs=68.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      .+..| |+||++.+||   ++|+++|.+||+|++++|+.      +||||||+|.++++|++||+.||+++|.+++|+|+
T Consensus         6 ~~~wL~VgNL~~~~te---~~L~~lF~q~G~V~~~~l~~------~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~   76 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDG---PTLRTLCMQHGPLVSFHPYL------NQGIALCKYTTREEANKAQMALNNCVLANTTIFAE   76 (89)
T ss_dssp             CCCEEEEECCCTTCCC---HHHHHHHHHHSCEEEEEEET------TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             ccceEEEeCCCccCCH---HHHHHHHHhhCCEEEEEEcC------CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            46678 9999999999   99999999999999999975      58999999999999999999999999999999999


Q ss_pred             ecc
Q 023632           97 KAE   99 (279)
Q Consensus        97 ~a~   99 (279)
                      +|.
T Consensus        77 ~A~   79 (89)
T 2wbr_A           77 SPS   79 (89)
T ss_dssp             CCC
T ss_pred             ECC
Confidence            984

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.76  E-value=1.3e-18  Score=132.15  Aligned_cols=81  Identities=15%  Similarity=0.241  Sum_probs=73.3

Q ss_pred             hcCCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           12 FINRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        12 ~~~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ........++| |.|||+++++   ++|+++|++||+|++|+|+      ++++||||+|++.++|++||+.||+++|++
T Consensus        20 ~~~~~~~~~~l~V~nlp~~~~~---~~l~~~f~~~G~i~~~~~~------~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g   90 (101)
T 2la4_A           20 IRSAPPRVTTAYIGNIPHFATE---ADLIPLFQNFGFILDFKHY------PEKGCCFIKYDTHEQAAVCIVALANFPFQG   90 (101)
T ss_dssp             HTTSCSSCCEEEEESCCTTCCH---HHHHHHHHTTSCCSEEEEE------TTTTEEEEECSSHHHHHHHHHHHTTCEETT
T ss_pred             hhcCCCCCCEEEEcCCCcccCH---HHHHHHHHhCCCEEEEEEe------cCCCEEEEEECCHHHHHHHHHHhCCCeECC
Confidence            33445567889 9999999999   9999999999999999998      357899999999999999999999999999


Q ss_pred             ceeEEeeccCC
Q 023632           91 AQVEVKKAEPK  101 (279)
Q Consensus        91 ~~i~V~~a~~~  101 (279)
                      ++|+|++|+++
T Consensus        91 ~~l~V~~a~~~  101 (101)
T 2la4_A           91 RNLRTGWGKER  101 (101)
T ss_dssp             EECCCCBCCCC
T ss_pred             eEEEEEeccCC
Confidence            99999999864

>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=99.76  E-value=1.8e-18  Score=131.01  Aligned_cols=82  Identities=26%  Similarity=0.417  Sum_probs=74.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||+++++   ++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~v~~~~~------kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l   81 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITE---EEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQL   81 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCH---HHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCC
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHhhcCCeEEEEEecC------CCEEEEEECCHHHHHHHHHHhCCCEeCCceE
Confidence            34566889 9999999999   999999999999999999855      6899999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++++++....
T Consensus        82 ~v~~a~~~~~~~   93 (99)
T 2cpj_A           82 RVRFACHSASLT   93 (99)
T ss_dssp             EEEESSCCSCCC
T ss_pred             EEEEcCCCCCCC
Confidence            999998865543

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=1.8e-18  Score=130.69  Aligned_cols=81  Identities=14%  Similarity=0.195  Sum_probs=72.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +....++| |.|||+++++   ++|+++|++||+|+ ++|+.+    ++++||||+|+++++|++||+.||+++|++++|
T Consensus        15 ~~~~~~~l~V~nL~~~~t~---~~l~~~F~~~G~v~-~~~~~~----~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l   86 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARV---SDLKRALRELGSVP-LRLTWQ----GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTL   86 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCH---HHHHHHHHHTTCCC-SEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCC
T ss_pred             CCCCCCEEEEeCCCCcCcH---HHHHHHHHhcCCEE-EEEEcC----CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEE
Confidence            34557888 9999999999   99999999999997 677754    578999999999999999999999999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|++++++++
T Consensus        87 ~V~~a~~~~~   96 (97)
T 2e5j_A           87 RVALARQQRD   96 (97)
T ss_dssp             EEEECCCCCC
T ss_pred             EEEEcCCCCC
Confidence            9999988654

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.2e-19  Score=141.95  Aligned_cols=83  Identities=16%  Similarity=0.194  Sum_probs=76.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++||   ++|+++|++|+.|+++.++.++.++++++||||+|+++++|++||+ ||+++|++++|+
T Consensus        22 ~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~-~~g~~~~gr~i~   97 (124)
T 1wel_A           22 HEAGFCVYLKGLPFEAEN---KHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   97 (124)
T ss_dssp             CCCCCEEEEECCCTTCCH---HHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHH-hCCCeECCcEEE
Confidence            4456788 9999999999   9999999999999997777777899999999999999999999999 899999999999


Q ss_pred             EeeccCCC
Q 023632           95 VKKAEPKK  102 (279)
Q Consensus        95 V~~a~~~~  102 (279)
                      |.+|.++.
T Consensus        98 V~~a~~~~  105 (124)
T 1wel_A           98 VHPITKKG  105 (124)
T ss_dssp             EEEECHHH
T ss_pred             EEECCHHH
Confidence            99997654

>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=99.76  E-value=1.2e-18  Score=135.82  Aligned_cols=83  Identities=16%  Similarity=0.207  Sum_probs=73.1

Q ss_pred             CCCCCcee-eeCCCCC-CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC--CCccCC
Q 023632           15 RQTTTQKM-TGLSLTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN--KLELAG   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln--g~~l~g   90 (279)
                      +..+.++| |+|||++ ++|   ++|+++|++||+|++|+|+++      |+||||+|+++++|++||+.||  ..+|++
T Consensus        21 ~~~p~~~l~V~NLp~~~~te---~~L~~lF~~fG~V~~v~i~~~------kg~aFVef~~~~~A~~Ai~~l~~~~~~l~G   91 (112)
T 1x4f_A           21 KQELGRVIHLSNLPHSGYSD---SAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQG   91 (112)
T ss_dssp             SSCCCCEEEEESCCCSSCCS---HHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             cCCCCCEEEEeCCCCccCCH---HHHHHHHHhcCCEEEEEEecC------CCEEEEEECCHHHHHHHHHHhccCCceECC
Confidence            45567889 9999998 999   999999999999999999743      7899999999999999999875  567999


Q ss_pred             ceeEEeeccCCCCCCC
Q 023632           91 AQVEVKKAEPKKPNLP  106 (279)
Q Consensus        91 ~~i~V~~a~~~~~~~~  106 (279)
                      ++|+|++|++++....
T Consensus        92 r~l~V~~a~~~~~~~~  107 (112)
T 1x4f_A           92 RCVKVDLSEKYKKLVS  107 (112)
T ss_dssp             SCCEEEEECSCSSSSC
T ss_pred             EEEEEEECcccccccc
Confidence            9999999987765543

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=4.7e-19  Score=137.56  Aligned_cols=78  Identities=24%  Similarity=0.376  Sum_probs=72.3

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++||   ++|+++|++| .|++|+|++|+. ++++|||||+|+++++|++|| .||+++|+++.|+|.
T Consensus        15 ~~~~v~V~nLp~~~te---~dl~~~F~~~-~v~~v~i~~d~~-g~~~G~afV~F~~~~~a~~Al-~~~~~~~~gr~i~V~   88 (109)
T 2dnn_A           15 DDLYVSVHGMPFSAME---NDVRDFFHGL-RVDAVHLLKDHV-GRNNGNGLVKFLSPQDTFEAL-KRNRMLMIQRYVEVS   88 (109)
T ss_dssp             HHHEEEEECCCSSCCH---HHHHHHTTTS-CCCEEEECCCTT-CCCCSEEEEECSSHHHHHHHH-HTTTEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHhccC-CeeEEEEEECCC-CCCCeEEEEEECCHHHHHHHH-hcCCCeECCeEEEEE
Confidence            34688 9999999999   9999999999 999999999975 999999999999999999999 679999999999999


Q ss_pred             eccCC
Q 023632           97 KAEPK  101 (279)
Q Consensus        97 ~a~~~  101 (279)
                      .+.++
T Consensus        89 ~a~~~   93 (109)
T 2dnn_A           89 PATER   93 (109)
T ss_dssp             ECCHH
T ss_pred             ECCcc
Confidence            88754

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.62  E-value=4.2e-20  Score=144.20  Aligned_cols=86  Identities=17%  Similarity=0.263  Sum_probs=80.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEE--------EEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE--------HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~--------v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      ++.+.++| |.|||+++++   ++|+++|++|++|++        |+|++++.++++++||||+|+++++|++||+.||+
T Consensus         3 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g   79 (116)
T 2lcw_A            3 DNSDNNTIFVQGLGENVTI---ESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG   79 (116)
Confidence            34567888 9999999999   999999999999998        99999999999999999999999999999999999


Q ss_pred             CccCCceeEEeeccCCCC
Q 023632           86 LELAGAQVEVKKAEPKKP  103 (279)
Q Consensus        86 ~~l~g~~i~V~~a~~~~~  103 (279)
                      ++|++++|+|++|+++..
T Consensus        80 ~~~~g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           80 KEFSGNPIKVSFATRRAD   97 (116)
Confidence            999999999999987654

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.76  E-value=1.5e-18  Score=133.34  Aligned_cols=83  Identities=10%  Similarity=0.186  Sum_probs=75.0

Q ss_pred             CCCCCcee-eeCCCCCC------CcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc
Q 023632           15 RQTTTQKM-TGLSLTPV------TEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE   87 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~------te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~   87 (279)
                      .+...++| |.|||+++      ++   ++|+++|++||+|++|.|+  +.++++++||||+|+++++|++||+.||+++
T Consensus        11 ~~~~~~~l~V~nLp~~~~~~~~~t~---~~l~~~F~~~G~v~~v~i~--~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~   85 (105)
T 2nlw_A           11 ADGIDSVIVVDNVPQVGPDRLEKLK---NVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYK   85 (105)
T ss_dssp             CCSCCSEEEEESCCCCCTTTTTHHH---HHHHHHHGGGSCEEEEECC--CBTTBSCCEEEEEECSSSHHHHHHHHCSSEE
T ss_pred             CCCCCCEEEEeCCCcchhhhhHHHH---HHHHHHHhcCCCEEEEEee--CCCCCeeeEEEEEECCHHHHHHHHHHhCCcc
Confidence            34446788 99999999      67   8999999999999999988  4688999999999999999999999999999


Q ss_pred             cCCc-eeEEeeccCCC
Q 023632           88 LAGA-QVEVKKAEPKK  102 (279)
Q Consensus        88 l~g~-~i~V~~a~~~~  102 (279)
                      |+++ +|+|++|...+
T Consensus        86 ~~g~~~l~V~~a~~~~  101 (105)
T 2nlw_A           86 LDKQHTFRVNLFTDFD  101 (105)
T ss_dssp             CSTTCEEEEECSCCCC
T ss_pred             cCCCceEEEEEcchHh
Confidence            9998 99999997654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.75  E-value=6.1e-19  Score=134.29  Aligned_cols=85  Identities=24%  Similarity=0.484  Sum_probs=76.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .+...++| |.|||+++++   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+  |+++|++++|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~a~~Ai~--~~~~~~g~~l   78 (102)
T 2xs2_A            5 GKIMPNTVFVGGIDVRMDE---TEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE--SQINFHGKKL   78 (102)
T ss_dssp             CEEEEEEEEEECCCTTCCH---HHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSCCCHHHHTT--CCCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCeEEEEEEECC-CCCccceEEEEECCHHHHHHHHh--CCCeECCEEE
Confidence            34556889 9999999999   9999999999999999999998 99999999999999999999999  8899999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|.++.++....
T Consensus        79 ~v~~a~~~~~~~   90 (102)
T 2xs2_A           79 KLGPAIRKQNLS   90 (102)
T ss_dssp             EEEEEEECC---
T ss_pred             EEEECCcCcchh
Confidence            999998776543

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.75  E-value=4.9e-18  Score=144.80  Aligned_cols=88  Identities=24%  Similarity=0.474  Sum_probs=81.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+|
T Consensus       123 ~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~l~g~~~~g~~i~V  199 (216)
T 2qfj_A          123 RAFNRIYVASVHQDLSD---DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV  199 (216)
T ss_dssp             TTSCEEEEECCCTTCCH---HHHHHHHTTSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCBCSSSBCEE
T ss_pred             CCCcEEEEeCCCCcCCH---HHHHHHHhccCCeeEEEEEecCCCCCcCceEEEEecCHHHHHHHHHHccCCEeCCcEEEE
Confidence            456788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCCCCCC
Q 023632           96 KKAEPKKPNLPQ  107 (279)
Q Consensus        96 ~~a~~~~~~~~~  107 (279)
                      ++++++....+.
T Consensus       200 ~~a~~~~~~~~~  211 (216)
T 2qfj_A          200 GKAVTPPMPLLT  211 (216)
T ss_dssp             EECSSCSSTTSC
T ss_pred             EEecCCCCCCCC
Confidence            999987554443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.75  E-value=3.7e-18  Score=136.06  Aligned_cols=86  Identities=13%  Similarity=0.183  Sum_probs=73.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHH-HHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALD-EFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~-~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +..+.++| |.|||+++++++|. +|.++|++||+|++|.|++   +.++|+||||+|++.++|++||+.||+.+|.+++
T Consensus        25 ~~~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~---~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~  101 (127)
T 2a3j_A           25 HTEPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDL---SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNP  101 (127)
T ss_dssp             CCSCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECC---CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEecc---CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCE
Confidence            34556789 99999999993332 2457999999999998753   6788999999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++|+++..
T Consensus       102 l~V~~a~~~~~  112 (127)
T 2a3j_A          102 LVITFSETPQS  112 (127)
T ss_dssp             CEEEECCCCCH
T ss_pred             EEEEEccCcch
Confidence            99999987654

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.75  E-value=5.6e-19  Score=136.13  Aligned_cols=83  Identities=16%  Similarity=0.199  Sum_probs=76.7

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCC---eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGD---VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~---V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      +....++| |.|||+++|+   ++|+++|++|+.   |++|+|++|+. ++++|||||+|+++++|++||+ +|++.|++
T Consensus         7 ~~~~~~~l~V~nLp~~~te---~~l~~~F~~~g~~~~v~~v~i~~~~~-g~~~G~afV~F~~~~~a~~Al~-~~~~~~~g   81 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTM---EDVLNFFSDCRIRNGENGIHFLLNRD-GKRRGDALIEMESEQDVQKALE-KHRMYMGQ   81 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCS---HHHHHHTTTSCBTTTTTTEECCCCTT-STTCSEEEEEBSSHHHHHHHHT-TTTCCSSS
T ss_pred             CCCCccEEEEeCCCCCCCH---HHHHHHHHhcCCcCCcceEEEEECCC-CCEeeEEEEEECCHHHHHHHHH-hCcceeCC
Confidence            44567888 9999999999   999999999998   89999999987 9999999999999999999999 89999999


Q ss_pred             ceeEEeeccCCC
Q 023632           91 AQVEVKKAEPKK  102 (279)
Q Consensus        91 ~~i~V~~a~~~~  102 (279)
                      +.|+|.++.+++
T Consensus        82 r~i~V~~a~~~~   93 (107)
T 2lmi_A           82 RYVEVYEINNED   93 (107)
T ss_dssp             SCCCCEECCHHH
T ss_pred             eEEEEEECCHHH
Confidence            999999988654

>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=99.75  E-value=2e-18  Score=129.25  Aligned_cols=80  Identities=19%  Similarity=0.290  Sum_probs=70.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCC-eEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC-CccCCce
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGD-VQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-LELAGAQ   92 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~-V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng-~~l~g~~   92 (279)
                      ....++| |.|||+++||   ++|+++|++|++ |+.+.|+       +++||||+|+++++|++||+.||+ ++|++++
T Consensus         5 ~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~vv~~~~~~-------~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~   74 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTA---DDLRQLFGDRKLPLAGQVLL-------KSGYAFVDYPDQNWAIRAIETLSGKVELHGKI   74 (93)
T ss_dssp             CCCCCCEEEECCCTTCCH---HHHHHHHHHTTCCCSSCEEE-------ETTEEEECCSCHHHHHHHHHHHTTTCEETTEE
T ss_pred             CCCCcEEEEeCCCCCCCH---HHHHHHHHHcCCceEEEEEc-------CCCEEEEEECCHHHHHHHHHHccCCeeECCEE
Confidence            4567888 9999999999   999999999999 5655553       478999999999999999999999 9999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|++++++..+.
T Consensus        75 l~v~~a~~~~~~~   87 (93)
T 2cqh_A           75 MEVDYSVSKKLRS   87 (93)
T ss_dssp             CEEEECCCCCCCC
T ss_pred             EEEEEccCccccC
Confidence            9999998876544

>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=99.75  E-value=5e-19  Score=143.22  Aligned_cols=82  Identities=15%  Similarity=0.140  Sum_probs=73.6

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++||   ++|+++|++|+ |++|+|++|++ +++++||||+|+++++|++|| ++|+++|+++.|+
T Consensus        43 ~~~~~~lfV~nLp~~~te---~dL~~~F~~~G-i~~v~i~~d~~-g~srGfaFV~F~~~e~A~~Al-~~~g~~l~gR~i~  116 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATE---NDIYNFFSPLN-PVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM-SKDRANMQHRYIE  116 (139)
T ss_dssp             --CCCCEECCSCCTTCCH---HHHHHHHCSCC-CSEEECCCSSS-SCSSCCCEEECSHHHHHHHHT-TCCSCSSSSCCCC
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcC-CeEEEEEECCC-CCCceEEEEEeCCHHHHHHHH-hhCCCEECCEEEE
Confidence            3456788 9999999999   99999999999 67999999985 999999999999999999999 7799999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |.++.+++.
T Consensus       117 V~~a~~~~~  125 (139)
T 2hgn_A          117 LFLNSTTGA  125 (139)
T ss_dssp             CEECCCSCC
T ss_pred             EEECCCCCC
Confidence            999876543

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.75  E-value=1.9e-18  Score=133.49  Aligned_cols=78  Identities=21%  Similarity=0.451  Sum_probs=70.8

Q ss_pred             CCCCcee-eeCCCCC-CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           16 QTTTQKM-TGLSLTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ....++| |.|||++ +++   ++|+++|++||+|++|+|        +++||||+|+++++|++||+.||+++|++++|
T Consensus        24 ~~~~~~l~V~nl~~~~~t~---~~l~~~F~~~G~v~~v~i--------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l   92 (110)
T 1wf1_A           24 KSINSRVFIGNLNTALVKK---SDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTL   92 (110)
T ss_dssp             TTCSSEEEECSCCCSSCCH---HHHHHHHGGGSCCSEEEE--------ETTEEEEECSSSHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCcEEEEeCCCcccCCH---HHHHHHHHhCCCeEEEEE--------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            3445788 9999999 999   999999999999999998        47899999999999999999999999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|++++++++.
T Consensus        93 ~V~~a~~~~~~  103 (110)
T 1wf1_A           93 DINMAGEPKPD  103 (110)
T ss_dssp             CEEESCCCCSC
T ss_pred             EEEECCCCCCC
Confidence            99999865543

>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=99.75  E-value=5.9e-18  Score=124.32  Aligned_cols=77  Identities=27%  Similarity=0.460  Sum_probs=71.1

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc-CCCccCCc
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGA   91 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l-ng~~l~g~   91 (279)
                      +.+.+.++| |.|||+++++   ++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.| |+++|+++
T Consensus         7 ~~~~~~~~l~V~~l~~~~t~---~~l~~~f~~~G~i~~~~~~~~------kg~afV~f~~~~~A~~a~~~l~~~~~~~g~   77 (85)
T 2ytc_A            7 GEDKTITTLYVGGLGDTITE---TDLRNHFYQFGEIRTITVVQR------QQCAFIQFATRQAAEVAAEKSFNKLIVNGR   77 (85)
T ss_dssp             CSCSSCCCEEEECCTTTSCH---HHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHTTTTTCEETTE
T ss_pred             CCCCCccEEEEcCCCCCCCH---HHHHHHHHhCCCEeEEEEECC------CCEEEEEECCHHHHHHHHHHhcCCeeECCC
Confidence            345677889 9999999999   999999999999999999864      789999999999999999998 99999999


Q ss_pred             eeEEeecc
Q 023632           92 QVEVKKAE   99 (279)
Q Consensus        92 ~i~V~~a~   99 (279)
                      +|+|++|+
T Consensus        78 ~l~v~~ak   85 (85)
T 2ytc_A           78 RLNVKWGR   85 (85)
T ss_dssp             ECCEEECC
T ss_pred             EEEEEecC
Confidence            99999984

>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=99.74  E-value=3.9e-18  Score=143.30  Aligned_cols=88  Identities=30%  Similarity=0.546  Sum_probs=75.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+. ++++|++++|+|
T Consensus       102 ~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~A~~~-~~~~~~G~~i~v  177 (196)
T 1l3k_A          102 LTVKKIFVGGIKEDTEE---HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVNGHNCEV  177 (196)
T ss_dssp             -CCSEEEEECCTTTCCH---HHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHC-SCCEETTEECEE
T ss_pred             CCcceEEEeCCCCCCCH---HHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCHHHHHHHHHh-CCcEECCEEEEE
Confidence            345788 9999999999   99999999999999999999999999999999999999999999998 799999999999


Q ss_pred             eeccCCCCCCCCC
Q 023632           96 KKAEPKKPNLPQP  108 (279)
Q Consensus        96 ~~a~~~~~~~~~~  108 (279)
                      ++|.++.+.....
T Consensus       178 ~~a~~k~~~~~~~  190 (196)
T 1l3k_A          178 RKALSKQEMASAS  190 (196)
T ss_dssp             EECC---------
T ss_pred             EecCChhHhcccc
Confidence            9999987765443

>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=99.74  E-value=7.6e-19  Score=126.11  Aligned_cols=74  Identities=30%  Similarity=0.547  Sum_probs=70.8

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+. ++++|++++|+|++|
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 KIFVGGLSPDTPE---EKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCH---HHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTT-SSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHh-CCCeECCEEEEEEEC
Confidence            47 9999999999   99999999999999999999999999999999999999999999997 889999999999875

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.1e-17  Score=126.74  Aligned_cols=79  Identities=18%  Similarity=0.333  Sum_probs=71.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcC--CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQF--GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~--G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      ...+.++| |.|||+++++   ++|+++|++|  +.|++|+|+        ++||||+|+++++|++||+.||+++|+++
T Consensus        11 ~~~~~~~l~V~nLp~~~t~---~~l~~~F~~~g~g~v~~~~~~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~   79 (99)
T 2cpd_A           11 TMSSVKILYVRNLMLSTSE---EMIEKEFNNIKPGAVERVKKI--------RDYAFVHFSNREDAVEAMKALNGKVLDGS   79 (99)
T ss_dssp             CSSCCCEEEEESCCTTCCH---HHHHHHHHTTSTTCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHSSEEETTE
T ss_pred             ccCCcCEEEEeCCCCCCCH---HHHHHHHHhcCCcceEEEEEe--------CCeEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            34567888 9999999999   9999999999  999999875        56999999999999999999999999999


Q ss_pred             eeEEeeccCCCCC
Q 023632           92 QVEVKKAEPKKPN  104 (279)
Q Consensus        92 ~i~V~~a~~~~~~  104 (279)
                      +|+|++++++...
T Consensus        80 ~l~v~~a~~~~~~   92 (99)
T 2cpd_A           80 PIEVTLAKPVDKD   92 (99)
T ss_dssp             EEEEECCCCCCCC
T ss_pred             EEEEEECCCCCCC
Confidence            9999999876543

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.74  E-value=3.7e-18  Score=143.42  Aligned_cols=84  Identities=15%  Similarity=0.273  Sum_probs=78.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|.|+.++ ++++++||||+|+++++|++||+.||+++|++++|+|
T Consensus        86 ~~~~~l~V~nLp~~~te---~~L~~~F~~~G~I~~v~i~~d~-~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V  161 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSD---ADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI  161 (177)
T ss_dssp             TTCEEEEEECCCSCCCH---HHHHHHHHHTSCCSEEEECCCT-TSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEEECC-CCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEE
Confidence            346788 9999999999   9999999999999999999998 9999999999999999999999999999999999999


Q ss_pred             eeccCCCCC
Q 023632           96 KKAEPKKPN  104 (279)
Q Consensus        96 ~~a~~~~~~  104 (279)
                      ++|.+....
T Consensus       162 ~~a~~~~~~  170 (177)
T 2f3j_A          162 QLVASQIDL  170 (177)
T ss_dssp             EEESSGGGG
T ss_pred             EEecCCCCC
Confidence            999875443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.74  E-value=4.1e-18  Score=128.52  Aligned_cols=80  Identities=19%  Similarity=0.334  Sum_probs=70.4

Q ss_pred             CCCCCcee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +..+.++| |.|||+ ++++   ++|+++|++||+|++|+|.        ++||||+|+++++|++||+.||+++|.+++
T Consensus         6 ~~~~~~~l~V~nlp~~~~t~---~~l~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~   74 (96)
T 2kvi_A            6 NIPPKSRLFIGNLPLKNVSK---EDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIECESQEMNFGKK   74 (96)
T ss_dssp             ---CCEEEEEESSTTSCCCH---HHHHHHHTTTCCCCEEEEE--------TTEEEEEESCHHHHHHHHHHHTCSSCBTTT
T ss_pred             cCCCCCEEEEeCCCcccCCH---HHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCeeCCcE
Confidence            34567889 999998 9999   9999999999999999984        679999999999999999999999999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|++++++....
T Consensus        75 l~V~~a~~~~~~~   87 (96)
T 2kvi_A           75 LILEVSSSNARPQ   87 (96)
T ss_dssp             BCEEEEECCCC--
T ss_pred             EEEEEcCcCCCCC
Confidence            9999998765433

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.74  E-value=5.2e-18  Score=131.16  Aligned_cols=79  Identities=19%  Similarity=0.365  Sum_probs=71.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .+...++| |.|||+++++   ++|+++|++||+|++|+|+        ++||||+|+++++|++||+.||+.+|++++|
T Consensus        27 ~~~~~~~l~V~nLp~~~t~---~~L~~~F~~~G~i~~v~i~--------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l   95 (108)
T 2jvo_A           27 GELSNTRLFVRPFPLDVQE---SELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAKAIEEVHGKSFANQPL   95 (108)
T ss_dssp             -CCSCSEEEECSSCTTCCH---HHHHHHHTTTSCCCEEEEE--------TTEEEEECSSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCEEEEEEE--------CCEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            45677889 9999999999   9999999999999999998        6899999999999999999999999999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|++++++..+
T Consensus        96 ~V~~a~~~~~r  106 (108)
T 2jvo_A           96 EVVYSKLPAKR  106 (108)
T ss_dssp             EEESCSCCC--
T ss_pred             EEEEecCCCCC
Confidence            99999876543

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=5.6e-18  Score=127.37  Aligned_cols=81  Identities=16%  Similarity=0.223  Sum_probs=73.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEH-QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v-~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++| .|++++.+++    |||+|+++++|++||+.||+++|++++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~v~~~~~i~~~~~~~~----afV~f~~~~~a~~Ai~~l~g~~~~g~~   83 (96)
T 2e44_A           11 KRQRIRKLQIRNIPPHLQW---EVLDSLLVQYGVVESCEQVNTDSETAV----VNVTYSSKDQARQALDKLNGFQLENFT   83 (96)
T ss_dssp             CCCSCCCEEEEEECSSSCH---HHHHHHHHHHSCEEEEEEECCSSSSEE----EEEEESSHHHHHHHHHHHTTCBCSSCB
T ss_pred             CCCCCCEEEEEcCCCCCCH---HHHHHHHHhcCCeEEEEEeecCCCCCE----EEEEECCHHHHHHHHHHhCCCEECCcE
Confidence            34456788 9999999999   9999999999999999 5888876543    999999999999999999999999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+|++|++++
T Consensus        84 l~V~~a~~~~   93 (96)
T 2e44_A           84 LKVAYIPDEM   93 (96)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEEcCccc
Confidence            9999998873

>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=99.73  E-value=1.6e-18  Score=137.93  Aligned_cols=81  Identities=17%  Similarity=0.251  Sum_probs=73.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeE--EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQ--EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~--~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+.++| |+|||+++||   ++|+++|++| .|+  +|+|++|+. ++++|||||+|+++++|++||+. ++++|+++.
T Consensus        39 ~~~~~~lfVgnLp~~~te---~dL~~~F~~~-~i~~~~v~i~~d~~-GrsrGfaFV~F~~~e~A~~Al~~-~~~~l~gR~  112 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTK---EEIVQFFSGL-EIVPNGITLPVDPE-GKITGEAFVQFASQELAEKALGK-HKERIGHRY  112 (126)
T ss_dssp             SSSCCEEEEECCCTTCCH---HHHHHHTTTS-CEEEEEEECCCCSS-SSSCSEEEEEESSTTHHHHHHTT-TTCCBTTBC
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHhcC-CceeeEEEEEECCC-CCCceEEEEEECCHHHHHHHHHH-CCCEECCEE
Confidence            3456788 9999999999   9999999999 777  899999986 99999999999999999999997 679999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+|.++.+++
T Consensus       113 I~V~~a~~~e  122 (126)
T 2hgm_A          113 IEVFKSSQEE  122 (126)
T ss_dssp             CCCEEECHHH
T ss_pred             EEEEECCHHH
Confidence            9999987643

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.7e-18  Score=137.33  Aligned_cols=82  Identities=18%  Similarity=0.192  Sum_probs=74.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCe----EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDV----QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V----~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ..+.++| |.|||+++||   ++|+++|++|++|    ++|+|++|+ +++++|||||+|+++++|++||+. |+++|.+
T Consensus        20 ~~~~~~v~V~nLp~~~te---~dl~~~F~~~g~v~g~v~~v~i~~d~-~gr~~G~aFV~F~~~~~A~~Al~~-~~~~l~g   94 (123)
T 2dha_A           20 KENQVIVRMRGLPFTATA---EEVVAFFGQHCPITGGKEGILFVTYP-DGRPTGDAFVLFACEEYAQNALRK-HKDLLGK   94 (123)
T ss_dssp             CCSCCEEEECSCCTTCCH---HHHHHHHHTTSCCTTGGGGEEEEECT-TSCEEEEEEECCSSHHHHHHHHTT-TTEESSS
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhhCCccCCcceEEEEECC-CCCEeeEEEEEECCHHHHHHHHHh-CCCeeCC
Confidence            3456788 9999999999   9999999999976    689999994 899999999999999999999998 9999999


Q ss_pred             ceeEEeeccCCC
Q 023632           91 AQVEVKKAEPKK  102 (279)
Q Consensus        91 ~~i~V~~a~~~~  102 (279)
                      +.|+|..+.+++
T Consensus        95 R~i~V~~a~~~e  106 (123)
T 2dha_A           95 RYIELFRSTAAE  106 (123)
T ss_dssp             CEECCEEECHHH
T ss_pred             eEEEEEECCHHH
Confidence            999999887543

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.73  E-value=3.2e-18  Score=125.02  Aligned_cols=72  Identities=11%  Similarity=0.258  Sum_probs=66.9

Q ss_pred             cee-eeCCCCCC------CcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc-
Q 023632           20 QKM-TGLSLTPV------TEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA-   91 (279)
Q Consensus        20 ~~l-V~nLp~~~------te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~-   91 (279)
                      ++| |.|||+++      ++   ++|+++|++||+|++|+|+  +.++++++||||+|+++++|++||+.||+.+|+++ 
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~---~~l~~~F~~~G~i~~v~i~--~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~   76 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLK---NVIHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH   76 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHH---HHHHHHHHTTCCEEEEECC--CBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSS
T ss_pred             CEEEEeCCCCCcHHHHHHHH---HHHHHHHhhcCCeEEEEec--CCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCce
Confidence            678 99999999      77   9999999999999999988  45889999999999999999999999999999999 


Q ss_pred             eeEEe
Q 023632           92 QVEVK   96 (279)
Q Consensus        92 ~i~V~   96 (279)
                      +|+|.
T Consensus        77 ~l~V~   81 (81)
T 2krb_A           77 TFRVN   81 (81)
T ss_dssp             CCCCC
T ss_pred             eEEeC
Confidence            88873

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.5e-17  Score=124.30  Aligned_cols=81  Identities=16%  Similarity=0.238  Sum_probs=72.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.||  ++++   ++|+++|++||+|++|+|.      ++++||||+|+++++|++||+.||+++|++++|
T Consensus        11 ~~~~~~~l~V~n~--~~t~---~~l~~~F~~~G~i~~v~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l   79 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTP---TLLRGAFSPFGNIIDLSMD------PPRNCAFVTYEKMESADQAVAELNGTQVESVQL   79 (97)
T ss_dssp             CCCCCSEEEEECS--SCCH---HHHHHHHTTTSCEEEEEEE------TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEE
T ss_pred             CCCCCCEEEEcCC--CCCH---HHHHHHHhhCCCEEEEEec------CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEE
Confidence            34566788 9996  8999   9999999999999999985      457899999999999999999999999999999


Q ss_pred             EEeeccCCCCCCC
Q 023632           94 EVKKAEPKKPNLP  106 (279)
Q Consensus        94 ~V~~a~~~~~~~~  106 (279)
                      +|++++++....+
T Consensus        80 ~v~~a~~~~~~~~   92 (97)
T 1x5p_A           80 KVNIARKQPMLDS   92 (97)
T ss_dssp             EEECCSSCCCCCS
T ss_pred             EEEECCCCCCCCC
Confidence            9999988765543

>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=99.73  E-value=3.8e-18  Score=128.44  Aligned_cols=83  Identities=16%  Similarity=0.316  Sum_probs=74.2

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHH----HHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~----~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      +..+.++| |.|||+++++   ++|+    ++|++||+|++|+|++   ++++++||||+|+++++|++||+.||++.|+
T Consensus         4 ~~~~~~~l~V~nLp~~~~~---~~l~~~l~~~f~~~G~i~~v~i~~---~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~   77 (97)
T 1nu4_A            4 ETRPNHTIYINNLNEKIKK---DELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFY   77 (97)
T ss_dssp             --CCCSEEEEESCCTTSCH---HHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEET
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHHHHhCCCEEEEEEEc---CCCcCcEEEEEeCCHHHHHHHHHHhCCCEEC
Confidence            34567888 9999999999   8888    9999999999999873   5678899999999999999999999999999


Q ss_pred             CceeEEeeccCCCC
Q 023632           90 GAQVEVKKAEPKKP  103 (279)
Q Consensus        90 g~~i~V~~a~~~~~  103 (279)
                      +++|+|++++++..
T Consensus        78 g~~l~v~~a~~~~~   91 (97)
T 1nu4_A           78 DKPMRIQYAKTDSD   91 (97)
T ss_dssp             TEECEEEECSSCCT
T ss_pred             CcEEEEEEccCCCc
Confidence            99999999988654

>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=99.73  E-value=1.2e-17  Score=129.84  Aligned_cols=82  Identities=10%  Similarity=0.226  Sum_probs=74.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++||.|++|.|+++.   ++++||||+|.++++|++||+.||+..|+++.|+
T Consensus         5 ~~~~~~l~V~nlp~~~t~---~~l~~~F~~~G~v~~v~i~~~~---~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~   78 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITA---EEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLV   78 (115)
T ss_dssp             TTCCSEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEECST---TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCeEEEEEeeCC---CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEE
Confidence            3456788 9999999999   9999999999999999999764   4589999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |++++++..
T Consensus        79 v~~a~~~~~   87 (115)
T 3lqv_A           79 VLYYNANRA   87 (115)
T ss_dssp             EEECCHHHH
T ss_pred             EEEecCChh
Confidence            999987543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.73  E-value=3.5e-18  Score=128.55  Aligned_cols=82  Identities=20%  Similarity=0.315  Sum_probs=72.8

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ..+.+.++| |.|||+++++   ++|+++|++|++|+.|     +.++++++||||+|+++++|++||+.||+++|++++
T Consensus        11 ~~~~~~~~l~V~nL~~~~t~---~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~   82 (96)
T 1fjc_A           11 KKVRAARTLLAKNLSFNITE---DELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRS   82 (96)
T ss_dssp             STTTGGGEEEEESCCSSCCH---HHHHHHHCSEEEECCE-----EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEE
T ss_pred             ccCCCCCEEEEeCCCCCCCH---HHHHHHHhhCCcEEEe-----CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeE
Confidence            345567889 9999999999   9999999999877655     347889999999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++++++..
T Consensus        83 l~v~~a~~~~~   93 (96)
T 1fjc_A           83 VSLYYTGEKGG   93 (96)
T ss_dssp             EEEEECSSSCC
T ss_pred             EEEEEcCCCCC
Confidence            99999987644

>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=99.73  E-value=1e-17  Score=130.11  Aligned_cols=79  Identities=8%  Similarity=-0.000  Sum_probs=71.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      +...++| |.|||+++++   ++|+++|++||+|++|.|++      +++||||+|+++++|++||+.||+++|++++|+
T Consensus         7 ~~~~~~l~V~nLp~~~te---~~L~~~F~~~G~i~~v~i~~------~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   77 (111)
T 1whx_A            7 GRSKTVILAKNLPAGTLA---AEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLY   77 (111)
T ss_dssp             SEEEEEEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhcCCEEEEEEeC------CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEE
Confidence            3345788 9999999999   99999999999999999874      468999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |++|+....
T Consensus        78 V~~a~~~~~   86 (111)
T 1whx_A           78 LEWAPIGVF   86 (111)
T ss_dssp             EEEEETTTT
T ss_pred             EEECCCCcc
Confidence            999976543

>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=99.73  E-value=1.4e-17  Score=135.55  Aligned_cols=80  Identities=20%  Similarity=0.323  Sum_probs=74.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++++   ++|+++|++||+|++|+|+++     +++||||+|+++++|++||+.||+++|++++|
T Consensus        69 ~~~~~~~l~V~nl~~~~t~---~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l  140 (150)
T 2i2y_A           69 SCPLDCKVYVGNLGNNGNK---TELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRELDGRTLCGCRV  140 (150)
T ss_dssp             SSTTSCEEEEESCCSCCSC---HHHHHHHHHHSCEEEEEECSS-----SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhhCCEEEEEEeeC-----CCcEEEEEECCHHHHHHHHHHcCCCEECCeEE
Confidence            34566889 9999999999   999999999999999999877     58999999999999999999999999999999


Q ss_pred             EEeeccCCC
Q 023632           94 EVKKAEPKK  102 (279)
Q Consensus        94 ~V~~a~~~~  102 (279)
                      +|+++++++
T Consensus       141 ~v~~a~~~~  149 (150)
T 2i2y_A          141 RVELSNGEK  149 (150)
T ss_dssp             EEEECCCCC
T ss_pred             EEEEcCCCC
Confidence            999998764

>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=99.73  E-value=2e-17  Score=125.23  Aligned_cols=77  Identities=19%  Similarity=0.370  Sum_probs=70.5

Q ss_pred             CCCCCcee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ...+.++| |.|||+ ++++   ++|+++|++||+|++|+|.        ++||||+|+++++|++||+.||+..|++++
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~---~~L~~~F~~~G~v~~v~i~--------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~   86 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSK---EDLFRIFSPYGHIMQINIK--------NAFGFIQFDNPQSVRDAIEXESQEMNFGKK   86 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCH---HHHHHHHGGGSCEEEEEEC--------SSEEEEEESSHHHHHHHHHHHTTSEETTEE
T ss_pred             CCCCCCEEEEeCCCcccCCH---HHHHHHHHhcCCEEEEEEe--------CCEEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            45667889 999998 9999   9999999999999999983        689999999999999999999999999999


Q ss_pred             eEEeeccCCC
Q 023632           93 VEVKKAEPKK  102 (279)
Q Consensus        93 i~V~~a~~~~  102 (279)
                      |+|++++++.
T Consensus        87 l~V~~a~~~~   96 (97)
T 2xnq_A           87 LILEVSSSNA   96 (97)
T ss_dssp             CEEEECCCCC
T ss_pred             EEEEecCCCC
Confidence            9999997653

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.72  E-value=1.8e-17  Score=142.44  Aligned_cols=83  Identities=20%  Similarity=0.269  Sum_probs=77.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+.++| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.+|...+.++.|+|
T Consensus        13 ~p~~tlfVgnLp~~~te---~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~   89 (213)
T 4f02_A           13 YPMASLYVGDLHPDVTE---AMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRI   89 (213)
T ss_dssp             --CCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCcEEEEeCCCCCCCH---HHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccc
Confidence            456789 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      .++....
T Consensus        90 ~~~~~~~   96 (213)
T 4f02_A           90 MWSQRDP   96 (213)
T ss_dssp             EECCCCT
T ss_pred             ccccccc
Confidence            9887544

>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=99.72  E-value=1.5e-17  Score=129.97  Aligned_cols=83  Identities=13%  Similarity=0.107  Sum_probs=71.6

Q ss_pred             CCCCCCcee-e--eCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc--
Q 023632           14 NRQTTTQKM-T--GLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL--   88 (279)
Q Consensus        14 ~~~~~~~~l-V--~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l--   88 (279)
                      ....++++| |  .||+++++|   ++|+++|++||+|++|.|+.+      |+||||+|+++++|++||+.||+++|  
T Consensus        20 ~~~~pt~~L~V~Ng~L~~~~te---~~L~~~F~~fG~v~~v~i~~~------rgfaFV~f~~~~~A~~Ai~~lnG~~~~~   90 (114)
T 2cq2_A           20 TVSYATQSLVVANGGLGNGVSR---NQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVVD   90 (114)
T ss_dssp             CCSSCCSEEEEETCTGGGTCCH---HHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEEC
T ss_pred             CCCCCCCEEEEECCCCCCCCCH---HHHHHHHHhcCCeEEEEEeCC------CCEEEEEECCHHHHHHHHHHhCCCEEcc
Confidence            345567888 9  669999999   999999999999999988643      68999999999999999999999988  


Q ss_pred             ---CCceeEEeeccCCCCCC
Q 023632           89 ---AGAQVEVKKAEPKKPNL  105 (279)
Q Consensus        89 ---~g~~i~V~~a~~~~~~~  105 (279)
                         .+++|.|.+++......
T Consensus        91 ~lg~g~~l~v~~a~~~p~~~  110 (114)
T 2cq2_A           91 DLGQKITLYLNFVEKVQWSG  110 (114)
T ss_dssp             TTSCEEECEEEEESCCCCSS
T ss_pred             ccCCCcEEEEEecccCcccC
Confidence               68899999997654433

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=99.72  E-value=2.8e-17  Score=134.01  Aligned_cols=82  Identities=22%  Similarity=0.475  Sum_probs=77.8

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|.++++|++||+.||+..|.+++|+|++
T Consensus         2 ~~~l~v~nlp~~~~~---~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~   78 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQ---EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSY   78 (167)
T ss_dssp             CSEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             cceEEEcCCCCCCCH---HHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEe
Confidence            4788 9999999999   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023632           98 AEPKKP  103 (279)
Q Consensus        98 a~~~~~  103 (279)
                      +.++..
T Consensus        79 ~~~~~~   84 (167)
T 1fxl_A           79 ARPSSA   84 (167)
T ss_dssp             CCCCCG
T ss_pred             cCCCcc
Confidence            987543

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.72  E-value=3e-17  Score=133.72  Aligned_cols=82  Identities=21%  Similarity=0.402  Sum_probs=77.6

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+.+|++++|+
T Consensus        84 ~~~~~~l~v~nl~~~~t~---~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~  160 (166)
T 3md3_A           84 SDDTFNLFVGDLNVNVDD---ETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR  160 (166)
T ss_dssp             CTTCEEEEEESCCTTCCH---HHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCceEEECCCCCCCCH---HHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHhCCCccCCcEEE
Confidence            4456788 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccC
Q 023632           95 VKKAEP  100 (279)
Q Consensus        95 V~~a~~  100 (279)
                      |++|++
T Consensus       161 v~~a~~  166 (166)
T 3md3_A          161 INWAAK  166 (166)
T ss_dssp             EEESCC
T ss_pred             EEecCC
Confidence            999863

>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=99.72  E-value=2.4e-17  Score=134.88  Aligned_cols=83  Identities=22%  Similarity=0.377  Sum_probs=78.5

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||++.|.+++|+|+
T Consensus         2 ~~~~l~v~nlp~~~~~---~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~   78 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTD---RELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVS   78 (168)
T ss_dssp             CCSEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CccEEEEeCCCCCCCH---HHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEE
Confidence            35788 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      ++.++..
T Consensus        79 ~~~~~~~   85 (168)
T 1b7f_A           79 YARPGGE   85 (168)
T ss_dssp             ECCCCSS
T ss_pred             ecCCCcc
Confidence            9987654

>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=99.72  E-value=3.8e-17  Score=135.26  Aligned_cols=79  Identities=10%  Similarity=0.157  Sum_probs=70.8

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC--ceeE
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQVE   94 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g--~~i~   94 (279)
                      +..+| |.||++++||   ++|+++|++||+|++|+|+.++    +++||||+|+++++|++||+.||+.+|.+  ++|+
T Consensus        45 ~vl~l~VgNL~~~vte---d~L~~~Fs~fG~V~~V~i~~k~----~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~  117 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTL---DVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLR  117 (164)
T ss_dssp             CEEEEEECSCCSCCCH---HHHHHHHHHHSCEEEEEEEESS----SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEE
T ss_pred             ceEEEEEeCcCCCCCH---HHHHHHHHhcCCEEEEEEEeCC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEE
Confidence            34567 9999999999   9999999999999999987542    57899999999999999999999999966  9999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |++++++..
T Consensus       118 V~~Ak~~~l  126 (164)
T 1sjr_A          118 IDFSKLTSL  126 (164)
T ss_dssp             EEECSSSSC
T ss_pred             EEEecCCcc
Confidence            999998643

>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=99.71  E-value=2.5e-18  Score=138.89  Aligned_cols=88  Identities=23%  Similarity=0.311  Sum_probs=73.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEE--E---eecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQ--I---MRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~--i---~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      ..++++| |.|||++||+   ++|+++|++||.|+.|.  +   ++.+.++++++||||+|.+.++|++||+.||+++|.
T Consensus        42 ~~~~~~l~V~nLp~~~te---~~L~~~F~~~G~i~~~~~~~~~di~~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~  118 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQE---KDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLF  118 (143)
T ss_dssp             CSCCSEEEEEEECTTCCH---HHHHHHHGGGCCTTCHHHHHHCEEEEEEETTTEEEEEEECSSHHHHHHHHHHHTTBEET
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCcccccccceeeEEeccCCCcccEEEEEeCCHHHHHHHHHHhCCCEeC
Confidence            4567889 9999999999   99999999999987641  1   111247889999999999999999999999999999


Q ss_pred             CceeEEeeccCCCCCCC
Q 023632           90 GAQVEVKKAEPKKPNLP  106 (279)
Q Consensus        90 g~~i~V~~a~~~~~~~~  106 (279)
                      +++|+|++|+++.++..
T Consensus       119 g~~l~V~~a~~~~~~~~  135 (143)
T 3egn_A          119 GKPMVVQFARSARPKQD  135 (143)
T ss_dssp             TEECEEEECCCSCC---
T ss_pred             CcEEEEEECCCCCCccC
Confidence            99999999987655443

>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=99.71  E-value=2.1e-17  Score=122.59  Aligned_cols=76  Identities=11%  Similarity=0.160  Sum_probs=69.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||++++|   ++|+++|++| +|++|+|.      ++++||||+|+++++|++||+.||+++|++++|+|+
T Consensus         4 ~~~~l~V~nLp~~~t~---~~l~~~F~~~-~v~~~~i~------~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~   73 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNC---QEVHDLLKDY-DLKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCH---HHHHHHTCSS-CCCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHhhC-CeEEEEEe------CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEE
Confidence            45788 9999999999   9999999999 99999884      578999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +|..+..
T Consensus        74 ~a~~~~~   80 (88)
T 1wg1_A           74 LQPTDAL   80 (88)
T ss_dssp             ECCCCCC
T ss_pred             EcCCCce
Confidence            9976543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.71  E-value=5.2e-17  Score=128.81  Aligned_cols=75  Identities=19%  Similarity=0.290  Sum_probs=67.3

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHHcCCCccCC--ceeEE
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGF-GFITFDTEQAVDDLLAKGNKLELAG--AQVEV   95 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~-aFV~F~s~e~a~~Ai~~lng~~l~g--~~i~V   95 (279)
                      ..| |.||++.+++   ++|+++|++||+|++|+|+..      ++| |||+|+++++|++||+.||+.+|.+  ++|+|
T Consensus        26 l~l~V~NL~~~vt~---~~L~~~Fs~yG~V~~v~i~~~------~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V   96 (124)
T 2e5i_A           26 LLLSIQNPLYPITV---DVLYTVCNPVGKVQRIVIFKR------NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKI   96 (124)
T ss_dssp             EEEEEESCCSCCCH---HHHHHHHTTTSCEEEEEEEES------SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEE
T ss_pred             EEEEEcCcCCCCCH---HHHHHHHHhcCCEEEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEE
Confidence            345 8999999999   999999999999999999752      276 9999999999999999999999987  69999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ++|+++..
T Consensus        97 ~~Ak~~~l  104 (124)
T 2e5i_A           97 EYARPTRL  104 (124)
T ss_dssp             ECCSCSCC
T ss_pred             EEecCCcc
Confidence            99988753

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.70  E-value=4.1e-17  Score=137.17  Aligned_cols=84  Identities=20%  Similarity=0.400  Sum_probs=79.5

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+.+|++++|+|
T Consensus       112 ~~~~~l~v~nl~~~~~~---~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  188 (198)
T 2yh0_A          112 DSAHKLFIGGLPNYLND---DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV  188 (198)
T ss_dssp             CCCCEEEEECCCTTCCH---HHHHHHHHTBSCEEEEEEEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHHcCCccEEEEeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            456888 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ++|+++..
T Consensus       189 ~~a~~~~~  196 (198)
T 2yh0_A          189 QRASVGAK  196 (198)
T ss_dssp             EESCCCCC
T ss_pred             EECCCCCC
Confidence            99988654

>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=99.70  E-value=4.7e-17  Score=136.60  Aligned_cols=85  Identities=31%  Similarity=0.524  Sum_probs=77.5

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +....++| |.|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|.++++|++||+. ++++|+++.|
T Consensus         9 ~~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~-~~~~~~g~~l   84 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTD---ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVV   84 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhc-CCCEECCEEe
Confidence            45567889 9999999999   99999999999999999999999999999999999999999999988 8899999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|+++.++..
T Consensus        85 ~v~~~~~~~~   94 (196)
T 1l3k_A           85 EPKRAVSRED   94 (196)
T ss_dssp             EEEECCC---
T ss_pred             eeecccCccc
Confidence            9999877644

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.70  E-value=1e-16  Score=127.99  Aligned_cols=80  Identities=13%  Similarity=0.226  Sum_probs=71.2

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccE-EEEEEcCHHHHHHHHHHcCCCccCC--ce
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGF-GFITFDTEQAVDDLLAKGNKLELAG--AQ   92 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~-aFV~F~s~e~a~~Ai~~lng~~l~g--~~   92 (279)
                      .+..+| |.||++++|+   ++|+++|++||+|++|+|+.+.     ++| |||+|++.++|++||+.||+++|.+  ++
T Consensus        26 s~VL~I~V~NL~~~vte---~~L~~lFs~yG~V~~V~i~~~~-----~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~   97 (130)
T 3zzy_A           26 SPVLRIIVENLFYPVTL---DVLHQIFSKFGTVLKIITFTKN-----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCT   97 (130)
T ss_dssp             CSEEEEEEESCCSCCCH---HHHHHHHTTSSCEEEEEEEEET-----TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEE
T ss_pred             CceEEEEECCCCCCCCH---HHHHHHHhCcCCEEEEEEEcCC-----CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcE
Confidence            344566 9999999999   9999999999999999988642     678 9999999999999999999999998  89


Q ss_pred             eEEeeccCCCCC
Q 023632           93 VEVKKAEPKKPN  104 (279)
Q Consensus        93 i~V~~a~~~~~~  104 (279)
                      |+|++++++.-.
T Consensus        98 LrI~~ak~~~l~  109 (130)
T 3zzy_A           98 LRIDFSKLTSLN  109 (130)
T ss_dssp             EEEEECSCSSCC
T ss_pred             EEEEecCCCcee
Confidence            999999886543

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus}

Probab=99.70  E-value=2.4e-17  Score=122.97  Aligned_cols=80  Identities=29%  Similarity=0.546  Sum_probs=62.0

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ......++| |.|||+++||   ++|+++|++||+|++|+|+++     +||||||+|+++++|++++..  .+.+.+++
T Consensus         6 ~~~~~~~~l~V~~Lp~~~te---~~L~~~F~~~G~i~~v~i~~~-----srGfaFV~F~~~~~A~~~~~~--~~~~~g~~   75 (89)
T 3d2w_A            6 HHHHHGSKVFVGRCTEDMTA---EELQQFFCQYGEVVDVFIPKP-----FRAFAFVTFADDKVAQSLCGE--DLIIKGIS   75 (89)
T ss_dssp             -----CCEEEEESCCTTCCH---HHHHHHHTTTSCEEEEECCSS-----CCSEEEEEESCHHHHHHHTTC--EEEETTEE
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHhccCCEEEEEEeeC-----CCCEEEEEECCHHHHHHHcCC--CcccCCEE
Confidence            345677888 9999999999   999999999999999999875     689999999999999843221  34456999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++|+++..
T Consensus        76 v~v~~a~~k~~   86 (89)
T 3d2w_A           76 VHISNAEPKHN   86 (89)
T ss_dssp             EEEEECC----
T ss_pred             EEEEEcCCCCc
Confidence            99999988654

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=99.69  E-value=3.2e-17  Score=134.25  Aligned_cols=80  Identities=38%  Similarity=0.696  Sum_probs=76.1

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++++   ++|+++|++||+|++|+|+.++.++++++||||+|+++++|++||+ +|++.|++++|+|+
T Consensus        86 ~~~~l~V~nlp~~~t~---~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~~g~~i~V~  161 (167)
T 2cjk_A           86 KTGKIFVGGIGPDVRP---KEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ-NKFIDFKDRKIEIK  161 (167)
T ss_dssp             HCEEEEEEEECTTCCH---HHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHHH-CSEECSSSSCEEEE
T ss_pred             CCCeEEECCCCCCCCH---HHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHHh-CCCEEeCCeEEEEe
Confidence            35678 9999999999   9999999999999999999999999999999999999999999998 79999999999999


Q ss_pred             eccCC
Q 023632           97 KAEPK  101 (279)
Q Consensus        97 ~a~~~  101 (279)
                      +|+|+
T Consensus       162 ~a~pk  166 (167)
T 2cjk_A          162 RAEPR  166 (167)
T ss_dssp             ECCCC
T ss_pred             ecCCC
Confidence            99876

>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=99.69  E-value=7.3e-17  Score=132.69  Aligned_cols=80  Identities=21%  Similarity=0.426  Sum_probs=76.0

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+++|++++|+|
T Consensus        92 ~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  168 (172)
T 2g4b_A           92 PGAHKLFIGGLPNYLND---DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV  168 (172)
T ss_dssp             TTTTCEEEECCCTTCCH---HHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEESSTTHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEEcCCCcCCH---HHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEeCCHHHHHHHHHHcCCCEECCeEEEE
Confidence            345788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eecc
Q 023632           96 KKAE   99 (279)
Q Consensus        96 ~~a~   99 (279)
                      ++|.
T Consensus       169 ~~As  172 (172)
T 2g4b_A          169 QRAS  172 (172)
T ss_dssp             EECC
T ss_pred             EeCC
Confidence            9873

>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=99.69  E-value=1.8e-17  Score=122.78  Aligned_cols=79  Identities=33%  Similarity=0.571  Sum_probs=67.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||++++|   ++|+++|++||+|++|+|+++     +++||||+|+++++|++|+..  .+.+++++|+|
T Consensus         3 ~~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~-----~~g~afV~f~~~~~a~~~~~~--~~~~~g~~l~v   72 (88)
T 1wf0_A            3 SGSSGVFVGRCTGDMTE---DELREFFSQYGDVMDVFIPKP-----FRAFAFVTFADDQIAQSLCGE--DLIIKGISVHI   72 (88)
T ss_dssp             SCCCEEEEESCCSSSCH---HHHHHHSTTTSCCCEEECCSS-----CCSCCEEECSCHHHHHHTTTC--EEEETTEEEEE
T ss_pred             CCCcEEEEeCCCCCCCH---HHHHHHHHHcCCeeEEEEecC-----CCCEEEEEECCHHHHHHHhcC--CceeCCEEEEE
Confidence            456889 9999999999   999999999999999999865     689999999999999875443  35668999999


Q ss_pred             eeccCCCCCC
Q 023632           96 KKAEPKKPNL  105 (279)
Q Consensus        96 ~~a~~~~~~~  105 (279)
                      ++++++....
T Consensus        73 ~~a~~~~~~~   82 (88)
T 1wf0_A           73 SNAEPKHNSN   82 (88)
T ss_dssp             ECCCCCCCCC
T ss_pred             EecCCCCCCC
Confidence            9998876544

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.68  E-value=1e-16  Score=124.69  Aligned_cols=78  Identities=21%  Similarity=0.315  Sum_probs=67.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCC---CCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHST---SRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~t---g~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      ....++| |.|||++++|   ++|+++|++||+|+ +.|+.++.+   +++++||||+|+++++|++||+.|+  .|+++
T Consensus         5 ~~~~~~lfVgnLp~~~te---~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~   78 (114)
T 2dnl_A            5 SSGSRKVFVGGLPPDIDE---DEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGK   78 (114)
T ss_dssp             SSCCCCEEEECCCTTCCH---HHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTE
T ss_pred             CCCCCEEEEcCCCCCCCH---HHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCc
Confidence            3456888 9999999999   99999999999999 888888877   6999999999999999999999983  46666


Q ss_pred             eeEEeecc
Q 023632           92 QVEVKKAE   99 (279)
Q Consensus        92 ~i~V~~a~   99 (279)
                      .|.|..+.
T Consensus        79 ~~~~~~~~   86 (114)
T 2dnl_A           79 LYLCVSSP   86 (114)
T ss_dssp             EEEEECCS
T ss_pred             EEEeccCC
Confidence            66665444

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.68  E-value=7e-17  Score=138.74  Aligned_cols=81  Identities=22%  Similarity=0.412  Sum_probs=74.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++||   ++|+++|++||+|++|+|++|+  ..+++||||+|+++++|++||++||+++|++++|+|+
T Consensus       102 ~~~~l~v~nl~~~~t~---~~l~~~F~~~G~i~~~~i~~d~--~~~~g~~fV~f~~~~~a~~Ai~~lng~~~~g~~i~V~  176 (213)
T 4f02_A          102 GVGNIFIKNLDKSIDN---KALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVG  176 (213)
T ss_dssp             CTTEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEEET--TEEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             ccccceECCcccccHH---HHHHHHHhhcCCeEEEEeeccC--CCCceEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            35678 9999999999   9999999999999999999985  4479999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +|+++++
T Consensus       177 ~a~~~~~  183 (213)
T 4f02_A          177 RFKSRKE  183 (213)
T ss_dssp             ECCCHHH
T ss_pred             EcCCCcc
Confidence            9987654

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.67  E-value=5.8e-17  Score=128.34  Aligned_cols=77  Identities=12%  Similarity=0.217  Sum_probs=70.0

Q ss_pred             cee-eeCC----CCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcC----HHH----HHHHHH--HcC
Q 023632           20 QKM-TGLS----LTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT----EQA----VDDLLA--KGN   84 (279)
Q Consensus        20 ~~l-V~nL----p~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s----~e~----a~~Ai~--~ln   84 (279)
                      ++| |.||    |+.|+|   ++|+++|++||+|++|.|+.|+.|++++|||||+|.+    +++    |.+||+  .||
T Consensus         3 ~kI~VgnL~~~~~~~tte---~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~ln   79 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQD---ISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESS   79 (136)
T ss_dssp             CEEEEEESSSSCCCCCCH---HHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTT
T ss_pred             cEEEEeCCCCCCCCCCCH---HHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhc
Confidence            577 9999    999999   9999999999999999999999999999999999996    333    889998  789


Q ss_pred             CCccCCceeEEeecc
Q 023632           85 KLELAGAQVEVKKAE   99 (279)
Q Consensus        85 g~~l~g~~i~V~~a~   99 (279)
                      +..|++++|+|++.+
T Consensus        80 g~~I~Gr~irV~ln~   94 (136)
T 2j8a_A           80 GCFIMGFKFEVILNK   94 (136)
T ss_dssp             CEEETTEEEEEEECC
T ss_pred             CCeecCcEEEEEECc
Confidence            999999999999764

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3e-16  Score=117.67  Aligned_cols=81  Identities=7%  Similarity=0.073  Sum_probs=68.1

Q ss_pred             CCCce-e-eeCCCCCCCcccH-HHHHHHHhcC-CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           17 TTTQK-M-TGLSLTPVTEPAL-DEFKDFFMQF-GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        17 ~~~~~-l-V~nLp~~~te~~~-~~L~~~F~~~-G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      ++..+ | |.|||+++++++| ++|+++|++| |+|++|       |+   |||||+|++.++|++||+.||+.+|.+++
T Consensus         6 ~p~~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~V-------tg---G~AfV~F~~~esA~~A~~~l~G~~l~gr~   75 (96)
T 2diu_A            6 SGCHTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSI-------TG---CSAILRFINQDSAERAQKRMENEDVFGNR   75 (96)
T ss_dssp             CCSSEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEEC-------CT---TCEEEEESSHHHHHHHHHHHTTCCSSSSC
T ss_pred             CCcceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEE-------ec---CEEEEEECCHHHHHHHHHHhcCCccCCce
Confidence            34455 8 9999999999332 2377999999 599998       33   99999999999999999999999999999


Q ss_pred             eEEeeccCCCCCCCC
Q 023632           93 VEVKKAEPKKPNLPQ  107 (279)
Q Consensus        93 i~V~~a~~~~~~~~~  107 (279)
                      |+|++|+.+.+.-..
T Consensus        76 i~v~~A~~~sd~~~~   90 (96)
T 2diu_A           76 IIVSFTPKNRELCET   90 (96)
T ss_dssp             CEEESSCCSCCCCCC
T ss_pred             EEEEecCCCcceeEe
Confidence            999999987665543

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.67  E-value=2.2e-16  Score=121.58  Aligned_cols=85  Identities=15%  Similarity=0.067  Sum_probs=72.0

Q ss_pred             CCCcee-eeCCCC--CCCcccHHHHHHHHhcCCCeEEEEEeecCCC-CCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           17 TTTQKM-TGLSLT--PVTEPALDEFKDFFMQFGDVQEHQIMRDHST-SRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        17 ~~~~~l-V~nLp~--~~te~~~~~L~~~F~~~G~V~~v~i~~d~~t-g~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .++++| |.||..  ++.++..++|+++|++||+|++|.|++++.+ .+++||+||+|+++++|++||+.||+.+|++++
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~Gr~   85 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRV   85 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGGSCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhcCCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECCcE
Confidence            456778 999963  3322222899999999999999999998764 689999999999999999999999999999999


Q ss_pred             eEEeeccCC
Q 023632           93 VEVKKAEPK  101 (279)
Q Consensus        93 i~V~~a~~~  101 (279)
                      |+|+++.+.
T Consensus        86 i~v~~a~~~   94 (105)
T 2pe8_A           86 VKACFYNLD   94 (105)
T ss_dssp             CEEEECCHH
T ss_pred             EEEEEcCHH
Confidence            999999753

>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=99.67  E-value=3e-16  Score=128.32  Aligned_cols=80  Identities=20%  Similarity=0.444  Sum_probs=75.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC--ce
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQ   92 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g--~~   92 (279)
                      ....++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+..|++  ++
T Consensus        86 ~~~~~~l~v~nl~~~~t~---~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~  162 (168)
T 1b7f_A           86 SIKDTNLYVTNLPRTITD---DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQP  162 (168)
T ss_dssp             TTTTCEEEEESCCTTCCH---HHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             cCCCCCEEEeCCCCCCCH---HHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhcCCEecCCCeE
Confidence            3456788 9999999999   9999999999999999999999899999999999999999999999999999987  99


Q ss_pred             eEEeec
Q 023632           93 VEVKKA   98 (279)
Q Consensus        93 i~V~~a   98 (279)
                      |+|++|
T Consensus       163 l~V~~A  168 (168)
T 1b7f_A          163 LSVRLA  168 (168)
T ss_dssp             CEEEEC
T ss_pred             EEEEeC
Confidence            999886

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.67  E-value=2e-16  Score=128.80  Aligned_cols=80  Identities=19%  Similarity=0.305  Sum_probs=74.2

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||+++|+   ++|+++|++||+|++|+|++++ ++++++||||+|.++++|++||+.||+..|.+++|+|+++
T Consensus         1 R~l~V~nlp~~~t~---~~l~~~f~~~G~i~~v~i~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~   76 (166)
T 3md3_A            1 RVLYVGNLDKAITE---DILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWA   76 (166)
T ss_dssp             CEEEEEEEETTCCH---HHHHHHHGGGSCEEEEEEECCC-C-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCH---HHHHHHHHhcCCeEEEEEEECC-CCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEc
Confidence            578 9999999999   9999999999999999999997 4679999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023632           99 EPKKP  103 (279)
Q Consensus        99 ~~~~~  103 (279)
                      .++..
T Consensus        77 ~~~~~   81 (166)
T 3md3_A           77 FQSQQ   81 (166)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            77654

>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=99.67  E-value=1.9e-16  Score=130.22  Aligned_cols=79  Identities=25%  Similarity=0.450  Sum_probs=72.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC---Cce
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA---GAQ   92 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~---g~~   92 (279)
                      ...++| |.|||+++|+   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+..|.   +++
T Consensus        93 ~~~~~l~v~nl~~~~t~---~~l~~~F~~~G~i~~v~~~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~~~  168 (175)
T 3nmr_A           93 VEDRKLFIGMISKKCTE---NDIRVMFSSFGQIEECRILRGP-DGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGCSSP  168 (175)
T ss_dssp             GGGSEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECT-TSCEEEEEEEEESSHHHHHHHHHHHTTSCCCTTCSSC
T ss_pred             CCCCeEEEcCCCCcCCH---HHHHHHHHhCCCEEEEEEEECC-CCCEEEEEEEEECCHHHHHHHHHHhcCCcccCCCCCC
Confidence            356788 9999999999   9999999999999999999996 6899999999999999999999999998777   499


Q ss_pred             eEEeecc
Q 023632           93 VEVKKAE   99 (279)
Q Consensus        93 i~V~~a~   99 (279)
                      |+|++|.
T Consensus       169 l~V~~ad  175 (175)
T 3nmr_A          169 MVVKFAD  175 (175)
T ss_dssp             CEEEECC
T ss_pred             eEEEecC
Confidence            9999984

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.67  E-value=1.8e-16  Score=135.09  Aligned_cols=83  Identities=20%  Similarity=0.407  Sum_probs=74.7

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||++.|.+++|+|
T Consensus        26 ~~~~~l~V~nLp~~~t~---~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v  102 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGE---DTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV  102 (216)
T ss_dssp             HHHTEEEEECCCTTCCH---HHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEE
T ss_pred             CcCCEEEEECCCCCCCH---HHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEE
Confidence            345788 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      .++..+.
T Consensus       103 ~~~~~~~  109 (216)
T 2qfj_A          103 GRPSNIG  109 (216)
T ss_dssp             ECCSCCG
T ss_pred             ecCCCcc
Confidence            8876553

>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=99.66  E-value=2.3e-16  Score=124.01  Aligned_cols=83  Identities=14%  Similarity=0.116  Sum_probs=71.7

Q ss_pred             CCcee-eeCC--CCCCCcccHHHHHHHHhcCCCeEEEEEeecCC----CCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           18 TTQKM-TGLS--LTPVTEPALDEFKDFFMQFGDVQEHQIMRDHS----TSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        18 ~~~~l-V~nL--p~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~----tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ++++| |.||  |.++.++..++|+++|++||+|++|+|++++.    +.+++||+||+|+++++|++||+.||+..|++
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            57788 9998  34444433489999999999999999999865    45788999999999999999999999999999


Q ss_pred             ceeEEeeccC
Q 023632           91 AQVEVKKAEP  100 (279)
Q Consensus        91 ~~i~V~~a~~  100 (279)
                      ++|+|+++..
T Consensus        99 R~i~v~~~~~  108 (118)
T 3ue2_A           99 RKVVAEVYDQ  108 (118)
T ss_dssp             EECEEEEECH
T ss_pred             cEEEEEEcCh
Confidence            9999998864

>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=99.65  E-value=2.4e-16  Score=116.03  Aligned_cols=71  Identities=21%  Similarity=0.430  Sum_probs=65.7

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcC----C-------CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQF----G-------DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~----G-------~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      .+.++| |.|||+++++   ++|+++|++|    +       +|++|+|+++      ++||||+|+++++|++|| .||
T Consensus         4 ~~~~~l~V~nLp~~~t~---~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~------kg~afV~f~~~~~a~~A~-~l~   73 (87)
T 2hzc_A            4 GSARRLYVGNIPFGITE---EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFD   73 (87)
T ss_dssp             GGGGEEEEESCCTTCCH---HHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS------SSEEEEEESSHHHHHHHG-GGT
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHHHhhhcccccCCCCcceEEEecCC------CcEEEEEcCCHHHHHHHH-hcC
Confidence            456889 9999999999   9999999999    8       9999998865      789999999999999999 999


Q ss_pred             CCccCCceeEEee
Q 023632           85 KLELAGAQVEVKK   97 (279)
Q Consensus        85 g~~l~g~~i~V~~   97 (279)
                      +++|++++|+|+.
T Consensus        74 g~~~~g~~l~V~r   86 (87)
T 2hzc_A           74 GIIFQGQSLKIRR   86 (87)
T ss_dssp             TCEETTEECEEEC
T ss_pred             CCEECCeEEEEeC
Confidence            9999999999974

>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=99.65  E-value=5.1e-16  Score=126.52  Aligned_cols=79  Identities=28%  Similarity=0.442  Sum_probs=73.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce--e
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ--V   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~--i   93 (279)
                      ...++| |.|||+++++   ++|+++|++||+|++|+|+.++.++++++||||+|+++++|++||+.||+.+|.++.  |
T Consensus        86 ~~~~~l~v~nl~~~~t~---~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~~~i  162 (167)
T 1fxl_A           86 IRDANLYVSGLPKTMTQ---KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI  162 (167)
T ss_dssp             GTTCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             CCCCcEEECCCCCcCCH---HHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHHHHHhcCCccCCCccce
Confidence            456788 9999999999   999999999999999999999989999999999999999999999999999999965  7


Q ss_pred             EEeec
Q 023632           94 EVKKA   98 (279)
Q Consensus        94 ~V~~a   98 (279)
                      +|++|
T Consensus       163 ~v~~A  167 (167)
T 1fxl_A          163 TVKFA  167 (167)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            88775

>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=99.65  E-value=5.1e-16  Score=127.64  Aligned_cols=83  Identities=27%  Similarity=0.450  Sum_probs=75.0

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCC--CcccEEEEEEcCHHHHHHHHHHcCCCccC---Cc
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTS--RSRGFGFITFDTEQAVDDLLAKGNKLELA---GA   91 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg--~~rG~aFV~F~s~e~a~~Ai~~lng~~l~---g~   91 (279)
                      +.++| |.|||+++|+   ++|+++|++||+|++|+|++++.++  ++++||||+|.++++|++||+.||+..+.   .+
T Consensus         2 ~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~   78 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSE---KDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHH   78 (175)
T ss_dssp             CCEEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSS
T ss_pred             CceEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCcc
Confidence            46788 9999999999   9999999999999999999999887  89999999999999999999999998776   67


Q ss_pred             eeEEeeccCCCC
Q 023632           92 QVEVKKAEPKKP  103 (279)
Q Consensus        92 ~i~V~~a~~~~~  103 (279)
                      .|.|.++.++..
T Consensus        79 ~~~~~~~~~~~~   90 (175)
T 3nmr_A           79 PIQMKPADSEKN   90 (175)
T ss_dssp             CCEEEECGGGCC
T ss_pred             ceEEcccccccc
Confidence            888888776544

>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=99.64  E-value=5.5e-16  Score=132.96  Aligned_cols=77  Identities=16%  Similarity=0.218  Sum_probs=71.3

Q ss_pred             CCcee-eeCCC-CCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           18 TTQKM-TGLSL-TPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp-~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..++| |.||| +++++   ++|+++|++||+|++|+|++++     ++||||+|+++++|++||+.||+++|.+++|+|
T Consensus         3 ~~~~l~V~nL~~~~~~~---~~L~~~F~~~G~v~~v~i~~~~-----~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v   74 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNC---DRVFNVFCLYGNVEKVKFMKSK-----PGAAMVEMADGYAVDRAITHLNNNFMFGQKMNV   74 (205)
T ss_dssp             CCSEEEEECCCTTTCCH---HHHHHHHTTTSCEEEEEECTTS-----TTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCcccCCH---HHHHHHHHhcCCeEEEEEecCC-----CCEEEEEECCHHHHHHHHHHhCCCEECCceEEE
Confidence            46788 99999 89999   9999999999999999998763     799999999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      ++++.+.
T Consensus        75 ~~s~~~~   81 (205)
T 3tyt_A           75 CVSKQPA   81 (205)
T ss_dssp             EECSCSC
T ss_pred             EEccCCc
Confidence            9987544

>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=99.64  E-value=9.1e-16  Score=119.02  Aligned_cols=87  Identities=11%  Similarity=0.205  Sum_probs=70.8

Q ss_pred             CCCCCcee-eeCCCCCCC--cc------cHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           15 RQTTTQKM-TGLSLTPVT--EP------ALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~t--e~------~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      ....+++| |.||....+  ++      ..++|+++|++||+|++|.| .++   .+++||||+|+++++|++||+.||+
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~---~~~G~afV~f~~~~~A~~Ai~~lng   86 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQTLDG   86 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETT---CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecC---CCCEEEEEEECCHHHHHHHHHHcCC
Confidence            44567888 999954432  10      01799999999999999966 554   3799999999999999999999999


Q ss_pred             CccCCceeEEeeccCCCCCC
Q 023632           86 LELAGAQVEVKKAEPKKPNL  105 (279)
Q Consensus        86 ~~l~g~~i~V~~a~~~~~~~  105 (279)
                      +.|++++|+|+++.++....
T Consensus        87 ~~~~gr~l~v~~a~~~~~~~  106 (112)
T 2dit_A           87 RWFGGRQITAQAWDGTTDYQ  106 (112)
T ss_dssp             CEETTEECEEEECCSCCCSS
T ss_pred             CEECCcEEEEEEeCCCCCcc
Confidence            99999999999998865543

>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=99.62  E-value=1.3e-15  Score=135.62  Aligned_cols=84  Identities=17%  Similarity=0.314  Sum_probs=75.3

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHH----HHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFK----DFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL   88 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~----~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l   88 (279)
                      .+...+++| |.|||+++++   ++|+    ++|++||+|++|+|++   ++++++||||+|+++++|++||+.||+++|
T Consensus         4 ~~~~~~~~l~V~nlp~~~~~---~~l~~~L~~~F~~~G~i~~v~~~~---~~~~~g~afV~f~~~~~a~~A~~~l~g~~~   77 (282)
T 3pgw_A            4 PETRPNHTIYINNLNEKIKK---DELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPF   77 (282)
T ss_pred             CCCCCCCEEEEeCCCCCCCH---HHHHHHHHHHHhccCCeEEEEEcC---CCCcceEEEEEECCHHHHHHHHHHhcCCee
Confidence            345667889 9999999999   7755    8999999999999885   678899999999999999999999999999


Q ss_pred             CCceeEEeeccCCCC
Q 023632           89 AGAQVEVKKAEPKKP  103 (279)
Q Consensus        89 ~g~~i~V~~a~~~~~  103 (279)
                      .+++|+|++++.+..
T Consensus        78 ~g~~l~v~~a~~~~~   92 (282)
T 3pgw_A           78 YDKPMRIQYAKTDSD   92 (282)
T ss_pred             CCcEEEEEEeccCcc
Confidence            999999999976543

>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=99.62  E-value=1.1e-15  Score=117.65  Aligned_cols=85  Identities=15%  Similarity=0.164  Sum_probs=71.7

Q ss_pred             CCCcee-eeCC--CCCCCcc-----cHHHHHHHHhcCCCeEEEEEeecCCC--CCcccEEEEEEcCHHHHHHHHHHcCCC
Q 023632           17 TTTQKM-TGLS--LTPVTEP-----ALDEFKDFFMQFGDVQEHQIMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKL   86 (279)
Q Consensus        17 ~~~~~l-V~nL--p~~~te~-----~~~~L~~~F~~~G~V~~v~i~~d~~t--g~~rG~aFV~F~s~e~a~~Ai~~lng~   86 (279)
                      .+++.| |.|+  |.++.++     ..++|+++|++||+|++|+|++++.+  .+++||+||+|+++++|++||+.||+.
T Consensus         3 ~ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~   82 (105)
T 3v4m_A            3 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   82 (105)
T ss_dssp             SCCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCC
Confidence            356777 9988  4444431     12689999999999999999998765  468999999999999999999999999


Q ss_pred             ccCCceeEEeeccCC
Q 023632           87 ELAGAQVEVKKAEPK  101 (279)
Q Consensus        87 ~l~g~~i~V~~a~~~  101 (279)
                      .|++++|+|+++.+.
T Consensus        83 ~f~GR~i~v~~~~~~   97 (105)
T 3v4m_A           83 KFANRVVVTKYCDPD   97 (105)
T ss_dssp             EETTEECEEEEECHH
T ss_pred             EeCCCEEEEEEeCHH
Confidence            999999999988653

>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=99.62  E-value=6.2e-16  Score=126.50  Aligned_cols=79  Identities=35%  Similarity=0.663  Sum_probs=73.3

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ++++| |.|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|.++++|++||+.  .+.|+++.|.|.
T Consensus         2 ~~~~l~v~nLp~~~t~---~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~--~~~~~g~~i~v~   76 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTE---DNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKT--QHILDGKVIDPK   76 (167)
T ss_dssp             GGGEEEECSCCTTCCH---HHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHHS--CCEETTEECCCE
T ss_pred             CCcEEEEeCCCCCCCH---HHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHhc--ccccCCeEcccc
Confidence            45788 9999999999   99999999999999999999999999999999999999999999996  468999999999


Q ss_pred             eccCC
Q 023632           97 KAEPK  101 (279)
Q Consensus        97 ~a~~~  101 (279)
                      ++.++
T Consensus        77 ~~~~~   81 (167)
T 2cjk_A           77 RAIPR   81 (167)
T ss_dssp             ECCCH
T ss_pred             cccch
Confidence            88654

>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=99.60  E-value=2.4e-15  Score=130.48  Aligned_cols=81  Identities=14%  Similarity=0.184  Sum_probs=74.2

Q ss_pred             CCCCCcee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....++| |.|||+ ++++   ++|+++|++||+|++|+|++++     ++||||+|.++++|++||+.||+..|.+++
T Consensus        30 ~~~~~~~l~V~nLp~~~~te---~~L~~~F~~~G~i~~v~i~~~~-----~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~  101 (229)
T 2adc_A           30 AGAGNSVLLVSNLNPERVTP---QSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKP  101 (229)
T ss_dssp             GCCCCSEEEEESCCTTTCCH---HHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSB
T ss_pred             CCCCCCEEEEeCCCcccCCH---HHHHHHHHhCCCeEEEEEEECC-----CCEEEEEECCHHHHHHHHHHhCCCeECCeE
Confidence            34567889 999999 9999   9999999999999999999885     789999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++++++..
T Consensus       102 l~v~~a~~~~~  112 (229)
T 2adc_A          102 IRITLSKHQNV  112 (229)
T ss_dssp             CEEECCSCCCC
T ss_pred             EEEEEecCccc
Confidence            99999986643

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.60  E-value=1.5e-15  Score=133.29  Aligned_cols=81  Identities=16%  Similarity=0.250  Sum_probs=69.9

Q ss_pred             CCCCCcee-eeCCCCCC---------CcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           15 RQTTTQKM-TGLSLTPV---------TEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~---------te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      .+...++| |+|||+++         +|   ++|+++|++||+|++|+|+.+      |+||||+|+++++|++||++||
T Consensus       130 ~~~~~rtLfVgnL~~~~~~~~~~~~~tE---e~L~~~F~~fG~I~~v~v~~~------kG~AFV~F~~~~~Ae~A~~am~  200 (240)
T 3u1l_A          130 FRKKNKTLYVGGIDGALNSKHLKPAQIE---SRIRFVFSRLGDIDRIRYVES------KNCGFVKFKYQANAEFAKEAMS  200 (240)
T ss_dssp             -CCCCCEEEEECTTGGGTTCCCCHHHHH---HHHHHHHHTTSCEEEEEEEGG------GTEEEEEESSHHHHHHHHHHHT
T ss_pred             cccCCceeecCCCChhhhcccccccCcH---HHHHHHHHccCCEEEEEEECC------CCEEEEEeCCHHHHHHHHHHhC
Confidence            34567899 99999998         68   999999999999999999854      7899999999999999999999


Q ss_pred             CCcc------------CCceeEEeeccCCCCC
Q 023632           85 KLEL------------AGAQVEVKKAEPKKPN  104 (279)
Q Consensus        85 g~~l------------~g~~i~V~~a~~~~~~  104 (279)
                      ++.|            .++.|.|++|+++..+
T Consensus       201 g~~l~~~~~~e~~~~~~gr~L~V~wA~~~pnp  232 (240)
T 3u1l_A          201 NQTLLLPSDKEWDDRREGTGLLVKWANEDPDP  232 (240)
T ss_dssp             TCCCCCTTSTTGGGGGGSCCCEEEECC-----
T ss_pred             CCEEeccccccccccCCCCEEEEEEccCCCCH
Confidence            9999            8999999999875443

>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=99.60  E-value=1.5e-15  Score=125.37  Aligned_cols=77  Identities=21%  Similarity=0.338  Sum_probs=70.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++++   ++|+++|++|++|..+     ..++++++||||+|+++++|++||+.||+.+|++++|+|
T Consensus        97 ~~~~~l~v~nlp~~~t~---~~l~~~F~~~g~v~~~-----~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~i~v  168 (175)
T 1fje_B           97 RAARTLLAKNLSFNITE---DELKEVFEDALEIRLV-----SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSL  168 (175)
T ss_dssp             GGGGEEEEESCCSSCCH---HHHHHHCTTCSEEEEE-----CSSSSCCSEEEEECSSHHHHHHHHHHHTEEEETTEEEEE
T ss_pred             ccCCEEEEeCCCCCCCH---HHHHHHHHhcCeEEEe-----cCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            355788 9999999999   9999999999987665     458899999999999999999999999999999999999


Q ss_pred             eeccCC
Q 023632           96 KKAEPK  101 (279)
Q Consensus        96 ~~a~~~  101 (279)
                      ++|+++
T Consensus       169 ~~a~~k  174 (175)
T 1fje_B          169 YYTGEK  174 (175)
T ss_dssp             EECSSC
T ss_pred             EecCCC
Confidence            999875

>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=99.60  E-value=3.1e-15  Score=127.18  Aligned_cols=77  Identities=16%  Similarity=0.208  Sum_probs=71.2

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |.|||+++|+   ++|+++|++||+|++|+|++++ +++++|||||+|+++++|++||+.++ .+|++++|+|++
T Consensus       109 ~~~l~V~nLp~~~t~---~~L~~~F~~~G~v~~v~i~~~~-~~~~kG~aFVeF~~~e~A~~A~~~~~-~~~~Gr~l~V~~  183 (193)
T 2voo_A          109 NRSVYIKGFPTDATL---DDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVETPG-QKYKETDLLILF  183 (193)
T ss_dssp             HTEEEEECCCTTCCH---HHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESSHHHHHHHHHCTT-CEETTEECEEEE
T ss_pred             cCEEEecCCCCcCCH---HHHHHHHhcCCCEEEEEEEECC-CCCcccEEEEEECCHHHHHHHHHhCC-CeECCEEEEEEE
Confidence            4678 9999999999   9999999999999999999986 58999999999999999999998864 699999999998


Q ss_pred             ccC
Q 023632           98 AEP  100 (279)
Q Consensus        98 a~~  100 (279)
                      ++.
T Consensus       184 ~~~  186 (193)
T 2voo_A          184 KDD  186 (193)
T ss_dssp             TTT
T ss_pred             hHH
Confidence            765

>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=99.59  E-value=1.8e-15  Score=135.22  Aligned_cols=81  Identities=19%  Similarity=0.306  Sum_probs=74.9

Q ss_pred             CCCcee-eeCCCCC-CCcccHHHHHHHHhcCCCeEEEEEeecCC-CCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           17 TTTQKM-TGLSLTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~-tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...++| |.|||++ +++   ++|+++|++||+|++|+|++++. |+++++||||+|.++++|++|| .||+++|.+++|
T Consensus       208 ~~~~~l~v~nlp~~~~t~---~~l~~~F~~~G~v~~v~i~~~~~~tg~~~g~afV~F~~~~~A~~A~-~l~g~~~~g~~i  283 (292)
T 2ghp_A          208 LEGREIMIRNLSTELLDE---NLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL-QMNRSLLGNREI  283 (292)
T ss_dssp             CTTTEEEEEEECTTTCCH---HHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHG-GGTTEEETTEEE
T ss_pred             CCCceEEEECCCcccCCH---HHHHHHHhccCCeeEEEEEecCCcCCCCceEEEEEeCCHHHHHHHH-HhcCCEECCcEE
Confidence            456788 9999999 999   99999999999999999999876 6999999999999999999999 999999999999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|++|+++
T Consensus       284 ~V~~a~~k  291 (292)
T 2ghp_A          284 SVSLADKK  291 (292)
T ss_dssp             EEEECCCC
T ss_pred             EEEEecCC
Confidence            99999876

>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=99.59  E-value=6.5e-15  Score=131.10  Aligned_cols=86  Identities=15%  Similarity=0.259  Sum_probs=80.1

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++++   ++|+++|++||+|++|+|++++.++++++||||+|.++++|++||+.||+..|++++|+
T Consensus        92 ~~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~  168 (284)
T 3smz_A           92 QPTDALLCVANLPPSLTQ---QQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLY  168 (284)
T ss_dssp             CCCSCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECE
T ss_pred             cCCCCEEEEcCCCCcCCH---HHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            3456788 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |+++.++...
T Consensus       169 v~~a~~~~~~  178 (284)
T 3smz_A          169 VHWTDAGQLT  178 (284)
T ss_dssp             EEECCGGGCC
T ss_pred             EEECCCCCCC
Confidence            9999876543

>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=99.59  E-value=4.1e-15  Score=132.41  Aligned_cols=86  Identities=13%  Similarity=0.226  Sum_probs=79.0

Q ss_pred             CCCCCcee-eeCCCCCC-CcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSLTPV-TEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~-te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....++| |.|||+++ ++   ++|+++|++||.|++|+|++++ ++++++||||+|+++++|++||+.||+.+|++++
T Consensus       180 ~~~~~~~l~v~nlp~~~~~~---~~l~~~f~~~G~i~~v~i~~~~-~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~  255 (284)
T 3smz_A          180 ALLHSRCLCVDRLPPGFNDV---DALCRALSAVHSPTFCQLACGQ-DGQLKGFAVLEYETAEMAEEAQQQADGLSLGGSH  255 (284)
T ss_dssp             TTTSCSEEEEECCCTTCCCH---HHHHHHTCSSSCCSEEEEEECS-SCCEEEEEEEECSSHHHHHHHHHHHTTCEETTEE
T ss_pred             ccCCccEEEEecCCcccCCH---HHHHHHhhCCCCeEEEEEEECC-CCCcccEEEEEeCCHHHHHHHHHHhCCCccCCeE
Confidence            34566788 99999995 99   9999999999999999999986 7899999999999999999999999999999999


Q ss_pred             eEEeeccCCCCC
Q 023632           93 VEVKKAEPKKPN  104 (279)
Q Consensus        93 i~V~~a~~~~~~  104 (279)
                      |+|++++++..+
T Consensus       256 l~v~~a~~~~~~  267 (284)
T 3smz_A          256 LRVSFCAPGPPG  267 (284)
T ss_dssp             CEEEECCSSSCH
T ss_pred             EEEEEecCCCcc
Confidence            999999887653

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.57  E-value=3.7e-15  Score=125.70  Aligned_cols=78  Identities=14%  Similarity=0.195  Sum_probs=72.3

Q ss_pred             CCcee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           18 TTQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..++| |.|||+ ++++   ++|+++|++||+|++|+|++++     ++||||+|+++++|++||+.||+..|.+++|+|
T Consensus         2 ~~~~l~v~nlp~~~~~~---~~l~~~F~~~G~i~~v~i~~~~-----~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v   73 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTP---QSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRI   73 (198)
T ss_dssp             CCCEEEEECCCSSSCCH---HHHHHHHHTTCCCSEEECSTTC-----SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEE
T ss_pred             CCcEEEEeCCCcccCCH---HHHHHHHHhcCCEEEEEEEeCC-----CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEE
Confidence            45788 999999 9999   9999999999999999999875     789999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ++++++..
T Consensus        74 ~~a~~~~~   81 (198)
T 1qm9_A           74 TLSKHQNV   81 (198)
T ss_dssp             EECCCCSC
T ss_pred             EEecCCCc
Confidence            99987643

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=2.8e-14  Score=108.81  Aligned_cols=77  Identities=16%  Similarity=0.232  Sum_probs=63.9

Q ss_pred             Ccee-eeCCC-------CCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           19 TQKM-TGLSL-------TPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        19 ~~~l-V~nLp-------~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      .++| |.-..       .+++|   ++|+++|++||+|++|.|+     .++++||||+|+++++|++||+.++  .+.+
T Consensus        10 ~~~~~v~w~~~~~~~~~~~~te---~~L~~~F~~~G~V~~v~i~-----~~~rGfaFVeF~~~~~A~~Ai~~~~--~~~g   79 (100)
T 2d9o_A           10 TPKLKLKWKCKKEDESKGGYSK---DVLLRLLQKYGEVLNLVLS-----SKKPGTAVVEFATVKAAELAVQNEV--GLVD   79 (100)
T ss_dssp             SCEEEEECCCCSSCSCCCSCCH---HHHHHHHHTTSCEEEEEEE-----SSSSSEEEEEESCHHHHHHHHHTCC--BCSS
T ss_pred             cceEEEeeeccCccCcCCCCCH---HHHHHHHHhcCCEEEEEEc-----cCCCCEEEEEECCHHHHHHHHHhcC--CCCC
Confidence            4566 65443       45888   9999999999999999998     3679999999999999999999954  4679


Q ss_pred             ceeEEeeccCCCCCC
Q 023632           91 AQVEVKKAEPKKPNL  105 (279)
Q Consensus        91 ~~i~V~~a~~~~~~~  105 (279)
                      ++|+|++++++....
T Consensus        80 ~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           80 NPLKISWLEGQPQDA   94 (100)
T ss_dssp             SBCEEECSSCCCCCC
T ss_pred             CeEEEEEccCCCCCC
Confidence            999999998765443

>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=99.57  E-value=8.5e-15  Score=130.24  Aligned_cols=77  Identities=13%  Similarity=0.195  Sum_probs=71.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-Cce
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~~   92 (279)
                      .....++| |.|||+++++   ++|+++|++||.|++|+|+.++     ++||||+|++.++|++||+.||+++|. +++
T Consensus       203 ~~~~~~~l~v~nl~~~~~~---~~l~~~F~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~  274 (282)
T 3pgw_A          203 ENPPNHILFLTNLPEETNE---LMLSMLFNQFPGFKEVRLVPGR-----HDIAFVEFDNEVQAGAARDALQGFKITQNNA  274 (282)
T ss_pred             CCCCCCEEEEeCCCCcCCH---HHHHHHHHhcCCeEEEEEecCC-----CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCE
Confidence            34456788 9999999999   9999999999999999999764     589999999999999999999999999 999


Q ss_pred             eEEeecc
Q 023632           93 VEVKKAE   99 (279)
Q Consensus        93 i~V~~a~   99 (279)
                      |+|++|+
T Consensus       275 l~v~~ak  281 (282)
T 3pgw_A          275 MKISFAK  281 (282)
T ss_pred             EEEEEec
Confidence            9999986

>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=99.56  E-value=1.5e-15  Score=116.71  Aligned_cols=75  Identities=13%  Similarity=0.234  Sum_probs=63.4

Q ss_pred             eeCCCCCCCcccH--------HHHHHHH-hcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           23 TGLSLTPVTEPAL--------DEFKDFF-MQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        23 V~nLp~~~te~~~--------~~L~~~F-~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +.+||+++++++|        ++|+++| ++||+|++|+|++++ +++++|||||+|+++++|++||+.||+..|++++|
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            5677788887222        3444555 999999999999886 47899999999999999999999999999999999


Q ss_pred             EEeec
Q 023632           94 EVKKA   98 (279)
Q Consensus        94 ~V~~a   98 (279)
                      +|+++
T Consensus        99 ~v~~s  103 (104)
T 1jmt_A           99 HAELS  103 (104)
T ss_dssp             CEEEC
T ss_pred             EEEEc
Confidence            99886

>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=99.55  E-value=9.6e-16  Score=126.59  Aligned_cols=84  Identities=18%  Similarity=0.300  Sum_probs=73.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +..+.++| |.|||+++|+   ++|+++|++|+.|.. .++++..++++++||||+|.++++|++||+ ||+++|.+++|
T Consensus         9 ~~~~~~~l~V~nLp~~~t~---~~l~~~f~~~g~~~~-~~~~~~~~~~~~g~afV~f~~~~~a~~A~~-l~g~~~~g~~l   83 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSV---AELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEI   83 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCH---HHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEE
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHHhCCcce-EEEEECCCCccccEEEEEECCHHHHHHHHh-cCCCEeCCeEE
Confidence            45677889 9999999999   999999999998766 345555688899999999999999999995 89999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|+++.++..
T Consensus        84 ~v~~~~~~~~   93 (175)
T 1fje_B           84 KLEKPKGRDS   93 (175)
T ss_dssp             EEECCCCSSC
T ss_pred             EEecCCCccc
Confidence            9999987654

>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=99.54  E-value=2.1e-14  Score=124.52  Aligned_cols=77  Identities=14%  Similarity=0.245  Sum_probs=70.7

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-Ccee
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQV   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~~i   93 (279)
                      .+.++| |.|||+++++   ++|+++|++|| +|++|+|+.+     .++||||+|++.++|++||+.||+.+|. +++|
T Consensus       149 ~~~~~l~V~nlp~~~t~---~~l~~~f~~~G~~i~~v~i~~~-----~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l  220 (229)
T 2adc_A          149 PPSATLHLSNIPPSVSE---EDLKVLFSSNGGVVKGFKFFQK-----DRKMALIQMGSVEEAVQALIDLHNHDLGENHHL  220 (229)
T ss_dssp             CSCSEEEEECCCTTCCH---HHHHHHHHTTSCCEEEEEECSS-----STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCCCEEEEeCCCccCCH---HHHHHHHHHcCCCeeEEEEEEC-----CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeE
Confidence            346888 9999999999   99999999999 9999999653     3689999999999999999999999999 9999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|++++++
T Consensus       221 ~v~~a~~~  228 (229)
T 2adc_A          221 RVSFSKST  228 (229)
T ss_dssp             EEEECSSC
T ss_pred             EEEEecCC
Confidence            99999875

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.53  E-value=1e-14  Score=122.97  Aligned_cols=77  Identities=14%  Similarity=0.245  Sum_probs=70.8

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-Ccee
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GAQV   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~~i   93 (279)
                      .++++| |.|||+++++   ++|+++|++|| +|++|+|+.+.     +++|||+|+++++|++||+.||+++|. +++|
T Consensus       118 ~~~~~l~v~nl~~~~~~---~~l~~~f~~~G~~v~~v~i~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l  189 (198)
T 1qm9_A          118 PPSATLHLSNIPPSVSE---EDLKVLFSSNGGVVKGFKFFQKD-----RKMALIQMGSVEEAVQALIDLHNHDLGENHHL  189 (198)
T ss_dssp             CCCCEEEECCCCTTCCH---HHHHHHHHHTTSCCCEEEESSTT-----SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSC
T ss_pred             CCccEEEEeCCCCCCCH---HHHHHHHHHcCCCceEEEEEeCC-----CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeE
Confidence            346788 9999999999   99999999999 99999997642     789999999999999999999999999 9999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|++++++
T Consensus       190 ~v~~a~~~  197 (198)
T 1qm9_A          190 RVSFSKST  197 (198)
T ss_dssp             CEEEECCC
T ss_pred             EEEeeccc
Confidence            99999875

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A

Probab=99.52  E-value=1.3e-14  Score=124.28  Aligned_cols=77  Identities=14%  Similarity=0.195  Sum_probs=68.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCe--EEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc--
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDV--QEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA--   91 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V--~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~--   91 (279)
                      .+.++| |.|||+++||   ++|+++|++||.|  ++|+|+.++  +++++||||+|+++++|++||+.||+++|.++  
T Consensus       121 ~p~~~l~v~NLp~~~t~---~~L~~~F~~~G~v~~~~v~~~~~~--~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~  195 (205)
T 3tyt_A          121 HPSNVLHFFNAPLEVTE---ENFFEICDELGVKRPTSVKVFSGK--SERSSSGLLEWDSKSDALETLGFLNHYQMKNPNG  195 (205)
T ss_dssp             CCCSEEEEEEECTTCCH---HHHHHHHHHHTCCCCSEEEECSCC--SSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSS
T ss_pred             CCcceEEEeCCCCCCCH---HHHHHHHHhcCCcceEEEEEEcCC--CCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCC
Confidence            345789 9999999999   9999999999999  899998875  45679999999999999999999999999876  


Q ss_pred             --eeEEeec
Q 023632           92 --QVEVKKA   98 (279)
Q Consensus        92 --~i~V~~a   98 (279)
                        +|.|++|
T Consensus       196 ~~p~~vk~~  204 (205)
T 3tyt_A          196 PYPYTLKLC  204 (205)
T ss_dssp             SSCEECEEE
T ss_pred             CcceEEEec
Confidence              5777765

>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=99.51  E-value=2.7e-14  Score=126.30  Aligned_cols=84  Identities=21%  Similarity=0.291  Sum_probs=74.2

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC-CccC---Cc
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-LELA---GA   91 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng-~~l~---g~   91 (279)
                      .+.++| |.|||+++|+   ++|+++|++||+|++|+|+.| .++++++||||+|++.++|++||+.||+ ..+.   ++
T Consensus        94 ~~~~~l~v~nl~~~~t~---~~l~~~F~~~G~i~~v~i~~~-~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~r  169 (261)
T 3sde_A           94 THGAALTVKNLSPVVSN---ELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGDGAFLLTTTPR  169 (261)
T ss_dssp             CCSSEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEEE-TTSCEEEEEEEEESSHHHHHHHHHHHHHSCEESSSSCC
T ss_pred             ccCCcccccCCCCCCCH---HHHHHHHHhcCCeEEEEeeeC-CCCCcCcEEEEEeCCHHHHHHHHHHhcCCeEEecCCCc
Confidence            345788 9999999999   999999999999999999999 5899999999999999999999999954 4443   99


Q ss_pred             eeEEeeccCCCCC
Q 023632           92 QVEVKKAEPKKPN  104 (279)
Q Consensus        92 ~i~V~~a~~~~~~  104 (279)
                      +|.|+++.+..+.
T Consensus       170 ~i~v~~~~~~~~~  182 (261)
T 3sde_A          170 PVIVEPMEQFDDE  182 (261)
T ss_dssp             BCEEEECCCEESS
T ss_pred             eEEEeeccccCcc
Confidence            9999999876443

>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=99.50  E-value=3e-14  Score=127.30  Aligned_cols=84  Identities=15%  Similarity=0.192  Sum_probs=70.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCC-CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFG-DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G-~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ...++| |.|||+++++   ++|+++|++|| +|++|+|++++. +++++||||+|.++++|++||+.||++.|.+++|+
T Consensus       115 ~~~~~l~v~nlp~~~t~---~~l~~~f~~~G~~i~~v~i~~~~~-~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~  190 (292)
T 2ghp_A          115 LTECTLWMTNFPPSYTQ---RNIRDLLQDINVVALSIRLPSLRF-NTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLV  190 (292)
T ss_dssp             CCSCEEEEECCCTTCCH---HHHHHHHHHTTCCCCEEECC--------CCEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCEEEEECCCCCCCH---HHHHHHHHHhCCCeEEEEEEeCCC-CCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            356788 9999999999   99999999999 999999999875 78899999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |+++.++...
T Consensus       191 v~~a~~~~~~  200 (292)
T 2ghp_A          191 TKVSNPLEKS  200 (292)
T ss_dssp             EEECCCC---
T ss_pred             EEECCCCccc
Confidence            9999876543

>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=99.50  E-value=2.7e-14  Score=126.33  Aligned_cols=77  Identities=29%  Similarity=0.442  Sum_probs=70.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++|+   ++|+++|++||+|++|+|+++      ++||||+|.++++|++||+.||++.|.++.|+
T Consensus        19 ~~~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~~------kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~   89 (261)
T 3sde_A           19 YTQRCRLFVGNLPTDITE---EDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKAELDGTILKSRPLR   89 (261)
T ss_dssp             SCGGGEEEEESCCTTCCH---HHHHHHTGGGCCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHHHhcCCEEEEEEeCC------CcEEEEEECCHHHHHHHHHHcCCcEECCceeE
Confidence            3455788 9999999999   999999999999999999754      68999999999999999999999999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |+++.+.
T Consensus        90 v~~a~~~   96 (261)
T 3sde_A           90 IRFATHG   96 (261)
T ss_dssp             EEECCCS
T ss_pred             eeecccC
Confidence            9998753

>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=99.49  E-value=6e-14  Score=115.10  Aligned_cols=76  Identities=21%  Similarity=0.437  Sum_probs=67.1

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcC----C-------CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQF----G-------DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~----G-------~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      +.++| |.|||+++|+   ++|+++|++|    +       .|.++++.++      ++||||+|.++++|++|| .||+
T Consensus         3 ~~~~l~V~nLp~~~t~---~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~------~g~afV~f~~~~~A~~A~-~~~~   72 (172)
T 2g4b_A            3 SARRLYVGNIPFGITE---EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD------KNFAFLEFRSVDETTQAM-AFDG   72 (172)
T ss_dssp             GGGEEEEESCCTTCCH---HHHHHHHHHHHHHTTCCSSSSCSEEEEEEETT------TTEEEEEESSHHHHHHHG-GGTT
T ss_pred             cccEEEEcCCCcccCH---HHHHHHHHHHhhhcccccCCCCceeeeEecCC------CCEEEEEeCCHHHHHHHH-HhCC
Confidence            45788 9999999999   9999999999    6       7777776543      789999999999999999 8999


Q ss_pred             CccCCceeEEeeccCCCC
Q 023632           86 LELAGAQVEVKKAEPKKP  103 (279)
Q Consensus        86 ~~l~g~~i~V~~a~~~~~  103 (279)
                      +.|.+++|+|+++.+...
T Consensus        73 ~~~~g~~i~v~~~~~~~~   90 (172)
T 2g4b_A           73 IIFQGQSLKIRRPHDYQP   90 (172)
T ss_dssp             CEETTEECEEECCSSCCC
T ss_pred             cEecCceeeecCCcccCC
Confidence            999999999998876543

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.47  E-value=1.2e-13  Score=115.81  Aligned_cols=76  Identities=20%  Similarity=0.410  Sum_probs=66.0

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcC----C-------CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQF----G-------DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~----G-------~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      ..++| |.|||+++||   ++|+++|++|    +       .|+++++.      ++++||||+|.++++|++|| .||+
T Consensus         3 ~~~~l~V~nLp~~~te---~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~------~~~g~afV~F~~~~~A~~Al-~l~g   72 (198)
T 2yh0_A            3 MARRLYVGNIPFGITE---EAMMDFFNAQMRLGGLTQAPGNPVLAVQIN------QDKNFAFLEFRSVDETTQAM-AFDG   72 (198)
T ss_dssp             -CCEEEEESCCTTCCH---HHHHHHHHHHHHHHTCCSSSSCSEEEEEEE------TTTTEEEEEESCSHHHHHHG-GGTT
T ss_pred             ceeEEEEcCCCCCCCH---HHHHHHHHHHHhhcccccCCCCceEEeEec------CCCCEEEEEeCCHHHHHHHH-HhcC
Confidence            46789 9999999999   9999999999    5       56666554      45799999999999999999 8899


Q ss_pred             CccCCceeEEeeccCCCC
Q 023632           86 LELAGAQVEVKKAEPKKP  103 (279)
Q Consensus        86 ~~l~g~~i~V~~a~~~~~  103 (279)
                      +.|.+++|+|+++.++..
T Consensus        73 ~~~~g~~i~v~~~~~~~~   90 (198)
T 2yh0_A           73 IIFQGQSLKIRRPHDYQP   90 (198)
T ss_dssp             EEETTEEEEEECCCCCCC
T ss_pred             CEEcCceEEEeCCCCCCC
Confidence            999999999999877643

>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=99.44  E-value=2.4e-13  Score=106.13  Aligned_cols=80  Identities=15%  Similarity=0.105  Sum_probs=65.2

Q ss_pred             CCCcee-eeCCCCCCC--c-----ccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc
Q 023632           17 TTTQKM-TGLSLTPVT--E-----PALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL   88 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~t--e-----~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l   88 (279)
                      .+++.| |.|+=....  +     +..++|+++|++||+|++|.|+++.    ++||+||+|+++++|++||+.||+.+|
T Consensus         5 ~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~----~~G~~fV~f~~~e~A~~Ai~~lnG~~f   80 (114)
T 3s6e_A            5 LATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS----AQGNVYVKCPSIAAAIAAVNALHGRWF   80 (114)
T ss_dssp             CCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC----TTCCEEEECSSHHHHHHHHHHHTTCEE
T ss_pred             CCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC----CcEEEEEEECCHHHHHHHHHHhCCCEE
Confidence            456677 888732221  1     1126889999999999999997663    589999999999999999999999999


Q ss_pred             CCceeEEeeccC
Q 023632           89 AGAQVEVKKAEP  100 (279)
Q Consensus        89 ~g~~i~V~~a~~  100 (279)
                      ++++|+|+++..
T Consensus        81 ~GR~i~v~~~~~   92 (114)
T 3s6e_A           81 AGKMITAAYVPL   92 (114)
T ss_dssp             TTEECEEEEECH
T ss_pred             CCEEEEEEEEcH
Confidence            999999998864

>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=99.39  E-value=4.8e-13  Score=123.12  Aligned_cols=76  Identities=14%  Similarity=0.166  Sum_probs=64.9

Q ss_pred             CCCCCcee-eeC--CCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC--
Q 023632           15 RQTTTQKM-TGL--SLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA--   89 (279)
Q Consensus        15 ~~~~~~~l-V~n--Lp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~--   89 (279)
                      .+.++++| |.|  |++.+||   ++|+++|++||+|++|.|+.      .|+||||+|++.++|++||+.||++++.  
T Consensus        14 ~~~ps~~l~VgN~gl~~~~te---~~L~~~F~~~G~V~~v~~~~------~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~   84 (345)
T 3tht_A           14 VSYATQSLVVANGGLGNGVSR---NQLLPVLEKCGLVDALLMPP------NKPYSFARYRTTEESKRAYVTLNGKEVVDD   84 (345)
T ss_dssp             CSSCCSEEEEETCSGGGTCCH---HHHHHHHHTTSCEEEEECCT------TCSEEEEEESSHHHHHHHHHHTTTCEEECT
T ss_pred             cCCCCCEEEEEcCCCCCCCCH---HHHHHHHHhcCCeEEEEEeC------CCCEEEEEECCHHHHHHHHHHhCCCccccc
Confidence            46678889 999  5889999   99999999999999987753      4789999999999999999999999883  


Q ss_pred             -Cc--eeEEeecc
Q 023632           90 -GA--QVEVKKAE   99 (279)
Q Consensus        90 -g~--~i~V~~a~   99 (279)
                       ++  .|.|.+++
T Consensus        85 ~g~~~~ly~~~~~   97 (345)
T 3tht_A           85 LGQKITLYLNFVE   97 (345)
T ss_dssp             TSCEEECEEEECS
T ss_pred             cCCceEEEEEEee
Confidence             34  56777664

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.32  E-value=3.5e-12  Score=94.72  Aligned_cols=76  Identities=18%  Similarity=0.308  Sum_probs=62.1

Q ss_pred             CCcee-eeCCCC----C-CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCc
Q 023632           18 TTQKM-TGLSLT----P-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGA   91 (279)
Q Consensus        18 ~~~~l-V~nLp~----~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~   91 (279)
                      +..+| |.-++.    + ..++.+.+|++.|++||+|..++|+.|+        +||+|++.++|.+||+ ||+++|+++
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~--------~fVtF~d~~sAlaAi~-mnG~~v~Gr   76 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK--------MWVTFLEGSSALNVLS-LNGKELLNR   76 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS--------EEEEESSHHHHHHGGG-GTTCEETTE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC--------EEEEECChHHHHHHHh-cCCeEeCCe
Confidence            34455 665552    2 2333347899999999999999999884        8999999999999998 899999999


Q ss_pred             eeEEeeccCCC
Q 023632           92 QVEVKKAEPKK  102 (279)
Q Consensus        92 ~i~V~~a~~~~  102 (279)
                      .|+|+++++.-
T Consensus        77 ~LkV~lkt~dW   87 (91)
T 2dnr_A           77 TITIALKSPSG   87 (91)
T ss_dssp             EEEEEECCCSS
T ss_pred             EEEEEeCCCCc
Confidence            99999988753

>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=99.24  E-value=3.5e-11  Score=103.58  Aligned_cols=84  Identities=14%  Similarity=0.129  Sum_probs=67.3

Q ss_pred             CCCcee-eeCCC--CCCCcccHHHHHHHHhcCCCeEEEEEeecC----CCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           17 TTTQKM-TGLSL--TPVTEPALDEFKDFFMQFGDVQEHQIMRDH----STSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        17 ~~~~~l-V~nLp--~~~te~~~~~L~~~F~~~G~V~~v~i~~d~----~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      ..+..+ +.++-  .++.+++.++|++.|++||+|++|.|+++.    .+.+++|++||+|+++++|++||+.||+..++
T Consensus       122 ~~s~v~~l~n~v~~~e~~~e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~  201 (222)
T 3dxb_A          122 MESTVMVLRNMVDPKDIDDDLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFA  201 (222)
T ss_dssp             CBCSEEEEESSCCGGGCCTTHHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSS
T ss_pred             cccccchhhcCCCHHHHHHHHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceEC
Confidence            334444 55442  233333337999999999999999998654    45589999999999999999999999999999


Q ss_pred             CceeEEeeccC
Q 023632           90 GAQVEVKKAEP  100 (279)
Q Consensus        90 g~~i~V~~a~~  100 (279)
                      +|+|.|+++..
T Consensus       202 gr~i~~~~~~~  212 (222)
T 3dxb_A          202 GRKVVAEVYDQ  212 (222)
T ss_dssp             SSBCEEEECCH
T ss_pred             CeEEEEEEcCH
Confidence            99999998764

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.21  E-value=3.5e-11  Score=94.53  Aligned_cols=76  Identities=16%  Similarity=0.223  Sum_probs=66.4

Q ss_pred             CCCCCcee-eeCCCCC-CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcC-HHHHHHHHHHcC--CCccC
Q 023632           15 RQTTTQKM-TGLSLTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDT-EQAVDDLLAKGN--KLELA   89 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s-~e~a~~Ai~~ln--g~~l~   89 (279)
                      .-++.+.| |.||+++ +++   ++|+++|++|++|+.|+|+++..      +|||+|.+ +++|++||++||  +.+|+
T Consensus        14 ~~~~G~il~v~~l~~~~~sr---edLke~F~~~G~V~~Vd~~~g~~------tgfVrf~~~~~~A~~av~~ln~~~~~i~   84 (121)
T 1owx_A           14 EEKIGCLLKFSGDLDDQTCR---EDLHILFSNHGEIKWIDFVRGAK------EGIILFKEKAKEALGKAKDANNGNLQLR   84 (121)
T ss_dssp             SCCCCCEEEEEESCCSSCCH---HHHHHHTCSSCCEEEEECCTTCS------EEEEEESSCHHHHHHHHHHTTTSCBCTT
T ss_pred             cccCCeEEEEecCCCCcCCH---HHHHHHHHhcCCEEEEEEecCCC------EEEEEECCChHHHHHHHHHhhcCCcEEe
Confidence            34556677 9999999 999   99999999999999999998864      59999999 899999999995  68899


Q ss_pred             CceeEEeecc
Q 023632           90 GAQVEVKKAE   99 (279)
Q Consensus        90 g~~i~V~~a~   99 (279)
                      +..++|+...
T Consensus        85 g~~~~~evL~   94 (121)
T 1owx_A           85 NKEVTWEVLE   94 (121)
T ss_dssp             SSSEEEEECC
T ss_pred             CcEEEEEECC
Confidence            9988887644

>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=99.19  E-value=2e-11  Score=91.13  Aligned_cols=76  Identities=13%  Similarity=0.225  Sum_probs=62.8

Q ss_pred             CCCCCcee-eeCCCCC------CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc
Q 023632           15 RQTTTQKM-TGLSLTP------VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE   87 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~------~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~   87 (279)
                      .-++..+| |.-++.+      ..++.+.+|.+.|++||+|..|+|+.|+        +||+|.+.++|.+||+ ||+++
T Consensus        11 ~GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~--------~fVtF~d~~sAl~AI~-ldG~~   81 (95)
T 1ufw_A           11 QGPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ--------MLVTFADSHSALSVLD-VDGMK   81 (95)
T ss_dssp             CCCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE--------EEEECSCSHHHHHHHH-GGGSE
T ss_pred             cCCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc--------EEEEEcChHHHHHHHh-cCCee
Confidence            34556677 8877643      3433346799999999999999999884        9999999999999999 89999


Q ss_pred             cCCceeEEeecc
Q 023632           88 LAGAQVEVKKAE   99 (279)
Q Consensus        88 l~g~~i~V~~a~   99 (279)
                      |+++.|+|++..
T Consensus        82 v~Gr~L~V~~k~   93 (95)
T 1ufw_A           82 VKGRAVKISGPS   93 (95)
T ss_dssp             ETTEEEEEECCC
T ss_pred             eCCeEEEEeccC
Confidence            999999998754

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.79  E-value=2.1e-08  Score=76.47  Aligned_cols=74  Identities=12%  Similarity=0.109  Sum_probs=66.9

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcC-----CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQF-----GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~-----G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      +.+.++| |-+||..|++   +.|++|++++     +.|++|.+..|.      +=|+|+|+|+.+|-||.-+||+.+|+
T Consensus        18 ~~~~rtiaL~~ipDtvnd---arIr~lve~~~~i~~g~i~KI~L~pDH------~GAivef~d~~~AgKasLaL~G~ef~   88 (117)
T 2l9w_A           18 KELETLICLFPLSDKVSP---SLICQFLQEEIHINEKDIRKILLVSDF------NGAIIIFRDSKFAAKMLMILNGSQFQ   88 (117)
T ss_dssp             TTTTSCEEEECCCTTCCH---HHHHHHHHHHTCCCTTTCSEEEEETTT------TEEEEECSCHHHHHHHHHHHSSEEET
T ss_pred             ccCCcEEEEecCCCCCCH---HHHHHHHhhhhccCccceeEEEEecCC------CceEEEEccchhhHHHHhhcCCeeec
Confidence            3457889 9999999999   9999999999     999999998885      47999999999999999999999999


Q ss_pred             CceeEEeec
Q 023632           90 GAQVEVKKA   98 (279)
Q Consensus        90 g~~i~V~~a   98 (279)
                      +++|+|-..
T Consensus        89 gr~Lr~gTv   97 (117)
T 2l9w_A           89 GKVIRSGTI   97 (117)
T ss_dssp             TEEEEEECH
T ss_pred             CeEEEecCH
Confidence            999998643

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.47  E-value=1.5e-06  Score=65.52  Aligned_cols=75  Identities=24%  Similarity=0.336  Sum_probs=62.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcC-----CCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQF-----GDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~-----G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ...++| |.|||+++++   +.|+-+|++-     |+|++|+...        .-|+|+|.+.+.|+++|++ ..+.|++
T Consensus         6 ~~~~~I~V~~lPp~~~~---e~L~LYFEn~rrsGGG~V~~v~~~~--------~~AvItF~d~~va~rVL~k-~~H~L~~   73 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPD---ELLTLYFENRRRSGGGPVLSWQRLG--------CGGVLTFREPADAERVLAQ-ADHELHG   73 (104)
T ss_dssp             CCCCEEEEESCCTTSCH---HHHHHHHHCTTTTCCCCEEEEEEET--------TEEEEEESSHHHHHHHHTC-SCCBSSS
T ss_pred             cCccEEEEECCCCCCCh---hHheEEEeCCCcCCCceeeEEEEcC--------CcEEEEEcChHHHHHHhcC-CcceecC
Confidence            345788 9999999999   9999999872     6888887653        3799999999999999988 5789999


Q ss_pred             ceeEEeeccCCCC
Q 023632           91 AQVEVKKAEPKKP  103 (279)
Q Consensus        91 ~~i~V~~a~~~~~  103 (279)
                      .+|.|....++..
T Consensus        74 ~~LsV~P~~~~~~   86 (104)
T 2dhx_A           74 AQLSLRPAPPRAP   86 (104)
T ss_dssp             SBCEEEECCCCCC
T ss_pred             eEEEEEcCCCCCc
Confidence            9999987665543

>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=98.30  E-value=2.8e-06  Score=64.26  Aligned_cols=78  Identities=15%  Similarity=0.226  Sum_probs=64.7

Q ss_pred             Ccee-eeCCCCCC-CcccH-HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           19 TQKM-TGLSLTPV-TEPAL-DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        19 ~~~l-V~nLp~~~-te~~~-~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .++| |.||+.+| +.+++ ++++++|.+|.++.....++.-.      =..|.|.++++|.+|-.+||...|++++|+|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR------Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK------RVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT------EEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce------EEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3556 99999877 44555 68899999999998887775531      4579999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      -++++..
T Consensus        79 YFgq~~~   85 (104)
T 1wey_A           79 YFAQTLH   85 (104)
T ss_dssp             ECCCCSS
T ss_pred             EecCCCC
Confidence            9998543

>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=98.19  E-value=3.2e-06  Score=65.61  Aligned_cols=79  Identities=11%  Similarity=0.110  Sum_probs=58.7

Q ss_pred             hhhhcCCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCc
Q 023632            9 LTMFINRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLE   87 (279)
Q Consensus         9 ~~~~~~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~   87 (279)
                      .+....+....+.| |-++|.+.+    +.|.++|++||+|+++....      ..-+-.|.|+++.+|++||.+ |+..
T Consensus        14 ~~l~~~~~~~~~wVtVFGFp~~~~----~~VL~~F~~~G~Iv~~~~~~------~~NWihI~Y~s~~~A~rAL~k-NG~i   82 (119)
T 1wwh_A           14 DSLTSEDHLDDTWVTVFGFPQASA----SYILLQFAQYGNILKHVMSN------TGNWMHIRYQSKLQARKALSK-DGRI   82 (119)
T ss_dssp             -------CGGGGEEEEECCCGGGH----HHHHHHHHTTSCEEEEEECS------SSSEEEEEESSHHHHHHHHTT-TTCE
T ss_pred             cccCCCCCCCCCEEEEECCCHHHH----HHHHHHHHhhCcEEEeccCC------CCCeEEEEeCCHHHHHHHHHh-CCeE
Confidence            33333445566778 999998865    67888999999999987621      134899999999999999999 9999


Q ss_pred             cCC-ceeEEeec
Q 023632           88 LAG-AQVEVKKA   98 (279)
Q Consensus        88 l~g-~~i~V~~a   98 (279)
                      |++ ..|-|++.
T Consensus        83 i~g~~mIGV~p~   94 (119)
T 1wwh_A           83 FGESIMIGVKPC   94 (119)
T ss_dssp             ETTTEECEEEEC
T ss_pred             ecCCEEEEEEEC
Confidence            984 66777664

>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=97.85  E-value=8e-05  Score=55.17  Aligned_cols=79  Identities=8%  Similarity=0.103  Sum_probs=59.3

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCC--cccEEEEEEcCHHHHHHHHHHcCCCccCCc-----
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSR--SRGFGFITFDTEQAVDDLLAKGNKLELAGA-----   91 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~--~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~-----   91 (279)
                      ++| |++||+.+||   +++.+.+....++.....+.-+.+.+  ...-|+|.|.+.|++...++.++++.+.+.     
T Consensus         2 ~KvVIRrLPP~Lte---eeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~D~kg~~~   78 (91)
T 1uw4_A            2 SKVVIRRLPPTLTK---EQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEY   78 (91)
T ss_dssp             CEEEEEEECTTCCH---HHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEE
T ss_pred             cEEEEeCCCCCCCH---HHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEEcCCCCEe
Confidence            456 9999999999   99999999887776666655443332  224699999999999999999999877543     


Q ss_pred             eeEEeeccCC
Q 023632           92 QVEVKKAEPK  101 (279)
Q Consensus        92 ~i~V~~a~~~  101 (279)
                      +..|++|.-+
T Consensus        79 ~a~VE~AP~q   88 (91)
T 1uw4_A           79 PAIVEFAPFQ   88 (91)
T ss_dssp             ECEEEECSSC
T ss_pred             eeEEEEcCCC
Confidence            2356666433

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=97.80  E-value=4e-05  Score=57.14  Aligned_cols=56  Identities=11%  Similarity=0.225  Sum_probs=46.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      ...+.| | .+|.++..   .||.++|+.|+. ..|+.+.|.       .|||.|.+++.|..||+.++
T Consensus        14 ~r~HVf~l-~FP~ewKt---~DI~~lFs~fgg-v~I~WidDT-------sAlvvf~~~~~a~~al~~i~   70 (100)
T 1whv_A           14 KRDHVLHV-TFPKEWKT---SDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             CCCSEEEE-ECCTTCCH---HHHHHHHTTTCS-CCCEEEETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             CCCeEEEE-eCChhhhh---HHHHHHhhccCC-EEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            344566 7 99999999   999999999984 456667664       79999999999999999763

>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=97.59  E-value=7.1e-05  Score=55.97  Aligned_cols=53  Identities=11%  Similarity=0.208  Sum_probs=45.7

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      +.| | .+|.++..   .||.++|+.|+ -..|+.+.|.       .|||.|.+++.|..||..++
T Consensus         7 HV~~l-~FP~ewKt---~Di~~lFs~fg-gv~I~WidDT-------sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKT---SDLYQLFSAFG-NIQISWIDDT-------SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCH---HHHHHHTTTSE-EEEEEEEETT-------EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhh---HHHHHHHhccC-CEEEEEEcCC-------eEEEEecCHHHHHHHHHhcc
Confidence            456 7 99999999   99999999998 4567777774       79999999999999999764

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=97.34  E-value=0.00032  Score=52.36  Aligned_cols=78  Identities=6%  Similarity=0.040  Sum_probs=52.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCc--ccEEEEEEcCHHHHHHHHHHcCCCccCCc----
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRS--RGFGFITFDTEQAVDDLLAKGNKLELAGA----   91 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~--rG~aFV~F~s~e~a~~Ai~~lng~~l~g~----   91 (279)
                      +.+| |+.||+.+||   ++|.+.+..+=++.-...+.-+.+.+.  -.-|+|.|++.|++....+.++++.+.+.    
T Consensus         9 ~~KvVIRrLPP~Lte---e~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~D~kg~~   85 (97)
T 2l08_A            9 SHMVVIRRLPPGLTK---EQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFLDSKGLE   85 (97)
T ss_dssp             CCCEEEECCCSCSCH---HHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEECTTCCE
T ss_pred             ceeEEEeCCCCCCCH---HHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEeCCCCE
Confidence            4456 9999999999   888887776544432222222222211  24589999999999999999998776543    


Q ss_pred             -eeEEeecc
Q 023632           92 -QVEVKKAE   99 (279)
Q Consensus        92 -~i~V~~a~   99 (279)
                       +..|++|.
T Consensus        86 ~~a~VE~AP   94 (97)
T 2l08_A           86 YPAVVEFAP   94 (97)
T ss_dssp             EEEEEEECC
T ss_pred             eeeEEEecC
Confidence             34556553

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=97.28  E-value=0.00015  Score=56.98  Aligned_cols=75  Identities=17%  Similarity=0.268  Sum_probs=55.4

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEE-EEEeec--------CCCCC-----cccEEEEEEcCHHHHHHHHHHcC
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQE-HQIMRD--------HSTSR-----SRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~-v~i~~d--------~~tg~-----~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      ..| |-+.|++.++    .+.+.|++||.|++ +.+.++        +.+.+     ...+..|+|+++.+|++||.+ |
T Consensus         8 ~~VtVFGFp~~~~~----~VI~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~-N   82 (132)
T 3p3d_A            8 LAILVFGYPETMAN----QVIAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLE-N   82 (132)
T ss_dssp             CEEEEECCCGGGHH----HHHHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTT-T
T ss_pred             eEEEEEecCHHHHH----HHHHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHh-C
Confidence            455 8899888774    67788999999876 222210        00111     245889999999999999999 9


Q ss_pred             CCccCCceeEEeecc
Q 023632           85 KLELAGAQVEVKKAE   99 (279)
Q Consensus        85 g~~l~g~~i~V~~a~   99 (279)
                      +..|++..|=|++..
T Consensus        83 G~ii~G~mIGV~Py~   97 (132)
T 3p3d_A           83 GAVFNGVLLGVIPYT   97 (132)
T ss_dssp             TCEETTEECEEEECC
T ss_pred             CeEeCcEEEEEEECC
Confidence            999999988887764

>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=96.95  E-value=0.00055  Score=54.84  Aligned_cols=35  Identities=3%  Similarity=0.002  Sum_probs=29.4

Q ss_pred             EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC
Q 023632           50 EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL   86 (279)
Q Consensus        50 ~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~   86 (279)
                      .++|+++..  +++||+||+|.++++|++||+.++..
T Consensus         2 ~~kl~ln~~--~~~G~~fV~f~~~~~A~~al~~~~~~   36 (158)
T 2kn4_A            2 QYKLILNGK--TLKGETTTEAVDAATAEKVFKQYAND   36 (158)
T ss_dssp             EEEEEEECS--SCEEEEEEECSSHHHHHHHHHHHHHH
T ss_pred             cEEEEecCc--cccchhHHHHHHHHhHHHHHHhhccc
Confidence            467777754  68999999999999999999887653

>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=96.49  E-value=0.0014  Score=52.11  Aligned_cols=42  Identities=10%  Similarity=0.056  Sum_probs=37.9

Q ss_pred             CCCcccEEEEEEcCHHHHHHHHHHc-CCCccCCceeEEeeccCC
Q 023632           59 TSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGAQVEVKKAEPK  101 (279)
Q Consensus        59 tg~~rG~aFV~F~s~e~a~~Ai~~l-ng~~l~g~~i~V~~a~~~  101 (279)
                      ..+.+|+++|+|.++++|++||+++ |+.+|++ .|+|+++..+
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            4577999999999999999999999 9999999 9999988653

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=96.34  E-value=0.0012  Score=62.63  Aligned_cols=55  Identities=15%  Similarity=0.378  Sum_probs=41.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHH
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAK   82 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~   82 (279)
                      .+.| |. +|.++++   ++|.++|++||+|.++.+.+++     .-||.|||.++++++++++.
T Consensus        53 ~rsv~v~-~~~~~~~---~~l~~y~~~~g~i~~~~~~~~~-----g~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           53 QRTVLIH-CPEKISE---NKFLKYLSQFGPINNHFFYESF-----GLYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HTEEEEE-ECCC------CHHHHHHGGGSCCCCEEEECSS-----SEEEEEECC---CCHHHHSS
T ss_pred             cceEEEE-cCCCCCH---HHHHHHHHhcCCcceEEEEccC-----CeEEEEEeCCHHHHHHHHhc
Confidence            4667 86 7999999   9999999999999999887654     35999999999999988765

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=93.81  E-value=0.12  Score=49.64  Aligned_cols=54  Identities=11%  Similarity=0.235  Sum_probs=44.2

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      ...+ |. +|..|..   .+|+++|+.|+. .+|+.+.|.       .|||.|.+.++|+.+++.++
T Consensus       440 ~~vl~v~-f~~~~~~---~~i~~~fs~fg~-v~V~widdt-------~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKT---SDLYQLFSAFGN-IQISWIDDT-------SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCH---HHHHHHGGGGCC-CEEEECSSS-------EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCH---HHHHHHHHhcCC-EEEEEEcCC-------eEEEEECCHHHHHHHHHHHH
Confidence            3456 76 8889998   999999999995 456665553       79999999999999999875

>2g0c_A ATP-dependent RNA helicase DBPA; RNA recognition motif, hydrolase; 1.70A {Bacillus subtilis} PDB: 3moj_B

Probab=88.58  E-value=0.77  Score=31.76  Aligned_cols=55  Identities=18%  Similarity=0.251  Sum_probs=37.7

Q ss_pred             HHHHHHHhcCC-----CeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           36 DEFKDFFMQFG-----DVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        36 ~~L~~~F~~~G-----~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      .+|..++..-.     .|-.|+|..+        |.||+-.. +.++++++.|+...+.+++|.|+.++
T Consensus        16 ~~ivg~i~~~~gi~~~~IG~I~i~d~--------~s~v~v~~-~~~~~~~~~l~~~~i~g~~~~v~~~~   75 (76)
T 2g0c_A           16 VDFVGTIAKIDGVSADDIGIITIMDN--------ASYVEILN-GKGPHVLKVMKNTTVKGKQLKVNKAN   75 (76)
T ss_dssp             HHHHHHHHTSTTCCGGGEEEEEECSS--------CEEEEECT-TCHHHHHHHHTTCCC---CCCEEECC
T ss_pred             HHHHHHHHHccCCChhhccEEEEeCC--------cEEEEECH-HHHHHHHHHhccccCcCceEEEEECC
Confidence            66666665443     3456776544        78998875 45778899999999999999998764

>4eyt_A Telomerase associated protein P65; RNA, LA protein, LARP7, RRM, XRRM, RNA binding protein; 2.50A {Tetrahymena thermophila} PDB: 4erd_A

Probab=86.52  E-value=3.4  Score=30.08  Aligned_cols=68  Identities=13%  Similarity=0.042  Sum_probs=47.9

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC-------CccC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK-------LELA   89 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng-------~~l~   89 (279)
                      ..+.| |-|||..+-.   .++.-.....|---.|..+        .+-|.|.|.+.++...||++|-.       ++|.
T Consensus        11 qnclikiinipqgtlk---aevvlavrhlgyefycdyi--------dgqamirfqnsdeqrlaiqkllnhnnnklqieir   79 (129)
T 4eyt_A           11 QNCLIKIINIPQGTLK---AEVVLAVRHLGYEFYCDYI--------DGQAMIRFQNSDEQRLAIQKLLNHNNNKLQIEIR   79 (129)
T ss_dssp             CSCEEEEECCCTTCCH---HHHHHHHHTTCCCEEEEEC--------SSCEEEEESSHHHHHHHHHHHEETTTTEEEEEET
T ss_pred             hCcEEEEEecCCCcee---eeeEEeehhcCeeEeeeee--------cCeeEEEecCChHHHHHHHHHHhcCCCEEEEEEc
Confidence            45677 9999999888   7777666666654455544        24689999999999999987622       2445


Q ss_pred             CceeEEe
Q 023632           90 GAQVEVK   96 (279)
Q Consensus        90 g~~i~V~   96 (279)
                      ++.+.|-
T Consensus        80 gqicdvi   86 (129)
T 4eyt_A           80 GQICDVI   86 (129)
T ss_dssp             TEEEEEE
T ss_pred             ceeeeee
Confidence            5555554

---

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	279
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	3e-14
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	2e-13
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-11
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	4e-11
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	5e-11
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	6e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	7e-11
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	0.002
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	2e-10
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-10
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	1e-09
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-09
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	1e-09
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-09
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	3e-09
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-09
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	4e-09
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-08
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-08
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	1e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-07
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-07
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	2e-06
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-06
d2dita1	99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	2e-06
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	3e-06
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-05
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	3e-05
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	5e-05
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	5e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	5e-05
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	7e-05
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-05
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	9e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	2e-04
d1o0pa_	104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	0.003

>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 = 64.6 bits (157), Expect = 3e-14
 Identities = 22/88 (25%), Positives = 44/88 (50%), Gaps = 6/88 (6%)

Query: 15  RQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 74
           ++T+   + GL     TE    + K++F  FG+V   Q+ +D  T  S+GFGF+ F   +
Sbjct: 6   QKTSDLIVLGLPWK-TTE---QDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 75  AVDDLLAKGNKLELAGAQVEVKKAEPKK 102
               ++++ + ++  G   + K    K+
Sbjct: 62  TQVKVMSQRHMID--GRWCDCKLPNSKQ 87

>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 = 62.7 bits (152), Expect = 2e-13
 Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 5/92 (5%)

Query: 14  NRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 73
            R   T     L+   +      + +DFF   G V++ +I+ D ++ RS+G  ++ F   
Sbjct: 15  ERDARTVFCMQLAAR-IRP---RDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 70

Query: 74  QAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL 105
           Q+V   +       L G  + V+ ++ +K  L
Sbjct: 71  QSVPLAIGL-TGQRLLGVPIIVQASQAEKNRL 101

>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 = 56.9 bits (137), Expect = 2e-11
 Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
            E   ++ +++F  FG+V+  ++  D+ T++ RGF FITF  E+ V  ++ K     + 
Sbjct: 11 TPE---EKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYH-NVG 66

Query: 90 GAQVEVKKA 98
           ++ E+K A
Sbjct: 67 LSKCEIKVA 75

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 56.1 bits (135), Expect = 4e-11
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 5/75 (6%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQAVDDLLAK-GNKLE 87
             +    E ++ F  FG+++  ++ +  + T   RGFGF+ F T+Q          +   
Sbjct: 20  ANQ---REIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTH 76

Query: 88  LAGAQVEVKKAEPKK 102
           L G ++ ++ A+ + 
Sbjct: 77  LYGRRLVLEWADSEV 91

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.8 bits (134), Expect = 5e-11
 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 3/74 (4%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           V +         F+ FGD+ + QI  D+ T + RGF F+ F+  +     +   N+ EL 
Sbjct: 17  VDD---KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELF 73

Query: 90  GAQVEVKKAEPKKP 103
           G  + V  A+P + 
Sbjct: 74  GRTIRVNLAKPMRI 87

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 6e-11
 Identities = 23/69 (33%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           T+    + KD+F +FG+V +  +  D  T RSRGFGF+ F   ++VD ++ +    +L 
Sbjct: 11 TTK---KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEH-KLN 66

Query: 90 GAQVEVKKA 98
          G  ++ K+A
Sbjct: 67 GKVIDPKRA 75

>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 = 57.7 bits (138), Expect = 7e-11
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 4/92 (4%)

Query: 11  MFINRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITF 70
                 T  +   G       E      +D+F Q+G ++  +IM D  + + RGF F+TF
Sbjct: 90  RPGAHLTVKKIFVGGIKEDTEE---HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146

Query: 71  DTEQAVDDLLAKGNKLELAGAQVEVKKAEPKK 102
           D   +VD ++ +     + G   EV+KA  K+
Sbjct: 147 DDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQ 177

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 183

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.1 bits (82), Expect = 0.002
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK 85
           T+   +  +  F Q+G + +  +MRD +T RSRGFGF+T+ T + VD  +     
Sbjct: 18 TTD---ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPH 70

>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 = 54.2 bits (130), Expect = 2e-10
 Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 3/70 (4%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          VTE       + F   G +   ++ RD  T RS G+ ++ F      +  L   N   + 
Sbjct: 12 VTE---AMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIK 68

Query: 90 GAQVEVKKAE 99
          G  V +  ++
Sbjct: 69 GKPVRIMWSQ 78

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 4/92 (4%)

Query: 14  NRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 73
             Q  T  + GL    V+E       + F+Q G V    + +D  T + +G+GF+ F +E
Sbjct: 6   RNQDATVYVGGLDEK-VSE---PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSE 61

Query: 74  QAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL 105
           +  D  +   + ++L G  + V KA     NL
Sbjct: 62  EDADYAIKIMDMIKLYGKPIRVNKASAHNKNL 93

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 7/77 (9%)

Query: 30  VTEPALDEFKDFFMQFGDVQEH--QIMRDHSTSRSRGFGFITFDTEQAVDDLLAK--GNK 85
                 +E  +   +  +               ++RGF F+ +++ +A      K    +
Sbjct: 13  KKR---EEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR 69

Query: 86  LELAGAQVEVKKAEPKK 102
           ++L G Q+ V  AEP+ 
Sbjct: 70  IQLWGHQIAVDWAEPEI 86

>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 = 52.0 bits (124), Expect = 1e-09
 Identities = 24/69 (34%), Positives = 39/69 (56%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           T+   +  +  F Q+G + +  +MRD +T RSRGFGF+T+ T + VD  +      ++ 
Sbjct: 18 TTD---ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAM-NARPHKVD 73

Query: 90 GAQVEVKKA 98
          G  VE K+A
Sbjct: 74 GRVVEPKRA 82

>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 = 51.5 bits (123), Expect = 1e-09
 Identities = 28/69 (40%), Positives = 44/69 (63%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           T+   +  +++F QFG+V+E  +MRD  T RSRGFGF+TF  +  VD +LA+ ++ EL 
Sbjct: 12 TTQ---EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELD 67

Query: 90 GAQVEVKKA 98
             ++ K A
Sbjct: 68 SKTIDPKVA 76

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-09
 Identities = 22/67 (32%), Positives = 40/67 (59%), Gaps = 1/67 (1%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           +  ++++ Q+G + +  +MRD ++ RSRGFGF+TF +   VD  +A      + G  VE 
Sbjct: 35  ESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPH-SIDGRVVEP 93

Query: 96  KKAEPKK 102
           K+A  ++
Sbjct: 94  KRAVARE 100

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.2 bits (122), Expect = 2e-09
 Identities = 16/75 (21%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           + +   D+ K+    FG ++   +++D +T  S+G+ F  +      D  +A  N ++L 
Sbjct: 13  LND---DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 69

Query: 90  GAQVEVKKAEPKKPN 104
             ++ V++A     N
Sbjct: 70  DKKLLVQRASVGAKN 84

>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 = 50.9 bits (121), Expect = 3e-09
 Identities = 22/75 (29%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQ-IMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL 88
           + E       D F  FG + +   IMRD  T  S+G+ FI F +  A D  +   N   L
Sbjct: 10  IDE---KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYL 66

Query: 89  AGAQVEVKKAEPKKP 103
               + V  A  K  
Sbjct: 67  CNRPITVSYAFKKDS 81

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 50.4 bits (120), Expect = 3e-09
 Identities = 18/78 (23%), Positives = 31/78 (39%), Gaps = 7/78 (8%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIM---RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL 86
            TE   +  K  F + G ++   I           S GFGF+ +   +     L +    
Sbjct: 10  TTE---ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGH 66

Query: 87  ELAGAQVEVKKAEPK-KP 103
            + G ++EV+ +E   KP
Sbjct: 67  TVDGHKLEVRISERATKP 84

>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 = 50.1 bits (119), Expect = 4e-09
 Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           T    ++ K +F QFG V +  +M D +T+R RGFGF+TF++E  V+ +    +  E+ 
Sbjct: 11 TTV---EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI-HFHEIN 66

Query: 90 GAQVEVKKA 98
             VE KKA
Sbjct: 67 NKMVECKKA 75

>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 = 48.8 bits (116), Expect = 2e-08
 Identities = 17/99 (17%), Positives = 38/99 (38%), Gaps = 10/99 (10%)

Query: 15  RQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 74
           +++ T  +  LS    TE   ++  + F + GD+++  +  D     + GF F+ + +  
Sbjct: 5   KKSCTLYVGNLSFY-TTE---EQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRA 60

Query: 75  AVDDLLAKGNKLELAGAQVEVKKAEPKKPNLPQPSYRRY 113
             ++ +   N   L    +        K        R+Y
Sbjct: 61  DAENAMRYINGTRLDDRIIRTDWDAGFKEG------RQY 93

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 47.9 bits (113), Expect = 3e-08
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 3/71 (4%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
            T+      +D       V     +     + SR F +I   +++     + K N L++ 
Sbjct: 13  YTQ---RNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIE 69

Query: 90  GAQVEVKKAEP 100
           G  +  K + P
Sbjct: 70  GYTLVTKVSNP 80

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.9 bits (113), Expect = 5e-08
 Identities = 19/98 (19%), Positives = 41/98 (41%), Gaps = 12/98 (12%)

Query: 14  NRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQI--------MRDHSTSRSRGF 65
           +   +   + GL+ + VT    D+  DFF Q G V+ ++           D  T + +G 
Sbjct: 5   DSDNSAIYVQGLNDS-VTL---DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGD 60

Query: 66  GFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEPKKP 103
             ++++        +   +  +  G++++V  A  K P
Sbjct: 61  ATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPP 98

>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 = 47.0 bits (111), Expect = 6e-08
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
            E      +D+F Q+G ++  +IM D  + + RGF F+TFD   +VD ++ +     + 
Sbjct: 14 TEE---HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQ-KYHTVN 69

Query: 90 GAQVEVKKA 98
          G   EV+KA
Sbjct: 70 GHNCEVRKA 78

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 3/75 (4%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
             E      +  F ++G + E  +++D  T RSRGFGF+TF+      D +   N   + 
Sbjct: 17  TNE---QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD 73

Query: 90  GAQVEVKKAEPKKPN 104
           G Q+ V +A     N
Sbjct: 74  GRQIRVDQAGKSSDN 88

>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 = 46.3 bits (109), Expect = 1e-07
 Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           +T+   +EF+  F   G+++  +++RD  T +S G+GF+ +   +  +  +   N L L 
Sbjct: 14  MTQ---EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQ 70

Query: 90  GAQVEVKKAEP 100
              ++V  A P
Sbjct: 71  TKTIKVSYARP 81

>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 = 45.3 bits (107), Expect = 3e-07
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          +T+   D+    F ++G + +  I+RD  T R RG  F+ ++  +   + ++  N +   
Sbjct: 18 ITD---DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPE 74

Query: 90 GA--QVEVKKA 98
          G    + V+ A
Sbjct: 75 GGSQPLSVRLA 85

>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 = 45.8 bits (108), Expect = 3e-07
 Identities = 7/77 (9%), Positives = 28/77 (36%), Gaps = 3/77 (3%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           +E  D F ++G +++ ++        +RG  ++ ++      +     +   +    + V
Sbjct: 22  EEMYDIFGKYGPIRQIRVGNTP---ETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV 78

Query: 96  KKAEPKKPNLPQPSYRR 112
                 +      + ++
Sbjct: 79  LYYNANRAFQKMDTKKK 95

>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 = 45.2 bits (107), Expect = 4e-07
 Identities = 14/74 (18%), Positives = 30/74 (40%), Gaps = 8/74 (10%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
            + +  F ++G +    + +        GF F+ +  E+     +A  +   +AG  +++
Sbjct: 31  SDVEAIFSKYGKIVGCSVHK--------GFAFVQYVNERNARAAVAGEDGRMIAGQVLDI 82

Query: 96  KKAEPKKPNLPQPS 109
             A   K N   PS
Sbjct: 83  NLAAEPKVNRSGPS 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 = 43.1 bits (101), Expect = 2e-06
 Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           +T+    E    F   G +   +IMRD+ T  S G+ F+ F +E      +   N + + 
Sbjct: 14  MTD---RELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVR 70

Query: 90  GAQVEVKKAEP 100
             +++V  A P
Sbjct: 71  NKRLKVSYARP 81

>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 = 43.5 bits (102), Expect = 2e-06
 Identities = 15/95 (15%), Positives = 37/95 (38%), Gaps = 11/95 (11%)

Query: 11  MFINRQTTTQKMTGLSLTPVTEPAL---------DEFKDFFMQFGDVQEHQIMRDHSTSR 61
           ++ N Q ++Q   GL    V++  +         + F +   ++G+V+E  +  +     
Sbjct: 9   IYRNPQNSSQSADGLRSA-VSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNL-GDH 66

Query: 62  SRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK 96
             G  ++ F  E+  +  +   N     G  +  +
Sbjct: 67  LVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAE 101

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 8/66 (12%), Positives = 24/66 (36%), Gaps = 4/66 (6%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++ +    +FG +++  +   H      G   ++F   +  D  +   +     G Q+  
Sbjct: 34  EDLRVECSKFGQIRKLLLFDRHP----DGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 89

Query: 96  KKAEPK 101
           +  +  
Sbjct: 90  QAWDGT 95

>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 = 42.3 bits (99), Expect = 3e-06
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 5/71 (7%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          +T+    E +  F Q+G +   +I+ D  T  SRG GFI FD     ++ +   N  + +
Sbjct: 18 MTQ---KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPS 74

Query: 90 GA--QVEVKKA 98
          GA   + VK A
Sbjct: 75 GATEPITVKFA 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 = 42.3 bits (99), Expect = 3e-06
 Identities = 12/73 (16%), Positives = 26/73 (35%), Gaps = 9/73 (12%)

Query: 30  VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
            +E   +  +  F         ++ +       R + F+ F   +   + +   N   L 
Sbjct: 20  TSE---EMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLD 70

Query: 90  GAQVEVKKAEPKK 102
           G+ +EV  A+P  
Sbjct: 71  GSPIEVTLAKPVD 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 = 40.3 bits (94), Expect = 1e-05
 Identities = 12/69 (17%), Positives = 32/69 (46%), Gaps = 4/69 (5%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
          V++    + ++ F +FG +++  +  D  + RS G   + F+ +      + + N + L 
Sbjct: 12 VSD---ADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLD 67

Query: 90 GAQVEVKKA 98
          G  + ++  
Sbjct: 68 GRPMNIQLV 76

>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 = 40.1 bits (93), Expect = 2e-05
 Identities = 18/66 (27%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA 89
           TE    + ++ F ++G + +  I+ D  + RSRGF F+ F+      +   + N +EL 
Sbjct: 21 TTE---RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELD 77

Query: 90 GAQVEV 95
          G ++ V
Sbjct: 78 GRRIRV 83

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 39.3 bits (91), Expect = 3e-05
 Identities = 9/63 (14%), Positives = 22/63 (34%)

Query: 36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
          DE  DFF  +  +     ++ +      G   + F++       +   N   +   +V++
Sbjct: 24 DEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKL 83

Query: 96 KKA 98
             
Sbjct: 84 VLG 86

>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 = 39.2 bits (91), Expect = 5e-05
 Identities = 14/92 (15%), Positives = 35/92 (38%), Gaps = 11/92 (11%)

Query: 14  NRQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE 73
           + +  T    G++   +T+      +  F  FG + E ++  +        + F+ F T 
Sbjct: 15  SPKNCTVYCGGIASG-LTD---QLMRQTFSPFGQIMEIRVFPEKG------YSFVRFSTH 64

Query: 74  QAVDDLLAKGNKLELAGAQVEVKKAEPKKPNL 105
           ++    +   N   + G  V+    +   P++
Sbjct: 65  ESAAHAIVSVNGTTIEGHVVKCYWGKE-SPDM 95

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 5e-05
 Identities = 9/73 (12%), Positives = 26/73 (35%), Gaps = 6/73 (8%)

Query: 36  DEFKDFFMQFGDVQE-----HQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG 90
           +   DFF     +          +     ++ + F F+ F +       +A  + +   G
Sbjct: 16  EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAF-DGIIFQG 74

Query: 91  AQVEVKKAEPKKP 103
             +++++    +P
Sbjct: 75  QSLKIRRPHDYQP 87

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 7/75 (9%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           DE ++FF Q+GDV +  I +       R F F+TF  +Q        G  L + G  V +
Sbjct: 20  DELREFFSQYGDVMDVFIPKPF-----RAFAFVTFADDQIAQS--LCGEDLIIKGISVHI 72

Query: 96  KKAEPKKPNLPQPSY 110
             AEPK  +   PS 
Sbjct: 73  SNAEPKHNSNSGPSS 87

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.4 bits (89), Expect = 7e-05
 Identities = 10/68 (14%), Positives = 24/68 (35%), Gaps = 6/68 (8%)

Query: 34  ALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV 93
           +       F Q+G++ +H +           +  I + ++      L+K  ++      +
Sbjct: 16  SASYILLQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALSKDGRIFGESIMI 69

Query: 94  EVKKAEPK 101
            VK    K
Sbjct: 70  GVKPCIDK 77

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 38.5 bits (89), Expect = 8e-05
 Identities = 21/90 (23%), Positives = 32/90 (35%), Gaps = 9/90 (10%)

Query: 15  RQTTTQKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQ 74
           R   T     LS   +TE   DE K+ F         +I       +S+G  +I F +E 
Sbjct: 14  RAARTLLAKNLSFN-ITE---DELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEA 64

Query: 75  AVDDLLAKGNKLELAGAQVEVKKAEPKKPN 104
             +  L +    E+ G  V +     K   
Sbjct: 65  DAEKNLEEKQGAEIDGRSVSLYYTGEKGGT 94

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Calcipressin-1
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.6 bits (89), Expect = 9e-05
 Identities = 12/86 (13%), Positives = 27/86 (31%), Gaps = 6/86 (6%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
            +F+  F  +      Q  +            I F    +  D   + +K E  G ++++
Sbjct: 25  AKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEMKL 78

Query: 96  KKAEPKKPNLPQPSYRRYNNPKPAYG 121
             A+         +    +   P+ G
Sbjct: 79  YFAQTLHIGSSHLAPPNPDKSGPSSG 104

>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 = 37.8 bits (87), Expect = 2e-04
 Identities = 15/68 (22%), Positives = 28/68 (41%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV 95
           ++ +  F  +G + E     D  T + +GF F+TF   +      A+ +     G  + V
Sbjct: 23  EDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHV 82

Query: 96  KKAEPKKP 103
             +  KK 
Sbjct: 83  LPSTIKKE 90

>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 = 34.2 bits (78), Expect = 0.003
 Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 2/69 (2%)

Query: 36  DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGF--ITFDTEQAVDDLLAKGNKLELAGAQV 93
           ++ +D   ++G V+  +I R        G G   + F +       +      + A   V
Sbjct: 29  EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88

Query: 94  EVKKAEPKK 102
             K  +P  
Sbjct: 89  VTKYCDPDS 97

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	279
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.88
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.87
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.87
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.87
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.87
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.87
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.86
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.86
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.86
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.86
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.86
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.86
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.86
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.85
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.85
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.85
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.85
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.85
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.85
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.84
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.84
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.84
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.84
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.84
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.84
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.84
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.83
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.83
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.83
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.83
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.83
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.83
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.82
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.82
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.82
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.82
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.81
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.8
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.8
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.8
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.8
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.79
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.79
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.79
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.78
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.78
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.78
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.78
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.77
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.77
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.76
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.76
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.76
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.76
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.76
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.76
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.75
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.75
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.75
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.75
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.75
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.75
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.74
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.74
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.73
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.73
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.71
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.71
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.7
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.69
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.69
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.69
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.68
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.65
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.64
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	99.62
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.54
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.53
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.51
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.5
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.49
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.47
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	98.03
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.85
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.58
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	96.1
d2cfxa2	77	Transcriptional regulator LrpC {Bacillus subtilis	82.97

>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=99.88  E-value=1.7e-22  Score=152.33  Aligned_cols=87  Identities=18%  Similarity=0.282  Sum_probs=81.1

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||++++|   ++|+++|++|++|++|+|++|+.|+++++||||+|+++++|++||+.||+++|++++|+
T Consensus         5 ~~~~~~lfV~nL~~~~t~---~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~   81 (99)
T d1whwa_           5 SSGSGRLFVRNLSYTSSE---EDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLH   81 (99)
T ss_dssp             CCSCEEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEE
T ss_pred             CCCCCEEEEECCCCcCCH---HHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3456789 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCCCC
Q 023632           95 VKKAEPKKPNL  105 (279)
Q Consensus        95 V~~a~~~~~~~  105 (279)
                      |++|+++++..
T Consensus        82 V~~a~~~~~~~   92 (99)
T d1whwa_          82 VLPSTIKKEAS   92 (99)
T ss_dssp             EEECCCCSTTC
T ss_pred             EEECCCCCccC
Confidence            99999876543

>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=99.87  E-value=3.3e-22  Score=149.22  Aligned_cols=85  Identities=24%  Similarity=0.402  Sum_probs=80.0

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ....++| |.|||+++|+   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+.||+++|++++|+
T Consensus         6 ~~~~~tlfV~nLp~~~t~---~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~   82 (93)
T d1x5ua1           6 RNQDATVYVGGLDEKVSE---PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIR   82 (93)
T ss_dssp             CCTTTEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCcCCH---HHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEE
Confidence            3445789 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCC
Q 023632           95 VKKAEPKKP  103 (279)
Q Consensus        95 V~~a~~~~~  103 (279)
                      |++|+++..
T Consensus        83 V~~A~~~~~   91 (93)
T d1x5ua1          83 VNKASAHNK   91 (93)
T ss_dssp             EEETTTTSC
T ss_pred             EEEcCCCCC
Confidence            999988654

>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=99.87  E-value=3e-22  Score=147.87  Aligned_cols=84  Identities=19%  Similarity=0.302  Sum_probs=78.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +..+.++| |.|||+++|+   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||+.+|++++|
T Consensus         3 ~s~~~~~l~V~nL~~~~t~---~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l   79 (88)
T d1rk8a_           3 RSVEGWILFVTSIHEEAQE---DEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTI   79 (88)
T ss_dssp             CCC-CEEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEE
Confidence            34556788 9999999999   9999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|++|.++
T Consensus        80 ~V~~a~~k   87 (88)
T d1rk8a_          80 QVDWCFVK   87 (88)
T ss_dssp             EEEESEEC
T ss_pred             EEEEecCC
Confidence            99999875

>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=99.87  E-value=3.7e-22  Score=159.39  Aligned_cols=85  Identities=21%  Similarity=0.429  Sum_probs=80.0

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++|+||||+|.+.++|++||+.||+++|++++|+|+
T Consensus        41 ~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~  117 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDE---VQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             TTSEEEEESCSTTCCH---HHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCH---HHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            34678 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCCC
Q 023632           97 KAEPKKPNL  105 (279)
Q Consensus        97 ~a~~~~~~~  105 (279)
                      +|+++.++.
T Consensus       118 ~a~~~~~~p  126 (139)
T d1u6fa1         118 LAASGHQRP  126 (139)
T ss_dssp             ESSCCCCCC
T ss_pred             EcCCCCCCC
Confidence            998776554

>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=99.87  E-value=2.3e-22  Score=146.28  Aligned_cols=79  Identities=23%  Similarity=0.401  Sum_probs=76.1

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |.|||+++||   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||++.|.+++|+|++
T Consensus         2 ~t~l~V~nLp~~~t~---~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~   78 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTD---RELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSY   78 (82)
T ss_dssp             CSEEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCEEEEeCCCCCCCH---HHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4578 9999999999   99999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q 023632           98 AEP  100 (279)
Q Consensus        98 a~~  100 (279)
                      |+|
T Consensus        79 a~p   81 (82)
T d1b7fa1          79 ARP   81 (82)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            976

>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=99.87  E-value=1.5e-22  Score=149.81  Aligned_cols=83  Identities=28%  Similarity=0.466  Sum_probs=79.0

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++|+   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.||++.|++++|+|+
T Consensus         4 ~~~tlfV~nLp~~~te---~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~   80 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDD---KVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN   80 (89)
T ss_dssp             CCSCEEEESCCSSCCH---HHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCcEEEEeCCCCcCCH---HHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45788 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +|+|++.
T Consensus        81 ~a~p~~~   87 (89)
T d2cqba1          81 LAKPMRI   87 (89)
T ss_dssp             ECCCCCC
T ss_pred             EeCCCCC
Confidence            9987654

>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=99.86  E-value=4.2e-22  Score=147.63  Aligned_cols=84  Identities=19%  Similarity=0.374  Sum_probs=79.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |.|||.++++   ++|+++|++||+|++|+|++|+.|+++++||||+|++.++|++||+.||+..|++++|+
T Consensus         5 ~~~~~~i~V~nLp~~~t~---~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~   81 (90)
T d2cq0a1           5 ADDNATIRVTNLSEDTRE---TDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILN   81 (90)
T ss_dssp             CSSSEEEEEESCCTTCCH---HHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3456789 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCC
Q 023632           95 VKKAEPKK  102 (279)
Q Consensus        95 V~~a~~~~  102 (279)
                      |++|+|+.
T Consensus        82 v~~akp~~   89 (90)
T d2cq0a1          82 VEWAKPST   89 (90)
T ss_dssp             EEESSCCC
T ss_pred             EEeeeCCC
Confidence            99998764

>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=99.86  E-value=7.6e-22  Score=143.43  Aligned_cols=78  Identities=23%  Similarity=0.496  Sum_probs=75.5

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |+|||++++|   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||++.|++++|+|++|
T Consensus         3 t~l~V~nLp~~~te---~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~A   79 (82)
T d1fxla1           3 TNLIVNYLPQNMTQ---EEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYA   79 (82)
T ss_dssp             SEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCH---HHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            568 9999999999   999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cC
Q 023632           99 EP  100 (279)
Q Consensus        99 ~~  100 (279)
                      +|
T Consensus        80 kP   81 (82)
T d1fxla1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             eC
Confidence            76

>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=99.86  E-value=6.6e-22  Score=145.12  Aligned_cols=81  Identities=21%  Similarity=0.406  Sum_probs=77.2

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      .+| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+.||+++|.+++|+|++|
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   78 (85)
T d2u2fa_           2 HKLFIGGLPNYLND---DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRA   78 (85)
T ss_dssp             CCEEEETCCSSCCS---HHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEEC
T ss_pred             CEEEEECCCCCCCH---HHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            478 9999999999   999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCC
Q 023632           99 EPKKP  103 (279)
Q Consensus        99 ~~~~~  103 (279)
                      ++..+
T Consensus        79 ~~~~~   83 (85)
T d2u2fa_          79 SVGAK   83 (85)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            86543

>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=99.86  E-value=8.4e-22  Score=149.70  Aligned_cols=86  Identities=27%  Similarity=0.454  Sum_probs=78.7

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +++.+.++| |+|||++++|   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||+.+|. +|++++
T Consensus         5 ~~d~~~~~lfV~nLp~~~te---~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~   80 (103)
T d2cqda1           5 QKDTTFTKIFVGGLPYHTTD---ASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRK   80 (103)
T ss_dssp             CCSCSSSEEEEECCCSSCCH---HHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEE
T ss_pred             CCCCCCcEEEEeCCCCcCcH---HHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEE
Confidence            445566789 9999999999   99999999999999999999999999999999999999999999999875 799999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++|.++..
T Consensus        81 l~V~~a~~~~~   91 (103)
T d2cqda1          81 ANVNLAYLGAK   91 (103)
T ss_dssp             CEEEESTTTCC
T ss_pred             EEEEEcCCCCC
Confidence            99999986543

>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=99.86  E-value=1.1e-21  Score=146.26  Aligned_cols=84  Identities=15%  Similarity=0.213  Sum_probs=78.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..+++| |+|||+++|+   ++|+++|++||+|++|+|++++.++++++||||+|+++++|++||+.||+.+|++++|+|
T Consensus         5 ~~s~tlfV~nlp~~~te---~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   81 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTE---EQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT   81 (93)
T ss_dssp             TTCCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            356789 9999999999   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ++|...++
T Consensus        82 ~~a~~~~~   89 (93)
T d1h2vz_          82 DWDAGFKE   89 (93)
T ss_dssp             EEESCCCT
T ss_pred             EEcCCCCC
Confidence            99876443

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=8.2e-22  Score=146.23  Aligned_cols=84  Identities=24%  Similarity=0.398  Sum_probs=77.0

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ...+++| |.|||+++||   ++|+++|++||+|++|+|++|+.|+++||||||+|.++++|++||+.+  +.|+++.|+
T Consensus         5 ~~~~~~lfV~nLp~~~te---~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~~~--~~l~Gr~i~   79 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTE---QDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQR--HMIDGRWCD   79 (90)
T ss_dssp             CCCCCCEEEESCCSSCCH---HHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHSC--EEETTEEEE
T ss_pred             CcCCCeEEEECCCCCCCH---HHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHhcC--CccCCEEeE
Confidence            3456778 9999999999   999999999999999999999999999999999999999999999864  489999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |++|.+++.+
T Consensus        80 v~~a~~k~~~   89 (90)
T d2cqga1          80 CKLPNSKQSQ   89 (90)
T ss_dssp             EECCCTTCCC
T ss_pred             EEeCCCCCCC
Confidence            9999887654

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=7.5e-22  Score=149.71  Aligned_cols=86  Identities=17%  Similarity=0.351  Sum_probs=80.8

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .++.++| |.|||++++|   ++|+++|++||+|++|+|+.++.++++|+||||+|+++++|++||++||+++|.+++|+
T Consensus        15 ~p~~~~l~V~nLp~~~te---~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~   91 (102)
T d2cpza1          15 GPEGANLFIYHLPQEFGD---QDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLK   91 (102)
T ss_dssp             CSTTCCEEEESCCSSCCH---HHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEE
Confidence            3455778 9999999999   99999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |++|+++.++
T Consensus        92 V~~a~~k~~~  101 (102)
T d2cpza1          92 VQLKRSKNDS  101 (102)
T ss_dssp             EECCCCSCCC
T ss_pred             EEEeCCCCCC
Confidence            9999987654

>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=99.85  E-value=2e-21  Score=142.35  Aligned_cols=80  Identities=20%  Similarity=0.444  Sum_probs=75.1

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC--ce
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQ   92 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g--~~   92 (279)
                      +.+.++| |.|||++++|   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+..+.+  ++
T Consensus         3 ~~~~t~lfV~nlp~~~te---~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~   79 (85)
T d1b7fa2           3 SIKDTNLYVTNLPRTITD---DQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQP   79 (85)
T ss_dssp             TTTTCEEEEESCCTTCCH---HHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSC
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeE
Confidence            3456679 9999999999   9999999999999999999999999999999999999999999999999999976  88


Q ss_pred             eEEeec
Q 023632           93 VEVKKA   98 (279)
Q Consensus        93 i~V~~a   98 (279)
                      |+|++|
T Consensus        80 l~V~~A   85 (85)
T d1b7fa2          80 LSVRLA   85 (85)
T ss_dssp             CEEEEC
T ss_pred             EEEEEC
Confidence            999987

>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=99.85  E-value=1.4e-21  Score=144.59  Aligned_cols=84  Identities=29%  Similarity=0.505  Sum_probs=79.3

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |+|||++|++   ++|+++|++||+|++|.+++++.++++++||||+|+++++|++||+.||+++|++++|+|+
T Consensus         4 ~~~kifV~nLp~~~t~---~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~   80 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNE---QSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD   80 (90)
T ss_dssp             CCSEEEEESCCTTCCH---HHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEE
T ss_pred             CCCEEEEECCCCcCCH---HHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45779 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCCC
Q 023632           97 KAEPKKPN  104 (279)
Q Consensus        97 ~a~~~~~~  104 (279)
                      +|.++.++
T Consensus        81 ~a~~~~~~   88 (90)
T d1x5sa1          81 QAGKSSDN   88 (90)
T ss_dssp             EEECCCCC
T ss_pred             EcCCCCCC
Confidence            99877654

>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=99.85  E-value=3.1e-21  Score=144.15  Aligned_cols=86  Identities=22%  Similarity=0.406  Sum_probs=78.8

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCC-CCCcccEEEEEEcCHHHHHHHHHHc-CCCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHS-TSRSRGFGFITFDTEQAVDDLLAKG-NKLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~-tg~~rG~aFV~F~s~e~a~~Ai~~l-ng~~l~g~   91 (279)
                      +...+++| |.|||++++|   ++|+++|++||+|++|+|++++. ++++++||||+|+++++|++||+.| |+.+|+++
T Consensus         4 ~~~~~~~l~V~nLp~~~~e---~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr   80 (94)
T d2cpha1           4 KKQTTSKILVRNIPFQANQ---REIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGR   80 (94)
T ss_dssp             CSSCCCCEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSC
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCE
Confidence            44566788 9999999999   99999999999999999998864 8899999999999999999999998 89999999


Q ss_pred             eeEEeeccCCCC
Q 023632           92 QVEVKKAEPKKP  103 (279)
Q Consensus        92 ~i~V~~a~~~~~  103 (279)
                      +|+|++|+++..
T Consensus        81 ~l~V~~A~~~~~   92 (94)
T d2cpha1          81 RLVLEWADSEVT   92 (94)
T ss_dssp             BCEEEECCCCCC
T ss_pred             EEEEEEcCCCCC
Confidence            999999987654

>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=99.85  E-value=2.2e-21  Score=140.54  Aligned_cols=76  Identities=22%  Similarity=0.309  Sum_probs=74.1

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      +| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+.||+..|++++|+|++|+
T Consensus         2 slfV~nL~~~~te---~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTE---AMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCH---HHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            58 9999999999   9999999999999999999999999999999999999999999999999999999999999985

>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=99.85  E-value=2.9e-21  Score=141.63  Aligned_cols=79  Identities=27%  Similarity=0.431  Sum_probs=74.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC--cee
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--AQV   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g--~~i   93 (279)
                      .+.++| |.|||+++||   ++|+++|++||+|++|+|++|+.++++++||||+|+++++|++||+.||+++|++  ++|
T Consensus         4 ~k~~~lfV~nLp~~~te---~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i   80 (85)
T d1fxla2           4 IRDANLYVSGLPKTMTQ---KELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI   80 (85)
T ss_dssp             GTTCEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCC
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEE
Confidence            455779 9999999999   9999999999999999999999999999999999999999999999999999987  569


Q ss_pred             EEeec
Q 023632           94 EVKKA   98 (279)
Q Consensus        94 ~V~~a   98 (279)
                      +|++|
T Consensus        81 ~V~~A   85 (85)
T d1fxla2          81 TVKFA   85 (85)
T ss_dssp             EEEEC
T ss_pred             EEEeC
Confidence            99886

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins A2/B1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.85  E-value=5.9e-22  Score=150.67  Aligned_cols=82  Identities=32%  Similarity=0.579  Sum_probs=77.0

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |+|||+++++   ++|+++|++||+|++|.|++|+.|.++++||||+|.+.++|++||+ ++++.|++++|+|++
T Consensus        20 ~~~lfVgnLp~~~te---~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~-~~~~~l~G~~i~V~~   95 (103)
T d1x4ba1          20 FRKLFIGGLSFETTE---ESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA-ARPHSIDGRVVEPKR   95 (103)
T ss_dssp             HTEEEEECCTTCCCH---HHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHT-SCSEEETTEEEEEEC
T ss_pred             CCEEEEeCCCCcCCH---HHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHH-hCCCeECCEEEEEEE
Confidence            4689 9999999999   9999999999999999999999999999999999999999999996 589999999999999


Q ss_pred             ccCCCCC
Q 023632           98 AEPKKPN  104 (279)
Q Consensus        98 a~~~~~~  104 (279)
                      |++++++
T Consensus        96 a~~ke~~  102 (103)
T d1x4ba1          96 AVAREES  102 (103)
T ss_dssp             CSSCCCC
T ss_pred             CcccCCC
Confidence            9987653

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=4e-21  Score=140.59  Aligned_cols=80  Identities=33%  Similarity=0.542  Sum_probs=75.0

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+. +++.|+++.|+|
T Consensus         4 e~~~~lfV~nlp~~~te---~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~-~~~~i~Gr~i~V   79 (84)
T d1l3ka1           4 EQLRKLFIGGLSFETTD---ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEP   79 (84)
T ss_dssp             GGGGEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEE
T ss_pred             CCCcEEEEECCCCCCCH---HHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHh-CCCEECCEEEEE
Confidence            345789 9999999999   99999999999999999999999999999999999999999999985 889999999999


Q ss_pred             eeccC
Q 023632           96 KKAEP  100 (279)
Q Consensus        96 ~~a~~  100 (279)
                      +.|.+
T Consensus        80 ~~A~s   84 (84)
T d1l3ka1          80 KRAVS   84 (84)
T ss_dssp             EECCC
T ss_pred             EeeeC
Confidence            99863

>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=99.84  E-value=1.3e-21  Score=140.89  Aligned_cols=75  Identities=41%  Similarity=0.655  Sum_probs=72.1

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++|+||||+|+++++|++||++ |.++|++++|+|++|
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 CKMFIGGLSWQTTQ---EGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQ-SRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCS---HHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHT-TTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCH---HHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHc-CCCEECCeEEEEEEC
Confidence            478 9999999999   99999999999999999999999999999999999999999999984 999999999999987

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.84  E-value=3.9e-21  Score=140.10  Aligned_cols=76  Identities=24%  Similarity=0.450  Sum_probs=72.9

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      .+.++| |.|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|+++++|++||++||+++|++++|+|
T Consensus         7 ~~~~~l~V~nL~~~~te---~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           7 DPNCCLGVFGLSLYTTE---RDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CGGGCEEEESCCSSCCH---HHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            446788 9999999999   999999999999999999999999999999999999999999999999999999999987

>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=99.84  E-value=1.3e-21  Score=148.60  Aligned_cols=83  Identities=23%  Similarity=0.442  Sum_probs=78.4

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |+|||++++|   ++|+++|++||+|++|+|++++.|+++++||||+|.++++|++||+.||+++|.+++|+|+
T Consensus         7 ~~rtl~V~nLp~~~te---~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~   83 (104)
T d1p1ta_           7 SLRSVFVGNIPYEATE---EQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVD   83 (104)
T ss_dssp             HHSCEEEESCCTTSCH---HHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEE
T ss_pred             CCCEEEEECCCCcCCH---HHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            35679 9999999999   9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +|.+++.
T Consensus        84 ~a~~~~~   90 (104)
T d1p1ta_          84 NAASEKN   90 (104)
T ss_dssp             ETTCTTH
T ss_pred             ECCCCCC
Confidence            9987643

>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=99.84  E-value=7.7e-21  Score=140.73  Aligned_cols=85  Identities=20%  Similarity=0.315  Sum_probs=77.2

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +++.+.++| |.|||+++||   ++|+++|++||+|++|+|++|+.+.  ++||||+|+++++|++||+.||++.|.++.
T Consensus         3 ~d~~~~~tl~V~nLp~~~te---~~l~~~F~~~G~i~~v~i~~d~~~~--~~~afV~f~~~~~A~~A~~~l~~~~~~g~~   77 (90)
T d2cqia1           3 EDDGQPRTLYVGNLSRDVTE---VLILQLFSQIGPCKSCKMITEHTSN--DPYCFVEFYEHRDAAAALAAMNGRKILGKE   77 (90)
T ss_dssp             CCSCCCCEEEEESCCTTCCH---HHHHHHHHHHSCEEEEEEECCCCSS--CCEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCH---HHHHHHHHhcCCceeeeeecccCcc--ceeeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            445667889 9999999999   9999999999999999999987654  789999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++|+++..
T Consensus        78 i~v~~a~~~~~   88 (90)
T d2cqia1          78 VKVNWATTPSS   88 (90)
T ss_dssp             EEEEECCCTTC
T ss_pred             EEEEEcCCCCC
Confidence            99999987543

>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=99.84  E-value=1.1e-20  Score=140.86  Aligned_cols=85  Identities=22%  Similarity=0.436  Sum_probs=77.6

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      +.+...++| |.|||+++++   ++|+++|++||+|++|+|++++.  .+++||||+|+++++|++||+.||+.+|++++
T Consensus         6 ~~~~~~~~l~v~nLp~~~t~---~~L~~~F~~~G~v~~v~~~~~~~--~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~   80 (93)
T d2cq3a1           6 ESKSTPKRLHVSNIPFRFRD---PDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKLHGTVVEGRK   80 (93)
T ss_dssp             CCSCCCCEEEEESCCTTCCH---HHHHHHGGGTSCEEEEEEECCTT--TTCCEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             CCCCCCCEEEEECCCCCCCH---HHHHHHHhhcceeeecccccccc--CCcceeEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            345667789 9999999999   99999999999999999999864  36899999999999999999999999999999


Q ss_pred             eEEeeccCCCC
Q 023632           93 VEVKKAEPKKP  103 (279)
Q Consensus        93 i~V~~a~~~~~  103 (279)
                      |+|++|+++..
T Consensus        81 l~V~~A~~r~~   91 (93)
T d2cq3a1          81 IEVNNATARVM   91 (93)
T ss_dssp             CEEEECCSSCC
T ss_pred             EEEEecCcCCC
Confidence            99999988654

>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=99.84  E-value=2.9e-21  Score=140.71  Aligned_cols=79  Identities=29%  Similarity=0.393  Sum_probs=74.3

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEE-EEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEH-QIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v-~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      | |.|||+++||   ++|+++|++||+|+++ +|++|+.|+++++||||+|+++++|++||+.||++.|++++|+|++|.
T Consensus         1 lfV~nLp~~~te---~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~   77 (83)
T d1x5ta1           1 IFIGNLDPEIDE---KLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAF   77 (83)
T ss_dssp             EEEECCCTTCCH---HHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESC
T ss_pred             CEEcCCCCcCcH---HHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEec
Confidence            6 9999999999   9999999999999764 789999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q 023632          100 PKKP  103 (279)
Q Consensus       100 ~~~~  103 (279)
                      +++.
T Consensus        78 ~k~~   81 (83)
T d1x5ta1          78 KKDS   81 (83)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            7654

>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=99.83  E-value=5.1e-21  Score=140.06  Aligned_cols=77  Identities=21%  Similarity=0.374  Sum_probs=72.0

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCC---CcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTS---RSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg---~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      | |+|||+++|+   ++|+++|++||+|++|+|++++.+.   ++||||||+|+++++|++||+.||+++|++++|+|++
T Consensus         1 LfV~nLp~~~t~---~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~   77 (85)
T d2cpfa1           1 LFIKNLNFSTTE---ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRI   77 (85)
T ss_dssp             EEEESCCTTCCH---HHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEEC
T ss_pred             CEEcCCCCCCCH---HHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            6 9999999999   9999999999999999999987765   4689999999999999999999999999999999999


Q ss_pred             ccCC
Q 023632           98 AEPK  101 (279)
Q Consensus        98 a~~~  101 (279)
                      |+++
T Consensus        78 a~~~   81 (85)
T d2cpfa1          78 SERA   81 (85)
T ss_dssp             SSCS
T ss_pred             CCCC
Confidence            8654

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein d0
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.83  E-value=4.7e-21  Score=137.19  Aligned_cols=74  Identities=35%  Similarity=0.623  Sum_probs=70.6

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++++||||+|.++++|++||+ ++.+.|++++|+|+.|
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 KMFIGGLSWDTTK---KDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD-QKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCH---HHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHH-TCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCH---HHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHh-cCCCEECCCEEEeeEC
Confidence            47 9999999999   9999999999999999999999999999999999999999999998 5899999999999865

>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=99.83  E-value=6.1e-21  Score=137.60  Aligned_cols=76  Identities=17%  Similarity=0.332  Sum_probs=72.7

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      +| |.|||++++|   ++|+++|++||+|++|+|++++ ++++++||||+|+++++|++||+.||+++|++++|+|++|.
T Consensus         2 rl~V~nLp~~~~~---~~l~~~F~~~G~v~~~~i~~~~-~g~~~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~l~V~~a~   77 (78)
T d1no8a_           2 KLLVSNLDFGVSD---ADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCH---HHHHHHHHHHSCEEEEEESCSS-CCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCH---HHHHHHHHHhCCCeEEEEEEee-ccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            57 9999999999   9999999999999999999996 89999999999999999999999999999999999999986


Q ss_pred             C
Q 023632          100 P  100 (279)
Q Consensus       100 ~  100 (279)
                      +
T Consensus        78 S   78 (78)
T d1no8a_          78 S   78 (78)
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=99.83  E-value=4.4e-21  Score=139.15  Aligned_cols=78  Identities=17%  Similarity=0.212  Sum_probs=68.7

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||+++||   ++|+++|++||+|+.+.++.++.++++++||||+|+++++|++||+.||++.|++++|+|++|
T Consensus         2 ~tl~v~nLp~~~t~---~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a   78 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQ---RNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVS   78 (81)
T ss_dssp             CEEEEECCCTTCCH---HHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             cEEEEECCCCcCCH---HHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            688 9999999999   999999999999999999988889999999999999999999999999999999999999999


Q ss_pred             cC
Q 023632           99 EP  100 (279)
Q Consensus        99 ~~  100 (279)
                      +|
T Consensus        79 ~P   80 (81)
T d2ghpa1          79 NP   80 (81)
T ss_dssp             CC
T ss_pred             cC
Confidence            86

>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=99.83  E-value=6.4e-22  Score=149.93  Aligned_cols=80  Identities=20%  Similarity=0.383  Sum_probs=75.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +.++| |.|||++++|   ++|+++|++||+|++|+|++|+.|+++||||||+|+++++|++||+ ||+..|++++|+|+
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~   92 (101)
T d2cq4a1          17 DARTVFCMQLAARIRP---RDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIG-LTGQRLLGVPIIVQ   92 (101)
T ss_dssp             HHTEEEEESCCTTCCH---HHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHH-HTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCCCH---HHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            45689 9999999999   9999999999999999999999999999999999999999999996 89999999999999


Q ss_pred             eccCC
Q 023632           97 KAEPK  101 (279)
Q Consensus        97 ~a~~~  101 (279)
                      +|+++
T Consensus        93 ~a~~~   97 (101)
T d2cq4a1          93 ASQAE   97 (101)
T ss_dssp             EHHHH
T ss_pred             ECCCC
Confidence            98764

>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=99.83  E-value=6.2e-21  Score=140.95  Aligned_cols=80  Identities=23%  Similarity=0.422  Sum_probs=74.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      ..+| |.|||+++++   ++|+++|++||+|++|+|+.++.  .+++||||+|+++++|++||+.||++.|++++|+|++
T Consensus         8 ~~~l~V~nLp~~~t~---~~l~~~F~~~G~v~~~~i~~~~~--~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~   82 (89)
T d1cvja2           8 VGNIFIKNLDKSIDN---KALYDTFSAFGNILSCKVVCDEN--GSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR   82 (89)
T ss_dssp             TTEEEEESCCSSCCH---HHHHHHHHTTSCEEEEEECCBTT--BCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEE
T ss_pred             CCEEEEeCCCCCCCH---HHHHHHHHhcCCceEEEEEeecC--CCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4568 9999999999   99999999999999999999864  4689999999999999999999999999999999999


Q ss_pred             ccCCCC
Q 023632           98 AEPKKP  103 (279)
Q Consensus        98 a~~~~~  103 (279)
                      |+++++
T Consensus        83 a~~~~~   88 (89)
T d1cvja2          83 FKSRKE   88 (89)
T ss_dssp             CCCTTT
T ss_pred             CCCCCC
Confidence            988765

>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=99.82  E-value=1.2e-20  Score=142.22  Aligned_cols=88  Identities=20%  Similarity=0.314  Sum_probs=79.4

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeE--------EEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQ--------EHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~--------~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      +++.+.++| |.|||+++||   ++|+++|++||+|+        .+.+++++.++++++||||+|.++++|++||+.||
T Consensus         3 ~~~~~~~~i~V~nLp~~~te---~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~   79 (101)
T d2cpea1           3 DEDSDNSAIYVQGLNDSVTL---DDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFD   79 (101)
T ss_dssp             CCCCCCCEEEEECCCTTCCH---HHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHT
T ss_pred             CCCCCCCEEEEECCCCcCCH---HHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhC
Confidence            345667889 9999999999   99999999999884        56778888899999999999999999999999999


Q ss_pred             CCccCCceeEEeeccCCCCC
Q 023632           85 KLELAGAQVEVKKAEPKKPN  104 (279)
Q Consensus        85 g~~l~g~~i~V~~a~~~~~~  104 (279)
                      +++|++++|+|++|+++.++
T Consensus        80 g~~~~gr~i~V~~a~~~~p~   99 (101)
T d2cpea1          80 GKDFQGSKLKVSLARKKPPM   99 (101)
T ss_dssp             TCEETTEECEEECSSCCCCS
T ss_pred             CCEECCEEEEEEEcCCCCCC
Confidence            99999999999999876554

>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=99.82  E-value=2.2e-20  Score=139.89  Aligned_cols=86  Identities=24%  Similarity=0.348  Sum_probs=78.3

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC------CCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN------KLE   87 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln------g~~   87 (279)
                      +..+.++| |+|||+++||   ++|+++|++||+|+++.|+.++.+.++++||||+|.++++|++||+.||      +..
T Consensus         4 ~~~~~~tlfV~nLp~~~te---~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~   80 (98)
T d1x4ha1           4 DVTEGKTVFIRNLSFDSEE---EALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLK   80 (98)
T ss_dssp             CCCCCCCEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEE
T ss_pred             CCCCCCEEEEcCCCCcCCH---HHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcE
Confidence            34456788 9999999999   9999999999999999999999999999999999999999999999886      567


Q ss_pred             cCCceeEEeeccCCCC
Q 023632           88 LAGAQVEVKKAEPKKP  103 (279)
Q Consensus        88 l~g~~i~V~~a~~~~~  103 (279)
                      |++++|+|++|+++.+
T Consensus        81 ~~gr~l~v~~a~~k~~   96 (98)
T d1x4ha1          81 LDGRQLKVDLAVTRDE   96 (98)
T ss_dssp             SSSCEEEEECCCCCCC
T ss_pred             ECCEEEEEEECCCCCc
Confidence            8999999999987654

>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=99.82  E-value=4.7e-21  Score=137.34  Aligned_cols=74  Identities=30%  Similarity=0.547  Sum_probs=70.6

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +| |+|||+++||   ++|+++|++||+|++|+|++|+.|+++||||||+|+++++|++||+. +.++|+++.|+|+.|
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 KIFVGGLSPDTPE---EKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK-KYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCH---HHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTC-SSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCH---HHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhh-CCCEECCEEeEEEEC
Confidence            57 9999999999   99999999999999999999999999999999999999999999986 678999999999876

>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=99.82  E-value=3.3e-20  Score=133.71  Aligned_cols=77  Identities=31%  Similarity=0.600  Sum_probs=73.1

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |+|||+++||   ++|+++|++||+|+.+.|+.++.+.++++||||+|.++|+|++||+ +|+++|++++|+|++
T Consensus         2 ~r~lfV~nLp~~~te---~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~-~~~~~l~Gr~i~V~~   77 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEE---HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNCEVRK   77 (79)
T ss_dssp             CSEEEEECCTTTCCH---HHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHH-CSCCEETTEECEEEE
T ss_pred             CCEEEECCCCCcCCH---HHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHH-hCCCEECCEEEEEEE
Confidence            5789 9999999999   9999999999999999999999999999999999999999999996 699999999999998


Q ss_pred             cc
Q 023632           98 AE   99 (279)
Q Consensus        98 a~   99 (279)
                      |.
T Consensus        78 A~   79 (79)
T d1l3ka2          78 AL   79 (79)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>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=99.81  E-value=2.5e-20  Score=136.84  Aligned_cols=82  Identities=17%  Similarity=0.283  Sum_probs=70.6

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeec-CCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRD-HSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d-~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .+.++| |.|||++++++  ++|+++|++||+|++|+|+.+ +.++++++||||+|+++++|++||+ ||+++|++++|+
T Consensus         2 ~e~~~l~V~nLp~~~t~e--d~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~-~n~~~~~gr~l~   78 (86)
T d2ghpa3           2 LEGREIMIRNLSTELLDE--NLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQ-MNRSLLGNREIS   78 (86)
T ss_dssp             CTTTEEEEEEECTTTCCH--HHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGG-GTTEEETTEEEE
T ss_pred             CCCCEEEEECCCCCcccH--HHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHh-cCCCEECCEEEE
Confidence            356889 99999998750  459999999999999998764 5689999999999999999999996 899999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |++|+++
T Consensus        79 V~~a~~k   85 (86)
T d2ghpa3          79 VSLADKK   85 (86)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            9999875

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=6.7e-20  Score=139.00  Aligned_cols=86  Identities=21%  Similarity=0.348  Sum_probs=74.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~-~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .+.++| |.|||+++||   ++|+++|++|+ |++++|+.++ .++++++||||+|+++++|++|+ +||+++|++++|+
T Consensus        13 ~p~~~v~V~nLp~~~te---~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~-~~~~~~~~gr~l~   87 (104)
T d1wi8a_          13 SPPYTAFLGNLPYDVTE---ESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL-SLNEESLGNKRIR   87 (104)
T ss_dssp             SSCEEEEEESCCSSCCH---HHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHH-GGGTCEETTEECE
T ss_pred             CCCCEEEEeCCCCcCCH---HHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHH-HcCCCEECCEEEE
Confidence            456789 9999999999   99999999998 7777777665 47889999999999999998776 5899999999999


Q ss_pred             EeeccCCCCCCCC
Q 023632           95 VKKAEPKKPNLPQ  107 (279)
Q Consensus        95 V~~a~~~~~~~~~  107 (279)
                      |++|++++.....
T Consensus        88 V~~a~~~~~~~~~  100 (104)
T d1wi8a_          88 VDVADQAQDKDSG  100 (104)
T ss_dssp             EEECCCCCCCCCC
T ss_pred             EEECCCCCCCCCC
Confidence            9999887665443

>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=99.80  E-value=3.2e-20  Score=132.30  Aligned_cols=74  Identities=38%  Similarity=0.608  Sum_probs=71.2

Q ss_pred             ee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           21 KM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        21 ~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +| |+|||+++||   ++|+++|++||.|+.+.+++++.++++++||||+|+++++|++||+ +|+++|++++|+|++|
T Consensus         1 rlfV~nLp~~~te---~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~-~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTV---EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE-IHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCH---HHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHH-CSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCH---HHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHh-cCCCEECCeEEEEEEC
Confidence            47 9999999999   9999999999999999999999999999999999999999999997 8999999999999986

>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=99.80  E-value=1.5e-19  Score=137.24  Aligned_cols=88  Identities=15%  Similarity=0.172  Sum_probs=78.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +..+..+| |.|||+++||   ++|+++|+.++.|+.+.++.++.++++++||||+|+++++|++||+ +|++.|+++.|
T Consensus        11 ~~~~~~~v~v~nLP~~~te---~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~-~~~~~i~gR~i   86 (104)
T d1wg5a_          11 DTANDGFVRLRGLPFGCSK---EEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK-KHKERIGHRYI   86 (104)
T ss_dssp             SCSCCCEEEEESCCTTCCH---HHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHT-TTTCCSSSSCC
T ss_pred             CCCCCcEEEEeCCCCCCCH---HHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHh-hCCCEEcceEE
Confidence            34455678 9999999999   9999999999999987777777899999999999999999999996 79999999999


Q ss_pred             EEeeccCCCCCCC
Q 023632           94 EVKKAEPKKPNLP  106 (279)
Q Consensus        94 ~V~~a~~~~~~~~  106 (279)
                      +|.++.+++...+
T Consensus        87 ~V~~~~~~~~~~s   99 (104)
T d1wg5a_          87 EIFKSSRAEVRTS   99 (104)
T ss_dssp             EEEEECTTTSCCS
T ss_pred             EEEECCHHHhccC
Confidence            9999988765543

>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=99.80  E-value=8.1e-21  Score=143.50  Aligned_cols=86  Identities=23%  Similarity=0.257  Sum_probs=80.3

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..++++| |.|||.++++   ++|+++|++||.|+.+.|+.++.++++++||||+|.++++|++||+.||+++|.+++|+
T Consensus        15 ~~ps~tl~V~nLp~~~t~---~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~   91 (102)
T d2cpxa1          15 GEPNKVLYLKNLSPRVTE---RDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   91 (102)
T ss_dssp             CSCCSEEEEECCCTTCCH---HHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCCEEEEeCCCCCCCH---HHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEE
Confidence            3456889 9999999999   99999999999999999999888999999999999999999999999999999999999


Q ss_pred             EeeccCCCCC
Q 023632           95 VKKAEPKKPN  104 (279)
Q Consensus        95 V~~a~~~~~~  104 (279)
                      |++|++++++
T Consensus        92 V~~ak~k~~r  101 (102)
T d2cpxa1          92 IEFGKNKKQR  101 (102)
T ss_dssp             EEECCCCSCC
T ss_pred             EEeCCCcccC
Confidence            9999987654

>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=99.79  E-value=1.7e-19  Score=135.13  Aligned_cols=79  Identities=16%  Similarity=0.351  Sum_probs=72.6

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ..+..++| |.|||.+++|   ++|+++|++||+|++|+|+.+      |+||||+|+++++|++||+.||+++|.+++|
T Consensus        14 ~~~~~~~l~v~nL~~~~te---~~L~~~F~~fG~i~~v~i~~~------kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l   84 (96)
T d1x4ga1          14 SSPKNCTVYCGGIASGLTD---QLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAIVSVNGTTIEGHVV   84 (96)
T ss_dssp             SCSSCCEEEEECCSSCCCH---HHHHHHHHHHSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHTTCEETTEEC
T ss_pred             CCCCCCEEEEcCCCCCCCH---HHHHHHHHHhCCceEEEEEec------ceEEEEEECCHHHHHHHHHHhCCCEECCEEE
Confidence            34556789 9999999999   999999999999999999976      6899999999999999999999999999999


Q ss_pred             EEeeccCCC
Q 023632           94 EVKKAEPKK  102 (279)
Q Consensus        94 ~V~~a~~~~  102 (279)
                      +|++++++.
T Consensus        85 ~v~~ak~~p   93 (96)
T d1x4ga1          85 KCYWGKESP   93 (96)
T ss_dssp             EEECCCCCC
T ss_pred             EEEEcCCCC
Confidence            999997654

>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=99.79  E-value=2.3e-19  Score=133.94  Aligned_cols=80  Identities=13%  Similarity=0.346  Sum_probs=72.1

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      ..+.++| |.|||+++|+   ++|+++|++|++|+.|+++.+   ..+++||||+|+++++|++||+.||+++|++++|+
T Consensus        11 ~~~~~~l~V~nLp~~~t~---~~l~~~F~~~G~v~~~~~~~~---~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~   84 (95)
T d1x4aa1          11 GNNDCRIYVGNLPPDIRT---KDIEDVFYKYGAIRDIDLKNR---RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLR   84 (95)
T ss_dssp             CCCSSEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEECCS---SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHHhcCCceEEEEeccc---ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEE
Confidence            3455679 9999999999   999999999999999987654   35689999999999999999999999999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |++|++.
T Consensus        85 V~~a~~~   91 (95)
T d1x4aa1          85 VEFPRSG   91 (95)
T ss_dssp             EECCCCC
T ss_pred             EEeccCC
Confidence            9998764

>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=99.79  E-value=1.4e-19  Score=136.12  Aligned_cols=80  Identities=18%  Similarity=0.354  Sum_probs=69.9

Q ss_pred             CCCCCcee-eeCCC-CCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce
Q 023632           15 RQTTTQKM-TGLSL-TPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ   92 (279)
Q Consensus        15 ~~~~~~~l-V~nLp-~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~   92 (279)
                      .....++| |.||| +.+++   ++|+++|++||+|++|+|.        |+||||+|+++++|++||++||+++|++++
T Consensus        11 ~~~~~~~lfV~nL~~~~~~~---~~L~~~F~~~G~i~~~~i~--------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~   79 (98)
T d1wf2a_          11 PRSMNSRVFIGNLNTLVVKK---SDVEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAVAGEDGRMIAGQV   79 (98)
T ss_dssp             CSSCCCCEEEEEECTTTCCH---HHHHHSSTTSSCEEEEEEE--------TEEEEEEESSHHHHHHHHHTTTTCEETTEE
T ss_pred             CCCCCcEEEEeCCCcccCCH---HHHHHHHhhcCCEEEEEEe--------CCeEEEEECCHHHHHHHHHHcCCCEECCEE
Confidence            34455678 99997 56788   8999999999999999983        689999999999999999999999999999


Q ss_pred             eEEeeccCCCCCC
Q 023632           93 VEVKKAEPKKPNL  105 (279)
Q Consensus        93 i~V~~a~~~~~~~  105 (279)
                      |+|++|++++...
T Consensus        80 l~V~~a~~~~~~~   92 (98)
T d1wf2a_          80 LDINLAAEPKVNR   92 (98)
T ss_dssp             CEEEETTSCCCCS
T ss_pred             EEEEECCCCCCCC
Confidence            9999998755443

>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=99.78  E-value=6.9e-20  Score=134.69  Aligned_cols=76  Identities=17%  Similarity=0.195  Sum_probs=68.4

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |+|||++|++   ++|+++|++||+|++|+|++|       +||||+|+++++|++||+.||+.+|+++.|+|.++
T Consensus         1 nrvfV~nlp~~~~~---~~l~~~F~~~G~v~~~~i~~~-------g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~   70 (87)
T d3begb1           1 NRVVVSGLPPSGSW---QDLKDHMREAGDVCYADVYRD-------GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYI   70 (87)
T ss_dssp             CCEEEEECCSSCCT---THHHHHHGGGSCEEEEEECTT-------SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBC
T ss_pred             CeEEEECCCCcCCH---HHHHHHHhhhccccccccccc-------ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEE
Confidence            367 9999999999   999999999999999998754       69999999999999999999999999999999988


Q ss_pred             cCCCCCC
Q 023632           99 EPKKPNL  105 (279)
Q Consensus        99 ~~~~~~~  105 (279)
                      +++.+..
T Consensus        71 ~~~~~~~   77 (87)
T d3begb1          71 RVKVDGP   77 (87)
T ss_dssp             EEEECC-
T ss_pred             ecCcCCC
Confidence            7655443

>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=99.78  E-value=3.4e-19  Score=133.23  Aligned_cols=85  Identities=19%  Similarity=0.254  Sum_probs=75.6

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCC-eEEEEEeecC-CCCCcccEEEEEEcCHHHHHHHHHHcCC--CccCCceeE
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGD-VQEHQIMRDH-STSRSRGFGFITFDTEQAVDDLLAKGNK--LELAGAQVE   94 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~-V~~v~i~~d~-~tg~~rG~aFV~F~s~e~a~~Ai~~lng--~~l~g~~i~   94 (279)
                      ++| |+|||.++++   ++|+++|++|++ |++|+|++|+ .++++++||||+|+++++|++||+.|+.  ..+.+++|+
T Consensus         2 ~rLyV~nLp~~~te---~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~   78 (96)
T d2disa1           2 CRLFIGGIPKMKKR---EEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   78 (96)
T ss_dssp             EEEEEECCCTTSCH---HHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             CEEEEcCCCCcCCH---HHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEE
Confidence            678 9999999999   999999999996 8999999885 4688999999999999999999999864  566799999


Q ss_pred             EeeccCCCCCCCC
Q 023632           95 VKKAEPKKPNLPQ  107 (279)
Q Consensus        95 V~~a~~~~~~~~~  107 (279)
                      |++|+|++++.+.
T Consensus        79 V~~A~p~~~~~~~   91 (96)
T d2disa1          79 VDWAEPEIDVDED   91 (96)
T ss_dssp             EEESCSSCSTTTC
T ss_pred             EEEcCCCCCCChH
Confidence            9999987766543

>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=99.78  E-value=2.2e-19  Score=135.84  Aligned_cols=85  Identities=18%  Similarity=0.134  Sum_probs=74.2

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      +....++| |.|||+++||   ++|+++|+.|+ |++|.|+++. ++++++||||+|+++++|++||+ ||+++|++|.|
T Consensus        11 ~~~~~~~v~v~nLp~~~te---~dl~~~F~~~~-~~~v~~~~~~-~g~~~G~afVeF~~~~~a~~Al~-~~~~~i~gR~I   84 (102)
T d1weza_          11 QSTTGHCVHMRGLPYRATE---NDIYNFFSPLN-PMRVHIEIGP-DGRVTGEADVEFATHEDAVAAMA-KDKANMQHRYV   84 (102)
T ss_dssp             CCSSSCEEEEESCCTTCCH---HHHHHSSCSCC-CSEEEEEESS-SSCEEEEEEEECSSSHHHHHHHT-TSSCCSSSSCC
T ss_pred             cCCCCCEEEEeCCCCcCCH---HHHHHHHhccC-cceeeeEEec-CCcceEEEEEEECCHHHHHHHHH-cCCCEECCEEE
Confidence            44556788 9999999999   99999999997 5578888875 67899999999999999999986 69999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|.++.++....
T Consensus        85 ~V~~s~~~~~~~   96 (102)
T d1weza_          85 ELFLNSTAGTSG   96 (102)
T ss_dssp             EEEEECCCCCCC
T ss_pred             EEEEcCCCCCCC
Confidence            999998765443

>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=99.78  E-value=1.4e-19  Score=136.63  Aligned_cols=82  Identities=20%  Similarity=0.365  Sum_probs=75.4

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .+.+.++| |.|||++|+|   ++|+++|++||+|+.+.|+.+. +.++++||||+|+++++|++||+.||+.+|.+++|
T Consensus        14 ~~~~~~~lfV~nLp~~~te---~~L~~~F~~~G~i~~~~~~~~~-~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~   89 (101)
T d1x5oa1          14 QEQDPTNLYISNLPLSMDE---QELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPG   89 (101)
T ss_dssp             CCCCTTEEEEESCCTTCCH---HHHHHTTTTTSCEEEEEEEECS-SSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTT
T ss_pred             ccCCCCEEEEeCCCCCCCH---HHHHHHHhhcccccceeeeccc-ccccccceeEEeCCHHHHHHHHHHhCCCEECCcCC
Confidence            44556789 9999999999   9999999999999999999885 78999999999999999999999999999999999


Q ss_pred             EEeeccC
Q 023632           94 EVKKAEP  100 (279)
Q Consensus        94 ~V~~a~~  100 (279)
                      .|.+++|
T Consensus        90 ~v~~~~P   96 (101)
T d1x5oa1          90 VSAPTEP   96 (101)
T ss_dssp             SCCCSSC
T ss_pred             ccCCCCC
Confidence            9987765

>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=99.77  E-value=2.2e-20  Score=138.69  Aligned_cols=81  Identities=17%  Similarity=0.304  Sum_probs=73.8

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      +....+| |.|||+++|+   ++|+++|++||+|++|+|+.+ .++++++||||+|+++++|++||+ ||+++|++++|+
T Consensus        10 ~~~~~~ifV~nL~~~~te---~~l~~~F~~~G~i~~~~v~~~-~~g~~kg~afv~F~~~e~a~~Al~-~~g~~~~g~~i~   84 (91)
T d1fjeb1          10 STTPFNLFIGNLNPNKSV---AELKVAISELFAKNDLAVVDV-RTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIK   84 (91)
T ss_dssp             CSSSEEEEEECCCTTSCH---HHHHHHHHHHHHHHTCCCCEE-EEETTTTEEEEEESSHHHHHHHHH-GGGEEETTEEEE
T ss_pred             CCCCcEEEEeCccCcchH---HHHHHHHhcCCcEEEeeeeec-CCCCccEEeEEeeCCHHHHHHHHh-cCCcEECCEEEE
Confidence            4455688 9999999999   999999999999999988755 589999999999999999999996 899999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |++|+++
T Consensus        85 V~~ak~k   91 (91)
T d1fjeb1          85 LEKPKGR   91 (91)
T ss_dssp             EECCCCS
T ss_pred             EEecCCC
Confidence            9999864

>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=99.77  E-value=5.2e-19  Score=134.88  Aligned_cols=77  Identities=14%  Similarity=0.202  Sum_probs=70.0

Q ss_pred             Ccee-eeCCCC-CCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           19 TQKM-TGLSLT-PVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        19 ~~~l-V~nLp~-~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      +++| |.|||+ .|||   ++|+++|++||+|++|+|++++     ++||||+|+++++|++||+.||++.|++++|+|+
T Consensus         2 ~~~l~V~nL~p~~~te---~~L~~~F~~fG~I~~v~i~~~~-----kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~   73 (109)
T d2adca1           2 NSVLLVSNLNPERVTP---QSLFILFGVYGDVQRVKILFNK-----KENALVQMADGNQAQLAMSHLNGHKLHGKPIRIT   73 (109)
T ss_dssp             CSEEEEESCCTTTCCH---HHHHHHHHHHTCEEEEEECCTT-----SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEE
T ss_pred             CCEEEEeCCCcccCCH---HHHHHHHhhccccceEEEEecc-----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4678 999965 5999   9999999999999999999874     7899999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +++.+..
T Consensus        74 ~s~~~~~   80 (109)
T d2adca1          74 LSKHQNV   80 (109)
T ss_dssp             CCSCCCC
T ss_pred             ECCCCCC
Confidence            9976543

>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=99.77  E-value=1.9e-19  Score=131.83  Aligned_cols=80  Identities=13%  Similarity=0.201  Sum_probs=71.5

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .+..++| |.|||++++|   +||+++|+.|+.|.++.++.+..+++++++|||+|+++++|++||++||+++|.+++|+
T Consensus         6 ~p~~~~l~v~nLp~~~~~---~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~   82 (86)
T d2cqpa1           6 KPGPTIIKVQNMPFTVSI---DEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVK   82 (86)
T ss_dssp             CCSSEEEEEESCCTTCCH---HHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECE
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEE
Confidence            3456678 9999999999   99999999999997754455556899999999999999999999999999999999999


Q ss_pred             Eeec
Q 023632           95 VKKA   98 (279)
Q Consensus        95 V~~a   98 (279)
                      |++|
T Consensus        83 v~l~   86 (86)
T d2cqpa1          83 LVLG   86 (86)
T ss_dssp             EEES
T ss_pred             EEEC
Confidence            9875

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=7e-19  Score=135.35  Aligned_cols=79  Identities=10%  Similarity=0.213  Sum_probs=72.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..+++| |.|||+++|+   ++|+++|++||+|++|+|+.+   .+++|||||+|.+.++|++||+.||++.|++++|+|
T Consensus         5 ~~~r~l~V~nLp~~~te---~~l~~~F~~~G~v~~i~~~~~---~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   78 (114)
T d2f9da1           5 EVNRILYIRNLPYKITA---EEMYDIFGKYGPIRQIRVGNT---PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVV   78 (114)
T ss_dssp             TCCSEEEEESCCTTCCH---HHHHHHHHTTSCEEEEEEECS---TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCEEEEECCCCCCCH---HHHHHHHhhcCCeEeeccccc---CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            346788 9999999999   999999999999999999865   456899999999999999999999999999999999


Q ss_pred             eeccCC
Q 023632           96 KKAEPK  101 (279)
Q Consensus        96 ~~a~~~  101 (279)
                      +++.++
T Consensus        79 ~~a~~~   84 (114)
T d2f9da1          79 LYYNAN   84 (114)
T ss_dssp             EECCHH
T ss_pred             EEcCCC
Confidence            998754

>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=99.76  E-value=1e-18  Score=127.10  Aligned_cols=78  Identities=15%  Similarity=0.208  Sum_probs=70.7

Q ss_pred             CCCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC-Cc
Q 023632           14 NRQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA-GA   91 (279)
Q Consensus        14 ~~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~-g~   91 (279)
                      .+++++++| |.|||+++++   ++|+++|++||+|++|+|++++     ++||||+|++.++|++||+.||+..|. ++
T Consensus         3 ~~~pP~~tl~V~nLp~~~t~---~~l~~~f~~~G~i~~v~~~~~~-----~g~afV~f~~~~~A~~A~~~l~g~~~~~~~   74 (83)
T d2b0ga1           3 TEQPPNQILFLTNLPEETNE---MMLSMLFNQFPGFKEVRLVPNR-----HDIAFVEFTTELQSNAAKEALQGFKITPTH   74 (83)
T ss_dssp             CCCSCCSEEEEESCCTTCCH---HHHHHHHTTSTTEEEEEECTTT-----CSCEEEEESSHHHHHHHHHHHTTCBSSTTC
T ss_pred             CCCCCCCEEEEECCCCCCCH---HHHHhhhccCccEEEeeeeccc-----ceeEEEecCCHHHHHHHHHHhCCcEeCCCc
Confidence            355677899 9999999999   9999999999999999998653     689999999999999999999998885 68


Q ss_pred             eeEEeecc
Q 023632           92 QVEVKKAE   99 (279)
Q Consensus        92 ~i~V~~a~   99 (279)
                      +|+|++|+
T Consensus        75 ~i~v~~ak   82 (83)
T d2b0ga1          75 AMKITFAK   82 (83)
T ss_dssp             BCEEEECC
T ss_pred             EEEEEEec
Confidence            99999986

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=5.5e-19  Score=129.29  Aligned_cols=77  Identities=16%  Similarity=0.203  Sum_probs=71.6

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++|+   ++|+++|++||+|++|+|++++ ++++|+||||+|+++++|++||+ +++++|.+++|+|+
T Consensus         5 ~~rtvfV~nlp~~~te---~~l~~~F~~~G~v~~v~l~~~~-~~~~kG~afV~f~~~e~a~~al~-~~~~~~~g~~l~v~   79 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATL---DDIKEWLEDKGQVLNIQMRRTL-HKAFKGSIFVVFDSIESAKKFVE-TPGQKYKETDLLIL   79 (85)
T ss_dssp             HTTEEEEECCCTTCCH---HHHHHHHTTSCCEEEEEEEECT-TCCEEEEEEEEESCHHHHHHHHT-CCCCEETTEECEEE
T ss_pred             CcCEEEEECCCCCCCH---HHHHHHHHHhcccccceeeeec-cCCcceEEEEEEcCHHHHHHHHH-HCCCEECCEEEEEE
Confidence            45789 9999999999   9999999999999999998885 88999999999999999999996 59999999999999


Q ss_pred             ecc
Q 023632           97 KAE   99 (279)
Q Consensus        97 ~a~   99 (279)
                      +++
T Consensus        80 ~~~   82 (85)
T d1zh5a2          80 FKD   82 (85)
T ss_dssp             EGG
T ss_pred             EcC
Confidence            864

>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=99.76  E-value=1.9e-19  Score=132.57  Aligned_cols=80  Identities=33%  Similarity=0.563  Sum_probs=70.1

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ..+++| |.|||+++||   ++|+++|++||+|++|+++.     ++++||||+|+++++|++||+  ++++|++++|+|
T Consensus         3 ~~s~~lfV~nLp~~~te---~~L~~~F~~~G~v~~v~~~~-----~~~gfafV~f~~~~~a~~a~~--~~~~i~g~~l~v   72 (88)
T d1wf0a_           3 SGSSGVFVGRCTGDMTE---DELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQSLCG--EDLIIKGISVHI   72 (88)
T ss_dssp             SCCCEEEEESCCSSSCH---HHHHHHSTTTSCCCEEECCS-----SCCSCCEEECSCHHHHHHTTT--CEEEETTEEEEE
T ss_pred             CCCCEEEEeCCCCCCCH---HHHHHHHHHcCCceEEEEee-----ccCceEEEEECCHHHHHHHHh--CCCEECCEEeEE
Confidence            356788 9999999999   99999999999999998754     357899999999999999986  678999999999


Q ss_pred             eeccCCCCCCC
Q 023632           96 KKAEPKKPNLP  106 (279)
Q Consensus        96 ~~a~~~~~~~~  106 (279)
                      ++|+++.....
T Consensus        73 ~~a~~k~~~~~   83 (88)
T d1wf0a_          73 SNAEPKHNSNS   83 (88)
T ss_dssp             ECCCCCCCCCS
T ss_pred             EeCCCCCCCCC
Confidence            99988765443

>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=99.76  E-value=6.3e-19  Score=129.27  Aligned_cols=75  Identities=27%  Similarity=0.475  Sum_probs=70.1

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |.|||+++++   ++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||+.+|++++|+|++
T Consensus         8 ~~~l~V~nLp~~~~~---~~l~~~F~~~G~i~~i~~~~~------k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~   78 (86)
T d2cpja1           8 RSRLFVGNLPPDITE---EEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRF   78 (86)
T ss_dssp             TTEEEEESCCTTCCH---HHHHHHTSTTCCCSEEEEETT------TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEE
T ss_pred             CCEEEEECCCCCCCH---HHHHHHHHHhCCceEeeeecc------cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            4578 9999999999   999999999999999999866      57999999999999999999999999999999999


Q ss_pred             ccCCC
Q 023632           98 AEPKK  102 (279)
Q Consensus        98 a~~~~  102 (279)
                      |.++.
T Consensus        79 A~~~~   83 (86)
T d2cpja1          79 ACHSA   83 (86)
T ss_dssp             SSCCS
T ss_pred             CCCcC
Confidence            98764

>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=99.76  E-value=6.5e-19  Score=134.67  Aligned_cols=76  Identities=8%  Similarity=0.021  Sum_probs=69.4

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||+++++   ++|+++|++||+|++|.|..      +++||||+|+++++|++||+.||++.|.+++|.|+
T Consensus         9 ~~~~l~V~nLp~~~t~---~~L~~~F~~fG~I~~v~l~~------~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~   79 (111)
T d1whxa_           9 SKTVILAKNLPAGTLA---AEIQETFSRFGSLGRVLLPE------GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLE   79 (111)
T ss_dssp             EEEEEEEESCCTTCCH---HHHHHHHHTTSCEEEEECCS------SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCEEEEECCCCCCCH---HHHHhhhhccCCccEEEeec------cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEE
Confidence            44678 9999999999   99999999999999998853      46899999999999999999999999999999999


Q ss_pred             eccCCC
Q 023632           97 KAEPKK  102 (279)
Q Consensus        97 ~a~~~~  102 (279)
                      +|....
T Consensus        80 ~a~~~~   85 (111)
T d1whxa_          80 WAPIGV   85 (111)
T ss_dssp             EEETTT
T ss_pred             ECCCCc
Confidence            987654

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 9 (SFRS9)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=6.3e-19  Score=132.45  Aligned_cols=79  Identities=13%  Similarity=0.161  Sum_probs=71.4

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ....+| |.|||+++++   ++|+++|++||+|++|+|.+       ++||||+|.++++|++||++||+.+|+++.|+|
T Consensus        13 ~~~~~i~V~Nlp~~~~~---~~L~~~F~~~G~v~~~~i~~-------~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v   82 (98)
T d1wg4a_          13 RSDFRVLVSGLPPSGSW---QDLKDHMREAGDVCYADVQK-------DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGET   82 (98)
T ss_dssp             SCSCEEEEECCCSSCCH---HHHHHHHTTSSCEEEEEEET-------TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCE
T ss_pred             CCCCEEEEECCCCCCCH---HHHHHHHHhhcccccccccc-------cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEE
Confidence            445678 9999999999   99999999999999999864       479999999999999999999999999999999


Q ss_pred             eeccCCCCCC
Q 023632           96 KKAEPKKPNL  105 (279)
Q Consensus        96 ~~a~~~~~~~  105 (279)
                      .+++++.++.
T Consensus        83 ~~~~~~~~~~   92 (98)
T d1wg4a_          83 SYIRVYPERS   92 (98)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEecCCCCC
Confidence            9998765544

>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=99.76  E-value=5.7e-19  Score=130.34  Aligned_cols=76  Identities=13%  Similarity=0.206  Sum_probs=69.0

Q ss_pred             CCcee-eeCCCCCCCcccHHHH---HHHHhcCCCeEEEEEeecCCCCCc---ccEEEEEEcCHHHHHHHHHHcCCCccCC
Q 023632           18 TTQKM-TGLSLTPVTEPALDEF---KDFFMQFGDVQEHQIMRDHSTSRS---RGFGFITFDTEQAVDDLLAKGNKLELAG   90 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L---~~~F~~~G~V~~v~i~~d~~tg~~---rG~aFV~F~s~e~a~~Ai~~lng~~l~g   90 (279)
                      ..++| |.|||+++++   ++|   +++|++||+|++|.|++|+.+..+   ++||||+|+++++|++||+.||+.+|++
T Consensus         7 q~n~vyV~nLp~~~t~---~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~g   83 (89)
T d2cpia1           7 QKNLVFVVGLSQRLAD---PEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDG   83 (89)
T ss_dssp             CSSCEEEEEECTTTCC---HHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETT
T ss_pred             ecCEEEEECCCCccCH---HHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECC
Confidence            45678 9999999999   888   778999999999999999876654   4899999999999999999999999999


Q ss_pred             ceeEEe
Q 023632           91 AQVEVK   96 (279)
Q Consensus        91 ~~i~V~   96 (279)
                      ++|+|.
T Consensus        84 r~lkvS   89 (89)
T d2cpia1          84 RTLKAS   89 (89)
T ss_dssp             EEEEEE
T ss_pred             EEEEEC
Confidence            999984

>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=99.75  E-value=6e-19  Score=131.91  Aligned_cols=81  Identities=20%  Similarity=0.317  Sum_probs=72.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ...+.++| |.|||++|||   ++|+++|++|+.|..++     .++++++||||+|+++++|++||+.||+++|++++|
T Consensus        12 ~~~~~~~l~V~nL~~~~te---~~l~~~F~~~g~v~~~~-----~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i   83 (96)
T d1fjca_          12 KVRAARTLLAKNLSFNITE---DELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV   83 (96)
T ss_dssp             TTTGGGEEEEESCCSSCCH---HHHHHHHCSEEEECCEE-----ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEE
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHHHHhcccceeee-----ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEE
Confidence            34456889 9999999999   99999999999876653     267889999999999999999999999999999999


Q ss_pred             EEeeccCCCC
Q 023632           94 EVKKAEPKKP  103 (279)
Q Consensus        94 ~V~~a~~~~~  103 (279)
                      +|++|.++..
T Consensus        84 ~V~~a~~k~~   93 (96)
T d1fjca_          84 SLYYTGEKGG   93 (96)
T ss_dssp             EEEECSSSCC
T ss_pred             EEEEeCCCCC
Confidence            9999988755

>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=99.75  E-value=3.1e-18  Score=125.77  Aligned_cols=79  Identities=14%  Similarity=0.192  Sum_probs=70.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc-CCcee
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL-AGAQV   93 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l-~g~~i   93 (279)
                      .+++++| |.|||++++|   ++|+++|++||.|+++.++.+    +.++||||+|+++++|++||++||+..| ++++|
T Consensus         7 ~pPs~tL~V~NLp~~~te---~~l~~~F~~~G~v~~~~~~~~----~~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l   79 (88)
T d2adca2           7 FPPSATLHLSNIPPSVSE---EDLKVLFSSNGGVVKGFKFFQ----KDRKMALIQMGSVEEAVQALIDLHNHDLGENHHL   79 (88)
T ss_dssp             CCSCSEEEEECCCTTCCH---HHHHHHHHTTSCCEEEEEECS----SSTTCEEEEESSHHHHHHHHHHHTTCBSSSSCBC
T ss_pred             CCCCCEEEEECCCCCCCH---HHHHHHhhccCCEEEEEEeee----cccceeEEEECCHHHHHHHHHhccCCEecCCCEE
Confidence            3567889 9999999999   999999999999998877654    3478999999999999999999999988 58999


Q ss_pred             EEeeccCC
Q 023632           94 EVKKAEPK  101 (279)
Q Consensus        94 ~V~~a~~~  101 (279)
                      +|++++++
T Consensus        80 ~v~~sk~~   87 (88)
T d2adca2          80 RVSFSKST   87 (88)
T ss_dssp             EEEECSSC
T ss_pred             EEEeCCCC
Confidence            99999764

>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=99.75  E-value=1.1e-18  Score=128.52  Aligned_cols=79  Identities=9%  Similarity=0.118  Sum_probs=67.2

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      .+++| |.|||++|++   +||+++|++|+ |+.+.+.      ++++||||+|+++++|++||++||+++|++++|+|+
T Consensus         4 ~s~~i~V~nLp~~~t~---~~l~~lF~~~G-~~~~~~~------~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~   73 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNC---QEVHDLLKDYD-LKYCYVD------RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQ   73 (88)
T ss_dssp             CCCCEEEESCCSSCCH---HHHHHHTCSSC-CCCEEEE------GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCEEEEeCCCCccCh---HHHHHHHHhcC-ceeeeee------ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            35678 9999999999   99999999999 3334332      457899999999999999999999999999999999


Q ss_pred             eccCCCCCCC
Q 023632           97 KAEPKKPNLP  106 (279)
Q Consensus        97 ~a~~~~~~~~  106 (279)
                      +++++.....
T Consensus        74 ~a~~~~~~~~   83 (88)
T d1wg1a_          74 LQPTDALLCS   83 (88)
T ss_dssp             ECCCCCCCSC
T ss_pred             EcCCCCCCCC
Confidence            9976654443

>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=99.75  E-value=4.9e-19  Score=131.10  Aligned_cols=83  Identities=13%  Similarity=0.288  Sum_probs=71.0

Q ss_pred             CCcee-eeCCCCCCCcccH-HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           18 TTQKM-TGLSLTPVTEPAL-DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~-~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ++++| |+|||++++++|| +.|.++|++||+|++|+|.+   +.++++||||+|+++++|++||+.||+++|++++|+|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~---~~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v   78 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCH---HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEee---eccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45789 9999999999433 23356789999999998754   4667899999999999999999999999999999999


Q ss_pred             eeccCCCC
Q 023632           96 KKAEPKKP  103 (279)
Q Consensus        96 ~~a~~~~~  103 (279)
                      ++|+++.+
T Consensus        79 ~~ak~~~~   86 (91)
T d1nu4a_          79 QYAKTDSD   86 (91)
T ss_dssp             EECSSCCT
T ss_pred             EEeCCCch
Confidence            99987654

>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=99.75  E-value=2.5e-18  Score=125.76  Aligned_cols=77  Identities=16%  Similarity=0.268  Sum_probs=69.8

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ..++| |.|||++++|   ++|+++|++|+.|+.+++.+      +++||||+|.++++|++||+.||+++|.+++|+|+
T Consensus         7 ~~k~l~V~nLp~~~te---~~l~~~F~~~g~i~~~~~~~------~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~   77 (86)
T d2cpda1           7 SVKILYVRNLMLSTSE---EMIEKEFNNIKPGAVERVKK------IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVT   77 (86)
T ss_dssp             CCCEEEEESCCTTCCH---HHHHHHHHTTSTTCEEEEEE------CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCH---HHHHHhhcccceeeeEEEcc------ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45789 9999999999   99999999999998887754      46899999999999999999999999999999999


Q ss_pred             eccCCCC
Q 023632           97 KAEPKKP  103 (279)
Q Consensus        97 ~a~~~~~  103 (279)
                      +|+|+..
T Consensus        78 ~akP~~~   84 (86)
T d2cpda1          78 LAKPVDK   84 (86)
T ss_dssp             CCCCCCC
T ss_pred             eccCCCC
Confidence            9987654

>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=99.75  E-value=5.3e-19  Score=127.89  Aligned_cols=76  Identities=21%  Similarity=0.280  Sum_probs=68.5

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCC-ccCCceeEEee
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKL-ELAGAQVEVKK   97 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~-~l~g~~i~V~~   97 (279)
                      ++| |+|||+++||   ++|+++|++||.|.+++++++      |+||||+|.++++|++||+.||+. +|++++|+|++
T Consensus         2 n~l~V~nLp~~~te---~~L~~~F~~~G~i~~~~~~~~------rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~   72 (80)
T d2cqha1           2 NKLYIGNLSPAVTA---DDLRQLFGDRKLPLAGQVLLK------SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   72 (80)
T ss_dssp             CCEEEECCCTTCCH---HHHHHHHHHTTCCCSSCEEEE------TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CEEEEECCCCCCCH---HHHHHHHHHhCcEEEeEEecc------cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEE
Confidence            468 9999999999   999999999999988777654      689999999999999999999985 69999999999


Q ss_pred             ccCCCCC
Q 023632           98 AEPKKPN  104 (279)
Q Consensus        98 a~~~~~~  104 (279)
                      |.+++++
T Consensus        73 a~~k~~r   79 (80)
T d2cqha1          73 SVSKKLR   79 (80)
T ss_dssp             CCCCCCC
T ss_pred             cCCcCcC
Confidence            9987654

>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=99.75  E-value=2.3e-18  Score=131.40  Aligned_cols=82  Identities=13%  Similarity=0.193  Sum_probs=72.4

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCcc--CCce
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLEL--AGAQ   92 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l--~g~~   92 (279)
                      ..++.+| |.|||++|||   ++|+++|++||+|++|+|++++    +++||||+|+++++|++||+.||+++|  .+++
T Consensus         4 ~s~~~~v~V~NL~~~vte---~~L~~~F~~~G~i~~~~i~~~~----~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~   76 (108)
T d2adba1           4 QSPVLRIIVENLFYPVTL---DVLHQIFSKFGTVLKIITFTKN----NQFQALLQYADPVSAQHAKLSLDGQNIYNACCT   76 (108)
T ss_dssp             CCCEEEEESCSCCSTTHH---HHHHHHHTTTSCEEEEEEEEET----TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCC
T ss_pred             CCCeEEEEEeCcCCCCCH---HHHHHHHccCCcEEEEEEEeeC----CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcE
Confidence            3456677 9999999999   9999999999999999999774    489999999999999999999999988  4788


Q ss_pred             eEEeeccCCCCC
Q 023632           93 VEVKKAEPKKPN  104 (279)
Q Consensus        93 i~V~~a~~~~~~  104 (279)
                      |+|.+++++...
T Consensus        77 l~v~~s~~~~~~   88 (108)
T d2adba1          77 LRIDFSKLTSLN   88 (108)
T ss_dssp             CEEEECSSCSCC
T ss_pred             EEEEecCCcccc
Confidence            999998876543

>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=99.75  E-value=3.4e-19  Score=126.08  Aligned_cols=70  Identities=14%  Similarity=0.348  Sum_probs=67.4

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      | |.|||+++||   ++|+++|++||+|+++++++++.+.++++||||+|+++++|++||+.||+++|+++.|+
T Consensus         1 lyV~nLp~~~te---~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTD---QDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCH---HHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCH---HHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            6 9999999999   99999999999999999999999999999999999999999999999999999998774

>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=99.74  E-value=3.6e-18  Score=127.89  Aligned_cols=79  Identities=18%  Similarity=0.302  Sum_probs=70.9

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCC--c
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAG--A   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g--~   91 (279)
                      +.+++++| |.|||++|+|   ++|+++|++||+|++|+|+++      ++||||+|+++++|++||+.||+.+|.+  +
T Consensus        13 ~~~Ps~tl~V~nLp~~~t~---~~l~~~f~~~G~i~~~~~~~~------~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~   83 (97)
T d1whya_          13 KANPTTRLWVGGLGPNTSL---AALAREFDRFGSIRTIDHVKG------DSFAYIQYESLDAAQAACAKMRGFPLGGPDR   83 (97)
T ss_dssp             CCCCCSCEEEECCCSSCCH---HHHHHHHHTTSCEEEEEECSS------SCCEEEEESSHHHHHHHHHHHTTCBCSSSSC
T ss_pred             CCCCCCEEEEcCCCCCCCH---HHHHHHHHhhcccceEeeecc------ccEEEeccCCHHHHHHHHHHhCCCEeCCCce
Confidence            44567889 9999999999   999999999999999999765      5699999999999999999999999986  5


Q ss_pred             eeEEeeccCCC
Q 023632           92 QVEVKKAEPKK  102 (279)
Q Consensus        92 ~i~V~~a~~~~  102 (279)
                      +|+|++|++.+
T Consensus        84 ~l~v~~ak~~~   94 (97)
T d1whya_          84 RLRVDFAKSGP   94 (97)
T ss_dssp             BCEEEECCCCC
T ss_pred             EEEEEeCCCCC
Confidence            89999998643

>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=99.74  E-value=2.7e-18  Score=123.74  Aligned_cols=75  Identities=17%  Similarity=0.280  Sum_probs=68.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEV   95 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V   95 (279)
                      ...++| |.||+  +||   ++|+++|++||+|++|+|.++      ++||||+|+++++|++||++||+.+|++++|+|
T Consensus         3 ~~~~ti~V~~~~--~te---~~L~~~F~~~G~I~~v~~~~~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V   71 (79)
T d2bz2a1           3 RKGNTLYVYGED--MTP---TLLRGAFSPFGNIIDLSMDPP------RNCAFVTYEKMESADQAVAELNGTQVESVQLKV   71 (79)
T ss_dssp             CCCCEEEEECSS--CCH---HHHHHHHSTTCCCSCEEEETT------TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEE
T ss_pred             CCCCEEEEECCC--CCH---HHHHHHHhccCccceeeeccC------CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEE
Confidence            456789 99996  899   999999999999999998755      579999999999999999999999999999999


Q ss_pred             eeccCCC
Q 023632           96 KKAEPKK  102 (279)
Q Consensus        96 ~~a~~~~  102 (279)
                      ++|+++.
T Consensus        72 ~~a~~~P   78 (79)
T d2bz2a1          72 NIARKQP   78 (79)
T ss_dssp             EECCSSC
T ss_pred             EEecCCC
Confidence            9997653

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.73  E-value=5.1e-18  Score=121.17  Aligned_cols=73  Identities=8%  Similarity=0.117  Sum_probs=66.7

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      ++| |.|||+++++   ++|+++|++||+|++|+|+.++..  .++||||+|+++++|++||+ +|+++|++++|+|+++
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 TTVLVKNLPKSYNQ---NKVYKYFKHCGPIIHVDVADSLKK--NFRFARIEFARYDGALAAIT-KTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCH---HHHHHHHGGGSCEEEEEEEECTTS--SSEEEEEEESSHHHHHHHHT-TTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCH---HHHHHHHhcCCceEEEEEEeeccc--cceEEEEEEcchHHhHHHHH-hcCcEECCEEEEEEEC
Confidence            367 9999999999   999999999999999999998754  35699999999999999996 6999999999999876

>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=99.73  E-value=1.4e-17  Score=126.21  Aligned_cols=82  Identities=12%  Similarity=0.168  Sum_probs=72.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc--CCCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l--ng~~l~g~   91 (279)
                      +..++++| |.|||++|||   ++|+++|++||+|++|+|+++      |++|||+|+++++|++||+.|  +...|.++
T Consensus        11 ~~~ps~~l~v~nlp~~~te---~~l~~~F~~fG~I~~~~~~~~------k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~   81 (104)
T d1wexa_          11 KVSVSPVVHVRGLCESVVE---ADLVEALEKFGTICYVMMMPF------KRQALVEFENIDSAKECVTFAADVPVYIAGQ   81 (104)
T ss_dssp             CCCCCSEEEEESCCSSCCH---HHHHHHHTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCBSSSS
T ss_pred             cCCCCCEEEEeCCCCCCCH---HHHHHhhhhcccceEEEEEec------ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeE
Confidence            45667889 9999999999   999999999999999998754      679999999999999999977  56788999


Q ss_pred             eeEEeeccCCCCCC
Q 023632           92 QVEVKKAEPKKPNL  105 (279)
Q Consensus        92 ~i~V~~a~~~~~~~  105 (279)
                      +|+|++++.++...
T Consensus        82 ~l~v~~s~~~~~~~   95 (104)
T d1wexa_          82 QAFFNYSTSKRITR   95 (104)
T ss_dssp             BCEEEECSSSSCCC
T ss_pred             EEEEEEcCCCccCC
Confidence            99999998765443

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.1e-18  Score=130.41  Aligned_cols=80  Identities=10%  Similarity=0.047  Sum_probs=71.3

Q ss_pred             CCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEe
Q 023632           18 TTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVK   96 (279)
Q Consensus        18 ~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~   96 (279)
                      ...+| |.|||+++|+   ++|+++|+.|+.|+++.++.+..+++++|||||+|+++++|++||+ ||++.|++++|+|+
T Consensus         7 ~~~~v~v~nLp~~~t~---~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~-~n~~~i~gr~i~V~   82 (103)
T d2cpya1           7 AKVCAHITNIPFSITK---MDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSER-LHRKKLNGREAFVH   82 (103)
T ss_dssp             CCCEEEEESCCTTSCH---HHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGG-GCSEEETTEEEEEE
T ss_pred             CceEEEEeCCCCCCCH---HHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHh-cCCCeECCcEEEEE
Confidence            34568 9999999999   9999999999999876566666799999999999999999999996 79999999999999


Q ss_pred             eccCC
Q 023632           97 KAEPK  101 (279)
Q Consensus        97 ~a~~~  101 (279)
                      ++.++
T Consensus        83 ~~~~~   87 (103)
T d2cpya1          83 VVTLE   87 (103)
T ss_dssp             EECHH
T ss_pred             ECCHH
Confidence            87654

>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=99.71  E-value=4.2e-18  Score=140.55  Aligned_cols=86  Identities=30%  Similarity=0.553  Sum_probs=79.0

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      .....++| |.|||+++|+   ++|+++|+.||+|+.|.|++|+.++++++||||+|+++++|++||+ ++.+.|++++|
T Consensus        93 ~~~~~~~i~V~~lp~~~te---~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~Al~-~~~~~~~G~~i  168 (183)
T d1u1qa_          93 AHLTVKKIFVGGIKEDTEE---HHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI-QKYHTVNGHNC  168 (183)
T ss_dssp             TTCCCSEEEEECCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHT-SSCEEETTEEE
T ss_pred             cccccceeEEccCCCcCCH---HHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHHHHHH-hCCCeECCEEE
Confidence            44566788 9999999999   9999999999999999999999999999999999999999999997 58889999999


Q ss_pred             EEeeccCCCCC
Q 023632           94 EVKKAEPKKPN  104 (279)
Q Consensus        94 ~V~~a~~~~~~  104 (279)
                      +|++|.+|+++
T Consensus       169 ~V~~A~~k~e~  179 (183)
T d1u1qa_         169 EVRKALSKQEM  179 (183)
T ss_dssp             EEEECCCHHHH
T ss_pred             EEEecCCcccc
Confidence            99999887544

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=3.4e-17  Score=120.17  Aligned_cols=79  Identities=16%  Similarity=0.219  Sum_probs=71.1

Q ss_pred             CCCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc--CCCccCCc
Q 023632           15 RQTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGA   91 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l--ng~~l~g~   91 (279)
                      +..++++| |+|||+++++   ++|+++|++||.|++|+|+++      ++||||+|+++++|++||+.+  +...|.++
T Consensus         4 ~~~Ps~~l~V~nLp~~~t~---~~L~~~f~~~G~i~~v~~~~~------~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~   74 (88)
T d2cq1a1           4 DGAPSRVLHIRKLPGEVTE---TEVIALGLPFGKVTNILMLKG------KNQAFLELATEEAAITMVNYYSAVTPHLRNQ   74 (88)
T ss_dssp             CSSCCSEEEEESCCTTCCH---HHHHHTTTTTSCEEEEEEETT------TTEEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCCCEEEEeCCCCCCCH---HHHHHHHhccccccccccccc------ceEEEEEeCCHHHHHHHHHHHccCCCccCCC
Confidence            45678899 9999999999   999999999999999998865      469999999999999999865  67899999


Q ss_pred             eeEEeeccCCC
Q 023632           92 QVEVKKAEPKK  102 (279)
Q Consensus        92 ~i~V~~a~~~~  102 (279)
                      +|+|++++.+.
T Consensus        75 ~l~v~~sk~~~   85 (88)
T d2cq1a1          75 PIYIQYSNHKE   85 (88)
T ss_dssp             ECEEEECSCSS
T ss_pred             EEEEEECCCCC
Confidence            99999997654

>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=99.69  E-value=3.1e-18  Score=131.60  Aligned_cols=82  Identities=16%  Similarity=0.201  Sum_probs=73.2

Q ss_pred             CCCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeE
Q 023632           16 QTTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVE   94 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~   94 (279)
                      .....+| |.|||+++||   ++|+++|+.|+.|+++.++.+..+++++|||||+|.++++|++||+ ||++.|+++.|+
T Consensus        15 ~~~~~~i~v~nLp~~~t~---~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~-~~~~~i~gR~i~   90 (112)
T d1wela1          15 HEAGFCVYLKGLPFEAEN---KHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALC-RHKQYMGNRFIQ   90 (112)
T ss_dssp             CCCCCEEEEECCCTTCCH---HHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHT-SCSBCSTTSCBE
T ss_pred             CCCCeEEEEecCCCcCcH---HHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHH-cCCCcCCCEEEE
Confidence            3445678 9999999999   9999999999999887677777799999999999999999999996 799999999999


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |.++.++
T Consensus        91 V~~~~~~   97 (112)
T d1wela1          91 VHPITKK   97 (112)
T ss_dssp             EEEECHH
T ss_pred             EEEcChH
Confidence            9988654

>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=99.69  E-value=4.8e-17  Score=123.31  Aligned_cols=83  Identities=14%  Similarity=0.179  Sum_probs=71.2

Q ss_pred             CCCcee-eeCCCCCC-CcccH-HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           17 TTTQKM-TGLSLTPV-TEPAL-DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~-te~~~-~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ..+++| |.||+.+| +++++ ++|+++|++||+|++|++++.      +++|||+|+++++|++||+.||++.|++++|
T Consensus         3 ~~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k~------~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l   76 (104)
T d1weya_           3 SGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS------FKRVRINFSNPLSAADARLRLHKTEFLGKEM   76 (104)
T ss_dssp             SCCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETT------TTEEEEECSSTTHHHHHHHTSTTSEETTEEC
T ss_pred             CCCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEecC------CCEEEEEECCHHHHHHHHHHhcccccCCCEe
Confidence            356788 99999987 44322 579999999999999999854      6799999999999999999999999999999


Q ss_pred             EEeeccCCCCCC
Q 023632           94 EVKKAEPKKPNL  105 (279)
Q Consensus        94 ~V~~a~~~~~~~  105 (279)
                      +|++|+++....
T Consensus        77 ~v~~a~~~~~~~   88 (104)
T d1weya_          77 KLYFAQTLHIGS   88 (104)
T ss_dssp             EEECCCCSSCCS
T ss_pred             EEeecccCCCCC
Confidence            999998765543

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Ribonucleoprotein PTB-binding 1, Raver-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.69  E-value=5.1e-17  Score=115.84  Aligned_cols=70  Identities=13%  Similarity=0.192  Sum_probs=62.8

Q ss_pred             e-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           22 M-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        22 l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      | |+|||+++++   ++|+++|++|+ |+.+++.      ++++||||+|+++++|++||+.||+.+|++++|+|++++.
T Consensus         1 i~V~nLp~~~t~---~~l~~~F~~~g-~~~~~~~------~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTN---QEVHDLLSDYE-LKYCFVD------KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCH---HHHHHHTTTSC-EEEEEEE------TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCH---HHHHHHHhccc-ccceeec------ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            5 9999999999   99999999998 5555443      4578999999999999999999999999999999999965


Q ss_pred             C
Q 023632          101 K  101 (279)
Q Consensus       101 ~  101 (279)
                      +
T Consensus        71 d   71 (75)
T d1wi6a1          71 D   71 (75)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.68  E-value=2.3e-17  Score=123.97  Aligned_cols=80  Identities=16%  Similarity=0.226  Sum_probs=70.3

Q ss_pred             CCCCCcee-eeCCCCC-CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHH--HcCCCccCC
Q 023632           15 RQTTTQKM-TGLSLTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLA--KGNKLELAG   90 (279)
Q Consensus        15 ~~~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~--~lng~~l~g   90 (279)
                      .....++| |.|||.+ +|+   ++|+++|++||+|++|.|+++      +++|||+|+++++|++||+  +++...|++
T Consensus        14 ~~~~~~~l~v~nLp~~~~te---~~l~~~F~~fG~V~~v~~~~~------k~~afV~f~~~~~A~~Ai~~~~~~~~~~~g   84 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSD---SAVLKLAEPYGKIKNYILMRM------KSQAFIEMETREDAMAMVDHCLKKALWFQG   84 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCS---HHHHTTTTTTSCCSEEEEETT------TTEEEEECSSHHHHHHHHHHHHHSCCCSSS
T ss_pred             CCCCCCEEEEeCCcCCccCH---HHHHhhhccccceeEEEEeec------CCcEEEEecchHHHHHHHHHHhcCCceECC
Confidence            34556788 9999985 899   999999999999999999866      5799999999999999998  468889999


Q ss_pred             ceeEEeeccCCCC
Q 023632           91 AQVEVKKAEPKKP  103 (279)
Q Consensus        91 ~~i~V~~a~~~~~  103 (279)
                      ++|+|++|+.+++
T Consensus        85 r~l~V~~s~~~~~   97 (99)
T d1x4fa1          85 RCVKVDLSEKYKK   97 (99)
T ss_dssp             SCCEEEEECSCSS
T ss_pred             EEEEEEEcCCccc
Confidence            9999999976653

>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=99.65  E-value=2.6e-18  Score=126.78  Aligned_cols=76  Identities=14%  Similarity=0.296  Sum_probs=66.8

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEe-----ecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCcee
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIM-----RDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQV   93 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~-----~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i   93 (279)
                      ++| |+|||+++||   ++|+++|++|+.|..+.|+     .+..+.++++||||+|+++|+|++||+ ||+++|++++|
T Consensus         2 RrlyVgNLp~~~te---~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~-l~g~~~~Gr~l   77 (90)
T d1u2fa_           2 RRLYVGNIPFGITE---EAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMA-FDGIIFQGQSL   77 (90)
T ss_dssp             CEEEECSCCTTCCT---THHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGG-GSSCCSSSSCC
T ss_pred             CEEEEcCCCCccch---HHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHh-hCCcEECCEEE
Confidence            678 9999999999   9999999999988766553     455678899999999999999999985 89999999999


Q ss_pred             EEeecc
Q 023632           94 EVKKAE   99 (279)
Q Consensus        94 ~V~~a~   99 (279)
                      +|++++
T Consensus        78 ~V~r~k   83 (90)
T d1u2fa_          78 KIRRPH   83 (90)
T ss_dssp             CCBCTT
T ss_pred             EECCCC
Confidence            997544

>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=99.64  E-value=1.6e-16  Score=117.05  Aligned_cols=79  Identities=15%  Similarity=0.114  Sum_probs=69.4

Q ss_pred             CCCCcee-eeCCCCC-CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHc--CCCccCCc
Q 023632           16 QTTTQKM-TGLSLTP-VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKG--NKLELAGA   91 (279)
Q Consensus        16 ~~~~~~l-V~nLp~~-~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~l--ng~~l~g~   91 (279)
                      ...+++| |.|||.. +|+   +||.++|++||+|++|+|+.++      .+|||+|++.++|++||+.|  +..+|.++
T Consensus         5 ~~~sr~v~v~nl~~~~~t~---~eL~~lF~~fG~I~~i~i~~~k------~~afV~f~~~~~A~~A~~~l~~~~~~~~gr   75 (89)
T d1x4da1           5 VETRRVVHIMDFQRGKNLR---YQLLQLVEPFGVISNHLILNKI------NEAFIEMATTEDAQAAVDYYTTTPALVFGK   75 (89)
T ss_dssp             CCCCCEEEEESCCCSSSHH---HHHHTTTGGGSCEEEEEECSSS------SCEEEEESSHHHHHHHHHHHHHSCCEETTE
T ss_pred             CCCCcEEEEECCCCCcCCH---HHHHHHHHhhCCeEEEEeeccc------eEEEEEEcchhhHHHHHHHHhhCCCccCCc
Confidence            4567888 9999986 789   9999999999999999998763      58999999999999999965  67889999


Q ss_pred             eeEEeeccCCCC
Q 023632           92 QVEVKKAEPKKP  103 (279)
Q Consensus        92 ~i~V~~a~~~~~  103 (279)
                      +|+|++|++.+.
T Consensus        76 ~l~V~~s~~~~~   87 (89)
T d1x4da1          76 PVRVHLSQKYKR   87 (89)
T ss_dssp             ECEEEEECCCTT
T ss_pred             eEEEEECCCccc
Confidence            999999976543

>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=99.62  E-value=3.5e-17  Score=124.08  Aligned_cols=75  Identities=13%  Similarity=0.250  Sum_probs=69.8

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      +.+ |.+++.+++|   ++|+++|++||+|++|+|+++ .+++++|||||+|+++++|++||+.||+++|++++|+|++.
T Consensus        28 ~~~~v~~~~~~~~e---d~l~e~f~k~G~I~~v~I~~~-~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFE---EVFTEMEEKYGEVEEMNVCDN-LGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHH---HHHHHHHHHTCCEEEEEECCS-SSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhH---HHHHHHhccCCCEEEEEeecC-CCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            456 8888889999   999999999999999999877 58999999999999999999999999999999999999875

>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=99.54  E-value=5.3e-15  Score=111.23  Aligned_cols=66  Identities=14%  Similarity=0.155  Sum_probs=57.8

Q ss_pred             CCCCCcee-eeC--CCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccC
Q 023632           15 RQTTTQKM-TGL--SLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELA   89 (279)
Q Consensus        15 ~~~~~~~l-V~n--Lp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~   89 (279)
                      ...++++| |.|  ||.++||   ++|+++|++||+|++|.++.+      ++||||+|++.++|++||+.||+++|.
T Consensus        14 ~~~pt~~l~V~ng~L~~~vte---~~L~~~F~~~G~i~~i~~~~~------k~~aFV~f~~~e~A~~A~~~lng~~i~   82 (101)
T d2cq2a1          14 VSYATQSLVVANGGLGNGVSR---NQLLPVLEKCGLVDALLMPPN------KPYSFARYRTTEESKRAYVTLNGKEVV   82 (101)
T ss_dssp             CSSCCSEEEEETCTGGGTCCH---HHHHHHHHHHSCEEEEECCTT------CSCEEEEESSHHHHHHHHHHTTTCEEE
T ss_pred             CCCCCceEEEECCCCCCCCCH---HHHHHHHHhhCcccEEeeccC------ccEEEEEECCHHHHHHHHHHhCCCCCC
Confidence            34556667 755  9999999   999999999999999988765      569999999999999999999998774

>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=99.53  E-value=1.1e-14  Score=109.06  Aligned_cols=85  Identities=9%  Similarity=0.183  Sum_probs=70.3

Q ss_pred             CCCCCcee-eeCC--CCCCCcc-----cH-HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           15 RQTTTQKM-TGLS--LTPVTEP-----AL-DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        15 ~~~~~~~l-V~nL--p~~~te~-----~~-~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      +....++| |.||  |.++.++     +| ++|++.|++||+|++|+|+.+    +++|||||+|+++++|++||+.||+
T Consensus         4 ~~~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~----~~~G~~fV~f~~~e~A~~A~~~lng   79 (99)
T d2dita1           4 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDR----HPDGVASVSFRDPEEADYCIQTLDG   79 (99)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETT----CTTCEEEEECSCHHHHHHHHHHSTT
T ss_pred             CCCCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCC----CCccEEEEEECCHHHHHHHHHHhCC
Confidence            34566788 9999  6554321     11 678999999999999998765    4579999999999999999999999


Q ss_pred             CccCCceeEEeeccCCCC
Q 023632           86 LELAGAQVEVKKAEPKKP  103 (279)
Q Consensus        86 ~~l~g~~i~V~~a~~~~~  103 (279)
                      ..|++++|+|+++.++..
T Consensus        80 ~~~~gr~i~v~~~~g~~~   97 (99)
T d2dita1          80 RWFGGRQITAQAWDGTTD   97 (99)
T ss_dssp             CEETTEECEEEECCSCCC
T ss_pred             cEECCEEEEEEEeCCcCC
Confidence            999999999999987654

>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=99.51  E-value=2.2e-14  Score=117.77  Aligned_cols=81  Identities=32%  Similarity=0.549  Sum_probs=73.4

Q ss_pred             Ccee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEee
Q 023632           19 TQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKK   97 (279)
Q Consensus        19 ~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~   97 (279)
                      .++| |+|||+++||   ++|+++|++||+|++|.|++++.++++++||||+|.++++|++|++. +...++.+.|.+..
T Consensus         6 ~r~lfV~nLp~~~te---~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~-~~~~~~~~~~~~~~   81 (183)
T d1u1qa_           6 LRKLFIGGLSFETTD---ESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA-RPHKVDGRVVEPKR   81 (183)
T ss_dssp             HHEEEEESCCTTCCH---HHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHT-CSCEETTEECEEEE
T ss_pred             CCEEEEECCCCCCCH---HHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHh-cCCcccccchhhhh
Confidence            3689 9999999999   99999999999999999999999999999999999999999999998 56778888888887


Q ss_pred             ccCCCC
Q 023632           98 AEPKKP  103 (279)
Q Consensus        98 a~~~~~  103 (279)
                      ..++..
T Consensus        82 ~~~~~~   87 (183)
T d1u1qa_          82 AVSRED   87 (183)
T ss_dssp             CCCTTG
T ss_pred             hhhccc
Confidence            765543

>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=99.50  E-value=3.8e-14  Score=106.97  Aligned_cols=84  Identities=15%  Similarity=0.164  Sum_probs=70.4

Q ss_pred             CCCcee-eeCC--CCCCCcc-----cHHHHHHHHhcCCCeEEEEEeecCCC--CCcccEEEEEEcCHHHHHHHHHHcCCC
Q 023632           17 TTTQKM-TGLS--LTPVTEP-----ALDEFKDFFMQFGDVQEHQIMRDHST--SRSRGFGFITFDTEQAVDDLLAKGNKL   86 (279)
Q Consensus        17 ~~~~~l-V~nL--p~~~te~-----~~~~L~~~F~~~G~V~~v~i~~d~~t--g~~rG~aFV~F~s~e~a~~Ai~~lng~   86 (279)
                      ++++.| |.||  |.++.++     .++||++.|++||+|++|.|++++.+  ...++++||+|+++++|++|++.||+.
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr   81 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGR   81 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSC
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCC
Confidence            357788 9999  6665431     12679999999999999999987654  345689999999999999999999999


Q ss_pred             ccCCceeEEeeccC
Q 023632           87 ELAGAQVEVKKAEP  100 (279)
Q Consensus        87 ~l~g~~i~V~~a~~  100 (279)
                      .+++|+|+|.++.+
T Consensus        82 ~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          82 KFANRVVVTKYCDP   95 (104)
T ss_dssp             CSSSSCCEEEEECH
T ss_pred             EECCeEEEEEEcCH
Confidence            99999999999864

>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=99.49  E-value=2.6e-14  Score=109.43  Aligned_cols=69  Identities=16%  Similarity=0.159  Sum_probs=60.6

Q ss_pred             eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCH-HHHHHHHHHcCCCccCCceeEEeeccC
Q 023632           23 TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTE-QAVDDLLAKGNKLELAGAQVEVKKAEP  100 (279)
Q Consensus        23 V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~-e~a~~Ai~~lng~~l~g~~i~V~~a~~  100 (279)
                      |+|||+++||   ++|+++|++||+|++|+|+++      ++||||+|+++ ++|.+||+.||+..|..+.++|.++..
T Consensus        16 vgnL~~~~te---e~Lk~~F~~fG~V~~v~i~~~------kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~~~   85 (113)
T d1owxa_          16 SGDLDDQTCR---EDLHILFSNHGEIKWIDFVRG------AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEVL   85 (113)
T ss_dssp             EESCCSSCCH---HHHHHHTCSSCCEEEEECCTT------CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEEC
T ss_pred             ECCCCCCCCH---HHHHHHHHhcCChheEEEecC------CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEeec
Confidence            9999999999   999999999999999999865      68999999985 789999999999888777666666543

>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=99.47  E-value=2.6e-14  Score=103.08  Aligned_cols=74  Identities=12%  Similarity=0.104  Sum_probs=62.3

Q ss_pred             CCCcee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCce-eE
Q 023632           17 TTTQKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQ-VE   94 (279)
Q Consensus        17 ~~~~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~-i~   94 (279)
                      ++.+.| |.+||+++++   +.| ++|++||+|+++++.++      ++||||+|+++++|++||+ +|+++|+++. |.
T Consensus         2 ~~~~wV~V~G~p~~~~~---~il-~~F~~~G~I~~~~~~~~------~~~~fV~f~~~~~A~~Al~-~nG~~~~g~~~vg   70 (81)
T d1wwha1           2 LDDTWVTVFGFPQASAS---YIL-LQFAQYGNILKHVMSNT------GNWMHIRYQSKLQARKALS-KDGRIFGESIMIG   70 (81)
T ss_dssp             GGGGEEEEECCCGGGHH---HHH-HHHHTTSCEEEEEECSS------SSEEEEEESSHHHHHHHHT-TTTCEETTTEECE
T ss_pred             CcccEEEEECCChHHHH---HHH-HHHHhhhhhheEEecCC------CCEEEEEEcccHHHHHHHh-cCCCeECCcEEEE
Confidence            345778 9999999887   666 47999999999987644      6799999999999999996 7999999984 67


Q ss_pred             EeeccCC
Q 023632           95 VKKAEPK  101 (279)
Q Consensus        95 V~~a~~~  101 (279)
                      |+.+..|
T Consensus        71 V~~~~~k   77 (81)
T d1wwha1          71 VKPCIDK   77 (81)
T ss_dssp             EEECCCH
T ss_pred             EEeCCCh
Confidence            8887654

>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=98.03  E-value=3.2e-06  Score=60.19  Aligned_cols=60  Identities=15%  Similarity=0.252  Sum_probs=52.2

Q ss_pred             CCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeec
Q 023632           30 VTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKA   98 (279)
Q Consensus        30 ~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a   98 (279)
                      .+|..+++|.+.|.+||+|.-|+++.|        ..+|+|.+-++|.+|++. ++++|.++.|+|...
T Consensus        33 FDe~l~~~Llq~l~~~GeViLvRFv~d--------~mwVTF~dG~SAL~al~l-~g~~v~G~~l~It~~   92 (95)
T d1ufwa_          33 FPEDLRTELMQTLGSYGTIVLVRINQG--------QMLVTFADSHSALSVLDV-DGMKVKGRAVKISGP   92 (95)
T ss_dssp             CCHHHHHHHHHHHHHHSCCSEEEEETT--------EEEEECSCSHHHHHHHHG-GGSEETTEEEEEECC
T ss_pred             CCHHHHHHHHHHHhhCCeEEEEEEeCC--------eEEEEECCcHHHHHHhcc-CCeEEcceEEEEecC
Confidence            344445788999999999999999987        589999999999999988 899999999999753

>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=97.85  E-value=3.7e-05  Score=55.10  Aligned_cols=78  Identities=8%  Similarity=0.106  Sum_probs=60.1

Q ss_pred             cee-eeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCc--ccEEEEEEcCHHHHHHHHHHcCCCccCCc-----
Q 023632           20 QKM-TGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRS--RGFGFITFDTEQAVDDLLAKGNKLELAGA-----   91 (279)
Q Consensus        20 ~~l-V~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~--rG~aFV~F~s~e~a~~Ai~~lng~~l~g~-----   91 (279)
                      ++| |+.||+++||   +++.+.+...+++.-.....-+.+-++  -.-|+|.|.+.+++....+.++++.+.+.     
T Consensus         2 tKvVvRrLPP~Lte---~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~D~~g~~~   78 (91)
T d1uw4a_           2 SKVVIRRLPPTLTK---EQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFLDNKGQEY   78 (91)
T ss_dssp             CEEEEEEECTTCCH---HHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEECTTCCEE
T ss_pred             ceEEEecCCCCCCH---HHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEEcCCCCEe
Confidence            355 9999999999   999999998888887766665544332  24699999999999999999999877543     


Q ss_pred             eeEEeeccC
Q 023632           92 QVEVKKAEP  100 (279)
Q Consensus        92 ~i~V~~a~~  100 (279)
                      +-.|++|.-
T Consensus        79 ~a~VE~AP~   87 (91)
T d1uw4a_          79 PAIVEFAPF   87 (91)
T ss_dssp             ECEEEECSS
T ss_pred             eeEEEEcCc
Confidence            235555543

>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=97.58  E-value=0.00012  Score=49.44  Aligned_cols=61  Identities=10%  Similarity=0.158  Sum_probs=51.9

Q ss_pred             HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCCCccCCceeEEeecc
Q 023632           36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNKLELAGAQVEVKKAE   99 (279)
Q Consensus        36 ~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng~~l~g~~i~V~~a~   99 (279)
                      +.|.++|+++++|.++.|.... ..  .-.|-|...+.++|..||..|+...|..++|.|.++.
T Consensus        11 q~L~~~f~~h~~V~sv~l~~~~-dg--~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1          11 QLLQEAFARHGKVKSVELSPHT-DY--QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHHSCEEEEEECSCC-ST--TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhheeEEEEEEEecc-CC--cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            5677899999999999886543 22  2368999999999999999999999999999999875

>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=96.10  E-value=0.0066  Score=43.32  Aligned_cols=54  Identities=15%  Similarity=0.247  Sum_probs=43.5

Q ss_pred             ceeeeCCCCCCCcccHHHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcC
Q 023632           20 QKMTGLSLTPVTEPALDEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGN   84 (279)
Q Consensus        20 ~~lV~nLp~~~te~~~~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~ln   84 (279)
                      +.+.-.+|.++..   .||.++|+.||.|.-..| .|.       -|||...+.|+|+.+++.++
T Consensus        17 HVf~~tFP~~Wk~---~dI~~lFSpfG~V~VswI-ddT-------Sa~V~L~~~e~~~~v~~~~~   70 (100)
T d1whva_          17 HVLHVTFPKEWKT---SDLYQLFSAFGNIQISWI-DDT-------SAFVSLSQPEQVQIAVNTSK   70 (100)
T ss_dssp             SEEEEECCTTCCH---HHHHHHHTTTCSCCCEEE-ETT-------EEEEECSCHHHHHHHHHHHH
T ss_pred             eeEEEeCCcccch---hHHHHHhcCCCceEEEEe-cCc-------eEEEEecCHHHHHHHHHHhc
Confidence            3336789999999   999999999998764444 442       79999999999999888754

>d2cfxa2 d.58.4.2 (A:64-140) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Dimeric alpha+beta barrel
family: Lrp/AsnC-like transcriptional regulator C-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=82.97  E-value=3.5  Score=26.72  Aligned_cols=46  Identities=15%  Similarity=0.240  Sum_probs=39.0

Q ss_pred             HHHHHHHhcCCCeEEEEEeecCCCCCcccEEEEEEcCHHHHHHHHHHcCC
Q 023632           36 DEFKDFFMQFGDVQEHQIMRDHSTSRSRGFGFITFDTEQAVDDLLAKGNK   85 (279)
Q Consensus        36 ~~L~~~F~~~G~V~~v~i~~d~~tg~~rG~aFV~F~s~e~a~~Ai~~lng   85 (279)
                      +++.+.+.++-+|.+|..+.    +...=+..|.+.|.++.++.|..+.+
T Consensus        16 ~~~~~~i~~~peV~e~~~vt----G~~D~il~v~~~d~~~l~~~i~~l~~   61 (77)
T d2cfxa2          16 ERFKSYIQTLPNIEFCYRIA----GAACYMLKINAESLEAVEDFINKTSP   61 (77)
T ss_dssp             HHHHHHHHTCTTEEEEEEEE----SSSSEEEEEEESSHHHHHHHHHHHTT
T ss_pred             HHHHHHHhcCchheEEEEEc----CCCCEEEEEEECCHHHHHHHHhhCCC
Confidence            78999999999999998874    44455788999999999999998864