Citrus Sinensis ID: 022058

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300---
Protein Sequence
MAAVADMPGDAAAANNTNNNKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH
Secondary Structure (PSIPRED)
cccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccccEEEccccccccccccEEEEEccccccHHHHHHHHHccccccccccccccccccccccccccccccccEEEEccccccccHHHHHHHHcccccEEEEEEEcccccccEEEEEEEccHHHHHHHHHccccEEccEEEEEccccccccccccccccccHHHHcccccEEEEccccccccHHHHHHHHHccccEEEEEEEEEcccccccEEEEEEEccHHHHHHHHHccccEEccEEEEEccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEcccccccccccccccccccEEEccccccccHHHHHHHHHHHccHHHHHccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccHHHHHcccccccEEEEEccccccccHHHHHHHHHHcccEEEEEEEEccccccEEEEEEEccHHHHHHHHHHcccEcccccEEEEccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHHHccccEEEEEEEEEcccccccEEEEEEccHHHHHHHHHHcccEEccccEEEEcccccccccccccccc
Coil and Loop (DISEMBL)
maavadmpgdaaaanntnnnknnnletkksesEFTVQKLVDMFTKlnplakeffpsyyhqhtdhhfsvinnnfaddnkqsaidnfnnnrrrrnNFNQGRKRLSGRafraqredsvrrtvyvsdidqnITEERLAGLfsscgqvvdcrvcgdphsvLRFAFVEFADEHGARAALNLGgtmlgyypvrvlpsktailpvnptflprsederemCSRTVyctnidkkvpQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCsgmvlgsqpirvspsktpvrprvtrpgmh
Flexible Loop (DISEMBL)
maavadmpgdaaaanntnnnknnnletkksesEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIdnfnnnrrrrnnfnqgrkrlsgrafraqredsvrrtvyvsdidqnITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLpsktailpvnptflprsedereMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLgsqpirvspsktpvrprvtrpgmh
Low Complexity Region (SEG)
maavadmpgdaaaanntnnnknnnLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDnfnnnrrrrnnfnQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH
Disordered region (IsUnstruct)
*********************************FTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFA*****************************************RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPR****REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLG***********************
Disordered Region (DISOPRED)
**************************TKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAI************************************VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP**************************VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRV*****************
Disordered Region (DISEMBL)
MAAVADMPGDAAAANNTNNNKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH
Disordered Region (DISPRO)
***********************NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHT*HHFSVINNN****N**SA******************************EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT******************MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAAVADMPGDxxxxxxxxxxxxxxxxxxxxxSEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH
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	303	2.2.26 [Sep-21-2011]
Q9LEB4	409	Polyadenylate-binding pro	N/A	no	0.564	0.418	0.289	3e-10
Q8WXA9	508	Splicing regulatory gluta	yes	no	0.273	0.163	0.404	3e-10
Q9JKL7	494	Splicing regulatory gluta	yes	no	0.273	0.168	0.404	6e-10
Q8BZX4	494	Splicing regulatory gluta	yes	no	0.273	0.168	0.404	6e-10
P21187	634	Polyadenylate-binding pro	yes	no	0.537	0.257	0.256	3e-09
Q5B630	732	Polyadenylate-binding pro	yes	no	0.514	0.213	0.28	4e-08
Q0U1G2	744	Polyadenylate-binding pro	N/A	no	0.580	0.236	0.260	6e-08
P31209	653	Polyadenylate-binding pro	yes	no	0.514	0.238	0.274	2e-07
Q60899	360	ELAV-like protein 2 OS=Mu	no	no	0.541	0.455	0.280	2e-07
P04147	577	Polyadenylate-binding pro	yes	no	0.511	0.268	0.258	2e-07

>sp|Q9LEB4|RBP45_NICPL Polyadenylate-binding protein RBP45 OS=Nicotiana plumbaginifolia GN=RBP45 PE=1 SV=1

 Score = 65.9 bits (159), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/197 (28%), Positives = 97/197 (49%), Gaps = 26/197 (13%)

Query: 111 REDSVRRTVYVSDIDQNIT----EERLAGLFSSC--GQVVDCRVCGDPHSVLRFAFVEFA 164
           R+DS   T++V D+  ++T    +E    ++SS    +VV  R+ G       + FV+FA
Sbjct: 170 RDDSAEHTIFVGDLAADVTDYILQETFKSVYSSVRGAKVVTDRITGRSKG---YGFVKFA 226

Query: 165 DE-HGARAALNLGGTMLGYYPVRVLPS---KTAILPVNPTFL-PR-SEDEREMCSRTVYC 218
           DE    RA   + G +    P+R+ P+   K    P   T+  P+ ++ E +  + T++ 
Sbjct: 227 DESEQLRAMTEMNGVLCSTRPMRIGPAANKKPVGTPQKATYQNPQATQGESDPNNTTIFV 286

Query: 219 TNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF---AVAESAILALNCS 275
             +D  V +  ++Q F     GE+  +++    V   R  FV+F   A AE A+ +LN  
Sbjct: 287 GGLDPTVAEEHLRQVFSPY--GELVHVKI----VAGKRCGFVQFGTRASAEQALSSLN-- 338

Query: 276 GMVLGSQPIRVSPSKTP 292
           G  LG Q IR+S  ++P
Sbjct: 339 GTQLGGQSIRLSWGRSP 355

Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.
Nicotiana plumbaginifolia (taxid: 4092)

>sp|Q8WXA9|SREK1_HUMAN Splicing regulatory glutamine/lysine-rich protein 1 OS=Homo sapiens GN=SREK1 PE=1 SV=1

 Score = 65.9 bits (159), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 113 DSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
           D +RRTVYV +++ Q  T ++L   F   G+V   R+ GD     RFAFVEFAD++    
Sbjct: 62  DEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPR 121

Query: 172 ALNLGGTMLGYYPVRVLPSKTAIL 195
           AL   G M G  P+++  S  AI+
Sbjct: 122 ALAFNGVMFGDRPLKINHSNNAIV 145

Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3.

Homo sapiens (taxid: 9606)

>sp|Q9JKL7|SREK1_RAT Splicing regulatory glutamine/lysine-rich protein 1 OS=Rattus norvegicus GN=Srek1 PE=1 SV=1

 Score = 65.1 bits (157), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 113 DSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
           D +RRTVYV +++ Q  T ++L   F   G+V   R+ GD     RFAFVEFAD++    
Sbjct: 65  DEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPR 124

Query: 172 ALNLGGTMLGYYPVRVLPSKTAIL 195
           AL   G M G  P+++  S  AI+
Sbjct: 125 ALAFNGVMFGDRPLKINHSNNAIV 148

Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3.

Rattus norvegicus (taxid: 10116)

>sp|Q8BZX4|SREK1_MOUSE Splicing regulatory glutamine/lysine-rich protein 1 OS=Mus musculus GN=Srek1 PE=2 SV=1

 Score = 65.1 bits (157), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 113 DSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
           D +RRTVYV +++ Q  T ++L   F   G+V   R+ GD     RFAFVEFAD++    
Sbjct: 65  DEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPR 124

Query: 172 ALNLGGTMLGYYPVRVLPSKTAIL 195
           AL   G M G  P+++  S  AI+
Sbjct: 125 ALAFNGVMFGDRPLKINHSNNAIV 148

Participates in the regulation of alternative splicing by modulating the activity of other splice facors. Inhibits the splicing activity of SFRS1, SFRS2 and SFRS6. Augments the splicing activity of SFRS3.

Mus musculus (taxid: 10090)

>sp|P21187|PABP_DROME Polyadenylate-binding protein OS=Drosophila melanogaster GN=pAbp PE=1 SV=3

 Score = 62.8 bits (151), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/191 (25%), Positives = 89/191 (46%), Gaps = 28/191 (14%)

Query: 105 RAFRAQREDSVRRT----VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FA 159
           R   +QR+ S+RR+    V++ ++D+ I  + +   FS+ G ++ C+V  D     + + 
Sbjct: 74  RIMWSQRDPSLRRSGVGNVFIKNLDRAIDNKAIYDTFSAFGNILSCKVATDEKGNSKGYG 133

Query: 160 FVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRT--- 215
           FV F  E  A  +++ + G +L    V V             F+PR E E+E+  +    
Sbjct: 134 FVHFETEEAANTSIDKVNGMLLNGKKVYV-----------GKFIPRKEREKELGEKAKLF 182

Query: 216 --VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR----IAFVEFAVAESAI 269
             VY  N  +     ++K+FFE    G++T  +++      ++    +AF     AE+A+
Sbjct: 183 TNVYVKNFTEDFDDEKLKEFFEPY--GKITSYKVMSKEDGKSKGFGFVAFETTEAAEAAV 240

Query: 270 LALNCSGMVLG 280
            ALN   M  G
Sbjct: 241 QALNGKDMGEG 251

Binds the poly(A) tail of mRNA.

Drosophila melanogaster (taxid: 7227)

>sp|Q5B630|PABP_EMENI Polyadenylate-binding protein, cytoplasmic and nuclear OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=pab1 PE=2 SV=2

 Score = 58.9 bits (141), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/175 (28%), Positives = 82/175 (46%), Gaps = 19/175 (10%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFAD-EHGARAALN 174
           ++YV ++D ++TE  L  LFSS GQV   RVC D  +   L +A+V + D  HG RA   
Sbjct: 43  SLYVGELDPSVTEAMLYELFSSIGQVASIRVCRDAVTRRSLGYAYVNYNDTAHGERALDE 102

Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           L  T++   P R++ S+            R    R+     V+  N+D  +    +   F
Sbjct: 103 LNYTLIKGKPCRIMWSQ------------RDPALRKTGQGNVFIKNLDSAIDNKALHDTF 150

Query: 235 EAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILAL-NCSGMVLGSQPIRVS 287
             A  G +   ++  D    ++   FV +  AE+A  A+ + +GM+L  + + V 
Sbjct: 151 --AAFGNILSCKVAQDEFGVSKGYGFVHYETAEAANNAIKHVNGMLLNDKKVFVG 203

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

>sp|Q0U1G2|PABP_PHANO Polyadenylate-binding protein, cytoplasmic and nuclear OS=Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) GN=PAB1 PE=3 SV=3

 Score = 58.5 bits (140), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 51/196 (26%), Positives = 94/196 (47%), Gaps = 20/196 (10%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEF-AD 165
           AQ+      ++YV ++D ++TE  L  LFSS GQV   RVC D  +   L +A+V + + 
Sbjct: 40  AQQAHQNSASLYVGELDPSVTEAMLFELFSSIGQVASIRVCRDAVTRRSLGYAYVNYNSS 99

Query: 166 EHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKV 225
           E G +A   L  T++   P R++ S+      +P         R+     V+  N+D  +
Sbjct: 100 EDGEKALEELNYTVIKGKPCRIMWSQR-----DPAL-------RKTGQGNVFIKNLDHAI 147

Query: 226 PQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILAL-NCSGMVLGSQP 283
               +   F  A  G +   ++  D + +++   FV +  AE+A  A+ + +GM+L  + 
Sbjct: 148 DNKALHDTF--AAFGNILSCKVAQDELGNSKGYGFVHYETAEAANNAIKHVNGMLLNEKK 205

Query: 284 IRVSPSKTPVRPRVTR 299
           + V     P + R+++
Sbjct: 206 VFVG-HHIPKKERMSK 220

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (taxid: 321614)

>sp|P31209|PABP_SCHPO Polyadenylate-binding protein, cytoplasmic and nuclear OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pab1 PE=1 SV=2

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 84/175 (48%), Gaps = 19/175 (10%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFAD-EHGARAALN 174
           ++YV ++D ++TE  L  LF+S G V   RVC D  +   L +A+V F + E G +A   
Sbjct: 81  SLYVGELDPSVTEAMLFELFNSIGPVASIRVCRDAVTRRSLGYAYVNFHNMEDGEKALDE 140

Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           L  T++   P R++ S+            R    R+M +  V+  N+D  +    +   F
Sbjct: 141 LNYTLIKGRPCRIMWSQ------------RDPSLRKMGTGNVFIKNLDPAIDNKALHDTF 188

Query: 235 EAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILAL-NCSGMVLGSQPIRVS 287
            A   G++   ++  D + + +   FV F   ESA  A+ + +GM+L  + + V 
Sbjct: 189 SAF--GKILSCKVAVDELGNAKGYGFVHFDSVESANAAIEHVNGMLLNDKKVYVG 241

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, involved in both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. In the cytoplasm, stimulates translation initiation and regulates mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN.

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

>sp|Q60899|ELAV2_MOUSE ELAV-like protein 2 OS=Mus musculus GN=Elavl2 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 85/189 (44%), Gaps = 25/189 (13%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGA 169
           EDS +  + V+ + QN+T+E L  LF S G++  C++  D  +   L + FV + D   A
Sbjct: 35  EDS-KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 93

Query: 170 RAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQA 228
             A+N L G  L    ++V  ++           P S   R+     +Y + + K + Q 
Sbjct: 94  EKAINTLNGLRLQTKTIKVSYAR-----------PSSASIRDA---NLYVSGLPKTMTQK 139

Query: 229 EVKQFFEAACGGEVTRLRLLGDHVH--STRIAFVEF---AVAESAILALNCSGMVLGSQP 283
           E++Q F     G +   R+L D V   S  + F+ F     AE AI  LN       ++P
Sbjct: 140 ELEQLFSQY--GRIITSRILVDQVTGISRGVGFIRFDKRIEAEEAIKGLNGQKPPGATEP 197

Query: 284 IRVSPSKTP 292
           I V  +  P
Sbjct: 198 ITVKFANNP 206

Binds RNA. Seems to recognize a GAAA motif. Can bind to its own 3'-UTR, the FOS 3'-UTR and the ID 3'-UTR.

Mus musculus (taxid: 10090)

>sp|P04147|PABP_YEAST Polyadenylate-binding protein, cytoplasmic and nuclear OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PAB1 PE=1 SV=4

 Score = 56.6 bits (135), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 81/178 (45%), Gaps = 23/178 (12%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP--HSVLRFAFVEFADEHGARAALNL 175
           ++YV D++ +++E  L  +FS  G V   RVC D    + L +A+V F D    R A+  
Sbjct: 39  SLYVGDLEPSVSEAHLYDIFSPIGSVSSIRVCRDAITKTSLGYAYVNFNDHEAGRKAIE- 97

Query: 176 GGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFE 235
               L Y P++    +      +P+        R+  S  ++  N+    P  + K  ++
Sbjct: 98  ---QLNYTPIKGRLCRIMWSQRDPSL-------RKKGSGNIFIKNLH---PDIDNKALYD 144

Query: 236 A-ACGGEVTRLRLLGDHVHSTR----IAFVEFAVAESAILALNCSGMVLGSQPIRVSP 288
             +  G++   ++  D    ++    + F E   A+ AI ALN  GM+L  Q I V+P
Sbjct: 145 TFSVFGDILSSKIATDENGKSKGFGFVHFEEEGAAKEAIDALN--GMLLNGQEIYVAP 200

Binds the poly(A) tail of mRNA. Appears to be an important mediator of the multiple roles of the poly(A) tail in mRNA biogenesis, stability and translation. In the nucleus, interacts with the nuclear cleavage factor IA (CFIA), which is required for both mRNA cleavage and polyadenylation. Is also required for efficient mRNA export to the cytoplasm. Acts in concert with a poly(A)-specific nuclease (PAN) to affect poly(A) tail shortening, which may occur concomitantly with either nucleocytoplasmic mRNA transport or translational initiation. Regulates PAN activity via interaction with the stimulator PAN3 or the inhibitor PBP1. In the cytoplasm, affects both translation and mRNA decay. Stimulates translation by interaction with translation initiation factor eIF4G, a subunit of the cap-binding complex eIF4F, bringing the 5'- and 3'-ends of the mRNA in proximity. The formation of this circular mRNP structure appears to be critical for the synergistic effects of the cap and the poly(A) tail in facilitating translation initiation, recycling of ribosomes, and mRNA stability. Also regulates translation termination by recruiting eukaryotic release factor 3 (eRF3). Interaction with eRF3 is also required for regulation of normal mRNA decay through translation termination-coupled poly(A) shortening, probably mediated by PAN. Loss of PAB1 from the mRNP after deadenylation triggers mRNA degradation. Inhibits the major cytoplasmic mRNA deadenylase CCR4-NOT complex. Is also associated peripherally with COPI vesicles through its interaction with ARF1, and this is required for correct localization of the asymmetrically distributed ASH1 mRNA.

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

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	303
224056565	307	predicted protein [Populus trichocarpa]	0.976	0.964	0.777	1e-133
358248658	296	uncharacterized protein LOC100779109 [Gl	0.960	0.983	0.75	1e-130
224114547	308	predicted protein [Populus trichocarpa]	0.891	0.876	0.829	1e-129
356556922	296	PREDICTED: polyadenylate-binding protein	0.960	0.983	0.756	1e-127
255578158	281	RNA-binding protein, putative [Ricinus c	0.920	0.992	0.776	1e-126
15231858	327	CTC-interacting domain 9 protein [Arabid	0.894	0.828	0.712	1e-115
225462109	292	PREDICTED: polyadenylate-binding protein	0.943	0.979	0.750	1e-115
388509636	313	unknown [Lotus japonicus]	0.980	0.948	0.705	1e-111
79319864	308	CTC-interacting domain 8 protein [Arabid	0.950	0.935	0.652	1e-109
51969708	295	putative RNA-binding protein [Arabidopsi	0.858	0.881	0.721	1e-109

>gi|224056565|ref|XP_002298913.1| predicted protein [Populus trichocarpa] gi|222846171|gb|EEE83718.1| predicted protein [Populus trichocarpa]

 Score =  479 bits (1232), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 244/314 (77%), Positives = 267/314 (85%), Gaps = 18/314 (5%)

Query: 1   MAAVADMPGDAAAANNTNNNKNN--------NLETK-KSESEFTVQKLVDMFTKLNPLAK 51
           MAAVA++  +AA A+N      N        + ETK  SESEFTVQKLVDMFTKLNPLAK
Sbjct: 1   MAAVAEITSEAAVASNNTTTAANKNDNNNNLDSETKPTSESEFTVQKLVDMFTKLNPLAK 60

Query: 52  EFFPSYYHQHT--DHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRA 109
           EFFPS Y ++   + HF    NNFA   KQSA DNF   +R+RNNFNQGR++L+GRA+RA
Sbjct: 61  EFFPSSYSKNNPNELHF----NNFAVPVKQSANDNFP--KRKRNNFNQGRRKLNGRAYRA 114

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
           Q+EDS+RRTVYVSDIDQ++TEERLAGLFS CGQVVDCRVCGDPHSVLRFAFVEFADE GA
Sbjct: 115 QQEDSIRRTVYVSDIDQHVTEERLAGLFSGCGQVVDCRVCGDPHSVLRFAFVEFADEQGA 174

Query: 170 RAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAE 229
           RAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMC+RTVYCTNIDKKV Q E
Sbjct: 175 RAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCTRTVYCTNIDKKVSQVE 234

Query: 230 VKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS 289
           VK FFE+ C GEVTRLRLLGD VHSTRIAFVEFA+AESAI+ALNCSGM LGSQP+RVSPS
Sbjct: 235 VKNFFESIC-GEVTRLRLLGDQVHSTRIAFVEFAMAESAIVALNCSGMALGSQPVRVSPS 293

Query: 290 KTPVRPRVTRPGMH 303
           KTPVRPRVTRP MH
Sbjct: 294 KTPVRPRVTRPAMH 307

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358248658|ref|NP_001240174.1| uncharacterized protein LOC100779109 [Glycine max] gi|255639113|gb|ACU19856.1| unknown [Glycine max]

 Score =  471 bits (1212), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 231/308 (75%), Positives = 262/308 (85%), Gaps = 17/308 (5%)

Query: 1   MAAVADMPGDAAAANNTNNNKNNNLETK-KSESEFTVQKLVDMFTKLNPLAKEFFPSYYH 59
           MAAVA++P DA           N +++K K+ESEF+VQKLVDMFTKLNPLAKEFFPS Y 
Sbjct: 1   MAAVAEIPADA-----------NKMDSKPKAESEFSVQKLVDMFTKLNPLAKEFFPSSYS 49

Query: 60  QHTDHHFSVINN----NFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSV 115
            + DH F   N      F    K SA +NF N+RRRRN+FNQGR+R+SGR+ +AQREDS+
Sbjct: 50  PNHDHGFQGFNQLSPTQFLVSTKPSANENFLNSRRRRNSFNQGRRRVSGRSLKAQREDSI 109

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNL 175
           RRTVYVS+IDQ++TEERLA LFSSCGQV+DCR+CGDPHSVLRFAFVEFADE+GAR ALNL
Sbjct: 110 RRTVYVSEIDQHVTEERLAALFSSCGQVIDCRICGDPHSVLRFAFVEFADEYGARTALNL 169

Query: 176 GGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFE 235
           GGT+LGYYPVRVLPSKTAILPVNPTFLPRS+DEREMC+RT+YCTNIDKKV QAEVK FFE
Sbjct: 170 GGTVLGYYPVRVLPSKTAILPVNPTFLPRSDDEREMCARTIYCTNIDKKVSQAEVKNFFE 229

Query: 236 AACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRP 295
           +AC GEV RLRLLGD VHSTRIAFVEFA+AESAI+ALNCSGM+LG+QPIRVSPSKTPVRP
Sbjct: 230 SAC-GEVMRLRLLGDQVHSTRIAFVEFAMAESAIIALNCSGMLLGTQPIRVSPSKTPVRP 288

Query: 296 RVTRPGMH 303
           RV RP  H
Sbjct: 289 RVPRPASH 296

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114547|ref|XP_002316790.1| predicted protein [Populus trichocarpa] gi|222859855|gb|EEE97402.1| predicted protein [Populus trichocarpa]

 Score =  466 bits (1200), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 228/275 (82%), Positives = 250/275 (90%), Gaps = 5/275 (1%)

Query: 29  KSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNN 88
           KSESEFTVQKLVDMFTKLNPLAKEFFPS Y+++    F +  NNF   NKQSA DNF   
Sbjct: 39  KSESEFTVQKLVDMFTKLNPLAKEFFPSSYNKNNPKQFHI--NNFPVPNKQSANDNFP-- 94

Query: 89  RRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRV 148
           +RRRN+FNQGR+RL+GRA+RAQREDS+RRTVYVSDIDQ++TEE+LAGLFS CGQVVDCR+
Sbjct: 95  KRRRNDFNQGRRRLNGRAYRAQREDSIRRTVYVSDIDQHVTEEQLAGLFSGCGQVVDCRI 154

Query: 149 CGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDE 208
           CGDP SVLRFAFVEFA E GARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLP+SEDE
Sbjct: 155 CGDPRSVLRFAFVEFAVEQGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPQSEDE 214

Query: 209 REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESA 268
           REMC+RTVYCTNI+KKV QAEVK FFE+ C GEVTRLRLLGDHVHSTRIAFVEFA+AESA
Sbjct: 215 REMCTRTVYCTNIEKKVSQAEVKNFFESIC-GEVTRLRLLGDHVHSTRIAFVEFAMAESA 273

Query: 269 ILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH 303
           I+ALNCSGMVLGSQP+RVSPSKTPVRPRVTR  +H
Sbjct: 274 IVALNCSGMVLGSQPVRVSPSKTPVRPRVTRLALH 308

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556922|ref|XP_003546769.1| PREDICTED: polyadenylate-binding protein, cytoplasmic and nuclear-like [Glycine max]

 Score =  459 bits (1180), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 233/308 (75%), Positives = 265/308 (86%), Gaps = 17/308 (5%)

Query: 1   MAAVADMPGDAAAANNTNNNKNNNLETK-KSESEFTVQKLVDMFTKLNPLAKEFFPSYYH 59
           MAAVA++P DA           N +++K K+ESEF+VQKLVDMFTKLNPLAKEFFPS Y 
Sbjct: 1   MAAVAEIPADA-----------NKMDSKPKAESEFSVQKLVDMFTKLNPLAKEFFPSSYS 49

Query: 60  QHTDHHFSVINN----NFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSV 115
            + D+ F   N     +F    K SA +NF NNRRRRN+FNQGR+++SGR+ +AQREDS+
Sbjct: 50  PNHDNRFQGFNQLSPTHFLVSTKPSADENFPNNRRRRNSFNQGRRKVSGRSLKAQREDSI 109

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNL 175
           RRTVYVS+IDQ++TEERLA LFSSCGQV+DCR+CGDPHSVLRFAFVEFADE+GAR ALNL
Sbjct: 110 RRTVYVSEIDQHVTEERLAALFSSCGQVIDCRICGDPHSVLRFAFVEFADEYGARTALNL 169

Query: 176 GGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFE 235
           GGT+LGYYPVRVLPSKTAILPVNPTFLPRS+DEREMC+RTVYCTNIDKKV QAEVK FFE
Sbjct: 170 GGTVLGYYPVRVLPSKTAILPVNPTFLPRSDDEREMCARTVYCTNIDKKVSQAEVKNFFE 229

Query: 236 AACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRP 295
           +AC GEV RLRLLGDHVHSTRIAFVEFA+AESAI+ALNCSGM+LG+QPIRVSPSKTPVRP
Sbjct: 230 SAC-GEVMRLRLLGDHVHSTRIAFVEFAMAESAIIALNCSGMLLGTQPIRVSPSKTPVRP 288

Query: 296 RVTRPGMH 303
           RVTRP  H
Sbjct: 289 RVTRPASH 296

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255578158|ref|XP_002529948.1| RNA-binding protein, putative [Ricinus communis] gi|223530546|gb|EEF32425.1| RNA-binding protein, putative [Ricinus communis]

 Score =  457 bits (1176), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 222/286 (77%), Positives = 254/286 (88%), Gaps = 7/286 (2%)

Query: 1   MAAVADMPGDAAAANNTNNNKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQ 60
           MAAVA++ G+ A A+N     N  +++    SEF+VQKLVDMFTKLNPLAKEFFPS Y+ 
Sbjct: 1   MAAVAEITGEVAIASN-----NKKMDSDVKNSEFSVQKLVDMFTKLNPLAKEFFPSSYNN 55

Query: 61  H-TDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTV 119
           +   H+F  +NN     +KQS IDNF++NRR+RNN+NQG++RL+GRA+RAQR+DS+RRTV
Sbjct: 56  NNITHNFLNLNNFAVVVDKQSPIDNFSSNRRKRNNYNQGKRRLNGRAYRAQRDDSIRRTV 115

Query: 120 YVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTM 179
           YVSDIDQ++TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGT+
Sbjct: 116 YVSDIDQHVTEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTV 175

Query: 180 LGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACG 239
           LGYYP RVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKK+ QAEVK FFE+ C 
Sbjct: 176 LGYYPFRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKISQAEVKTFFESTC- 234

Query: 240 GEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIR 285
           GEVTRLRLLGDHVHSTRIAFVEFA+AESAI+ALNCSGMV+G+QPIR
Sbjct: 235 GEVTRLRLLGDHVHSTRIAFVEFAMAESAIIALNCSGMVVGTQPIR 280

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231858|ref|NP_188063.1| CTC-interacting domain 9 protein [Arabidopsis thaliana] gi|11994215|dbj|BAB01337.1| unnamed protein product [Arabidopsis thaliana] gi|332642006|gb|AEE75527.1| CTC-interacting domain 9 protein [Arabidopsis thaliana]

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 201/282 (71%), Positives = 237/282 (84%), Gaps = 11/282 (3%)

Query: 29  KSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVIN-----NNFADDNKQSAID 83
           ++ES   + KLV MF KLNPLAKEFFPSYY    ++  +  N     ++F    KQS  +
Sbjct: 43  ETESRLDMHKLVAMFKKLNPLAKEFFPSYYDPKKNNQVAKANQFLPADDFETTKKQSGEE 102

Query: 84  -----NFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFS 138
                  ++N R+R N++QGR+RL+GR  +AQREDS+RRTVYVSDIDQ++TEE LAGLFS
Sbjct: 103 FDLDAKKDDNTRKRRNYSQGRRRLTGRISKAQREDSIRRTVYVSDIDQSVTEEGLAGLFS 162

Query: 139 SCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVN 198
           +CGQVVDCR+CGDPHSVLRFAFVEFAD+ GA  AL+LGGTMLG+YPVRVLPSKTAILPVN
Sbjct: 163 NCGQVVDCRICGDPHSVLRFAFVEFADDQGAHEALSLGGTMLGFYPVRVLPSKTAILPVN 222

Query: 199 PTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIA 258
           PTFLPRSEDEREMC+RT+YCTNIDKKV QA+V+ FFE+AC GEVTRLRLLGD +HSTRIA
Sbjct: 223 PTFLPRSEDEREMCTRTIYCTNIDKKVSQADVRNFFESAC-GEVTRLRLLGDQLHSTRIA 281

Query: 259 FVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRP 300
           FVEFA+A+SA+ ALNCSGMV+GSQPIRVSPSKTPVRPR+TRP
Sbjct: 282 FVEFALADSALSALNCSGMVVGSQPIRVSPSKTPVRPRITRP 323

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225462109|ref|XP_002277842.1| PREDICTED: polyadenylate-binding protein, cytoplasmic and nuclear [Vitis vinifera] gi|296088694|emb|CBI38144.3| unnamed protein product [Vitis vinifera]

 Score =  419 bits (1077), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 232/309 (75%), Positives = 257/309 (83%), Gaps = 23/309 (7%)

Query: 1   MAAVADMPGDAAAANNTNNNKNNNLETKKSESEFTV---QKLVDMFT--KLNPLAKEFFP 55
           MAA A+M G+A  A  ++ N +       S+SEF       +VDM +  KLNPLAKEFFP
Sbjct: 1   MAAGAEMSGEAVPAVPSSKNSD-------SKSEFGAGMQSMIVDMLSNLKLNPLAKEFFP 53

Query: 56  SYY-HQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDS 114
           S Y H H      +I  +F+ D+     D + NNRRRRNN+NQGR+RLSGRAFRAQREDS
Sbjct: 54  SSYSHDH------LIPTDFSKDSPN---DAYPNNRRRRNNYNQGRRRLSGRAFRAQREDS 104

Query: 115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
           +RRTVYVSDIDQ++TEERLA LFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN
Sbjct: 105 IRRTVYVSDIDQHVTEERLAALFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 164

Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMC+RTVYCTNIDKKV QAEVK FF
Sbjct: 165 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCARTVYCTNIDKKVSQAEVKNFF 224

Query: 235 EAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVR 294
           E AC GEV+RLRLLGDHVHSTRIAFVEFA+AESAI+ALNCSG+VLG+QPIRVSPSKTPVR
Sbjct: 225 ERAC-GEVSRLRLLGDHVHSTRIAFVEFAMAESAIVALNCSGLVLGTQPIRVSPSKTPVR 283

Query: 295 PRVTRPGMH 303
           PRV R  +H
Sbjct: 284 PRVPRATLH 292

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388509636|gb|AFK42884.1| unknown [Lotus japonicus]

 Score =  406 bits (1044), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 220/312 (70%), Positives = 255/312 (81%), Gaps = 15/312 (4%)

Query: 1   MAAVADMPGDAAAANNTNNNKNNNLETKKS-ESEFTVQKLVDMFTKLNPLAKEFFPSYYH 59
           MAA  ++P  ++A         + L++K + +SEF +QKLVD+FTKLNPLA+EF PS Y 
Sbjct: 1   MAAATEIP--SSADAAAAAATGSKLDSKPNLDSEFNMQKLVDIFTKLNPLAEEFIPSSYA 58

Query: 60  Q--HTDHHFSVIN----NNF---ADDNKQSAIDNF--NNNRRRRNNFNQGRKRLSGRAFR 108
              H DH     N    N F    ++NK  A D +   NNRRRRNNFNQG +R +GR  +
Sbjct: 59  AAAHRDHLHQGFNQWSPNPFLVNNNNNKPLADDQYPNANNRRRRNNFNQGGRRFTGRVLK 118

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHG 168
           AQREDSVRRTVYVSDIDQ++TEERLA LF++CG V+DCR+CGDPHSVLRFAFVEFADE+G
Sbjct: 119 AQREDSVRRTVYVSDIDQHVTEERLAALFTTCGSVIDCRICGDPHSVLRFAFVEFADEYG 178

Query: 169 ARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQA 228
           ARAALNL GT+LGYYPVRVLPSKTAILPVNPTFLPRS+DEREMCSRTVYCTNIDKKV QA
Sbjct: 179 ARAALNLSGTVLGYYPVRVLPSKTAILPVNPTFLPRSDDEREMCSRTVYCTNIDKKVSQA 238

Query: 229 EVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP 288
           EVK FFE +C GEVTR+RLLGDHVHSTRIAFVEFA+AESAI+AL+CSGM+LG+QP+RVSP
Sbjct: 239 EVKNFFEISC-GEVTRIRLLGDHVHSTRIAFVEFAIAESAIIALSCSGMLLGTQPVRVSP 297

Query: 289 SKTPVRPRVTRP 300
           SKTPVRPRV RP
Sbjct: 298 SKTPVRPRVPRP 309

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79319864|ref|NP_001031182.1| CTC-interacting domain 8 protein [Arabidopsis thaliana] gi|332194856|gb|AEE32977.1| CTC-interacting domain 8 protein [Arabidopsis thaliana]

 Score =  402 bits (1032), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 205/314 (65%), Positives = 245/314 (78%), Gaps = 26/314 (8%)

Query: 1   MAAVADMPGDAAAANN---TNNNKNNNLETK----------KSESEF-TVQKLVDMFTKL 46
           MAA+ +M  D+    N   T +    + ++K          KS+ E+  ++KLV MF KL
Sbjct: 1   MAAITEMATDSNDVINDGGTGDGIEKSTDSKPEIESDDLKPKSKPEYDQMKKLVAMFKKL 60

Query: 47  NPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK-RLSGR 105
           NP AKEFFPSY            N N +DD   +   +  +N++RRNN+NQGR+ RL GR
Sbjct: 61  NPEAKEFFPSYKR----------NTNQSDDFVIAIKPSGEDNKKRRNNYNQGRRVRLPGR 110

Query: 106 AFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFAD 165
           A +AQREDS+RRTVYVSDIDQ++TEE LAGLFSSCGQVVDCR+CGDP+SVLRFAFVEF+D
Sbjct: 111 ASKAQREDSIRRTVYVSDIDQSVTEEGLAGLFSSCGQVVDCRICGDPNSVLRFAFVEFSD 170

Query: 166 EHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKV 225
           + GAR+AL+LGGTM+GYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRT+YCTN+DK  
Sbjct: 171 DQGARSALSLGGTMIGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTIYCTNVDKNA 230

Query: 226 PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIR 285
            + +V  FF++AC GEVTRLRLLGD VHSTRIAFVEFA+AESA+ ALNCSG+VLGSQPIR
Sbjct: 231 TEDDVNTFFQSAC-GEVTRLRLLGDQVHSTRIAFVEFAMAESAVAALNCSGIVLGSQPIR 289

Query: 286 VSPSKTPVRPRVTR 299
           VSPSKTPVR R+TR
Sbjct: 290 VSPSKTPVRSRITR 303

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|51969708|dbj|BAD43546.1| putative RNA-binding protein [Arabidopsis thaliana] gi|51970080|dbj|BAD43732.1| putative RNA-binding protein [Arabidopsis thaliana]

 Score =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 197/273 (72%), Positives = 230/273 (84%), Gaps = 13/273 (4%)

Query: 29  KSESEF-TVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNN 87
           KS+ E+  ++KLV MF KLNP AKEFFPSY            N N +DD   +   +  +
Sbjct: 29  KSKPEYDQMKKLVAMFKKLNPEAKEFFPSYKR----------NTNQSDDFVIAIKPSGED 78

Query: 88  NRRRRNNFNQGRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC 146
           N++RRNN+NQGR+ RL GRA +AQREDS+RRTVYVSDIDQ++TEE LAGLFSSCGQVVDC
Sbjct: 79  NKKRRNNYNQGRRVRLPGRASKAQREDSIRRTVYVSDIDQSVTEEGLAGLFSSCGQVVDC 138

Query: 147 RVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSE 206
           R+CGDP+SVLRFAFVEF+D+ GAR+AL+LGGTM+GYYPVRVLPSKTAILPVNPTFLPRSE
Sbjct: 139 RICGDPNSVLRFAFVEFSDDQGARSALSLGGTMIGYYPVRVLPSKTAILPVNPTFLPRSE 198

Query: 207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAE 266
           DEREMCSRT+YCTN+DK   + +V  FF++AC GEVTRLRLLGD VHSTRIAFVEFA+AE
Sbjct: 199 DEREMCSRTIYCTNVDKNATEDDVNTFFQSAC-GEVTRLRLLGDQVHSTRIAFVEFAMAE 257

Query: 267 SAILALNCSGMVLGSQPIRVSPSKTPVRPRVTR 299
           SA+ ALNCSG+VLGSQPIRVSPSKTPVR R+TR
Sbjct: 258 SAVAALNCSGIVLGSQPIRVSPSKTPVRSRITR 290

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	303
TAIR|locus:2091657	327	CID9 "CTC-interacting domain 9	0.894	0.828	0.709	7.9e-101
TAIR|locus:2024842	314	CID8 "CTC-interacting domain 8	0.874	0.843	0.704	1.4e-96
TAIR|locus:2139242	336	CID12 "CTC-interacting domain	0.877	0.791	0.604	6.4e-83
TAIR|locus:2082961	353	CID10 "CTC-interacting domain	0.858	0.736	0.617	3.2e-81
TAIR|locus:2035629	406	CID11 "CTC-interacting domain	0.825	0.615	0.614	3.3e-79
TAIR|locus:2184022	320	CID13 "CTC-interacting domain	0.811	0.768	0.577	3.3e-70
UNIPROTKB|Q9LEB4	409	RBP45 "Polyadenylate-binding p	0.567	0.420	0.287	1e-09
TAIR|locus:2009036	407	PAB1 "poly(A) binding protein	0.570	0.425	0.263	1.3e-09
RGD|621696	494	Srek1 "splicing regulatory glu	0.303	0.186	0.382	9.9e-09
UNIPROTKB|Q9JKL7	494	Srek1 "Splicing regulatory glu	0.303	0.186	0.382	9.9e-09

TAIR|locus:2091657 CID9 "CTC-interacting domain 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 1000 (357.1 bits), Expect = 7.9e-101, P = 7.9e-101
 Identities = 200/282 (70%), Positives = 229/282 (81%)

Query:    29 KSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNF-ADD----NKQSA-- 81
             ++ES   + KLV MF KLNPLAKEFFPSYY    ++  +  N    ADD     KQS   
Sbjct:    43 ETESRLDMHKLVAMFKKLNPLAKEFFPSYYDPKKNNQVAKANQFLPADDFETTKKQSGEE 102

Query:    82 --IDXXXXXXXXXXXX-XQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFS 138
               +D              QGR+RL+GR  +AQREDS+RRTVYVSDIDQ++TEE LAGLFS
Sbjct:   103 FDLDAKKDDNTRKRRNYSQGRRRLTGRISKAQREDSIRRTVYVSDIDQSVTEEGLAGLFS 162

Query:   139 SCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVN 198
             +CGQVVDCR+CGDPHSVLRFAFVEFAD+ GA  AL+LGGTMLG+YPVRVLPSKTAILPVN
Sbjct:   163 NCGQVVDCRICGDPHSVLRFAFVEFADDQGAHEALSLGGTMLGFYPVRVLPSKTAILPVN 222

Query:   199 PTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIA 258
             PTFLPRSEDEREMC+RT+YCTNIDKKV QA+V+ FFE+ACG EVTRLRLLGD +HSTRIA
Sbjct:   223 PTFLPRSEDEREMCTRTIYCTNIDKKVSQADVRNFFESACG-EVTRLRLLGDQLHSTRIA 281

Query:   259 FVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRP 300
             FVEFA+A+SA+ ALNCSGMV+GSQPIRVSPSKTPVRPR+TRP
Sbjct:   282 FVEFALADSALSALNCSGMVVGSQPIRVSPSKTPVRPRITRP 323

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:2024842 CID8 "CTC-interacting domain 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 960 (343.0 bits), Expect = 1.4e-96, P = 1.4e-96
 Identities = 193/274 (70%), Positives = 224/274 (81%)

Query:    29 KSESEFT-VQKLVDMFTKLNPLAKEFFPSYYHQ-HTDHHFSVINNNFADDNKQSAIDXXX 86
             KS+ E+  ++KLV MF KLNP AKEFFPSY    +    F +      +DNK+ AI+   
Sbjct:    42 KSKPEYDQMKKLVAMFKKLNPEAKEFFPSYKRNTNQSDDFVIAIKPSGEDNKKVAINRRR 101

Query:    87 XXXXXXXXXXQGRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD 145
                       QGR+ RL GRA +AQREDS+RRTVYVSDIDQ++TEE LAGLFSSCGQVVD
Sbjct:   102 RNNYN-----QGRRVRLPGRASKAQREDSIRRTVYVSDIDQSVTEEGLAGLFSSCGQVVD 156

Query:   146 CRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRS 205
             CR+CGDP+SVLRFAFVEF+D+ GAR+AL+LGGTM+GYYPVRVLPSKTAILPVNPTFLPRS
Sbjct:   157 CRICGDPNSVLRFAFVEFSDDQGARSALSLGGTMIGYYPVRVLPSKTAILPVNPTFLPRS 216

Query:   206 EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA 265
             EDEREMCSRT+YCTN+DK   + +V  FF++ACG EVTRLRLLGD VHSTRIAFVEFA+A
Sbjct:   217 EDEREMCSRTIYCTNVDKNATEDDVNTFFQSACG-EVTRLRLLGDQVHSTRIAFVEFAMA 275

Query:   266 ESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTR 299
             ESA+ ALNCSG+VLGSQPIRVSPSKTPVR R+TR
Sbjct:   276 ESAVAALNCSGIVLGSQPIRVSPSKTPVRSRITR 309

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:0005737 "cytoplasm" evidence=ISM

GO:0005515 "protein binding" evidence=IPI

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

TAIR|locus:2139242 CID12 "CTC-interacting domain 12" [Arabidopsis thaliana (taxid:3702)]

 Score = 831 (297.6 bits), Expect = 6.4e-83, P = 6.4e-83
 Identities = 165/273 (60%), Positives = 204/273 (74%)

Query:    36 VQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFS----VINNNFADDNKQSAIDXXXXXXXX 91
             +++L ++ +KLNP+AKEF P    +   + F+     +NN F        ++        
Sbjct:    66 MRELHELLSKLNPMAKEFIPPSLTKPVVNGFNGGFFAVNNGFVAAGN-FPVNEDGSFRRK 124

Query:    92 XXXXXQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD 151
                  QG++R++ R   AQRE+ +RRTVYVSDIDQ +TEE+LAGLF   GQVVDCR+CGD
Sbjct:   125 KSFGQQGKRRMNPRTSLAQREEIIRRTVYVSDIDQQVTEEQLAGLFIGFGQVVDCRICGD 184

Query:   152 PHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREM 211
             P+SVLRFAF+EF DE GAR ALNL GTMLG+YPV+V+PSKTAI PVNPTFLPR+EDEREM
Sbjct:   185 PNSVLRFAFIEFTDEVGARTALNLSGTMLGFYPVKVMPSKTAIAPVNPTFLPRTEDEREM 244

Query:   212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA 271
             C+RT+YCTNIDKK+ Q ++K FFE+ CG EV RLRLLGD+ H TRI FVEF +AESAI A
Sbjct:   245 CARTIYCTNIDKKLTQTDIKLFFESVCG-EVYRLRLLGDYHHPTRIGFVEFVMAESAIAA 303

Query:   272 LNCSGMVLGSQPIRVSPSKTPVRPR-VTRPGMH 303
             LNCSG++LGS PIRVSPSKTPVR R + R  MH
Sbjct:   304 LNCSGVLLGSLPIRVSPSKTPVRSRAIPRHQMH 336

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS;IDA

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2082961 CID10 "CTC-interacting domain 10" [Arabidopsis thaliana (taxid:3702)]

 Score = 815 (292.0 bits), Expect = 3.2e-81, P = 3.2e-81
 Identities = 165/267 (61%), Positives = 201/267 (75%)

Query:    36 VQKLVDMFTKLNPLAKEFFP-SYYHQHTD--HHFSVINNNFADDNKQSAIDXXXXXXXXX 92
             ++ L D F+KLNP+A+EF P S     +    +     NNFA   K +  D         
Sbjct:    87 IKDLADAFSKLNPMAQEFVPPSLARSQSGVLRNGLGFTNNFAAPPKLA--DGNDHFPRRR 144

Query:    93 XXXXQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP 152
                 QG++R++ R   AQ++D +RRTVYVSDIDQ +TEE LAG+F +CGQVVDCRVCGDP
Sbjct:   145 RSFGQGKRRMNKRTSLAQKDDVIRRTVYVSDIDQQVTEENLAGVFINCGQVVDCRVCGDP 204

Query:   153 HSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMC 212
             +SVLRFAF+EF +E GARAAL++ GT+LG+YP++VLPSKTAI PVNPTFLPRSEDEREMC
Sbjct:   205 NSVLRFAFIEFTNEEGARAALSMSGTVLGFYPLKVLPSKTAIAPVNPTFLPRSEDEREMC 264

Query:   213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              RTVYCTNIDK++ Q ++K FFE  CG EV RLRL GD+ H TRIAFVEFA+AESAI AL
Sbjct:   265 VRTVYCTNIDKRITQIDLKGFFEMLCG-EVHRLRL-GDYHHQTRIAFVEFAMAESAIAAL 322

Query:   273 NCSGMVLGSQPIRVSPSKTPVRPRVTR 299
             +CSG+VLG+ PIRVSPSKTPVRP   R
Sbjct:   323 HCSGIVLGALPIRVSPSKTPVRPHFPR 349

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:2035629 CID11 "CTC-interacting domain 11" [Arabidopsis thaliana (taxid:3702)]

 Score = 796 (285.3 bits), Expect = 3.3e-79, P = 3.3e-79
 Identities = 161/262 (61%), Positives = 195/262 (74%)

Query:    36 VQKLVDMFTKLNPLAKEFFPSYYHQHTDH-----HFSVI-----NNNFADDNKQSAIDXX 85
             +++L ++F+KLNP+A+EF P   ++   +      F+       NN FA           
Sbjct:    83 MRELQELFSKLNPMAEEFVPPSLNKQGGNGVNGGFFTSAGSFFRNNGFAGTGN-GGYGNE 141

Query:    86 XXXXXXXXXXXQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD 145
                        QG++R++ R   AQRED +RRTVYVSD+DQ +TEE+LAGLF SCGQVVD
Sbjct:   142 NGGFRRKKSFGQGKRRMNARTSMAQREDVIRRTVYVSDLDQQVTEEQLAGLFVSCGQVVD 201

Query:   146 CRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRS 205
             CR+CGDP+SVLRFAF+EF DE GA  ALNL GTMLG+YPV+VLPSKTAI PVNPTFLPR+
Sbjct:   202 CRICGDPNSVLRFAFIEFTDEEGAMTALNLSGTMLGFYPVKVLPSKTAIAPVNPTFLPRT 261

Query:   206 EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA 265
             EDEREMC+RT+YCTNIDKKV Q++VK FFE+ CG EV RLRLLGD+ HSTRIAFVEF +A
Sbjct:   262 EDEREMCARTIYCTNIDKKVTQSDVKIFFESFCG-EVYRLRLLGDYQHSTRIAFVEFVMA 320

Query:   266 ESAILALNCSGMVLGSQPIRVS 287
             ESAI ALNCSG+VLGS PIR S
Sbjct:   321 ESAIAALNCSGVVLGSLPIRSS 342

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

GO:0046482 "para-aminobenzoic acid metabolic process" evidence=RCA

TAIR|locus:2184022 CID13 "CTC-interacting domain 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 711 (255.3 bits), Expect = 3.3e-70, P = 3.3e-70
 Identities = 145/251 (57%), Positives = 173/251 (68%)

Query:    46 LNPLAKEFFPSYYHQHTDHHFSVINNNFADDNK--QSAIDXXXXXXXXXXXXXQGRKRLS 103
             LNP+AKEF PS+  Q   HH     N F   N   +  I              +GR  ++
Sbjct:    66 LNPMAKEFVPSFLAQ--THHSEFWGNRFWFTNHFPKQTIFLIGQFATMRRNFGKGRPWIT 123

Query:   104 GRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEF 163
              +    Q ED ++RTVYVSDID  +TEE+LA LF SCGQVVDCR+CGD  S+LRFAF+EF
Sbjct:   124 KKTNLVQNEDMIKRTVYVSDIDNQVTEEQLASLFLSCGQVVDCRMCGDYKSILRFAFIEF 183

Query:   164 ADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDK 223
              D  GAR+AL   GTM G +P+RV  SKTAI PVNP+FLP+S+DE E C +TVYCTNIDK
Sbjct:   184 TDAEGARSALRKSGTMFGSHPIRVFMSKTAIAPVNPSFLPQSKDELEKCGKTVYCTNIDK 243

Query:   224 KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQP 283
             +V + E++ FF+  CG EV  LRLLGD  H TRIAFVEF +AESAI ALNCSG+VLG  P
Sbjct:   244 EVTKMELENFFKTVCG-EVHHLRLLGDFYHQTRIAFVEFKLAESAISALNCSGVVLGELP 302

Query:   284 IRVSPSKTPVR 294
             IRVSPSKTPVR
Sbjct:   303 IRVSPSKTPVR 313

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

UNIPROTKB|Q9LEB4 RBP45 "Polyadenylate-binding protein RBP45" [Nicotiana plumbaginifolia (taxid:4092)]

 Score = 163 (62.4 bits), Expect = 1.0e-09, P = 1.0e-09
 Identities = 57/198 (28%), Positives = 98/198 (49%)

Query:   110 QREDSVRRTVYVSDIDQNITE----ERLAGLFSSC--GQVVDCRVCGDPHSVLRFAFVEF 163
             +R+DS   T++V D+  ++T+    E    ++SS    +VV  R+ G       + FV+F
Sbjct:   169 RRDDSAEHTIFVGDLAADVTDYILQETFKSVYSSVRGAKVVTDRITGRSKG---YGFVKF 225

Query:   164 ADE-HGARAALNLGGTMLGYYPVRVLPS---KTAILPVNPTFL-PRS-EDEREMCSRTVY 217
             ADE    RA   + G +    P+R+ P+   K    P   T+  P++ + E +  + T++
Sbjct:   226 ADESEQLRAMTEMNGVLCSTRPMRIGPAANKKPVGTPQKATYQNPQATQGESDPNNTTIF 285

Query:   218 CTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF---AVAESAILALNC 274
                +D  V +  ++Q F     GE+  +++    V   R  FV+F   A AE A+ +LN 
Sbjct:   286 VGGLDPTVAEEHLRQVFSPY--GELVHVKI----VAGKRCGFVQFGTRASAEQALSSLN- 338

Query:   275 SGMVLGSQPIRVSPSKTP 292
              G  LG Q IR+S  ++P
Sbjct:   339 -GTQLGGQSIRLSWGRSP 355

GO:0005634 "nucleus" evidence=IDA

GO:0008143 "poly(A) RNA binding" evidence=IDA

TAIR|locus:2009036 PAB1 "poly(A) binding protein 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 162 (62.1 bits), Expect = 1.3e-09, P = 1.3e-09
 Identities = 52/197 (26%), Positives = 97/197 (49%)

Query:   101 RLSGRAFR---AQREDSVRRT----VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH 153
             +L G+  R   ++R+ S R +    V+V ++D++I  ++L  +FS+ G+V+ C+V  D  
Sbjct:     8 KLKGKPMRIMFSERDPSNRMSGRGNVFVKNLDESIDNKQLCDMFSAFGKVLSCKVARDAS 67

Query:   154 SVLR-FAFVEFADEHGARAALNL-GGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREM 211
              V + + FV+F  +     A N   GT++    + V P           F+ R + ++  
Sbjct:    68 GVSKGYGFVQFYSDLSVYTACNFHNGTLIRNQHIHVCP-----------FVSRGQWDKSR 116

Query:   212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-HVHSTRIAFVEFAVAESAIL 270
                 VY  N+ +    A++K+ F     GE+T   ++ D    S R  FV F  AE+A+ 
Sbjct:   117 VFTNVYVKNLVETATDADLKRLFGEF--GEITSAVVMKDGEGKSRRFGFVNFEKAEAAVT 174

Query:   271 ALN-CSGMVLGSQPIRV 286
             A+   +G+V+  + + V
Sbjct:   175 AIEKMNGVVVDEKELHV 191

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

RGD|621696 Srek1 "splicing regulatory glutamine/lysine-rich protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 156 (60.0 bits), Expect = 9.9e-09, P = 9.9e-09
 Identities = 36/94 (38%), Positives = 52/94 (55%)

Query:   113 DSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
             D +RRTVYV +++ Q  T ++L   F   G+V   R+ GD     RFAFVEFAD++    
Sbjct:    65 DEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPR 124

Query:   172 ALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRS 205
             AL   G M G  P+++  S  AI+   P   P++
Sbjct:   125 ALAFNGVMFGDRPLKINHSNNAIVKP-PEMTPQA 157

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005681 "spliceosomal complex" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA;ISO

GO:0006397 "mRNA processing" evidence=IEA

GO:0008380 "RNA splicing" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

UNIPROTKB|Q9JKL7 Srek1 "Splicing regulatory glutamine/lysine-rich protein 1" [Rattus norvegicus (taxid:10116)]

 Score = 156 (60.0 bits), Expect = 9.9e-09, P = 9.9e-09
 Identities = 36/94 (38%), Positives = 52/94 (55%)

Query:   113 DSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
             D +RRTVYV +++ Q  T ++L   F   G+V   R+ GD     RFAFVEFAD++    
Sbjct:    65 DEIRRTVYVGNLNSQTTTADQLLEFFKQVGEVKFVRMAGDETQPTRFAFVEFADQNSVPR 124

Query:   172 ALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRS 205
             AL   G M G  P+++  S  AI+   P   P++
Sbjct:   125 ALAFNGVMFGDRPLKINHSNNAIVKP-PEMTPQA 157

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: estExt_fgenesh4_pg.C_LG_I2967 hypothetical protein (308 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	303
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	9e-53
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	2e-52
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	1e-32
cd12225	77	cd12225, RRM1_2_CID8_like, RNA recognition motif 1	4e-32
cd12459	80	cd12459, RRM1_CID8_like, RNA recognition motif 1 i	1e-18
cd12460	82	cd12460, RRM2_CID8_like, RNA recognition motif 2 i	4e-18
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	4e-18
smart00360	73	smart00360, RRM, RNA recognition motif	6e-14
cd12260	85	cd12260, RRM2_SREK1, RNA recognition motif 2 in sp	4e-13
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	2e-12
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	2e-12
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	3e-11
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	6e-11
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	6e-11
cd00590	72	cd00590, RRM_SF, RNA recognition motif (RRM) super	1e-09
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	2e-09
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-09
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-09
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	5e-09
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	8e-09
smart00360	73	smart00360, RRM, RNA recognition motif	2e-08
cd12399	78	cd12399, RRM_HP0827_like, RNA recognition motif in	3e-08
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	3e-08
TIGR01622	457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	4e-08
cd12451	79	cd12451, RRM2_NUCLs, RNA recognition motif 2 in nu	6e-08
pfam14259	69	pfam14259, RRM_6, RNA recognition motif (a	7e-08
COG0724	306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-08
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	2e-07
cd12454	80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	2e-07
TIGR01628	562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-07
cd12336	75	cd12336, RRM_RBM7_like, RNA recognition motif in R	6e-07
cd12283	73	cd12283, RRM1_RBM39_like, RNA recognition motif 1	7e-07
cd12306	73	cd12306, RRM_II_PABPs, RNA recognition motif in ty	9e-07
cd12450	77	cd12450, RRM1_NUCLs, RNA recognition motif 1 found	2e-06
cd12378	80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	3e-06
cd12334	74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	4e-06
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	4e-06
TIGR01661	352	TIGR01661, ELAV_HUD_SF, ELAV/HuD family splicing f	4e-06
cd12398	75	cd12398, RRM_CSTF2_RNA15_like, RNA recognition mot	4e-06
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	5e-06
cd12381	79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	7e-06
cd12346	72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	8e-06
pfam00076	70	pfam00076, RRM_1, RNA recognition motif	1e-05
cd12268	68	cd12268, RRM_Vip1, RNA recognition motif in fissio	1e-05
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	1e-05
cd12298	78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-05
cd12344	81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	2e-05
cd12382	80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-05
cd12447	76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-05
cd12564	76	cd12564, RRM1_RBM19, RNA recognition motif 1 in RN	3e-05
cd12347	73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	3e-05
cd12230	82	cd12230, RRM1_U2AF65, RNA recognition motif 1 foun	3e-05
cd12650	78	cd12650, RRM1_Hu, RNA recognition motif 1 in the H	4e-05
cd12353	75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	4e-05
cd12551	77	cd12551, RRM_II_PABPN1L, RNA recognition motif in	4e-05
cd12297	78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	5e-05
cd12352	72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	7e-05
cd12354	73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	7e-05
cd12537	85	cd12537, RRM1_RBM23, RNA recognition motif 1 in ve	7e-05
cd12391	72	cd12391, RRM1_SART3, RNA recognition motif 1 in sq	8e-05
cd12608	69	cd12608, RRM1_CoAA, RNA recognition motif 1 in ver	8e-05
cd12320	76	cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition mot	8e-05
cd12565	76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	1e-04
cd12536	85	cd12536, RRM1_RBM39, RNA recognition motif 1 in ve	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	1e-04
cd12550	76	cd12550, RRM_II_PABPN1, RNA recognition motif in t	1e-04
pfam13893	56	pfam13893, RRM_5, RNA recognition motif	2e-04
cd12380	80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	2e-04
cd12240	78	cd12240, RRM_NCBP2, RNA recognition motif found in	2e-04
cd12448	73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	2e-04
cd12318	82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	3e-04
cd12249	78	cd12249, RRM1_hnRNPR_like, RNA recognition motif 1	3e-04
cd12325	72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	3e-04
cd12390	92	cd12390, RRM3_RAVER, RNA recognition motif 3 in ri	3e-04
cd12245	79	cd12245, RRM_scw1_like, RNA recognition motif in y	4e-04
cd12671	75	cd12671, RRM_CSTF2_CSTF2T, RNA recognition motif i	5e-04
cd12375	77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	5e-04
cd12228	84	cd12228, RRM_ENOX, RNA recognition motif (RRM) in	5e-04
cd12395	73	cd12395, RRM2_RBM34, RNA recognition motif 2 in RN	6e-04
cd12413	79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	6e-04
cd12487	78	cd12487, RRM1_DND1, RNA recognition motif 1 found	7e-04
cd12290	80	cd12290, RRM1_LARP7, RNA recognition motif 1 in La	8e-04
cd12441	73	cd12441, RRM_Nup53_like, RNA recognition motif in	9e-04
cd12296	71	cd12296, RRM1_Prp24, RNA recognition motif 1 in fu	0.001
cd12330	75	cd12330, RRM2_Hrp1p, RNA recognition motif 2 in ye	0.001
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.001
cd12259	76	cd12259, RRM_SRSF11_SREK1, RNA recognition motif i	0.001
cd12592	75	cd12592, RRM_RBM7, RNA recognition motif in verteb	0.001
cd12343	66	cd12343, RRM1_2_CoAA_like, RNA recognition motif 1	0.001
cd12771	83	cd12771, RRM1_HuB, RNA recognition motif 1 in vert	0.001
cd12272	72	cd12272, RRM2_PHIP1, RNA recognition motif 2 in Ar	0.002
cd12614	74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	0.002
cd12392	81	cd12392, RRM2_SART3, RNA recognition motif 2 in sq	0.002
cd12227	77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	0.002
cd12373	73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.002
cd12619	75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	0.002
cd12284	73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	0.003
cd12271	72	cd12271, RRM1_PHIP1, RNA recognition motif 1 in Ar	0.003
cd12257	72	cd12257, RRM1_RBM26_like, RNA recognition motif 1	0.003
cd12609	68	cd12609, RRM2_CoAA, RNA recognition motif 2 in ver	0.003
cd12301	74	cd12301, RRM1_2_PAR10_like, RNA recognition motif	0.003
cd12670	79	cd12670, RRM2_Nop12p_like, RNA recognition motif 2	0.003
cd12615	74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	0.004
cd12616	81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	0.004
cd12309	79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	0.004
cd12379	77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	0.004
cd12357	89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.004

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

 Score =  166 bits (423), Expect = 9e-53
 Identities = 67/80 (83%), Positives = 75/80 (93%)

Query: 115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
           +RRTVYVSDIDQ +TEE+LA LFS+CGQVVDCRVCGDP+SVLRFAF+EF DE GARAAL+
Sbjct: 1   IRRTVYVSDIDQQVTEEQLAALFSNCGQVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS 60

Query: 175 LGGTMLGYYPVRVLPSKTAI 194
           L GTMLG+YPVRVLPSKTAI
Sbjct: 61  LSGTMLGFYPVRVLPSKTAI 80

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score =  166 bits (421), Expect = 2e-52
 Identities = 67/83 (80%), Positives = 75/83 (90%), Gaps = 1/83 (1%)

Query: 210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAI 269
           EMC+RT+YCTNIDKKV Q++VK FFE+ CG EV+RLRLLGD+ HSTRIAFVEFA+AESAI
Sbjct: 1   EMCARTIYCTNIDKKVTQSDVKLFFESLCG-EVSRLRLLGDYHHSTRIAFVEFAMAESAI 59

Query: 270 LALNCSGMVLGSQPIRVSPSKTP 292
            ALNCSG VLGS PIRVSPSKTP
Sbjct: 60  AALNCSGAVLGSLPIRVSPSKTP 82

This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 82

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score =  115 bits (289), Expect = 1e-32
 Identities = 45/79 (56%), Positives = 56/79 (70%), Gaps = 2/79 (2%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
           RT++   ID  + + ++K+FF     GEVTR+RL GD  HS R AFVEFA AESA+ ALN
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNC--GEVTRVRLCGDRQHSARFAFVEFADAESALSALN 58

Query: 274 CSGMVLGSQPIRVSPSKTP 292
            SG +LG  P+RVSPSKTP
Sbjct: 59  LSGTLLGGHPLRVSPSKTP 77

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

>gnl|CDD|240671 cd12225, RRM1_2_CID8_like, RNA recognition motif 1 and 2 (RRM1, RRM2) in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score =  113 bits (285), Expect = 4e-32
 Identities = 41/77 (53%), Positives = 54/77 (70%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLG 176
           RT++V  ID +++E+ L   FS+CG+V   R+CGD     RFAFVEFAD   A +ALNL 
Sbjct: 1   RTIHVGGIDGSLSEDDLKEFFSNCGEVTRVRLCGDRQHSARFAFVEFADAESALSALNLS 60

Query: 177 GTMLGYYPVRVLPSKTA 193
           GT+LG +P+RV PSKT 
Sbjct: 61  GTLLGGHPLRVSPSKTP 77

This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 77

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

 Score = 78.6 bits (194), Expect = 1e-18
 Identities = 34/80 (42%), Positives = 49/80 (61%), Gaps = 2/80 (2%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
           RTVY ++ID++V + ++   F + CG +V   R+ GD     R AF+EF   E A  AL+
Sbjct: 3   RTVYVSDIDQQVTEEQLAALF-SNCG-QVVDCRVCGDPNSVLRFAFIEFTDEEGARAALS 60

Query: 274 CSGMVLGSQPIRVSPSKTPV 293
            SG +LG  P+RV PSKT +
Sbjct: 61  LSGTMLGFYPVRVLPSKTAI 80

This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 80

>gnl|CDD|240906 cd12460, RRM2_CID8_like, RNA recognition motif 2 in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins

 Score = 76.8 bits (189), Expect = 4e-18
 Identities = 37/77 (48%), Positives = 48/77 (62%), Gaps = 1/77 (1%)

Query: 117 RTVYVSDIDQNITEERLAGLFSS-CGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNL 175
           RT+Y ++ID+ +T+  +   F S CG+V   R+ GD H   R AFVEFA    A AALN 
Sbjct: 5   RTIYCTNIDKKVTQSDVKLFFESLCGEVSRLRLLGDYHHSTRIAFVEFAMAESAIAALNC 64

Query: 176 GGTMLGYYPVRVLPSKT 192
            G +LG  P+RV PSKT
Sbjct: 65  SGAVLGSLPIRVSPSKT 81

This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. Length = 82

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

 Score = 77.3 bits (191), Expect = 4e-18
 Identities = 33/83 (39%), Positives = 48/83 (57%)

Query: 113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAA 172
           + +RRT+YV ++D   T ++L   FS  G+V   R+ GD     R+AFVEFA++     A
Sbjct: 1   EEIRRTIYVGNLDPTTTADQLLEFFSQAGEVKYVRMAGDETQPTRYAFVEFAEQTSVINA 60

Query: 173 LNLGGTMLGYYPVRVLPSKTAIL 195
           L L G M G  P++V  S  AI+
Sbjct: 61  LKLNGAMFGGRPLKVNHSNNAIV 83

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 65.3 bits (160), Expect = 6e-14
 Identities = 28/73 (38%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL--RFAFVEFADEHGARAALN- 174
           T++V ++  + TEE L  LFS  G+V   R+  D  +     FAFVEF  E  A  AL  
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKALEA 60

Query: 175 LGGTMLGYYPVRV 187
           L G  L   P++V
Sbjct: 61  LNGKELDGRPLKV 73

Length = 73

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

 Score = 63.5 bits (155), Expect = 4e-13
 Identities = 31/80 (38%), Positives = 45/80 (56%), Gaps = 2/80 (2%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
           RT+Y  N+D      ++ +FF  A  GEV  +R+ GD    TR AFVEFA   S I AL 
Sbjct: 5   RTIYVGNLDPTTTADQLLEFFSQA--GEVKYVRMAGDETQPTRYAFVEFAEQTSVINALK 62

Query: 274 CSGMVLGSQPIRVSPSKTPV 293
            +G + G +P++V+ S   +
Sbjct: 63  LNGAMFGGRPLKVNHSNNAI 82

This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. . Length = 85

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

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 28/75 (37%), Positives = 42/75 (56%), Gaps = 6/75 (8%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAVAESAILA 271
           TV+   +  KV + ++ +FF  A  G+V  +R++ D  +S R   +A+VEF   ES  LA
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKA--GKVRDVRIIRDR-NSRRSKGVAYVEFYDEESVPLA 57

Query: 272 LNCSGMVLGSQPIRV 286
           L  +G  L  QPI V
Sbjct: 58  LGLTGQRLLGQPIMV 72

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

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

 Score = 61.2 bits (149), Expect = 2e-12
 Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN-LG 176
           ++V ++  + TEE L  LFS  G++   R+  D     + FAFVEF     A  AL  L 
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKFGEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEALN 60

Query: 177 GTMLGYYPVRV 187
           G  L    ++V
Sbjct: 61  GKELDGRKLKV 71

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|222631 pfam14259, RRM_6, RNA recognition motif (a

 Score = 57.9 bits (141), Expect = 3e-11
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 1/69 (1%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGG 177
           +YV ++  ++TEE L   FS  G+V   R+  +      FAFVEFA    A AAL  L G
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPYGKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKLNG 60

Query: 178 TMLGYYPVR 186
            +L    +R
Sbjct: 61  LVLDGRTLR 69

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

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

 Score = 57.2 bits (139), Expect = 6e-11
 Identities = 27/70 (38%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL-NLG 176
           ++V ++  + TEE L  LFS  G +   R+  D     + FAFVEF DE  A  AL  L 
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKFGPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEALN 60

Query: 177 GTMLGYYPVR 186
           G  LG   +R
Sbjct: 61  GKELGGRELR 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|240896 cd12450, RRM1_NUCLs, RNA recognition motif 1 found in nucleolin-like proteins mainly from plants

 Score = 57.3 bits (139), Expect = 6e-11
 Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALNLG 176
           T++V ++  +  ++ L   F  CG+VVD R+  D     + F  VEFA E GA+ AL   
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKECGEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALEKS 60

Query: 177 GTMLGYYPVRV 187
           G  L    +RV
Sbjct: 61  GEELLGREIRV 71

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

 Score = 53.1 bits (128), Expect = 1e-09
 Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-HVHSTRIAFVEFAVAESAILALNC 274
           ++  N+     + ++++ F     GE+  +R++ D    S   AFVEF   E A  AL  
Sbjct: 1   LFVGNLPPDTTEEDLRELFSKF--GEIESVRIVRDKDGKSKGFAFVEFESPEDAEKALEA 58

Query: 275 -SGMVLGSQPIRVS 287
            +G  L  + ++VS
Sbjct: 59  LNGKELDGRKLKVS 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|240841 cd12395, RRM2_RBM34, RNA recognition motif 2 in RNA-binding protein 34 (RBM34) and similar proteins

 Score = 53.3 bits (129), Expect = 2e-09
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALNL 175
           +V+V ++  +I EE L   F  CG V   R+  D  + +   F +V F  +     AL L
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRKTGIGKGFGYVLFKTKDSVALALKL 60

Query: 176 GGTMLGYYPVRV 187
            G  L    +RV
Sbjct: 61  NGIKLKGRKIRV 72

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

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

 Score = 53.0 bits (128), Expect = 2e-09
 Identities = 28/79 (35%), Positives = 37/79 (46%), Gaps = 11/79 (13%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--------FAFVEFADEHG 168
           R +YV ++D  + E+ L G+FS  G+V   R+   P             FAFV F D   
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKFGEVESIRI---PKKQDEKQGRLNNGFAFVTFKDASS 57

Query: 169 ARAALNLGGTMLGYYPVRV 187
           A  AL L GT LG   + V
Sbjct: 58  AENALQLNGTELGGRKISV 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|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family

 Score = 56.8 bits (137), Expect = 4e-09
 Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 6/97 (6%)

Query: 196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--H 253
               T  P +E ER+   RTV+   +  K  + ++ +FF     G+V  ++ + D     
Sbjct: 74  SGRNTKEPLTEAERD--DRTVFVLQLALKARERDLYEFFSKV--GKVRDVQCIKDRNSRR 129

Query: 254 STRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK 290
           S  +A+VEF   ES I AL  +G +L  +PI V  S+
Sbjct: 130 SKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQ 166

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

 Score = 51.5 bits (124), Expect = 5e-09
 Identities = 22/59 (37%), Positives = 37/59 (62%), Gaps = 1/59 (1%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALNL 175
           TV+VS++D ++ E+ L  LFS CG++ D R+  +     + +A+VEF +E   + AL L
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKCGEITDVRLVKNYKGKSKGYAYVEFENEESVQEALKL 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 = 56.0 bits (135), Expect = 8e-09
 Identities = 49/187 (26%), Positives = 82/187 (43%), Gaps = 28/187 (14%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFAD-EHGARAALNLG 176
           +YV ++D ++ E++L  LF+  G++    V  D     R FAFV F   E  A+A   + 
Sbjct: 181 LYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMN 240

Query: 177 GTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSR---------------TVYCTNI 221
           G  +G      L  +   L V      R+E E E+  +                +Y  N+
Sbjct: 241 GKKIG------LAKEGKKLYVGR-AQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNL 293

Query: 222 DKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILALN-CSGMVL 279
           D  V   ++++ F     GE+T  +++ D    +R   FV F+  E A  A+    G +L
Sbjct: 294 DDTVTDEKLRELFSEC--GEITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRML 351

Query: 280 GSQPIRV 286
           G +P+ V
Sbjct: 352 GGKPLYV 358

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

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

 Score = 50.3 bits (121), Expect = 2e-08
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 5/75 (6%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVH--STRIAFVEFAVAESAILAL 272
           T++  N+     + E+++ F     G+V  +RL+ D     S   AFVEF   E A  AL
Sbjct: 1   TLFVGNLPPDTTEEELRELFSKF--GKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL 58

Query: 273 NC-SGMVLGSQPIRV 286
              +G  L  +P++V
Sbjct: 59  EALNGKELDGRPLKV 73

Length = 73

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

 Score = 49.9 bits (120), Expect = 3e-08
 Identities = 26/73 (35%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL-N 174
            +YV ++  N+TEE L  LF   G+V   RV  D  +     F FVE      A AA+  
Sbjct: 1   NLYVGNLPYNVTEEDLKDLFGQFGEVTSARVITDRETGRSRGFGFVEMETAEEANAAIEK 60

Query: 175 LGGTMLGYYPVRV 187
           L GT  G   + V
Sbjct: 61  LNGTDFGGRTLTV 73

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

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 49.6 bits (119), Expect = 3e-08
 Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 2/70 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGG 177
           +YV ++D+ +TE+ LA LFS  G +  C++  +  +   +AFVE+ D   A AAL  + G
Sbjct: 1   LYVGNLDRTVTEDLLAELFSQIGPIKSCKLIREHGND-PYAFVEYYDHRSAAAALQTMNG 59

Query: 178 TMLGYYPVRV 187
            ++    ++V
Sbjct: 60  RLILGQEIKV 69

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

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

 Score = 53.7 bits (129), Expect = 4e-08
 Identities = 49/179 (27%), Positives = 71/179 (39%), Gaps = 13/179 (7%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL 173
            RTV+V  +     E  L   FS  G+V D +   D +S      A+VEF D      AL
Sbjct: 89  DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKAL 148

Query: 174 NLGGTMLGYYPVRVLPSKT----AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAE 229
            L G ML   P+ V  S+     A               +      +Y  N+   + + E
Sbjct: 149 ALTGQMLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLK------LYVGNLHFNITEQE 202

Query: 230 VKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS 287
           ++Q FE     E  +L    +   S    F++F  AE A  AL   +G  L  +PI+V 
Sbjct: 203 LRQIFEPFGDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKEALEVMNGFELAGRPIKVG 261

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

 Score = 48.9 bits (117), Expect = 6e-08
 Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 118 TVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARA 171
           T++V   D ++ E+ +       FSSCG++    +  D  +     FA++EF    G   
Sbjct: 1   TIFVKGFDSSLGEDDIRRSLTEHFSSCGEITRVSIPTDRETGASKGFAYIEFKSVDGVEK 60

Query: 172 ALNLGGTMLGYYPVRVLPS 190
           AL L G+ LG   + V  +
Sbjct: 61  ALELDGSDLGGGNLVVDEA 79

This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 48.3 bits (116), Expect = 7e-08
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL-NC 274
           +Y  N+   V + ++++FF     G+V  +RL+ +       AFVEFA  E A  AL   
Sbjct: 1   LYVRNLPPSVTEEDLREFFSPY--GKVEGVRLVRNKDRPRGFAFVEFASPEDAEAALKKL 58

Query: 275 SGMVLGSQPIR 285
           +G+VL  + +R
Sbjct: 59  NGLVLDGRTLR 69

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

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

 Score = 52.3 bits (124), Expect = 8e-08
 Identities = 48/270 (17%), Positives = 88/270 (32%), Gaps = 14/270 (5%)

Query: 21  KNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQS 80
             +   T+    E           +LN                    + +    ++ ++ 
Sbjct: 21  IESGKLTELLLKEEYGGLEEANSKELNLEVNSRKIESEISPPSKKRLLSSERKEENEREM 80

Query: 81  AIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSC 140
              N       +    +  +       R + ++    T++V ++  ++TEE L  LF   
Sbjct: 81  EEQNDGERGYTKEFEEELFRSSESPKSRQKSKEE-NNTLFVGNLPYDVTEEDLRELFKKF 139

Query: 141 GQVVDCRVCGDPHSVL--RFAFVEFADEHGARAAL-NLGGTMLGYYPVRVLPSKTAILP- 196
           G V   R+  D  +     FAFVEF  E  A  A+  L G  L   P+RV  ++ A  P 
Sbjct: 140 GPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQPASQPR 199

Query: 197 ---------VNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRL 247
                         L R +      S  +Y  N+  K  + E+   F++        L  
Sbjct: 200 SELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSRGDIVRASLPP 259

Query: 248 LGDHVHSTRIAFVEFAVAESAILALNCSGM 277
             D       +FV    ++ A+ + +    
Sbjct: 260 SKDGKIPKSRSFVGNEASKDALESNSRGNK 289

Length = 306

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

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 30/95 (31%), Positives = 49/95 (51%), Gaps = 6/95 (6%)

Query: 99  RKRLSGRAFRAQREDSVRRT----VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS 154
           R+    R F   +++   +     +YV ++D  +T+E+L  LFS CG++   +V  D   
Sbjct: 264 REAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSECGEITSAKVMLDEKG 323

Query: 155 VLR-FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
           V R F FV F++   A  A+  + G MLG  P+ V
Sbjct: 324 VSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYV 358

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

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

 Score = 47.3 bits (113), Expect = 2e-07
 Identities = 14/58 (24%), Positives = 31/58 (53%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL 173
           + +++V  +  ++T+E L   FS  G++++  +    +    FAF++F  E  A  A+
Sbjct: 3   KYSIFVGQLSPDVTKEELNERFSRHGKILEVNLIKRANHTNAFAFIKFEREQAAARAV 60

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 = 51.3 bits (123), Expect = 3e-07
 Identities = 47/176 (26%), Positives = 76/176 (43%), Gaps = 19/176 (10%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN- 174
           ++YV D+D ++TE +L  LF   G V+  RVC D  +   L + +V F +   A  AL  
Sbjct: 2   SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNFQNPADAERALET 61

Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           +    LG  P+R++ S+            R    R      ++  N+DK V    +   F
Sbjct: 62  MNFKRLGGKPIRIMWSQ------------RDPSLRRSGVGNIFVKNLDKSVDNKALFDTF 109

Query: 235 EAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILALN-CSGMVLGSQPIRVSP 288
                G +   ++  D    +R   FV F   ESA  A+   +GM+L  + + V  
Sbjct: 110 SKF--GNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQKVNGMLLNDKEVYVGR 163

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

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

 Score = 45.8 bits (109), Expect = 6e-07
 Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN 174
            RT++V ++D  +TEE L  LF   G +   ++  DP+   + FAFV F  E     A+ 
Sbjct: 1   DRTLFVGNLDARVTEEILYELFLQAGPLEGVKIPKDPNGKPKSFAFVTFKHEVSVPYAIQ 60

Query: 175 L 175
           L
Sbjct: 61  L 61

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

 Score = 45.7 bits (109), Expect = 7e-07
 Identities = 27/74 (36%), Positives = 35/74 (47%), Gaps = 6/74 (8%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR----FAFVEFADEHGARAAL 173
           TV+V  +   + E  L   FS  G+V D R+  D +S  R     A+VEF DE     AL
Sbjct: 1   TVFVMQLSLKVRERDLYEFFSKAGKVRDVRIIRDRNS--RRSKGVAYVEFYDEESVPLAL 58

Query: 174 NLGGTMLGYYPVRV 187
            L G  L   P+ V
Sbjct: 59  GLTGQRLLGQPIMV 72

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

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

 Score = 45.4 bits (108), Expect = 9e-07
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 12/77 (15%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRV-------CGDPHSVLRFAFVEFADEHGARA 171
           ++V ++D   T E L   F SCG +   R+        G P     FA++EF D+     
Sbjct: 2   IFVGNVDYGTTPEELQEHFKSCGTIN--RITILCDKFTGQPKG---FAYIEFLDKSSVEN 56

Query: 172 ALNLGGTMLGYYPVRVL 188
           AL L  +      ++V 
Sbjct: 57  ALLLNESEFRGRQIKVT 73

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

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

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 3/73 (4%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILALN 273
           T++  N+     Q ++++FF+    GEV  +R+  D    ++    VEFA  E A  AL 
Sbjct: 1   TLFVGNLSWSAEQDDLEEFFKEC--GEVVDVRIAQDDDGRSKGFGHVEFATEEGAQKALE 58

Query: 274 CSGMVLGSQPIRV 286
            SG  L  + IRV
Sbjct: 59  KSGEELLGREIRV 71

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

 Score = 44.4 bits (106), Expect = 3e-06
 Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 120 YVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LG 176
           YV D+  ++TE  L  +FS  G V+  RVC D  +   L +A+V F +   A  AL+ L 
Sbjct: 3   YVGDLHPDVTEAMLYEIFSPAGPVLSIRVCRDLITRRSLGYAYVNFQNPADAERALDTLN 62

Query: 177 GTMLGYYPVRVLPS 190
             ++   P+R++ S
Sbjct: 63  FDVIKGKPIRIMWS 76

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

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

 Score = 43.7 bits (104), Expect = 4e-06
 Identities = 26/75 (34%), Positives = 35/75 (46%), Gaps = 9/75 (12%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDC-----RVCGDPHSVLRFAFVEFADEHGARAAL 173
           VYV ++D+ +TEE L  LF   G VV+      RV         + FVEF  E  A  A+
Sbjct: 1   VYVGNLDEKVTEELLWELFIQAGPVVNVHIPKDRVTQAHQG---YGFVEFLSEEDADYAI 57

Query: 174 N-LGGTMLGYYPVRV 187
             +    L   P+RV
Sbjct: 58  KIMNMIKLYGKPIRV 72

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

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

 Score = 43.4 bits (103), Expect = 4e-06
 Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 120 YVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL--RFAFVEFADEHGARAAL-NLG 176
           YV ++  NITE+ L G+F   G++   ++  DP +     + F++FAD   A+ AL  L 
Sbjct: 2   YVGNLHFNITEDDLRGIFEPFGEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQLN 61

Query: 177 GTMLGYYPVRV 187
           G  L   P++V
Sbjct: 62  GFELAGRPIKV 72

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

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

 Score = 47.2 bits (112), Expect = 4e-06
 Identities = 45/178 (25%), Positives = 77/178 (43%), Gaps = 30/178 (16%)

Query: 126 QNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGY 182
           Q +T+E +  LF+S G++  C++  D  +   L + FV +     A  A+N L G  L  
Sbjct: 13  QTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQN 72

Query: 183 YPVRV---LPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACG 239
             ++V    PS  +I   N                 +Y + + K + Q E++  F     
Sbjct: 73  KTIKVSYARPSSDSIKGAN-----------------LYVSGLPKTMTQHELESIFSPF-- 113

Query: 240 GEVTRLRLLGDHVH--STRIAFVEF---AVAESAILALNCSGMVLGSQPIRVSPSKTP 292
           G++   R+L D+V   S  + F+ F     A+ AI  LN +     ++PI V  +  P
Sbjct: 114 GQIITSRILSDNVTGLSKGVGFIRFDKRDEADRAIKTLNGTTPSGCTEPITVKFANNP 171

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|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 = 43.4 bits (103), Expect = 4e-06
 Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 3/72 (4%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL-NL 175
           V+V +I  + TEE+L  +FS  G VV  R+  D  +     + F EF D   A +A+ NL
Sbjct: 1   VFVGNIPYDATEEQLIEIFSEVGPVVSFRLVTDRDTGKPKGYGFCEFEDIETAASAIRNL 60

Query: 176 GGTMLGYYPVRV 187
            G       +RV
Sbjct: 61  NGYEFNGRALRV 72

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

 Score = 43.1 bits (102), Expect = 5e-06
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQV--VDCRVCGDPHSVLRFAFVEFADEHGARAALNLG 176
           VYV  I    TE+ +   FS CG++  +D     D       AF+ F  E  A+ AL L 
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYCGEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALALD 60

Query: 177 GTMLGYYPVRV 187
           G  +G   ++V
Sbjct: 61  GEDMGGRFLKV 71

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

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

 Score = 43.0 bits (102), Expect = 7e-06
 Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 2/70 (2%)

Query: 120 YVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFAD-EHGARAALNLGG 177
           YV ++D +I +ERL   FS  G +   +V  D     + F FV F+  E   +A   + G
Sbjct: 5   YVKNLDDSIDDERLREEFSPFGTITSAKVMTDEKGRSKGFGFVCFSSPEEATKAVTEMNG 64

Query: 178 TMLGYYPVRV 187
            ++G  P+ V
Sbjct: 65  RIIGGKPLYV 74

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

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

 Score = 42.7 bits (101), Expect = 8e-06
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 15/75 (20%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRV-----CGDPHSVLRFAFVEFADEHGARAA 172
           TV+V  +D  +TE+ L  LF   G++V  ++     CG         FV+F     A AA
Sbjct: 3   TVFVGGLDPAVTEDELRSLFGPFGEIVYVKIPPGKGCG---------FVQFVHRAAAEAA 53

Query: 173 LN-LGGTMLGYYPVR 186
           +  L GT++G   +R
Sbjct: 54  IQQLQGTIIGGSRIR 68

This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. . Length = 72

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

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-HVHSTRIAFVEFAVAESAILAL-N 273
           ++  N+     + ++K  F     G +  +R++ D    S   AFVEF   E A  AL  
Sbjct: 1   LFVGNLPPDTTEEDLKDLFSKF--GPIESIRIVRDETGRSKGFAFVEFEDEEDAEKALEA 58

Query: 274 CSGMVLGSQPIR 285
            +G  LG + +R
Sbjct: 59  LNGKELGGRELR 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|240714 cd12268, RRM_Vip1, RNA recognition motif in fission yeast protein Vip1 and similar proteins

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGT 178
           VYVS+I    TE++++  FS CG++ +  +  D  S  + A + F     A+ AL L   
Sbjct: 1   VYVSNISPKTTEKQISDFFSFCGKISNLDLTNDGES--QTATITFEKPSAAKTALLLDNA 58

Query: 179 MLGYYPVRV 187
           +LG   ++V
Sbjct: 59  LLGGKVIQV 67

This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). . Length = 68

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 42.2 bits (100), Expect = 1e-05
 Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL 173
           TV V ++ ++ TE ++   F  CG++ + ++          A +EF  E  A AAL
Sbjct: 2   TVKVKNLPKDTTENKIRQFFKDCGEIREVKIVESEGG--LVAVIEFETEDEALAAL 55

This subfamily corresponds to the RRM1 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 = 71

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

 Score = 41.9 bits (99), Expect = 2e-05
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 7/80 (8%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRL-----LGDHVHSTRIAFVEFAVAESA 268
           R +Y  N+D K+ + +++  F     GEV  +R+           +   AFV F  A SA
Sbjct: 1   REIYVRNLDFKLDEDDLRGIFSKF--GEVESIRIPKKQDEKQGRLNNGFAFVTFKDASSA 58

Query: 269 ILALNCSGMVLGSQPIRVSP 288
             AL  +G  LG + I VS 
Sbjct: 59  ENALQLNGTELGGRKISVSL 78

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

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 17/64 (26%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL-N 174
           T+++ D++  + E  +   F+ CG+V   ++  +  +     + FVEFA    A  AL +
Sbjct: 1   TLWMGDLEPWMDEAYIYSAFAECGEVTSVKIIRNKQTGKSAGYGFVEFATHEAAEQALQS 60

Query: 175 LGGT 178
           L G 
Sbjct: 61  LNGK 64

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

>gnl|CDD|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 = 42.2 bits (100), Expect = 2e-05
 Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 2/59 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLR-FAFVEFADEHGARAALN 174
            ++VS +    TE+ L  LFS  G+V +  +  DP +   R F FV F     A AA+ 
Sbjct: 3   KLFVSGLSTRTTEKELEALFSKFGRVEEVLLMKDPETGESRGFGFVTFESVEDADAAIR 61

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

 Score = 41.6 bits (98), Expect = 2e-05
 Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 3/73 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALN- 174
           T++V ++  ++ +E L   F   G VV  RV  D  +     F +V+F     A+ A+  
Sbjct: 1   TLFVGNLSWSVDDEWLKAEFEKFGTVVGARVITDRETGRSRGFGYVDFESPEDAKKAIEA 60

Query: 175 LGGTMLGYYPVRV 187
           + G  L   P+ V
Sbjct: 61  MDGKELDGRPINV 73

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

 Score = 41.5 bits (98), Expect = 3e-05
 Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 5/71 (7%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFAD-EHGARAALNLG 176
           TVYV ++   +TEE L   FS  G + + RV  D      +AFV F   E  A A + + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFSPFGAIEEVRVFKDKG----YAFVRFDTHEAAATAIVAVN 57

Query: 177 GTMLGYYPVRV 187
           GT +    V+ 
Sbjct: 58  GTSINGQTVKC 68

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

>gnl|CDD|241008 cd12564, RRM1_RBM19, RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 121 VSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN 174
           V ++ + I E++L  LF + G + D ++        R F FV +  E  A+ AL 
Sbjct: 5   VKNLPKGIKEDKLRKLFEAFGTITDVQLKYTKDGKFRKFGFVGYKTEEEAQKALK 59

This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 76

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

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL 173
           +YV  + + + E+ L   F   G + D ++  D  +     FAFVEF +   A AA+
Sbjct: 1   LYVGGLAEEVDEKVLHAAFIPFGDIKDIQIPLDYETQKHRGFAFVEFEEPEDAAAAI 57

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|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins

 Score = 41.4 bits (98), Expect = 3e-05
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSC-----------GQVVDCRVCGDPHSVLRFAFVEFAD 165
           R +YV ++   ITEE L   F+               V+  ++  + +    FAFVEF  
Sbjct: 2   RRLYVGNLPPGITEEELVDFFNQAMLAAGLNQAPGNPVLSVQINPEKN----FAFVEFRT 57

Query: 166 EHGARAALNLGGTMLGYYPVRV 187
              A AAL L G +    P+++
Sbjct: 58  VEEATAALALDGIIFKGQPLKI 79

The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. Length = 82

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

 Score = 40.9 bits (96), Expect = 4e-05
 Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 3/58 (5%)

Query: 126 QNITEERLAGLFSSCGQVVDCRVCGD--PHSVLRFAFVEFADEHGARAALN-LGGTML 180
           QN+T++ +  LFSS G++  C++  D      L + FV + D   A  A+N L G  L
Sbjct: 11  QNMTQDEIRSLFSSIGEIESCKLIRDKVTGQSLGYGFVNYVDPEDAEKAINTLNGLRL 68

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

 Score = 40.8 bits (96), Expect = 4e-05
 Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 3/71 (4%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALN-L 175
           ++V D+   I  E L   F+  G++ D RV  D  +     + FV F  +  A  A+  +
Sbjct: 2   IFVGDLSPEIDTETLRAAFAPFGEISDARVVKDMQTGKSKGYGFVSFVKKEDAENAIQSM 61

Query: 176 GGTMLGYYPVR 186
            G  LG   +R
Sbjct: 62  NGQWLGGRAIR 72

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

>gnl|CDD|240995 cd12551, RRM_II_PABPN1L, RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2)

 Score = 41.0 bits (96), Expect = 4e-05
 Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 8/80 (10%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQV----VDC-RVCGDPHSVLRFAFVEFADEHGARAA 172
           +VYV ++D   T E L   FS CG +    + C +  G P     +A++EFA      AA
Sbjct: 1   SVYVGNVDYGSTAEELEAHFSGCGPINRVTILCDKFSGHPKG---YAYIEFATRDSVEAA 57

Query: 173 LNLGGTMLGYYPVRVLPSKT 192
           + L  +      ++VLP +T
Sbjct: 58  VALDESSFRGRVIKVLPKRT 77

This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. . Length = 77

>gnl|CDD|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 40.6 bits (96), Expect = 5e-05
 Identities = 17/68 (25%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP----HSVLRFAFVEFADEHGARAAL 173
           T++V++   +  +  +  LF   G+++  R    P    +   RF +V+F     A AA+
Sbjct: 2   TLWVTNFPPSFDQSDIRDLFEQYGEILSIRF---PSLRFNKTRRFCYVQFTSPESAAAAV 58

Query: 174 NLGGTMLG 181
            L    LG
Sbjct: 59  ALLNGKLG 66

This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. . Length = 78

>gnl|CDD|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR

 Score = 40.0 bits (94), Expect = 7e-05
 Identities = 19/74 (25%), Positives = 38/74 (51%), Gaps = 8/74 (10%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAILAL 272
           +Y  N+D+ V +  + + F  +  G +   +L+ +H +    AFVE+     A +A+  +
Sbjct: 1   LYVGNLDRTVTEDLLAELF--SQIGPIKSCKLIREHGNDP-YAFVEYYDHRSAAAALQTM 57

Query: 273 NCSGMVLGSQPIRV 286
           N  G ++  Q I+V
Sbjct: 58  N--GRLILGQEIKV 69

This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. Length = 72

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

 Score = 39.9 bits (94), Expect = 7e-05
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 7/77 (9%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA-LN 273
           TVY  N+   + + E+++ F     G +  +R+  D  +    AFV F   E+A  A + 
Sbjct: 2   TVYVGNLPHGLTEEELQRTFS--PFGAIEEVRVFKDKGY----AFVRFDTHEAAATAIVA 55

Query: 274 CSGMVLGSQPIRVSPSK 290
            +G  +  Q ++ S  K
Sbjct: 56  VNGTSINGQTVKCSWGK 72

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

>gnl|CDD|240981 cd12537, RRM1_RBM23, RNA recognition motif 1 in vertebrate probable RNA-binding protein 23 (RBM23)

 Score = 40.4 bits (94), Expect = 7e-05
 Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 4/80 (5%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL 270
           +RTV+C  +  ++   +++ FF A   G+V  +R++ D     S  IA+VEF   +S  L
Sbjct: 1   ARTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPL 58

Query: 271 ALNCSGMVLGSQPIRVSPSK 290
           A+  +G  L   PI V  S+
Sbjct: 59  AIGLTGQRLLGVPIIVQASQ 78

This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or 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). In contrast to RBM39, RBM23 contains only two RRMs. . Length = 85

>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 = 39.9 bits (94), Expect = 8e-05
 Identities = 24/74 (32%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILALN 273
           TV+ +N+D  VP+ E+++ F     GE+T +RL+ ++   ++  A+VEF   ES   AL 
Sbjct: 1   TVFVSNLDYSVPEDELRKLFSKC--GEITDVRLVKNYKGKSKGYAYVEFENEESVQEALK 58

Query: 274 CSGMVLGSQPIRVS 287
               ++  +P+ VS
Sbjct: 59  LDRELIKGRPMFVS 72

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

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

 Score = 39.8 bits (93), Expect = 8e-05
 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 9/64 (14%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGA-RAALNLG 176
           ++V ++D++ ++E L  LF + G V+ C       +V+R FAFV    E  A RA   L 
Sbjct: 3   IFVGNVDEDTSQEELRALFEAYGAVLSC-------AVMRQFAFVHLRGEAAADRAIEELN 55

Query: 177 GTML 180
           G  L
Sbjct: 56  GREL 59

This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. . Length = 69

>gnl|CDD|240766 cd12320, RRM6_RBM19_RRM5_MRD1, RNA recognition motif 6 in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 in multiple RNA-binding domain-containing protein 1 (MRD1)

 Score = 39.9 bits (94), Expect = 8e-05
 Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 129 TEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN-LGGTML 180
           T++ L  LFS  GQV   R+        R FAFVEF  +  A+ A+  L  T L
Sbjct: 13  TKKELRELFSPFGQVKSVRLPKKFDGSHRGFAFVEFVTKQEAQNAMEALKSTHL 66

This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. . Length = 76

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

 Score = 39.9 bits (94), Expect = 1e-04
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN 174
           + V ++ + +TE+RL   F S G+V D +V        R F FV F  E  A+ A+ 
Sbjct: 3   IIVKNLPKYVTEDRLREHFESKGEVTDVKVMRTRDGKSRRFGFVGFKSEEDAQQAVK 59

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|240980 cd12536, RRM1_RBM39, RNA recognition motif 1 in vertebrate RNA-binding protein 39 (RBM39)

 Score = 40.0 bits (93), Expect = 1e-04
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL 270
           +RTV+C  +  ++   ++++FF     G+V  +R++ D     S  IA+VEF    S  L
Sbjct: 1   ARTVFCMQLAARIRPRDLEEFFSTV--GKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPL 58

Query: 271 ALNCSGMVLGSQPIRVSPSK 290
           A+  +G  +   PI V  S+
Sbjct: 59  AIGLTGQRVLGVPIIVQASQ 78

This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. . Length = 85

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

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 21/56 (37%), Positives = 27/56 (48%), Gaps = 4/56 (7%)

Query: 136 LFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGGTMLGYYPVRVLPS 190
           LFS  G V   ++         FAFVEF+ E  A  A+  L G + G  P+RV  S
Sbjct: 4   LFSPFGNVEKIKLLKKKP---GFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|240994 cd12550, RRM_II_PABPN1, RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins

 Score = 39.4 bits (92), Expect = 1e-04
 Identities = 25/79 (31%), Positives = 40/79 (50%), Gaps = 8/79 (10%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQV----VDC-RVCGDPHSVLRFAFVEFADEHGARAA 172
           +VYV ++D   T E L   F  CG V    + C +  G P     FA++EF+D+   R A
Sbjct: 1   SVYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKG---FAYIEFSDKESVRTA 57

Query: 173 LNLGGTMLGYYPVRVLPSK 191
           L L  ++     ++V+P +
Sbjct: 58  LALDESLFRGRQIKVMPKR 76

This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. . Length = 76

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

 Score = 38.3 bits (90), Expect = 2e-04
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 4/51 (7%)

Query: 240 GEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL-NCSGMVLGSQPIRVSPS 289
           G V +++LL         AFVEF+  E+A  A+   +G++ G +P+RV  S
Sbjct: 9   GNVEKIKLLKKK---PGFAFVEFSTEEAAEKAVQYLNGVLFGGRPLRVDYS 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|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFAD-EHGARAALNLG 176
           VYV ++ +++ +E+L  LF   G++   +V  D     + F FV F + E   +A   L 
Sbjct: 4   VYVKNLGEDMDDEKLKELFGKYGKITSAKVMKDDEGKSKGFGFVNFENHEAAQKAVEELN 63

Query: 177 G 177
           G
Sbjct: 64  G 64

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

 Score = 39.1 bits (92), Expect = 2e-04
 Identities = 25/81 (30%), Positives = 35/81 (43%), Gaps = 21/81 (25%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRV-----------CGDPHSVLRFAFVEFADEH 167
           +YV ++    TEE++  LFS CG +   R+           CG       F FVE+    
Sbjct: 1   LYVGNLSFYTTEEQIYELFSRCGDIK--RIIMGLDRFTKTPCG-------FCFVEYYTRE 51

Query: 168 GARAALN-LGGTMLGYYPVRV 187
            A  A+  L GT L    +RV
Sbjct: 52  DAENAVKYLNGTKLDDRIIRV 72

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

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

 Score = 38.9 bits (91), Expect = 2e-04
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-L 175
           ++V ++  +  E+ +   F   G++   R+  DP S     F +VEF+ +  A+AAL+ L
Sbjct: 1   LFVGNLSFDADEDSIYEAFGEYGEISSVRLPTDPDSGRPKGFGYVEFSSQEAAQAALDAL 60

Query: 176 GGTMLGYYPVRV 187
           GGT L   PVR+
Sbjct: 61  GGTDLLGRPVRL 72

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

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

 Score = 38.7 bits (91), Expect = 3e-04
 Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 8/72 (11%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC-----GDPHSVLR--FAFVEFADEHGA 169
            T++V +++   TEE L   F  CG V    +        P  +L   + FVEF  +  A
Sbjct: 1   TTLFVKNLNFKTTEETLKKHFEKCGGVRSVTIAKKKDPKGPGKLLSMGYGFVEFKSKEAA 60

Query: 170 RAAL-NLGGTML 180
           + AL  L GT+L
Sbjct: 61  QKALKRLQGTVL 72

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

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 16/56 (28%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL 173
           V+V  I +++ E+ L  LF   G + + R+  D   + R +AFV + ++  A+ A+
Sbjct: 4   VFVGKIPRDLFEDELVPLFEKAGPIYELRLMMDFSGLNRGYAFVTYTNKEAAQRAV 59

This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. . Length = 78

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

 Score = 38.0 bits (89), Expect = 3e-04
 Identities = 21/58 (36%), Positives = 28/58 (48%), Gaps = 4/58 (6%)

Query: 120 YVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAALN 174
           ++  +  + TEE L   FS  G+VVDC +  DP +  R   F FV FAD       L 
Sbjct: 2   FIGGLSWDTTEESLREYFSKYGEVVDCVIMKDPITG-RSRGFGFVTFADPSSVDKVLA 58

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

 Score = 38.8 bits (91), Expect = 3e-04
 Identities = 27/88 (30%), Positives = 37/88 (42%), Gaps = 14/88 (15%)

Query: 117 RTVYVSD-----IDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGA- 169
           R ++V        D +I    L  LFS  G+   C++   P+   R FAFVE+A    A 
Sbjct: 3   RCLFVDRLPKTFRDVSI----LRKLFSQVGKPTFCQLAIAPNGQPRGFAFVEYATAEDAE 58

Query: 170 RAALNLGGTMLGYYPVRVL---PSKTAI 194
            A   L G  L   P+RV    P +   
Sbjct: 59  EAQQALNGHSLQGSPIRVSFGNPGRPGA 86

This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. . Length = 92

>gnl|CDD|240691 cd12245, RRM_scw1_like, RNA recognition motif in yeast cell wall integrity protein scw1 and similar proteins

 Score = 38.3 bits (90), Expect = 4e-04
 Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG 176
           T++V+++  N TEE L  LFS        ++       +   FVEF D   A  ALN L 
Sbjct: 4   TLFVANLGPNTTEEELRQLFSRQPGFRRLKMHNKGGGPV--CFVEFEDVSFATQALNSLQ 61

Query: 177 GTML 180
           G +L
Sbjct: 62  GAVL 65

This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. Length = 79

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

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 26/75 (34%), Positives = 37/75 (49%), Gaps = 9/75 (12%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVC-----GDPHSVLRFAFVEFADEHGARAAL 173
           V+V +I    TEE+L  +FS  G VV  R+      G P     + F E+ D+  A +A+
Sbjct: 1   VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKG---YGFCEYKDQETALSAM 57

Query: 174 -NLGGTMLGYYPVRV 187
            NL G  L    +RV
Sbjct: 58  RNLNGYELNGRQLRV 72

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

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

 Score = 37.7 bits (88), Expect = 5e-04
 Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 121 VSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN 174
           V+ + Q++T+E L  LF + G +  C++  D  +   L + FV++ DE+ A+ A+N
Sbjct: 5   VNYLPQDMTQEELRSLFEAIGPIESCKIVRDRITGQSLGYGFVDYVDENDAQKAIN 60

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

 Score = 37.8 bits (88), Expect = 5e-04
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 10/71 (14%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLG 176
           +TV+V  + +N TEE +  +F  CG+++  R+     S   F  + FA+E     A+ L 
Sbjct: 7   KTVFVGGLPENATEEIIREVFEQCGEIIAIRM-----SKKNFCHIRFAEEFAVDKAIYLS 61

Query: 177 GTMLGYYPVRV 187
           G     Y VR+
Sbjct: 62  G-----YRVRI 67

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

>gnl|CDD|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 = 20/76 (26%), Positives = 38/76 (50%), Gaps = 6/76 (7%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAVAESAILA 271
           +V+  N+   + + E+++ FE    G+V  +R++ D   +       +V F   +S  LA
Sbjct: 1   SVFVGNLPFDIEEEELRKHFEDC--GDVEAVRIVRDR-KTGIGKGFGYVLFKTKDSVALA 57

Query: 272 LNCSGMVLGSQPIRVS 287
           L  +G+ L  + IRV 
Sbjct: 58  LKLNGIKLKGRKIRVK 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|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins

 Score = 37.6 bits (88), Expect = 6e-04
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFA-DEHGARAALN 174
           T++V ++  + T+E+L   FS  G +  C V  D  S     F +V FA +E   RA   
Sbjct: 1   TLFVRNLPYDTTDEQLEEFFSEVGPIKRCFVVKDKGSKKCRGFGYVTFALEEDAKRALEE 60

Query: 175 LGGTMLGYYPVRV 187
              T  G   + V
Sbjct: 61  KKKTKFGGRKIHV 73

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|240931 cd12487, RRM1_DND1, RNA recognition motif 1 found in vertebrate dead end protein homolog 1 (DND1)

 Score = 37.5 bits (87), Expect = 7e-04
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 5/69 (7%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALNLGG 177
           V++  I Q++ E+RL  LF S G + + R+      + R FA+ +++D  GA AA+    
Sbjct: 4   VFIGKIPQDVYEDRLIPLFQSVGTLYEFRLMMTFSGLNRGFAYAKYSDRRGASAAI---- 59

Query: 178 TMLGYYPVR 186
             L  Y + 
Sbjct: 60  ATLHNYELP 68

This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 78

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

 Score = 37.3 bits (87), Expect = 8e-04
 Identities = 21/65 (32%), Positives = 27/65 (41%), Gaps = 16/65 (24%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVV---------DCRVCGDPHSVLRFAFVEFADEHG 168
           TVYV  + +N T E L  +FS  G VV            + G       FAF+EF     
Sbjct: 1   TVYVECLPKNATHEWLKAVFSKYGTVVYVSLPRYKHTGDIKG-------FAFIEFETPEE 53

Query: 169 ARAAL 173
           A+ A 
Sbjct: 54  AQKAC 58

This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. . Length = 80

>gnl|CDD|240887 cd12441, RRM_Nup53_like, RNA recognition motif in nucleoporin Nup53 and similar proteins

 Score = 36.8 bits (86), Expect = 9e-04
 Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 5/54 (9%)

Query: 137 FSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTML-GYYPVRVLP 189
           FSSCG +++ R     +    +  ++++    A  AL+  GT++ G   V V P
Sbjct: 21  FSSCGTILEVRYPPGAN----WIHLKYSSRLEAERALSKNGTIINGGVMVGVKP 70

This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. Length = 73

>gnl|CDD|240742 cd12296, RRM1_Prp24, RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNC 274
           TV   N+ K   + +++QFF+  C GE+  ++++        +A +EF   + A+ AL  
Sbjct: 2   TVKVKNLPKDTTENKIRQFFK-DC-GEIREVKIV--ESEGGLVAVIEFETEDEALAALTK 57

Query: 275 SGMVLGSQPIRVS 287
               LG   I VS
Sbjct: 58  DHKRLGGNEISVS 70

This subfamily corresponds to the RRM1 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 = 71

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

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 23/72 (31%), Positives = 32/72 (44%), Gaps = 4/72 (5%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAALNL 175
           ++V  +  ++TEE     FS  G+VVD ++  D H   R   F FV F  E       + 
Sbjct: 2   IFVGGLPPDVTEEEFKEYFSQFGKVVDAQLMQD-HDTGRSRGFGFVTFDSESAVERVFSA 60

Query: 176 GGTMLGYYPVRV 187
           G   LG   V V
Sbjct: 61  GMLELGGKQVEV 72

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

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 9/77 (11%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR----IAFVEFAVAESAIL 270
           TVY  N+   + + +V++FF+   G E+T +RL  D    T        V+FA  ES   
Sbjct: 1   TVYIGNLAWDITEDDVREFFK---GCEITSVRLATDK--ETGEFKGFGHVDFADEESLDA 55

Query: 271 ALNCSGMVLGSQPIRVS 287
           AL   G VL  +PIR++
Sbjct: 56  ALKLDGTVLCGRPIRIA 72

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

>gnl|CDD|240705 cd12259, RRM_SRSF11_SREK1, RNA recognition motif in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins

 Score = 36.5 bits (85), Expect = 0.001
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 4/67 (5%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVC---GDPHSVL-RFAFVEFADEHGARAAL 173
            V V+++    TEE++  LF   G++ + R+     D   VL +  FV++ D      AL
Sbjct: 1   VVQVTNVSPQATEEQMRTLFGFLGKIEELRLYPSDDDLAPVLSKVCFVKYEDPEDVGVAL 60

Query: 174 NLGGTML 180
           +L  T+ 
Sbjct: 61  HLTNTVF 67

This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. . Length = 76

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

 Score = 36.8 bits (85), Expect = 0.001
 Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALNL 175
           RT++V ++D  +TEE +  LF   G V+  ++  D     + FAFV F  E     A+NL
Sbjct: 2   RTLFVGNLDPKVTEELIFELFLQAGPVIKVKIPKDKDGKPKQFAFVNFKHEVSVPYAMNL 61

This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. . Length = 75

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

 Score = 36.4 bits (85), Expect = 0.001
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 7/63 (11%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGG 177
           ++V ++    T E L  LF   G V +C V      V  + FV   +E  A  A+  L G
Sbjct: 2   LFVGNLPDATTSEELRALFEKYGTVTECDV------VKNYGFVHMEEEEDAEDAIKALNG 55

Query: 178 TML 180
              
Sbjct: 56  YEF 58

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

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

 Score = 36.6 bits (84), Expect = 0.001
 Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 4/79 (5%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGA 169
           EDS +  + V+ + QN+T+E L  LF S G++  C++  D  +   L + FV + D   A
Sbjct: 1   EDS-KTNLIVNYLPQNMTQEELKSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDA 59

Query: 170 RAALN-LGGTMLGYYPVRV 187
             A+N L G  L    ++V
Sbjct: 60  EKAINTLNGLRLQTKTIKV 78

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

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 3/72 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNL 175
           TVY+ ++  +ITE+ +   F    ++   R+  D  +     F  V+FADE    AAL L
Sbjct: 1   TVYIGNLAWDITEDDVREFFK-GCEITSVRLATDKETGEFKGFGHVDFADEESLDAALKL 59

Query: 176 GGTMLGYYPVRV 187
            GT+L   P+R+
Sbjct: 60  DGTVLCGRPIRI 71

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

>gnl|CDD|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV-LRFAFVEFADEHGARAALN-LG 176
           +YV ++D  +TE+ L  +F   G V + ++  D ++  + + FVE+   H A  AL  L 
Sbjct: 1   LYVGNLDPRVTEDILKQIFQVGGPVQNVKIIPDKNNKGVNYGFVEYHQSHDAEIALQTLN 60

Query: 177 GTMLGYYPVRV 187
           G  +    +RV
Sbjct: 61  GRQIENNEIRV 71

This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. . Length = 74

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC----GDPHSVLRFAFVEFADEHGA-R 170
           +  ++VS +  ++T+E L  LF   G V   R+     G P      A+VE+ +E  A +
Sbjct: 2   KHKLFVSGLPFSVTKEELEKLFKKHGVVKSVRLVTNRSGKPKG---LAYVEYENESSASQ 58

Query: 171 AALNLGGTMLGYYPVRV 187
           A L + GT +    + V
Sbjct: 59  AVLKMDGTEIKEKTISV 75

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

>gnl|CDD|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 9/82 (10%)

Query: 212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA 271
           CS T++  ++ KKV + ++K  FE    GE+  +    D +     A+V     + A  A
Sbjct: 1   CSTTLWIGHLSKKVTEEDLKNLFEEY--GEIQSI----DMIPPRGCAYVCMETRQDAHRA 54

Query: 272 LN-CSGMVLGSQPIRVS--PSK 290
           L     + L  + I+V+  P+K
Sbjct: 55  LQKLRNVKLAGKKIKVAWAPNK 76

This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. Length = 77

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

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 4/70 (5%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGG 177
           VYV ++    T+  L   F   G +    V  +P     FAFVEF D   A  A+  L G
Sbjct: 2   VYVGNLGPRATKRELEDEFEKYGPLRSVWVARNPPG---FAFVEFEDPRDAEDAVRALDG 58

Query: 178 TMLGYYPVRV 187
             +    VRV
Sbjct: 59  RRICGNRVRV 68

This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. . Length = 73

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

 Score = 35.9 bits (83), Expect = 0.002
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-L 175
           ++V D+   +T+  L   FS+     D RV  D  S     + FV F  +  A  A+N +
Sbjct: 2   IFVGDLSPEVTDATLFAAFSAFPSCSDARVMWDMKSGRSRGYGFVSFRSQQDAENAINEM 61

Query: 176 GGTMLGYYPVRV 187
            G  LG  P+R 
Sbjct: 62  NGKWLGSRPIRC 73

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

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 5/74 (6%)

Query: 217 YCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAVAESAILAL-N 273
           Y  N+   + + +++  FE    GE+  ++L  D     S    F++FA AE A  AL  
Sbjct: 2   YVGNLHFNITEDDLRGIFEPF--GEIEFVQLQRDPETGRSKGYGFIQFADAEDAKKALEQ 59

Query: 274 CSGMVLGSQPIRVS 287
            +G  L  +PI+V 
Sbjct: 60  LNGFELAGRPIKVG 73

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

 Score = 35.4 bits (82), Expect = 0.003
 Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 4/73 (5%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLG--DHVHSTRIAFVEFAVAESAILALN 273
           VY   I     + E++ +F     GE+  L L+   D      IAF+ F   E+A  AL 
Sbjct: 1   VYVGGIPYYSTEDEIRSYFSYC--GEIEELDLMTFPDTGRFRGIAFITFKTEEAAKRALA 58

Query: 274 CSGMVLGSQPIRV 286
             G  +G + ++V
Sbjct: 59  LDGEDMGGRFLKV 71

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

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

 Score = 35.6 bits (83), Expect = 0.003
 Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 5/60 (8%)

Query: 116 RRTVYVSDI-DQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
             T+ V +I  +     +L   FS  G +V+ +V  +P S    A V+F+    A+ A  
Sbjct: 1   NTTLEVRNIPPELNNITKLNEHFSKFGTIVNIQVNYNPES----ALVQFSTSEEAKKAYR 56

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

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 7/63 (11%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG 177
           ++V ++    T + L GLF   G+VV+C    D      +AFV    E  A AA+  L G
Sbjct: 3   IFVGNVSATCTSDELRGLFEEFGRVVECDKVKD------YAFVHMEREEEALAAIEALNG 56

Query: 178 TML 180
             +
Sbjct: 57  KEV 59

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

>gnl|CDD|240747 cd12301, RRM1_2_PAR10_like, RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase PARP-10, RNA recognition motif 2 in PARP-14, RNA recognition motif in N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35), RNA-binding protein 43 (RBM43) and similar proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAAC---GGEVTRLRLLGDHVHSTRIAFVEFAVAESAI 269
           R V    + + V   +++ +FE      GG+VTR++ L +   S  + F +F VAE  +
Sbjct: 1   RCVLVAGLPETVSDDKLELYFENKRRSGGGDVTRVQYLREK-GSALVTFADFKVAERVV 58

This subfamily corresponds to the RRM1 and RRM2 of PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35) and RNA-binding protein 43 (RBM43). PARP-10 is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells. PARP-10 may also play a role in nuclear processes including the regulation of chromatin, gene transcription, and nuclear/cytoplasmic transport. PARP-10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM). PARP-14, also termed aggressive lymphoma protein 2, is a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. Like PARP-10, PARP-14 also includes two RRMs at the N-terminus. Nmi, also termed N-myc and STAT interactor, is an interferon inducible protein that interacts with c-Myc, N-Myc, Max and c-Fos, and other transcription factors containing bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc proteins, Nmi also associates with all the Stat family of transcription factors except Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can enhance Stat-mediated transcriptional activity through recruiting the Stat1 and Stat5 transcriptional coactivators, CREB-binding protein (CBP) and p300. IFP 35 is an interferon-induced leucine zipper protein that can specifically form homodimers. Distinct from known bZIP proteins, IFP 35 lacks a basic domain critical for DNA binding. In addition, IFP 35 may negatively regulate other bZIP transcription factors by protein-protein interaction. For instance, it can form heterodimers with B-ATF, a member of the AP1 transcription factor family. Both Nmi and IFP35 harbor one RRM. RBM43 is a putative RNA-binding protein containing one RRM, but its biological function remains unclear. . Length = 74

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

 Score = 35.6 bits (82), Expect = 0.003
 Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 2/61 (3%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALNLG 176
           V+V ++     EE L  +F  CG +   R+  DP + +   FA+V+F DE+    AL L 
Sbjct: 2   VFVGNLGFEDVEEGLWRVFGKCGGIEYVRIVRDPKTNVGKGFAYVQFKDENAVEKALLLN 61

Query: 177 G 177
            
Sbjct: 62  E 62

This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). . Length = 79

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

 Score = 35.4 bits (81), Expect = 0.004
 Identities = 18/56 (32%), Positives = 30/56 (53%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL 173
           T+YV ++ +++TE  +  LFS  G    C++  D      + FVEF +   A A+L
Sbjct: 1   TLYVGNLSRDVTEALILQLFSQIGPCKSCKMIMDTAGNDPYCFVEFFEHRHAAASL 56

This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 74

>gnl|CDD|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins

 Score = 35.5 bits (81), Expect = 0.004
 Identities = 19/56 (33%), Positives = 31/56 (55%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL 173
           T+YV ++ +++TE  +  LFS  G    C++  +  S   + FVEF +   A AAL
Sbjct: 1   TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 56

This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. . Length = 81

>gnl|CDD|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family

 Score = 35.5 bits (82), Expect = 0.004
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP---HSVLRFAFVEFAD-EHGARAA 172
           RT++V +++  ITEE L   F   G V D  +   P    +   +AFV+F + +   RA 
Sbjct: 3   RTLFVGNLEITITEEELRRAFERYGVVEDVDIKRPPRGQGNA--YAFVKFLNLDMAHRAK 60

Query: 173 LNLGGTMLGYYPVRV 187
           + + G  +G   +++
Sbjct: 61  VAMSGQYIGRNQIKI 75

This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. . Length = 79

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

 Score = 35.2 bits (82), Expect = 0.004
 Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN-LG 176
           +++ ++D++I  + L   FS+ G ++ C+V  D +   + + FV F  E  A  A+  + 
Sbjct: 5   IFIKNLDKSIDNKALYDTFSAFGNILSCKVATDENGGSKGYGFVHFETEEAAVRAIEKVN 64

Query: 177 GTMLG 181
           G +L 
Sbjct: 65  GMLLN 69

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

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

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 9/65 (13%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDC----RVCGDPHSVLRFAFVEFADEHGARA 171
           RR +YV  I  + T   L   F   G++ +     R  GD      + FV +     A  
Sbjct: 2   RRVIYVGKIPIDTTRSELRQRFQPFGEIEEITLHFRDDGD-----NYGFVTYRYACDAFR 56

Query: 172 ALNLG 176
           A+  G
Sbjct: 57  AIEHG 61

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	303
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
TIGR01628	562	PABP-1234 polyadenylate binding protein, human typ	100.0
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	100.0
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	100.0
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	100.0
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01649	481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	100.0
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	100.0
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	100.0
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	100.0
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	100.0
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	100.0
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	100.0
TIGR01645	612	half-pint poly-U binding splicing factor, half-pin	99.98
KOG0123	369	consensus Polyadenylate-binding protein (RRM super	99.97
TIGR01661	352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.97
TIGR01622	457	SF-CC1 splicing factor, CC1-like family. A homolog	99.97
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.96
KOG0144	510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.96
TIGR01659	346	sex-lethal sex-lethal family splicing factor. This	99.95
TIGR01648	578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.94
KOG0145	360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.94
TIGR01642	509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.94
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.94
KOG0117	506	consensus Heterogeneous nuclear ribonucleoprotein	99.94
KOG0148	321	consensus Apoptosis-promoting RNA-binding protein	99.93
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.93
KOG0127	678	consensus Nucleolar protein fibrillarin NOP77 (RRM	99.92
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.92
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.91
KOG0124	544	consensus Polypyrimidine tract-binding protein PUF	99.91
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.91
KOG0131	203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.89
KOG0109	346	consensus RNA-binding protein LARK, contains RRM a	99.86
KOG0110	725	consensus RNA-binding protein (RRM superfamily) [G	99.85
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.85
KOG0147	549	consensus Transcriptional coactivator CAPER (RRM s	99.84
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.84
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.81
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.8
KOG4205	311	consensus RNA-binding protein musashi/mRNA cleavag	99.77
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.76
KOG1190	492	consensus Polypyrimidine tract-binding protein [RN	99.75
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.75
KOG4211	510	consensus Splicing factor hnRNP-F and related RNA-	99.75
KOG4212	608	consensus RNA-binding protein hnRNP-M [RNA process	99.73
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
PLN03134	144	glycine-rich RNA-binding protein 4; Provisional	99.7
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.68
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.67
KOG1457	284	consensus RNA binding protein (contains RRM repeat	99.67
KOG0146	371	consensus RNA-binding protein ETR-3 (RRM superfami	99.63
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.63
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.6
PF00076	70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.59
PLN03120	260	nucleic acid binding protein; Provisional	99.59
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.58
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.57
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.57
KOG0122	270	consensus Translation initiation factor 3, subunit	99.55
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.55
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.54
KOG0122	270	consensus Translation initiation factor 3, subunit	99.53
KOG1456	494	consensus Heterogeneous nuclear ribonucleoprotein	99.53
KOG0125	376	consensus Ataxin 2-binding protein (RRM superfamil	99.51
PLN03120	260	nucleic acid binding protein; Provisional	99.51
PLN03121	243	nucleic acid binding protein; Provisional	99.5
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.48
PF14259	70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.48
KOG0105	241	consensus Alternative splicing factor ASF/SF2 (RRM	99.44
PLN03213	759	repressor of silencing 3; Provisional	99.44
smart00362	72	RRM_2 RNA recognition motif.	99.44
PLN03121	243	nucleic acid binding protein; Provisional	99.43
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.43
smart00362	72	RRM_2 RNA recognition motif.	99.43
KOG4206	221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.43
PLN03213	759	repressor of silencing 3; Provisional	99.41
KOG0149	247	consensus Predicted RNA-binding protein SEB4 (RRM	99.4
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	99.4
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.4
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	99.37
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.37
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.36
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.36
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.35
KOG0107	195	consensus Alternative splicing factor SRp20/9G8 (R	99.35
KOG0114	124	consensus Predicted RNA-binding protein (RRM super	99.35
smart00360	71	RRM RNA recognition motif.	99.35
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.34
KOG0111	298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.34
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.33
smart00360	71	RRM RNA recognition motif.	99.32
KOG0126	219	consensus Predicted RNA-binding protein (RRM super	99.31
cd00590	74	RRM RRM (RNA recognition motif), also known as RBD	99.31
KOG4207	256	consensus Predicted splicing factor, SR protein su	99.31
KOG0130	170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.3
KOG0121	153	consensus Nuclear cap-binding protein complex, sub	99.29
KOG0106	216	consensus Alternative splicing factor SRp55/B52/SR	99.28
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.28
KOG0113	335	consensus U1 small nuclear ribonucleoprotein (RRM	99.27
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	99.26
PF13893	56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.26
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.26
COG0724	306	RNA-binding proteins (RRM domain) [General functio	99.24
smart00361	70	RRM_1 RNA recognition motif.	99.21
smart00361	70	RRM_1 RNA recognition motif.	99.19
KOG0108	435	consensus mRNA cleavage and polyadenylation factor	99.16
KOG0120	500	consensus Splicing factor U2AF, large subunit (RRM	99.15
KOG1548	382	consensus Transcription elongation factor TAT-SF1	99.06
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	99.05
KOG0226	290	consensus RNA-binding proteins [General function p	99.04
KOG4210	285	consensus Nuclear localization sequence binding pr	99.02
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	99.0
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.99
KOG4454	267	consensus RNA binding protein (RRM superfamily) [G	98.97
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.91
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.9
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.9
KOG0153	377	consensus Predicted RNA-binding protein (RRM super	98.87
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.87
KOG1365	508	consensus RNA-binding protein Fusilli, contains RR	98.82
KOG0415	479	consensus Predicted peptidyl prolyl cis-trans isom	98.82
KOG1457	284	consensus RNA binding protein (contains RRM repeat	98.81
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.74
KOG0112	975	consensus Large RNA-binding protein (RRM superfami	98.74
KOG0132	894	consensus RNA polymerase II C-terminal domain-bind	98.74
KOG4661	940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.73
KOG4208	214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.72
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.65
KOG4210	285	consensus Nuclear localization sequence binding pr	98.65
KOG0533	243	consensus RRM motif-containing protein [RNA proces	98.64
KOG0128	881	consensus RNA-binding protein SART3 (RRM superfami	98.63
KOG0129	520	consensus Predicted RNA-binding protein (RRM super	98.58
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	98.56
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.55
KOG0151	877	consensus Predicted splicing regulator, contains R	98.54
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.53
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.52
KOG0151	877	consensus Predicted splicing regulator, contains R	98.52
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	98.51
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.49
KOG4307	944	consensus RNA binding protein RBM12/SWAN [General	98.48
PF04059	97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	98.48
KOG0116	419	consensus RasGAP SH3 binding protein rasputin, con	98.47
KOG4209	231	consensus Splicing factor RNPS1, SR protein superf	98.47
KOG0226	290	consensus RNA-binding proteins [General function p	98.41
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.4
KOG4660	549	consensus Protein Mei2, essential for commitment t	98.28
PF11608	90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	98.08
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.81
PF08777	105	RRM_3: RNA binding motif; InterPro: IPR014886 This	97.72
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.6
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.56
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.49
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	97.47
PF05172	100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.44
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.38
COG5175	480	MOT2 Transcriptional repressor [Transcription]	97.35
KOG1995	351	consensus Conserved Zn-finger protein [General fun	97.34
KOG2314	698	consensus Translation initiation factor 3, subunit	97.32
KOG1996	378	consensus mRNA splicing factor [RNA processing and	97.31
PF14605	53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.26
KOG2314	698	consensus Translation initiation factor 3, subunit	97.24
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	97.22
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	96.77
KOG3152	278	consensus TBP-binding protein, activator of basal	96.75
PF08952	146	DUF1866: Domain of unknown function (DUF1866) ; In	96.74
KOG2193	584	consensus IGF-II mRNA-binding protein IMP, contain	96.62
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.61
KOG3152	278	consensus TBP-binding protein, activator of basal	96.51
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.49
KOG2202	260	consensus U2 snRNP splicing factor, small subunit,	96.48
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	96.45
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.45
KOG4849	498	consensus mRNA cleavage factor I subunit/CPSF subu	96.44
KOG4676	479	consensus Splicing factor, arginine/serine-rich [R	96.32
KOG1855	484	consensus Predicted RNA-binding protein [General f	96.12
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	95.83
KOG1996	378	consensus mRNA splicing factor [RNA processing and	95.37
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	95.28
PF07576	110	BRAP2: BRCA1-associated protein 2; InterPro: IPR01	94.76
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	94.73
KOG2591	684	consensus c-Mpl binding protein, contains La domai	94.47
KOG2416	718	consensus Acinus (induces apoptotic chromatin cond	94.35
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.32
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	94.25
PF07292	88	NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909	94.21
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	94.21
PF10309	62	DUF2414: Protein of unknown function (DUF2414); In	94.2
KOG0115	275	consensus RNA-binding protein p54nrb (RRM superfam	94.04
PF08675	87	RNA_bind: RNA binding domain; InterPro: IPR014789	94.03
PF15023	166	DUF4523: Protein of unknown function (DUF4523)	93.59
KOG2135	526	consensus Proteins containing the RNA recognition	93.57
KOG2135	526	consensus Proteins containing the RNA recognition	93.25
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	93.2
PF03467	176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	92.96
KOG0804	493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	92.74
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.37
KOG2068	327	consensus MOT2 transcription factor [Transcription	92.33
PF04847	184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	92.12
KOG4285	350	consensus Mitotic phosphoprotein [Cell cycle contr	91.13
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	90.9
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	89.64
KOG2318	650	consensus Uncharacterized conserved protein [Funct	88.71
PF11767	66	SET_assoc: Histone lysine methyltransferase SET as	88.63
KOG2591	684	consensus c-Mpl binding protein, contains La domai	88.24
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	87.42
PF14111	153	DUF4283: Domain of unknown function (DUF4283)	87.03
KOG4574	1007	consensus RNA-binding protein (contains RRM and Pu	86.66
PF03880	74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	85.65
KOG2253	668	consensus U1 snRNP complex, subunit SNU71 and rela	85.26
PF10567	309	Nab6_mRNP_bdg: RNA-recognition motif; InterPro: IP	84.6

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=100.00  E-value=2.1e-44  Score=332.67  Aligned_cols=252  Identities=18%  Similarity=0.287  Sum_probs=204.9

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc--
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ--   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~--   97 (303)
                      .+|||+|||+++|+++|+++|++||+|.+|+|++++.++.++   ||+|     .+     .+    +|.+|+..+++  
T Consensus         4 ~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f-----~~-----~~----~A~~Ai~~l~g~~   69 (352)
T TIGR01661         4 TNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNY-----VR-----PE----DAEKAVNSLNGLR   69 (352)
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEE-----Cc-----HH----HHHHHHhhcccEE
Confidence            489999999999999999999999999999999998765544   9999     88     88    99999999987  


Q ss_pred             --CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHH
Q 022058           98 --GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAA  172 (303)
Q Consensus        98 --g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~A  172 (303)
                        |+. .+...  .........++|||+|||+++++++|+++|+.||.|..+.++.+..+  ++|||||+|.+.++|++|
T Consensus        70 l~g~~i~v~~a--~~~~~~~~~~~l~v~~l~~~~~~~~l~~~f~~~G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~~a  147 (352)
T TIGR01661        70 LQNKTIKVSYA--RPSSDSIKGANLYVSGLPKTMTQHELESIFSPFGQIITSRILSDNVTGLSKGVGFIRFDKRDEADRA  147 (352)
T ss_pred             ECCeeEEEEee--cccccccccceEEECCccccCCHHHHHHHHhccCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHH
Confidence              333 11111  11122335678999999999999999999999999999999987643  799999999999999999


Q ss_pred             HH-hCCcccCC--eeEEEeecCCCCCCCC------------CCC------------------------C-----------
Q 022058          173 LN-LGGTMLGY--YPVRVLPSKTAILPVN------------PTF------------------------L-----------  202 (303)
Q Consensus       173 i~-l~g~~~~g--~~i~v~~~~~~~~~~~------------~~~------------------------~-----------  202 (303)
                      ++ |||..+.|  ++|.|.++........            +..                        .           
T Consensus       148 i~~l~g~~~~g~~~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  227 (352)
T TIGR01661       148 IKTLNGTTPSGCTEPITVKFANNPSSSNSKGLLSQLEAVQNPQTTRVPLSTILTAAGIGPMHHAAARFRPSAGDFTAVLA  227 (352)
T ss_pred             HHHhCCCccCCCceeEEEEECCCCCcCCchhcCchhhcccCcccCCCCccccccccCCCCccCcccccccCcchhhhhhh
Confidence            98 99999876  7788888753321000            000                        0           


Q ss_pred             --------------CCc-c----------------cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC
Q 022058          203 --------------PRS-E----------------DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH  251 (303)
Q Consensus       203 --------------~~~-~----------------~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~  251 (303)
                                    ... .                ......+.+|||+|||+.+++++|+++|++|  |.|.+|+|++|.
T Consensus       228 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lfV~NL~~~~~e~~L~~~F~~f--G~v~~v~i~~d~  305 (352)
T TIGR01661       228 HQQQQHAVAQQHAAQRASPPATDGQTAGLAAGAQIAASDGAGYCIFVYNLSPDTDETVLWQLFGPF--GAVQNVKIIRDL  305 (352)
T ss_pred             hhhhhcccccccccccCCCccccccccccccCCCCCCCCCCCcEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeEcC
Confidence                          000 0                0001123479999999999999999999999  999999999985


Q ss_pred             --CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          252 --VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       252 --~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                        |.++|||||+|.+.++|.+|+. |||..|+|+.|+|.|+.+.
T Consensus       306 ~t~~skG~aFV~F~~~~~A~~Ai~~lnG~~~~gr~i~V~~~~~~  349 (352)
T TIGR01661       306 TTNQCKGYGFVSMTNYDEAAMAILSLNGYTLGNRVLQVSFKTNK  349 (352)
T ss_pred             CCCCccceEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEccCC
Confidence              7899999999999999999998 9999999999999998754

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

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

Probab=100.00  E-value=1.2e-39  Score=318.27  Aligned_cols=256  Identities=20%  Similarity=0.308  Sum_probs=209.6

Q ss_pred             CCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhccc-
Q 022058           21 KNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-   97 (303)
Q Consensus        21 ~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-   97 (303)
                      ..++|||+|||+++|+++|+++|++||.|.+|+++.+..++.++  ||+|     .+     .+    +|.+|+..+++ 
T Consensus        87 ~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F-----~~-----~e----~A~~Ai~~lng~  152 (562)
T TIGR01628        87 GVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHF-----EK-----EE----SAKAAIQKVNGM  152 (562)
T ss_pred             CCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEE-----CC-----HH----HHHHHHHHhccc
Confidence            35689999999999999999999999999999999988765555  9999     88     88    89999999887 


Q ss_pred             ---CCC-CCCchhhhhcc---CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHH
Q 022058           98 ---GRK-RLSGRAFRAQR---EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGA  169 (303)
Q Consensus        98 ---g~~-~~~~~~~~~~~---~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A  169 (303)
                         |+. .+........+   .....++|||+|||+++|+++|+++|+.||.|.++.++.+..+ ++|||||+|.+.++|
T Consensus       153 ~~~~~~i~v~~~~~~~~~~~~~~~~~~~l~V~nl~~~~tee~L~~~F~~fG~i~~~~i~~~~~g~~~G~afV~F~~~e~A  232 (562)
T TIGR01628       153 LLNDKEVYVGRFIKKHEREAAPLKKFTNLYVKNLDPSVNEDKLRELFAKFGEITSAAVMKDGSGRSRGFAFVNFEKHEDA  232 (562)
T ss_pred             EecCceEEEeccccccccccccccCCCeEEEeCCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHH
Confidence               222 11111111111   2234678999999999999999999999999999999998765 899999999999999


Q ss_pred             HHHHH-hCCcccC----CeeEEEeecCCCCCCC---CCCCCC-CcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCc
Q 022058          170 RAALN-LGGTMLG----YYPVRVLPSKTAILPV---NPTFLP-RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGG  240 (303)
Q Consensus       170 ~~Ai~-l~g~~~~----g~~i~v~~~~~~~~~~---~~~~~~-~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G  240 (303)
                      .+|++ +||..+.    |+.|.|.++.......   ...+.. ...........+|||+||+..+++++|+++|++|  |
T Consensus       233 ~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~er~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~~~~~~~~L~~~F~~~--G  310 (562)
T TIGR01628       233 AKAVEEMNGKKIGLAKEGKKLYVGRAQKRAEREAELRRKFEELQQERKMKAQGVNLYVKNLDDTVTDEKLRELFSEC--G  310 (562)
T ss_pred             HHHHHHhCCcEecccccceeeEeecccChhhhHHHHHhhHHhhhhhhhcccCCCEEEEeCCCCccCHHHHHHHHHhc--C
Confidence            99998 9999999    9999999875432110   000000 0011112345789999999999999999999999  9


Q ss_pred             ceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          241 EVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       241 ~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      .|.+|+|+.|. |.++|||||+|.+.++|.+|+. |||..++|+.|.|.++...
T Consensus       311 ~i~~~~i~~d~~g~~~g~gfV~f~~~~~A~~A~~~~~g~~~~gk~l~V~~a~~k  364 (562)
T TIGR01628       311 EITSAKVMLDEKGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRK  364 (562)
T ss_pred             CeEEEEEEECCCCCcCCeEEEEeCCHHHHHHHHHHhcCCeeCCceeEEEeccCc
Confidence            99999999985 8899999999999999999998 9999999999999998753

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

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

Probab=100.00  E-value=8.7e-40  Score=319.31  Aligned_cols=245  Identities=21%  Similarity=0.318  Sum_probs=206.6

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      .|||+|||+++|+++|+++|++||+|.+|+|++|..++.++   ||+|     .+     .+    +|++|+..+++   
T Consensus         2 sl~VgnLp~~vte~~L~~~F~~~G~v~~v~v~~d~~t~~s~G~afV~F-----~~-----~~----~A~~Al~~ln~~~i   67 (562)
T TIGR01628         2 SLYVGDLDPDVTEAKLYDLFKPFGPVLSVRVCRDSVTRRSLGYGYVNF-----QN-----PA----DAERALETMNFKRL   67 (562)
T ss_pred             eEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEE-----CC-----HH----HHHHHHHHhCCCEE
Confidence            69999999999999999999999999999999998866554   9999     88     88    99999998876   


Q ss_pred             -CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH
Q 022058           98 -GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN  174 (303)
Q Consensus        98 -g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~  174 (303)
                       |+. ++.+.............+|||+|||+++++++|+++|+.||.|.+|+++.+..+ ++|||||+|.+.++|.+|++
T Consensus        68 ~gk~i~i~~s~~~~~~~~~~~~~vfV~nLp~~~~~~~L~~~F~~~G~i~~~~i~~~~~g~skg~afV~F~~~e~A~~Ai~  147 (562)
T TIGR01628        68 GGKPIRIMWSQRDPSLRRSGVGNIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGKSRGYGFVHFEKEESAKAAIQ  147 (562)
T ss_pred             CCeeEEeecccccccccccCCCceEEcCCCccCCHHHHHHHHHhcCCcceeEeeecCCCCcccEEEEEECCHHHHHHHHH
Confidence             333 222211111112224567999999999999999999999999999999998766 89999999999999999998


Q ss_pred             -hCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-C
Q 022058          175 -LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-V  252 (303)
Q Consensus       175 -l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~  252 (303)
                       +||..+.|+.|.|..........         .......++|||+|||.++++++|+++|+.|  |.|.++.+.++. +
T Consensus       148 ~lng~~~~~~~i~v~~~~~~~~~~---------~~~~~~~~~l~V~nl~~~~tee~L~~~F~~f--G~i~~~~i~~~~~g  216 (562)
T TIGR01628       148 KVNGMLLNDKEVYVGRFIKKHERE---------AAPLKKFTNLYVKNLDPSVNEDKLRELFAKF--GEITSAAVMKDGSG  216 (562)
T ss_pred             HhcccEecCceEEEeccccccccc---------cccccCCCeEEEeCCCCcCCHHHHHHHHHhc--CCEEEEEEEECCCC
Confidence             99999999999997653221100         1122345789999999999999999999999  999999999885 7


Q ss_pred             CcccEEEEEEcCHHHHHHHHH-hCCceeC----CeeeEEeecCCCC
Q 022058          253 HSTRIAFVEFAVAESAILALN-CSGMVLG----SQPIRVSPSKTPV  293 (303)
Q Consensus       253 ~~~g~afV~f~~~e~A~~Ai~-l~g~~~~----g~~l~v~~a~~~~  293 (303)
                      +++|||||+|.+.++|.+|+. |||..+.    |+.|.|.++....
T Consensus       217 ~~~G~afV~F~~~e~A~~Av~~l~g~~i~~~~~g~~l~v~~a~~k~  262 (562)
T TIGR01628       217 RSRGFAFVNFEKHEDAAKAVEEMNGKKIGLAKEGKKLYVGRAQKRA  262 (562)
T ss_pred             CcccEEEEEECCHHHHHHHHHHhCCcEecccccceeeEeecccChh
Confidence            899999999999999999998 9999999    9999999886543

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

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

Probab=100.00  E-value=1e-39  Score=273.67  Aligned_cols=250  Identities=18%  Similarity=0.270  Sum_probs=209.3

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcccCCC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK  100 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~  100 (303)
                      +|.|-=||..+|++|||.||+..|+|++|++++|+-++++-   ||.|     ..     ++    ||++|++.+||-|-
T Consensus        43 NLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNY-----v~-----p~----DAe~AintlNGLrL  108 (360)
T KOG0145|consen   43 NLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY-----VR-----PK----DAEKAINTLNGLRL  108 (360)
T ss_pred             eeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeee-----cC-----hH----HHHHHHhhhcceee
Confidence            58889999999999999999999999999999999877765   9999     88     88    99999999998322


Q ss_pred             -----CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHH
Q 022058          101 -----RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL  173 (303)
Q Consensus       101 -----~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai  173 (303)
                           +++...  ...+.....+|||.+||..+|..+|+.+|++||.|..-+|+.|..+  ++|.|||.|...++|+.||
T Consensus       109 Q~KTIKVSyAR--PSs~~Ik~aNLYvSGlPktMtqkelE~iFs~fGrIItSRiL~dqvtg~srGVgFiRFDKr~EAe~AI  186 (360)
T KOG0145|consen  109 QNKTIKVSYAR--PSSDSIKDANLYVSGLPKTMTQKELEQIFSPFGRIITSRILVDQVTGLSRGVGFIRFDKRIEAEEAI  186 (360)
T ss_pred             ccceEEEEecc--CChhhhcccceEEecCCccchHHHHHHHHHHhhhhhhhhhhhhcccceecceeEEEecchhHHHHHH
Confidence                 222211  1223446788999999999999999999999999998899888776  8999999999999999999


Q ss_pred             H-hCCcccCC--eeEEEeecCCCCCCC----------CC----------------------------CCCCCcc------
Q 022058          174 N-LGGTMLGY--YPVRVLPSKTAILPV----------NP----------------------------TFLPRSE------  206 (303)
Q Consensus       174 ~-l~g~~~~g--~~i~v~~~~~~~~~~----------~~----------------------------~~~~~~~------  206 (303)
                      + |||+.-.|  .+|.|+++..+....          +|                            .|.|-..      
T Consensus       187 k~lNG~~P~g~tepItVKFannPsq~t~~a~ls~ly~sp~rr~~Gp~hh~~~r~r~~~~~~~~~~~~rfsP~~~d~m~~l  266 (360)
T KOG0145|consen  187 KGLNGQKPSGCTEPITVKFANNPSQKTNQALLSQLYQSPARRYGGPMHHQAQRFRLDNLLNPHAAQARFSPMTIDGMSGL  266 (360)
T ss_pred             HhccCCCCCCCCCCeEEEecCCcccccchhhhHHhhcCccccCCCcccchhhhhccccccchhhhhccCCCcccccccee
Confidence            9 99998876  789999985542100          00                            0111110      


Q ss_pred             -----cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCce
Q 022058          207 -----DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMV  278 (303)
Q Consensus       207 -----~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~  278 (303)
                           +.......+|||.||.++.+|.-||++|.+|  |.|..|+|++|-  ++++|||||++.+.++|..||. |||+.
T Consensus       267 ~~~~lp~~~~~g~ciFvYNLspd~de~~LWQlFgpF--GAv~nVKvirD~ttnkCKGfgFVtMtNYdEAamAi~sLNGy~  344 (360)
T KOG0145|consen  267 AGVNLPGGPGGGWCIFVYNLSPDADESILWQLFGPF--GAVTNVKVIRDFTTNKCKGFGFVTMTNYDEAAMAIASLNGYR  344 (360)
T ss_pred             eeeccCCCCCCeeEEEEEecCCCchHhHHHHHhCcc--cceeeEEEEecCCcccccceeEEEecchHHHHHHHHHhcCcc
Confidence                 1112346899999999999999999999999  999999999995  6899999999999999999998 99999


Q ss_pred             eCCeeeEEeecCC
Q 022058          279 LGSQPIRVSPSKT  291 (303)
Q Consensus       279 ~~g~~l~v~~a~~  291 (303)
                      +++|.|+|+|...
T Consensus       345 lg~rvLQVsFKtn  357 (360)
T KOG0145|consen  345 LGDRVLQVSFKTN  357 (360)
T ss_pred             ccceEEEEEEecC
Confidence            9999999999754

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

Probab=100.00  E-value=2.5e-39  Score=289.26  Aligned_cols=246  Identities=20%  Similarity=0.256  Sum_probs=206.7

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcccCC
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGR   99 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~   99 (303)
                      -.|||+.||-++.|+||+.||++.|+|.++||+.|+.++.++   ||.|     .+     .+    +|+.|++.+|+..
T Consensus        84 ~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf-----~~-----Ke----~Aq~Aik~lnn~E  149 (506)
T KOG0117|consen   84 CEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTF-----CT-----KE----EAQEAIKELNNYE  149 (506)
T ss_pred             ceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEe-----ec-----HH----HHHHHHHHhhCcc
Confidence            359999999999999999999999999999999997655544   9999     88     88    9999999999832


Q ss_pred             CCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCc-eeEEEEeeCCC---CCceEEEEEecCHHHHHHHHH-
Q 022058          100 KRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQ-VVDCRVCGDPH---SVLRFAFVEFADEHGARAALN-  174 (303)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~~~i~~~~~---~~~G~~fV~f~~~~~A~~Ai~-  174 (303)
                      -+....+  ...-...++.|||||||.+.++++|.+.+++.++ |.+|.+...+.   .+||||||+|.++..|..|.. 
T Consensus       150 ir~GK~i--gvc~Svan~RLFiG~IPK~k~keeIlee~~kVteGVvdVivy~~p~dk~KNRGFaFveYe~H~~Aa~aRrK  227 (506)
T KOG0117|consen  150 IRPGKLL--GVCVSVANCRLFIGNIPKTKKKEEILEEMKKVTEGVVDVIVYPSPDDKTKNRGFAFVEYESHRAAAMARRK  227 (506)
T ss_pred             ccCCCEe--EEEEeeecceeEeccCCccccHHHHHHHHHhhCCCeeEEEEecCccccccccceEEEEeecchhHHHHHhh
Confidence            2211111  1112336889999999999999999999998875 67777766443   389999999999999999996 


Q ss_pred             -hCC-cccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCC
Q 022058          175 -LGG-TMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV  252 (303)
Q Consensus       175 -l~g-~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~  252 (303)
                       +++ ..+.|..+.|.|+++...+        +++ .....+.|||+||+.++|++.|+++|++|  |.|++|+.++|  
T Consensus       228 l~~g~~klwgn~~tVdWAep~~e~--------ded-~ms~VKvLYVRNL~~~tTeE~lk~~F~~~--G~veRVkk~rD--  294 (506)
T KOG0117|consen  228 LMPGKIKLWGNAITVDWAEPEEEP--------DED-TMSKVKVLYVRNLMESTTEETLKKLFNEF--GKVERVKKPRD--  294 (506)
T ss_pred             ccCCceeecCCcceeeccCcccCC--------Chh-hhhheeeeeeeccchhhhHHHHHHHHHhc--cceEEeecccc--
Confidence             554 5568999999999754321        111 33456899999999999999999999999  99999999988  


Q ss_pred             CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCCCCCCCC
Q 022058          253 HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRPRVTRPG  301 (303)
Q Consensus       253 ~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~r~~r~~  301 (303)
                          ||||.|.++++|.+||+ |||++|+|..|.|.+|||+...+.+|+.
T Consensus       295 ----YaFVHf~eR~davkAm~~~ngkeldG~~iEvtLAKP~~k~k~~r~~  340 (506)
T KOG0117|consen  295 ----YAFVHFAEREDAVKAMKETNGKELDGSPIEVTLAKPVDKKKKERKA  340 (506)
T ss_pred             ----eeEEeecchHHHHHHHHHhcCceecCceEEEEecCChhhhccchhh
Confidence                99999999999999999 9999999999999999999999988854

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

Probab=100.00  E-value=5.5e-38  Score=300.11  Aligned_cols=242  Identities=20%  Similarity=0.224  Sum_probs=193.4

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhcccCCC
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK  100 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~  100 (303)
                      .+|||+|||+++|+++|+++|++||+|.+|+|++|..+..++  ||+|     .+     .+    +|++|+..|++-.-
T Consensus        59 ~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRGfaFV~F-----~~-----~e----~A~~Ai~~lng~~i  124 (578)
T TIGR01648        59 CEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRGYAFVTF-----CG-----KE----EAKEAVKLLNNYEI  124 (578)
T ss_pred             CEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccceEEEEe-----CC-----HH----HHHHHHHHcCCCee
Confidence            479999999999999999999999999999999996555554  9999     88     88    99999999987211


Q ss_pred             CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCc-eeEEEEeeC---CCCCceEEEEEecCHHHHHHHHH-h
Q 022058          101 RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQ-VVDCRVCGD---PHSVLRFAFVEFADEHGARAALN-L  175 (303)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~~~i~~~---~~~~~G~~fV~f~~~~~A~~Ai~-l  175 (303)
                      . ..+... -......++|||+|||+++++++|.+.|+.++. +.++.+...   ...++|||||+|.++++|..|+. |
T Consensus       125 ~-~Gr~l~-V~~S~~~~rLFVgNLP~~~TeeeL~eeFskv~egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL  202 (578)
T TIGR01648       125 R-PGRLLG-VCISVDNCRLFVGGIPKNKKREEILEEFSKVTEGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKL  202 (578)
T ss_pred             c-CCcccc-ccccccCceeEeecCCcchhhHHHHHHhhcccCCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHh
Confidence            0 000100 012234788999999999999999999999864 444444332   12379999999999999999997 6


Q ss_pred             CC--cccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCC
Q 022058          176 GG--TMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVH  253 (303)
Q Consensus       176 ~g--~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~  253 (303)
                      +.  ..+.|+.|.|.|+.+....         ........++|||+||+..+++++|+++|++|.+|.|++|.++++   
T Consensus       203 ~~gki~l~Gr~I~VdwA~p~~~~---------d~~~~~~~k~LfVgNL~~~~tee~L~~~F~~f~~G~I~rV~~~rg---  270 (578)
T TIGR01648       203 MPGRIQLWGHVIAVDWAEPEEEV---------DEDVMAKVKILYVRNLMTTTTEEIIEKSFSEFKPGKVERVKKIRD---  270 (578)
T ss_pred             hccceEecCceEEEEeecccccc---------cccccccccEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEeecC---
Confidence            53  4578999999998643211         011122357899999999999999999999973479999987653   


Q ss_pred             cccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCC
Q 022058          254 STRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRP  295 (303)
Q Consensus       254 ~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~  295 (303)
                         ||||+|.+.++|.+|++ |||..|.|+.|+|+|++|+...
T Consensus       271 ---fAFVeF~s~e~A~kAi~~lnG~~i~Gr~I~V~~Akp~~~~  310 (578)
T TIGR01648       271 ---YAFVHFEDREDAVKAMDELNGKELEGSEIEVTLAKPVDKK  310 (578)
T ss_pred             ---eEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEccCCCcc
Confidence               99999999999999998 9999999999999999987654

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.

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

Probab=100.00  E-value=5.6e-37  Score=258.56  Aligned_cols=228  Identities=22%  Similarity=0.299  Sum_probs=188.1

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhcccCCCCCC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLS  103 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~~~~  103 (303)
                      +|||+||++++||+-|-.||++.|+|++++|+.+.-     -|.+     +.                 ..  +.+.+  
T Consensus         8 tlyvgnld~~vte~~i~~lf~qig~v~~~k~i~~e~-----~v~w-----a~-----------------~p--~nQsk--   56 (321)
T KOG0148|consen    8 TLYVGNLDSTVTEDFIATLFNQIGSVTKTKVIFDEL-----KVNW-----AT-----------------AP--GNQSK--   56 (321)
T ss_pred             eEEeeccChhhHHHHHHHHHHhccccccceeehhhh-----cccc-----cc-----------------Cc--ccCCC--
Confidence            899999999999999999999999999999997732     2222     22                 00  11111  


Q ss_pred             chhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCccc
Q 022058          104 GRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTML  180 (303)
Q Consensus       104 ~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~  180 (303)
                             ........+||+.|...++-++|++.|.+||+|.+++|++|..+  |||||||.|.+.++|++||. |||++|
T Consensus        57 -------~t~~~hfhvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf~~k~dAEnAI~~MnGqWl  129 (321)
T KOG0148|consen   57 -------PTSNQHFHVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSFPNKEDAENAIQQMNGQWL  129 (321)
T ss_pred             -------CccccceeEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEeccchHHHHHHHHHhCCeee
Confidence                   11112566999999999999999999999999999999999987  89999999999999999998 999999


Q ss_pred             CCeeEEEeecCCCCCCCCCCCCCCc--ccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEE
Q 022058          181 GYYPVRVLPSKTAILPVNPTFLPRS--EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIA  258 (303)
Q Consensus       181 ~g~~i~v~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~a  258 (303)
                      ++|.|+..|+..+....+.....-+  -...++..++|||+|++..+++++|++.|++|  |.|..|+|.+++|    |+
T Consensus       130 G~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~f--G~I~EVRvFk~qG----Ya  203 (321)
T KOG0148|consen  130 GRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPF--GPIQEVRVFKDQG----YA  203 (321)
T ss_pred             ccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccC--CcceEEEEecccc----eE
Confidence            9999999999655421111100000  01224567899999999999999999999999  9999999999986    99


Q ss_pred             EEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCC
Q 022058          259 FVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRP  295 (303)
Q Consensus       259 fV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~  295 (303)
                      ||.|.+.|+|..||. |||.+++|+.+++.|.|.....
T Consensus       204 FVrF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~~~  241 (321)
T KOG0148|consen  204 FVRFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGDDG  241 (321)
T ss_pred             EEEecchhhHHHHHHHhcCceeCceEEEEeccccCCCC
Confidence            999999999999997 9999999999999999876544

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

Probab=100.00  E-value=2.6e-36  Score=288.95  Aligned_cols=249  Identities=20%  Similarity=0.272  Sum_probs=196.1

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc----CC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ----GR   99 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~----g~   99 (303)
                      +|+|+||++++|+++|+++|++||+|.+|.+.++..+ ...||+|     .+     .+    +|.+|+..||+    ++
T Consensus        98 ~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~~-~~afVef-----~~-----~~----~A~~A~~~Lng~~i~~~  162 (481)
T TIGR01649        98 RVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNNV-FQALVEF-----ES-----VN----SAQHAKAALNGADIYNG  162 (481)
T ss_pred             EEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCCc-eEEEEEE-----CC-----HH----HHHHHHHHhcCCcccCC
Confidence            5899999999999999999999999999999876532 1239999     88     88    99999998887    21


Q ss_pred             C-----------CCC-----chh-------h--------------hhc--------------------------------
Q 022058          100 K-----------RLS-----GRA-------F--------------RAQ--------------------------------  110 (303)
Q Consensus       100 ~-----------~~~-----~~~-------~--------------~~~--------------------------------  110 (303)
                      .           .+.     ...       .              ...                                
T Consensus       163 ~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~  242 (481)
T TIGR01649       163 CCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMG  242 (481)
T ss_pred             ceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCcccccCCCCCCcccccccCC
Confidence            0           000     000       0              000                                


Q ss_pred             ---------------------------cCCCCCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEE
Q 022058          111 ---------------------------REDSVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE  162 (303)
Q Consensus       111 ---------------------------~~~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~  162 (303)
                                                 ......++|||+|||+ .+++++|+++|+.||.|.+|+++.+.   +|||||+
T Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~yG~V~~vki~~~~---~g~afV~  319 (481)
T TIGR01649       243 PPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVYGNVERVKFMKNK---KETALIE  319 (481)
T ss_pred             CcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhcCCeEEEEEEeCC---CCEEEEE
Confidence                                       0012456899999998 69999999999999999999999864   5899999


Q ss_pred             ecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCC------------CCC----C-ccc------ccccccceEEE
Q 022058          163 FADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPT------------FLP----R-SED------EREMCSRTVYC  218 (303)
Q Consensus       163 f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~------------~~~----~-~~~------~~~~~~~~l~V  218 (303)
                      |.+.++|..|+. |||..|.|++|.|.+++.........            +..    + ...      ....+..+|||
T Consensus       320 f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~d~~~~~~~r~~~~~~~~~~~~~~ps~~L~v  399 (481)
T TIGR01649       320 MADPYQAQLALTHLNGVKLFGKPLRVCPSKQQNVQPPREGQLDDGLTSYKDYSSSRNHRFKKPGSANKNNIQPPSATLHL  399 (481)
T ss_pred             ECCHHHHHHHHHHhCCCEECCceEEEEEcccccccCCCCCcCcCCCcccccccCCccccCCCcccccccccCCCCcEEEE
Confidence            999999999998 99999999999999975432111000            000    0 000      01235679999


Q ss_pred             cCCCCCCCHHHHHHHhhhhcCcc--eeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCee------eEEeec
Q 022058          219 TNIDKKVPQAEVKQFFEAACGGE--VTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQP------IRVSPS  289 (303)
Q Consensus       219 ~nL~~~~t~~~L~~~F~~~~~G~--i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~------l~v~~a  289 (303)
                      +|||.++++++|+++|+.|  |.  |..+++..+.+..+|+|||+|.+.++|.+|+. |||+.|.++.      |+|+|+
T Consensus       400 ~NLp~~~tee~L~~lF~~~--G~~~i~~ik~~~~~~~~~~~gfVeF~~~e~A~~Al~~ln~~~l~~~~~~~~~~lkv~fs  477 (481)
T TIGR01649       400 SNIPLSVSEEDLKELFAEN--GVHKVKKFKFFPKDNERSKMGLLEWESVEDAVEALIALNHHQLNEPNGSAPYHLKVSFS  477 (481)
T ss_pred             ecCCCCCCHHHHHHHHHhc--CCccceEEEEecCCCCcceeEEEEcCCHHHHHHHHHHhcCCccCCCCCCccceEEEEec
Confidence            9999999999999999999  97  88898877665568899999999999999998 9999999985      999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      ++.
T Consensus       478 ~~~  480 (481)
T TIGR01649       478 TSR  480 (481)
T ss_pred             cCC
Confidence            865

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).

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

Probab=100.00  E-value=2.6e-36  Score=288.93  Aligned_cols=246  Identities=20%  Similarity=0.228  Sum_probs=191.0

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc-----
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-----   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-----   97 (303)
                      ..|||+|||+++|+++|+++|++||+|.+|.+++++   .-.||+|     .+     .+    +|++|+..++.     
T Consensus         3 ~vv~V~nLp~~~te~~L~~~f~~fG~V~~v~i~~~k---~~afVef-----~~-----~e----~A~~Ai~~~~~~~~~l   65 (481)
T TIGR01649         3 PVVHVRNLPQDVVEADLVEALIPFGPVSYVMMLPGK---RQALVEF-----ED-----EE----SAKACVNFATSVPIYI   65 (481)
T ss_pred             cEEEEcCCCCCCCHHHHHHHHHhcCCeeEEEEECCC---CEEEEEe-----Cc-----hH----HHHHHHHHhhcCCceE
Confidence            479999999999999999999999999999999753   1229999     88     77    89999986532     


Q ss_pred             -CCC-CCCchh----hhhc------cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecC
Q 022058           98 -GRK-RLSGRA----FRAQ------REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFAD  165 (303)
Q Consensus        98 -g~~-~~~~~~----~~~~------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~  165 (303)
                       |+. .+.+..    ....      ..+..-..|||+||++.+|+++|+++|+.||.|.+|.++++..  +|+|||+|.+
T Consensus        66 ~g~~l~v~~s~~~~~~~~~~~~~~~~~~~~~~~v~v~nl~~~vt~~~L~~~F~~~G~V~~v~i~~~~~--~~~afVef~~  143 (481)
T TIGR01649        66 RGQPAFFNYSTSQEIKRDGNSDFDSAGPNKVLRVIVENPMYPITLDVLYQIFNPYGKVLRIVTFTKNN--VFQALVEFES  143 (481)
T ss_pred             cCeEEEEEecCCcccccCCCCcccCCCCCceEEEEEcCCCCCCCHHHHHHHHhccCCEEEEEEEecCC--ceEEEEEECC
Confidence             333 111100    0000      0111223699999999999999999999999999999987654  4799999999


Q ss_pred             HHHHHHHHH-hCCcccCC--eeEEEeecCCCCCC------CC-----CCC------------CCCcc-------------
Q 022058          166 EHGARAALN-LGGTMLGY--YPVRVLPSKTAILP------VN-----PTF------------LPRSE-------------  206 (303)
Q Consensus       166 ~~~A~~Ai~-l~g~~~~g--~~i~v~~~~~~~~~------~~-----~~~------------~~~~~-------------  206 (303)
                      .++|.+|++ |||..|.|  +.|+|.|++.....      ..     +..            ..+..             
T Consensus       144 ~~~A~~A~~~Lng~~i~~~~~~l~v~~sk~~~l~v~~~~~~s~dyt~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  223 (481)
T TIGR01649       144 VNSAQHAKAALNGADIYNGCCTLKIEYAKPTRLNVKYNDDDSRDYTNPDLPGRRDPGLDQTHRQRQPALLGQHPSSYGHD  223 (481)
T ss_pred             HHHHHHHHHHhcCCcccCCceEEEEEEecCCCceeEecccCCCCCcCCCCCCCCCCCcCccccccccccccCCCccCCCc
Confidence            999999998 99999954  68999887642210      00     000            00000             


Q ss_pred             ---------------------------------------------cccccccceEEEcCCCC-CCCHHHHHHHhhhhcCc
Q 022058          207 ---------------------------------------------DEREMCSRTVYCTNIDK-KVPQAEVKQFFEAACGG  240 (303)
Q Consensus       207 ---------------------------------------------~~~~~~~~~l~V~nL~~-~~t~~~L~~~F~~~~~G  240 (303)
                                                                   .....+..+|||+|||+ .+++++|+++|+.|  |
T Consensus       224 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nL~~~~vt~~~L~~lF~~y--G  301 (481)
T TIGR01649       224 GYSSHGGPLAPLAGGDRMGPPHGPPSRYRPAYEAAPLAPAISSYGPAGGGPGSVLMVSGLHQEKVNCDRLFNLFCVY--G  301 (481)
T ss_pred             ccccCCCCCCcccccccCCCcccCCCCCcccccccccCccccccCCCCCCCCCEEEEeCCCCCCCCHHHHHHHHHhc--C
Confidence                                                         00012457999999998 69999999999999  9


Q ss_pred             ceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          241 EVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       241 ~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      .|.+|+|++++   +|+|||+|.+.++|..|+. |||..|.|+.|+|.+++..
T Consensus       302 ~V~~vki~~~~---~g~afV~f~~~~~A~~Ai~~lng~~l~g~~l~v~~s~~~  351 (481)
T TIGR01649       302 NVERVKFMKNK---KETALIEMADPYQAQLALTHLNGVKLFGKPLRVCPSKQQ  351 (481)
T ss_pred             CeEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEcccc
Confidence            99999999874   4799999999999999998 9999999999999998654

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).

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

Probab=100.00  E-value=7.4e-35  Score=278.05  Aligned_cols=252  Identities=17%  Similarity=0.265  Sum_probs=194.8

Q ss_pred             CCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc-
Q 022058           22 NNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-   97 (303)
Q Consensus        22 ~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-   97 (303)
                      +.+|||+|||+++|+++|+++|++||+|.+|+|+.++.++.++   ||+|     .+     .+    +|.+|+. +++ 
T Consensus        89 ~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF-----~~-----~e----~A~~Al~-l~g~  153 (457)
T TIGR01622        89 DRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEF-----YD-----VE----SVIKALA-LTGQ  153 (457)
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEE-----CC-----HH----HHHHHHH-hCCC
Confidence            4579999999999999999999999999999999998766554   9999     77     77    8888885 554 


Q ss_pred             ---CCC-CCCchhh----------hhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEE
Q 022058           98 ---GRK-RLSGRAF----------RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFV  161 (303)
Q Consensus        98 ---g~~-~~~~~~~----------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV  161 (303)
                         |++ .+.....          .........++|||+|||+.+++++|+++|+.||.|..|.++.+..+  ++|||||
T Consensus       154 ~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~G~i~~v~~~~d~~~g~~~g~afV  233 (457)
T TIGR01622       154 MLLGRPIIVQSSQAEKNRAAKAATHQPGDIPNFLKLYVGNLHFNITEQELRQIFEPFGDIEDVQLHRDPETGRSKGFGFI  233 (457)
T ss_pred             EECCeeeEEeecchhhhhhhhcccccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEE
Confidence               322 1100000          00001123588999999999999999999999999999999998765  7999999


Q ss_pred             EecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCC----------------------------------C-------C
Q 022058          162 EFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPV----------------------------------N-------P  199 (303)
Q Consensus       162 ~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~----------------------------------~-------~  199 (303)
                      +|.+.++|.+|+. |||..+.|++|.|.++.......                                  .       +
T Consensus       234 ~f~~~e~A~~A~~~l~g~~i~g~~i~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  313 (457)
T TIGR01622       234 QFHDAEEAKEALEVMNGFELAGRPIKVGYAQDSTYLLDAANTFEDIDKQQQMGKNLNTEEREQLMEKLDRDDGDGGLLIP  313 (457)
T ss_pred             EECCHHHHHHHHHhcCCcEECCEEEEEEEccCCCccccchhhhccccccccCCcCCCccchHHHHHhhccCCCCccccCC
Confidence            9999999999998 99999999999999954211000                                  0       0


Q ss_pred             -C------------------CCCC--------------cccc--cccccceEEEcCCCCCCC----------HHHHHHHh
Q 022058          200 -T------------------FLPR--------------SEDE--REMCSRTVYCTNIDKKVP----------QAEVKQFF  234 (303)
Q Consensus       200 -~------------------~~~~--------------~~~~--~~~~~~~l~V~nL~~~~t----------~~~L~~~F  234 (303)
                       .                  ..+.              ....  ......+|+|.||....+          .+||++.|
T Consensus       314 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~n~~~~~~~~~~~~~~~~~~dv~~e~  393 (457)
T TIGR01622       314 GTGSKIALMQKLQRDGIIDPNIPSRYATGALAIMARNSFVPSTNNNLATTCLVLSNMFDPATEEEPNFDNEILDDVKEEC  393 (457)
T ss_pred             CccchhhhhccccccccccccccccccccccccccCCCCCCcccCCCCCcEEEEecCCCCcccccchHHHHHHHHHHHHH
Confidence             0                  0000              0000  113457899999955433          36899999


Q ss_pred             hhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          235 EAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       235 ~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      ++|  |.|+.|.|...  .+.|++||+|.+.++|.+|++ |||..|+|+.|.+.|....
T Consensus       394 ~k~--G~v~~v~v~~~--~~~G~~fV~F~~~e~A~~A~~~lnGr~f~gr~i~~~~~~~~  448 (457)
T TIGR01622       394 SKY--GGVVHIYVDTK--NSAGKIYLKFSSVDAALAAFQALNGRYFGGKMITAAFVVND  448 (457)
T ss_pred             Hhc--CCeeEEEEeCC--CCceeEEEEECCHHHHHHHHHHhcCcccCCeEEEEEEEcHH
Confidence            999  99999998743  345899999999999999999 9999999999999997544

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.

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

Probab=100.00  E-value=2.5e-36  Score=268.86  Aligned_cols=254  Identities=19%  Similarity=0.255  Sum_probs=207.2

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcccCCC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK  100 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~  100 (303)
                      ++||+-+|-++||.|||++|++||.|.+|.|++|+.++.++   ||.|     .+     .+    +|.+|++.++.-+.
T Consensus        36 KlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~-----~t-----rk----~a~~a~~Alhn~kt  101 (510)
T KOG0144|consen   36 KLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKY-----YT-----RK----EADEAINALHNQKT  101 (510)
T ss_pred             hheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEe-----cc-----HH----HHHHHHHHhhcccc
Confidence            69999999999999999999999999999999999988766   9999     66     66    77788888776222


Q ss_pred             ------CCCchhhhhccCC-CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHH
Q 022058          101 ------RLSGRAFRAQRED-SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAA  172 (303)
Q Consensus       101 ------~~~~~~~~~~~~~-~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~A  172 (303)
                            .+..+....+++. ...+.||||.|+..++|.+++++|++||.|++|+|++|..+ +||||||.|.+.+.|..|
T Consensus       102 lpG~~~pvqvk~Ad~E~er~~~e~KLFvg~lsK~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~A  181 (510)
T KOG0144|consen  102 LPGMHHPVQVKYADGERERIVEERKLFVGMLSKQCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAA  181 (510)
T ss_pred             cCCCCcceeecccchhhhccccchhhhhhhccccccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHH
Confidence                  2222222333322 24788999999999999999999999999999999999887 999999999999999999


Q ss_pred             HH-hCCc-ccCC--eeEEEeecCCCCCCC---------------------------------------------------
Q 022058          173 LN-LGGT-MLGY--YPVRVLPSKTAILPV---------------------------------------------------  197 (303)
Q Consensus       173 i~-l~g~-~~~g--~~i~v~~~~~~~~~~---------------------------------------------------  197 (303)
                      |+ |||. .+.|  .+|.|+|+++.....                                                   
T Consensus       182 ika~ng~~tmeGcs~PLVVkFADtqkdk~~~~lqq~~~~~~qql~~~~~~~n~~~~~~l~~~~~~~~Qq~~~sqn~g~l~  261 (510)
T KOG0144|consen  182 IKALNGTQTMEGCSQPLVVKFADTQKDKDGKRLQQLNPALLQQLGNGQNPQNLASLGALSNGYQGPQQQTQQSQNVGTLG  261 (510)
T ss_pred             HHhhccceeeccCCCceEEEecccCCCchHHHHHhhhHHHHHHhcCCCCccchhhhhccCcccCchhhhccccCCCcccc
Confidence            99 9984 4555  899999987643200                                                   


Q ss_pred             -----CC--------------------------CC--------------C------CCc---------------------
Q 022058          198 -----NP--------------------------TF--------------L------PRS---------------------  205 (303)
Q Consensus       198 -----~~--------------------------~~--------------~------~~~---------------------  205 (303)
                           .+                          ..              .      +.+                     
T Consensus       262 g~~~L~~l~a~~~qq~~~~~~~~ta~q~~~~s~q~~pl~~qts~~~~~~~~~~~~~~ss~~~~s~~~~aq~~~~q~~p~t  341 (510)
T KOG0144|consen  262 GLPPLGPLNATQLQQAAALAAAATAAQKTASSTQGLPLRTQTSFPGSQTSPQSASAPSSSLSTSQNPLAQLGARQTFPGT  341 (510)
T ss_pred             cccCCCCcchhHHHHHHHhhhhcccccCCCCCcccCccccccCCccccCCCccccCccccCcccccchhhhhHhhcCCCC
Confidence                 00                          00              0      000                     


Q ss_pred             ---------------------------------------------------------------------------ccccc
Q 022058          206 ---------------------------------------------------------------------------EDERE  210 (303)
Q Consensus       206 ---------------------------------------------------------------------------~~~~~  210 (303)
                                                                                                 .+.+.
T Consensus       342 ~~~~n~~~~~a~a~~~sp~aa~~~~lq~~~ltp~~~~~~~~~tQa~q~~~q~a~~a~~~l~~q~~~~qq~~~~~~~q~eG  421 (510)
T KOG0144|consen  342 PANYNLAGGMAGAGTTSPVAASLANLQQIGLTPFAGAAALDHTQAMQQYAQSANLAAPGLVGQQATTQQAQMVGNGQVEG  421 (510)
T ss_pred             chhcccccccccccccCcccccccccccccCCChhhhhhHhHHHhhhHhhhhhhhcccchhhhhHhhhhhhcccCccccC
Confidence                                                                                       00113


Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      +.+..|||++||.+.-+.+|-..|.+|  |.|.+.++.-|+  +-+++|+||.|++..+|..||. |||+.+++++|+|.
T Consensus       422 peGanlfiyhlPqefgdq~l~~~f~pf--G~Vlsakvfidk~tnlskcfgfvSyen~~sa~~aI~amngfQig~KrlkVQ  499 (510)
T KOG0144|consen  422 PEGANLFIYHLPQEFGDQDLIATFQPF--GGVLSAKVFIDKVTNLSKCFGFVSYENAQSAQNAISAMNGFQIGSKRLKVQ  499 (510)
T ss_pred             CCccceeeeeCchhhhhHHHHHHhccc--cceeEEEEEEecccCHhhhcCcccccchhhhHHHHHHhcchhhccccceEE
Confidence            346789999999999999999999999  999999888886  7799999999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      ......
T Consensus       500 lk~~~~  505 (510)
T KOG0144|consen  500 LKRDRN  505 (510)
T ss_pred             eeeccC
Confidence            875443

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

Probab=100.00  E-value=5.7e-35  Score=266.69  Aligned_cols=253  Identities=22%  Similarity=0.286  Sum_probs=198.6

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc--
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ--   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~--   97 (303)
                      .+|||++|||+++.++|.++|+.+|||..+.++.++.....|   ||.|     +.     .+    |+++|+....+  
T Consensus         6 ~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtF-----am-----~E----D~qrA~~e~~~~k   71 (678)
T KOG0127|consen    6 ATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTF-----AM-----EE----DVQRALAETEQSK   71 (678)
T ss_pred             ceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceee-----eh-----Hh----HHHHHHHHhhcCc
Confidence            489999999999999999999999999999999998875544   9999     77     77    88888776654  


Q ss_pred             --CCC-CC---Cchhhhh---------------c-cC-----CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEee
Q 022058           98 --GRK-RL---SGRAFRA---------------Q-RE-----DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCG  150 (303)
Q Consensus        98 --g~~-~~---~~~~~~~---------------~-~~-----~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~  150 (303)
                        |+. .+   ..+....               + +.     ....-.|.|+||||.+.+.+|+.+|+.||.|.+|.|++
T Consensus        72 f~Gr~l~v~~A~~R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~G~V~Ei~IP~  151 (678)
T KOG0127|consen   72 FEGRILNVDPAKKRARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNFGKVVEIVIPR  151 (678)
T ss_pred             ccceecccccccccccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhcceEEEEEccc
Confidence              222 00   0000000               0 00     01144599999999999999999999999999999998


Q ss_pred             CCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCC--------------------------C---
Q 022058          151 DPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVN--------------------------P---  199 (303)
Q Consensus       151 ~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~--------------------------~---  199 (303)
                      ...+ -+|||||+|....+|..|++ +|+..|+||+|.|.|+-.......                          .   
T Consensus       152 k~dgklcGFaFV~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd~ye~ta~~~~~s~Kk~~~eEed~e~~~d~~~~~~  231 (678)
T KOG0127|consen  152 KKDGKLCGFAFVQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKDTYEDTAHEEKQSLKKAVKEEEDKEADEDDGKDFD  231 (678)
T ss_pred             CCCCCccceEEEEEeeHHHHHHHHHhccCceecCceeEEeeecccccccccchhhhhhhhhccchhhhcccccccccccc
Confidence            7776 57999999999999999999 999999999999999743211000                          0   


Q ss_pred             ----CCCCCc---------------------------c----------------cccccccceEEEcCCCCCCCHHHHHH
Q 022058          200 ----TFLPRS---------------------------E----------------DEREMCSRTVYCTNIDKKVPQAEVKQ  232 (303)
Q Consensus       200 ----~~~~~~---------------------------~----------------~~~~~~~~~l~V~nL~~~~t~~~L~~  232 (303)
                          .....+                           +                +.......+|||+|||+++|+++|.+
T Consensus       232 ~Ed~e~d~edeEe~D~~se~~ee~~~~Eee~~~vDd~e~S~~~~~~k~~q~k~~~en~~~~~tVFvRNL~fD~tEEel~~  311 (678)
T KOG0127|consen  232 EEDGEEDSEDEEETDGNSEAFEEGEESEEEEDDVDDEESSGKKESDKKAQNKTTRENITEGKTVFVRNLPFDTTEEELKE  311 (678)
T ss_pred             hhcccccccccccccccchhhhccccccccccccccccccccCcccchhccccccccccccceEEEecCCccccHHHHHH
Confidence                000000                           0                00011247899999999999999999


Q ss_pred             HhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-h-----CC-ceeCCeeeEEeecCC
Q 022058          233 FFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-C-----SG-MVLGSQPIRVSPSKT  291 (303)
Q Consensus       233 ~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l-----~g-~~~~g~~l~v~~a~~  291 (303)
                      +|++|  |.|.++.|+.++  +.++|.|||.|.+..+|+.||. .     .| ..|+||.|+|..+-+
T Consensus       312 ~fskF--G~v~ya~iV~~k~T~~skGtAFv~Fkt~~~~~~ci~~Aspa~e~g~~ll~GR~Lkv~~Av~  377 (678)
T KOG0127|consen  312 HFSKF--GEVKYAIIVKDKDTGHSKGTAFVKFKTQIAAQNCIEAASPASEDGSVLLDGRLLKVTLAVT  377 (678)
T ss_pred             HHHhh--ccceeEEEEeccCCCCcccceEEEeccHHHHHHHHHhcCccCCCceEEEeccEEeeeeccc
Confidence            99999  999999998885  8899999999999999999997 3     24 678999999998864

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

Probab=100.00  E-value=1e-33  Score=273.72  Aligned_cols=252  Identities=15%  Similarity=0.159  Sum_probs=188.8

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhcc------------CCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccc
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKL------------NPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNN   87 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~------------G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~   87 (303)
                      ....+|||+|||+++|+++|+++|.+|            ++|..+.+..++   .-.||+|     .+     .+    +
T Consensus       173 ~~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~~k---g~afVeF-----~~-----~e----~  235 (509)
T TIGR01642       173 RQARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINKEK---NFAFLEF-----RT-----VE----E  235 (509)
T ss_pred             ccccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECCCC---CEEEEEe-----CC-----HH----H
Confidence            344579999999999999999999985            345556654432   1229999     87     77    8


Q ss_pred             hHHhhhhccc----CCC-CCCchhhhh---------------------------ccCCCCCCEEEEcCCCCCCCHHHHHH
Q 022058           88 NRRRRNNFNQ----GRK-RLSGRAFRA---------------------------QREDSVRRTVYVSDIDQNITEERLAG  135 (303)
Q Consensus        88 A~~a~~~~~~----g~~-~~~~~~~~~---------------------------~~~~~~~~~l~V~nlp~~~t~~~l~~  135 (303)
                      |..|+ .|++    |.. .+..+....                           .......++|||+|||+.+++++|++
T Consensus       236 A~~Al-~l~g~~~~g~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~  314 (509)
T TIGR01642       236 ATFAM-ALDSIIYSNVFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKE  314 (509)
T ss_pred             Hhhhh-cCCCeEeeCceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHH
Confidence            88888 4665    322 111110000                           00112357899999999999999999


Q ss_pred             HhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCC----CC-----
Q 022058          136 LFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTF----LP-----  203 (303)
Q Consensus       136 ~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~----~~-----  203 (303)
                      +|+.||.|..+.++.+..+  ++|||||+|.+.++|..|+. |||..+.|+.|.|.++...........    .+     
T Consensus       315 ~f~~~G~i~~~~~~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~  394 (509)
T TIGR01642       315 LLESFGDLKAFNLIKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANQATIDTSNGMAPVTLLA  394 (509)
T ss_pred             HHHhcCCeeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccCCCCCCcccccccccccccc
Confidence            9999999999999998654  89999999999999999998 999999999999999754321110000    00     


Q ss_pred             C-----cccccccccceEEEcCCCCC--C--------CHHHHHHHhhhhcCcceeEEEEecCC-----CCcccEEEEEEc
Q 022058          204 R-----SEDEREMCSRTVYCTNIDKK--V--------PQAEVKQFFEAACGGEVTRLRLLGDH-----VHSTRIAFVEFA  263 (303)
Q Consensus       204 ~-----~~~~~~~~~~~l~V~nL~~~--~--------t~~~L~~~F~~~~~G~i~~v~i~~d~-----~~~~g~afV~f~  263 (303)
                      .     .......+..+|+|.|+...  +        ..++|+++|++|  |.|.+|.|+++.     +...|+|||+|.
T Consensus       395 ~~~~~~~~~~~~~~s~v~~l~N~~~~~~l~~d~~~~~~~edl~~~f~~~--G~v~~v~i~~~~~~~~~~~~~G~~fV~F~  472 (509)
T TIGR01642       395 KALSQSILQIGGKPTKVVQLTNLVTGDDLMDDEEYEEIYEDVKTEFSKY--GPLINIVIPRPNGDRNSTPGVGKVFLEYA  472 (509)
T ss_pred             ccchhhhccccCCCceEEEeccCCchhHhcCcchHHHHHHHHHHHHHhc--CCeeEEEeeccCcCCCcCCCcceEEEEEC
Confidence            0     00011235678999999642  1        136899999999  999999998752     345789999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          264 VAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       264 ~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      +.++|.+|+. |||..|+|+.|.|.|...
T Consensus       473 ~~e~A~~A~~~lnGr~~~gr~v~~~~~~~  501 (509)
T TIGR01642       473 DVRSAEKAMEGMNGRKFNDRVVVAAFYGE  501 (509)
T ss_pred             CHHHHHHHHHHcCCCEECCeEEEEEEeCH
Confidence            9999999998 999999999999999754

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

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

Probab=100.00  E-value=7.8e-33  Score=265.17  Aligned_cols=158  Identities=15%  Similarity=0.228  Sum_probs=132.9

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcc
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFN   96 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~   96 (303)
                      ....+|||+||++++|+++|+++|++||+|.+|+|+.|+.++.++   ||+|     .+     .+    +|++|+..+|
T Consensus       105 ~~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF-----~s-----~e----~A~~Ai~~ln  170 (612)
T TIGR01645       105 AIMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEY-----EV-----PE----AAQLALEQMN  170 (612)
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEe-----Cc-----HH----HHHHHHHhcC
Confidence            344589999999999999999999999999999999998765544   9999     88     88    9999999998


Q ss_pred             c----CCC-CCCchhhhh---------ccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEE
Q 022058           97 Q----GRK-RLSGRAFRA---------QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAF  160 (303)
Q Consensus        97 ~----g~~-~~~~~~~~~---------~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~f  160 (303)
                      +    |+. .+..+....         .......++|||+|||+++++++|+++|+.||.|.+|+|++++.+  ++||||
T Consensus       171 G~~i~GR~IkV~rp~~~p~a~~~~~~~~~~~~~~~rLfVgnLp~~vteedLk~lFs~FG~I~svrl~~D~~tgksKGfGF  250 (612)
T TIGR01645       171 GQMLGGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGF  250 (612)
T ss_pred             CeEEecceeeecccccccccccccccccccccccceEEeecCCCCCCHHHHHHHHhhcCCeeEEEEEecCCCCCcCCeEE
Confidence            7    444 222111110         011123568999999999999999999999999999999998765  799999


Q ss_pred             EEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          161 VEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       161 V~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      |+|.+.++|.+||. ||+..++|+.|+|.++.
T Consensus       251 VeFe~~e~A~kAI~amNg~elgGr~LrV~kAi  282 (612)
T TIGR01645       251 IEYNNLQSQSEAIASMNLFDLGGQYLRVGKCV  282 (612)
T ss_pred             EEECCHHHHHHHHHHhCCCeeCCeEEEEEecC
Confidence            99999999999998 99999999999998864

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.

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=100.00  E-value=3.3e-32  Score=248.34  Aligned_cols=169  Identities=21%  Similarity=0.407  Sum_probs=150.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++|+++|+++|+.||+|.+|+|+.|..+  ++|||||+|.++++|.+||+ ||+..+.+++|+|.
T Consensus       103 ~~~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF~~~e~A~~Ai~~LnG~~l~gr~i~V~  182 (346)
T TIGR01659       103 TNNSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDFGSEADSQRAIKNLNGITVRNKRLKVS  182 (346)
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEEccHHHHHHHHHHcCCCccCCceeeee
Confidence            3446889999999999999999999999999999999998765  89999999999999999998 99999999999999


Q ss_pred             ecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHH
Q 022058          189 PSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAE  266 (303)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e  266 (303)
                      ++++...              ....++|||+|||..+++++|+++|++|  |.|..+.|++|+  ++++|+|||+|.+.+
T Consensus       183 ~a~p~~~--------------~~~~~~lfV~nLp~~vtee~L~~~F~~f--G~V~~v~i~~d~~tg~~kG~aFV~F~~~e  246 (346)
T TIGR01659       183 YARPGGE--------------SIKDTNLYVTNLPRTITDDQLDTIFGKY--GQIVQKNILRDKLTGTPRGVAFVRFNKRE  246 (346)
T ss_pred             ccccccc--------------ccccceeEEeCCCCcccHHHHHHHHHhc--CCEEEEEEeecCCCCccceEEEEEECCHH
Confidence            8753211              1123689999999999999999999999  999999999985  788999999999999


Q ss_pred             HHHHHHH-hCCceeCC--eeeEEeecCCCCCCC
Q 022058          267 SAILALN-CSGMVLGS--QPIRVSPSKTPVRPR  296 (303)
Q Consensus       267 ~A~~Ai~-l~g~~~~g--~~l~v~~a~~~~~~r  296 (303)
                      +|.+||+ ||+..+.+  +.|+|.+++...+.+
T Consensus       247 ~A~~Ai~~lng~~~~g~~~~l~V~~a~~~~~~~  279 (346)
T TIGR01659       247 EAQEAISALNNVIPEGGSQPLTVRLAEEHGKAK  279 (346)
T ss_pred             HHHHHHHHhCCCccCCCceeEEEEECCcccccc
Confidence            9999999 99998865  799999998765544

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).

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

Probab=100.00  E-value=6.8e-32  Score=247.55  Aligned_cols=238  Identities=22%  Similarity=0.345  Sum_probs=205.1

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc-eeeeecchhhhhhchhhhccccchHHhhhhcccCCC-C
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH-HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK-R  101 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~-~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~-~  101 (303)
                      .|+|+   +++|+..|.++|+++|+|.+|++.+|. +..+. ||.|     .+     ++    +|.+|+..+|..-- .
T Consensus         3 sl~vg---~~v~e~~l~~~f~~~~~v~s~rvc~d~-tslgy~yvnf-----~~-----~~----da~~A~~~~n~~~~~~   64 (369)
T KOG0123|consen    3 SLYVG---PDVTEAMLFDKFSPAGPVLSIRVCRDA-TSLGYAYVNF-----QQ-----PA----DAERALDTMNFDVLKG   64 (369)
T ss_pred             ceecC---CcCChHHHHHHhcccCCceeEEEeecC-CccceEEEec-----CC-----HH----HHHHHHHHcCCcccCC
Confidence            57888   999999999999999999999999999 72233 9999     88     88    99999999998221 3


Q ss_pred             CCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc
Q 022058          102 LSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML  180 (303)
Q Consensus       102 ~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~  180 (303)
                      ...+++++++++..   |||.||+++++..+|.++|+.||.|.+|++.++.++++|| ||+|+++++|.+||+ +||..+
T Consensus        65 ~~~rim~s~rd~~~---~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~-FV~f~~e~~a~~ai~~~ng~ll  140 (369)
T KOG0123|consen   65 KPIRIMWSQRDPSL---VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGY-FVQFESEESAKKAIEKLNGMLL  140 (369)
T ss_pred             cEEEeehhccCCce---eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceee-EEEeCCHHHHHHHHHHhcCccc
Confidence            33456777777655   9999999999999999999999999999999999999999 999999999999999 999999


Q ss_pred             CCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEE
Q 022058          181 GYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAF  259 (303)
Q Consensus       181 ~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~af  259 (303)
                      .|+.|.|...........+    .. . .......+++.|++...+++.|..+|..+  |.|.++.++++. ++++||+|
T Consensus       141 ~~kki~vg~~~~~~er~~~----~~-~-~~~~~t~v~vk~~~~~~~~~~l~~~f~~~--g~i~s~~v~~~~~g~~~~~gf  212 (369)
T KOG0123|consen  141 NGKKIYVGLFERKEEREAP----LG-E-YKKRFTNVYVKNLEEDSTDEELKDLFSAY--GSITSVAVMRDSIGKSKGFGF  212 (369)
T ss_pred             CCCeeEEeeccchhhhccc----cc-c-hhhhhhhhheeccccccchHHHHHhhccc--CcceEEEEeecCCCCCCCccc
Confidence            9999999886443211111    11 1 22345779999999999999999999999  999999999985 77999999


Q ss_pred             EEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          260 VEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       260 V~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      |.|.++++|..|+. |||..+.+..+-|..+..
T Consensus       213 v~f~~~e~a~~av~~l~~~~~~~~~~~V~~aqk  245 (369)
T KOG0123|consen  213 VNFENPEDAKKAVETLNGKIFGDKELYVGRAQK  245 (369)
T ss_pred             eeecChhHHHHHHHhccCCcCCccceeeccccc
Confidence            99999999999999 999999999999888754

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

Probab=99.98  E-value=2.9e-31  Score=254.40  Aligned_cols=177  Identities=24%  Similarity=0.356  Sum_probs=151.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++.|+.+  ++|||||+|.+.++|++|++ |||..+.||.|+|.+..
T Consensus       106 ~~~rLfVGnLp~~~tEe~Lr~lF~~fG~I~sV~I~~D~~TgkskGfAFVeF~s~e~A~~Ai~~lnG~~i~GR~IkV~rp~  185 (612)
T TIGR01645       106 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  185 (612)
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHccCCEEEEEEeecCCCCCcCCeEEEEeCcHHHHHHHHHhcCCeEEecceeeecccc
Confidence            5688999999999999999999999999999999998765  89999999999999999998 99999999999998653


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~  269 (303)
                      ....  ....... ........++|||+|||+.+++++|+++|+.|  |.|.+|+|.+|.  ++++|||||+|.+.++|.
T Consensus       186 ~~p~--a~~~~~~-~~~~~~~~~rLfVgnLp~~vteedLk~lFs~F--G~I~svrl~~D~~tgksKGfGFVeFe~~e~A~  260 (612)
T TIGR01645       186 NMPQ--AQPIIDM-VQEEAKKFNRIYVASVHPDLSETDIKSVFEAF--GEIVKCQLARAPTGRGHKGYGFIEYNNLQSQS  260 (612)
T ss_pred             cccc--ccccccc-ccccccccceEEeecCCCCCCHHHHHHHHhhc--CCeeEEEEEecCCCCCcCCeEEEEECCHHHHH
Confidence            2211  0000000 01112235789999999999999999999999  999999999985  678999999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeecCCCCCCC
Q 022058          270 LALN-CSGMVLGSQPIRVSPSKTPVRPR  296 (303)
Q Consensus       270 ~Ai~-l~g~~~~g~~l~v~~a~~~~~~r  296 (303)
                      +|+. |||..++|+.|+|.++.+++..+
T Consensus       261 kAI~amNg~elgGr~LrV~kAi~pP~~~  288 (612)
T TIGR01645       261 EAIASMNLFDLGGQYLRVGKCVTPPDAL  288 (612)
T ss_pred             HHHHHhCCCeeCCeEEEEEecCCCcccc
Confidence            9998 99999999999999998765544

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.

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

Probab=99.97  E-value=2.4e-31  Score=243.99  Aligned_cols=253  Identities=20%  Similarity=0.313  Sum_probs=209.5

Q ss_pred             CcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc----CCC
Q 022058           25 LETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ----GRK  100 (303)
Q Consensus        25 ~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~----g~~  100 (303)
                      |||+||+.++|.++|.++|+.||+|.+|++..+.++..+.||+|     .+     ++    .|++|+..+||    ++.
T Consensus        79 ~~i~nl~~~~~~~~~~d~f~~~g~ilS~kv~~~~~g~kg~FV~f-----~~-----e~----~a~~ai~~~ng~ll~~kk  144 (369)
T KOG0123|consen   79 VFIKNLDESIDNKSLYDTFSEFGNILSCKVATDENGSKGYFVQF-----ES-----EE----SAKKAIEKLNGMLLNGKK  144 (369)
T ss_pred             eeecCCCcccCcHHHHHHHHhhcCeeEEEEEEcCCCceeeEEEe-----CC-----HH----HHHHHHHHhcCcccCCCe
Confidence            89999999999999999999999999999999998844449999     88     88    99999999998    333


Q ss_pred             CCCchh----h---hhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHH
Q 022058          101 RLSGRA----F---RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAA  172 (303)
Q Consensus       101 ~~~~~~----~---~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~A  172 (303)
                      ....+.    .   ........-..++|.|++.+++++.|..+|+.+|.|.++.++.+..+ ++||+||.|.++++|..|
T Consensus       145 i~vg~~~~~~er~~~~~~~~~~~t~v~vk~~~~~~~~~~l~~~f~~~g~i~s~~v~~~~~g~~~~~gfv~f~~~e~a~~a  224 (369)
T KOG0123|consen  145 IYVGLFERKEEREAPLGEYKKRFTNVYVKNLEEDSTDEELKDLFSAYGSITSVAVMRDSIGKSKGFGFVNFENPEDAKKA  224 (369)
T ss_pred             eEEeeccchhhhcccccchhhhhhhhheeccccccchHHHHHhhcccCcceEEEEeecCCCCCCCccceeecChhHHHHH
Confidence            111111    1   11111123456999999999999999999999999999999998877 899999999999999999


Q ss_pred             HH-hCCcccCCeeEEEeecCCCCCCC----CCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEE
Q 022058          173 LN-LGGTMLGYYPVRVLPSKTAILPV----NPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRL  247 (303)
Q Consensus       173 i~-l~g~~~~g~~i~v~~~~~~~~~~----~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i  247 (303)
                      ++ +|+..+++..+.|..+.......    .+.......+.......+|||.|++..++.+.|+.+|+.+  |.|.+++|
T Consensus       225 v~~l~~~~~~~~~~~V~~aqkk~e~~~~l~~~~~~~~~~~~~~~~~~nl~vknld~~~~~e~L~~~f~~~--GeI~s~kv  302 (369)
T KOG0123|consen  225 VETLNGKIFGDKELYVGRAQKKSEREAELKRKFEQEFAKRSVSLQGANLYVKNLDETLSDEKLRKIFSSF--GEITSAKV  302 (369)
T ss_pred             HHhccCCcCCccceeecccccchhhHHHHhhhhHhhhhhccccccccccccccCccccchhHHHHHHhcc--cceeeEEE
Confidence            99 99999999999999886532110    1111112222234556889999999999999999999999  99999999


Q ss_pred             ecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCC
Q 022058          248 LGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       248 ~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~  293 (303)
                      +.+. |.++|+|||.|.+.++|.+|+. +||..++++.|.|.++....
T Consensus       303 ~~~~~g~skG~gfV~fs~~eeA~~A~~~~n~~~i~~k~l~vav~qr~~  350 (369)
T KOG0123|consen  303 MVDENGKSKGFGFVEFSSPEEAKKAMTEMNGRLIGGKPLYVAVAQRKE  350 (369)
T ss_pred             EeccCCCccceEEEEcCCHHHHHHHHHhhChhhhcCCchhhhHHhhhc
Confidence            9985 8999999999999999999998 99999999999999986433

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor

Probab=99.97  E-value=1.2e-29  Score=234.21  Aligned_cols=163  Identities=24%  Similarity=0.443  Sum_probs=146.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ...+|||+|||+++++++|+++|+.||+|.+|+|++++.+  ++|||||+|.+.++|.+||. |||..+.|++|.|.++.
T Consensus         2 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~d~~~g~s~g~afV~f~~~~~A~~Ai~~l~g~~l~g~~i~v~~a~   81 (352)
T TIGR01661         2 SKTNLIVNYLPQTMTQEEIRSLFTSIGEIESCKLVRDKVTGQSLGYGFVNYVRPEDAEKAVNSLNGLRLQNKTIKVSYAR   81 (352)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHccCCEEEEEEEEcCCCCccceEEEEEECcHHHHHHHHhhcccEEECCeeEEEEeec
Confidence            3678999999999999999999999999999999998754  89999999999999999998 99999999999999975


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~  269 (303)
                      +...              .....+|||+|||..+++++|+++|++|  |.|..+.++.+.  +.++|||||+|.+.++|.
T Consensus        82 ~~~~--------------~~~~~~l~v~~l~~~~~~~~l~~~f~~~--G~i~~~~~~~~~~~~~~~g~~fv~f~~~~~A~  145 (352)
T TIGR01661        82 PSSD--------------SIKGANLYVSGLPKTMTQHELESIFSPF--GQIITSRILSDNVTGLSKGVGFIRFDKRDEAD  145 (352)
T ss_pred             cccc--------------ccccceEEECCccccCCHHHHHHHHhcc--CCEEEEEEEecCCCCCcCcEEEEEECCHHHHH
Confidence            3211              1123689999999999999999999999  999999999885  678999999999999999


Q ss_pred             HHHH-hCCceeCC--eeeEEeecCCCC
Q 022058          270 LALN-CSGMVLGS--QPIRVSPSKTPV  293 (303)
Q Consensus       270 ~Ai~-l~g~~~~g--~~l~v~~a~~~~  293 (303)
                      .|++ |||..+.|  ..|.|.++..+.
T Consensus       146 ~ai~~l~g~~~~g~~~~i~v~~a~~~~  172 (352)
T TIGR01661       146 RAIKTLNGTTPSGCTEPITVKFANNPS  172 (352)
T ss_pred             HHHHHhCCCccCCCceeEEEEECCCCC
Confidence            9998 99999877  678999987664

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

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

Probab=99.97  E-value=4.5e-29  Score=238.21  Aligned_cols=173  Identities=28%  Similarity=0.366  Sum_probs=148.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+.+++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+||.|+|..+.|++|.|.++..
T Consensus        88 ~~~~l~V~nlp~~~~~~~l~~~F~~~G~v~~v~i~~d~~~~~skg~afVeF~~~e~A~~Al~l~g~~~~g~~i~v~~~~~  167 (457)
T TIGR01622        88 DDRTVFVLQLALKARERDLYEFFSKVGKVRDVQCIKDRNSRRSKGVAYVEFYDVESVIKALALTGQMLLGRPIIVQSSQA  167 (457)
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeecCCCCCcceEEEEEECCHHHHHHHHHhCCCEECCeeeEEeecch
Confidence            5778999999999999999999999999999999998764  89999999999999999999999999999999988654


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                      ..........  ..........+|||+|||..+++++|+++|++|  |.|..|.|+.+.  |+++|||||+|.+.++|.+
T Consensus       168 ~~~~~~~~~~--~~~~~~p~~~~l~v~nl~~~~te~~l~~~f~~~--G~i~~v~~~~d~~~g~~~g~afV~f~~~e~A~~  243 (457)
T TIGR01622       168 EKNRAAKAAT--HQPGDIPNFLKLYVGNLHFNITEQELRQIFEPF--GDIEDVQLHRDPETGRSKGFGFIQFHDAEEAKE  243 (457)
T ss_pred             hhhhhhhccc--ccCCCCCCCCEEEEcCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            3211100000  000011235899999999999999999999999  999999999885  5889999999999999999


Q ss_pred             HHH-hCCceeCCeeeEEeecCC
Q 022058          271 ALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       271 Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      |+. |||..|.|+.|.|.|+..
T Consensus       244 A~~~l~g~~i~g~~i~v~~a~~  265 (457)
T TIGR01622       244 ALEVMNGFELAGRPIKVGYAQD  265 (457)
T ss_pred             HHHhcCCcEECCEEEEEEEccC
Confidence            998 999999999999999763

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.

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

Probab=99.96  E-value=3.5e-29  Score=235.51  Aligned_cols=244  Identities=20%  Similarity=0.299  Sum_probs=192.5

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhcccCC--C-
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGR--K-  100 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~--~-  100 (303)
                      -|+|||||..+..++|..+|..||+|..|-+|   .++...+|.|     ..     +.    +|+.|...|..-+  . 
T Consensus       387 vil~kNlpa~t~~~elt~~F~~fG~i~rvllp---~~G~~aiv~f-----l~-----p~----eAr~Afrklaysr~k~~  449 (725)
T KOG0110|consen  387 VILVKNLPAGTLSEELTEAFLRFGEIGRVLLP---PGGTGAIVEF-----LN-----PL----EARKAFRKLAYSRFKSA  449 (725)
T ss_pred             eeeeccCccccccHHHHHHhhcccccceeecC---cccceeeeee-----cC-----cc----chHHHHHHhchhhhccC
Confidence            58999999999999999999999999999776   2334449999     77     66    8888877765500  0 


Q ss_pred             ----------CCC--------------c----hhhh---------hccC-------------CCCCCEEEEcCCCCCCCH
Q 022058          101 ----------RLS--------------G----RAFR---------AQRE-------------DSVRRTVYVSDIDQNITE  130 (303)
Q Consensus       101 ----------~~~--------------~----~~~~---------~~~~-------------~~~~~~l~V~nlp~~~t~  130 (303)
                                .+.              .    +...         .+.+             ....+.|||.||+++++.
T Consensus       450 plyle~aP~dvf~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~  529 (725)
T KOG0110|consen  450 PLYLEWAPEDVFTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTL  529 (725)
T ss_pred             ccccccChhhhccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccch
Confidence                      000              0    0000         0000             001223999999999999


Q ss_pred             HHHHHHhhcCCceeEEEEeeCCCC-----CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCCCCC
Q 022058          131 ERLAGLFSSCGQVVDCRVCGDPHS-----VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPR  204 (303)
Q Consensus       131 ~~l~~~F~~~G~i~~~~i~~~~~~-----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~  204 (303)
                      ++|..+|...|.|.++.|...+..     |.|||||+|.+.++|++|++ |+|+.++|+.|.|..+........  .   
T Consensus       530 e~l~~~F~k~G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~~k~~~~~--g---  604 (725)
T KOG0110|consen  530 EDLEDLFSKQGTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISENKPASTV--G---  604 (725)
T ss_pred             hHHHHHHHhcCeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEeccCcccccc--c---
Confidence            999999999999999988875533     67999999999999999999 999999999999999862211110  0   


Q ss_pred             cccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCC
Q 022058          205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGS  281 (303)
Q Consensus       205 ~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g  281 (303)
                      .........+.|.|+|||+..+..+++.+|+.|  |.|.+|+|+...  +.++|||||.|.++.+|..|+. |.+..|.|
T Consensus       605 K~~~~kk~~tKIlVRNipFeAt~rEVr~LF~aF--GqlksvRlPKK~~k~a~rGF~Fv~f~t~~ea~nA~~al~STHlyG  682 (725)
T KOG0110|consen  605 KKKSKKKKGTKILVRNIPFEATKREVRKLFTAF--GQLKSVRLPKKIGKGAHRGFGFVDFLTPREAKNAFDALGSTHLYG  682 (725)
T ss_pred             cccccccccceeeeeccchHHHHHHHHHHHhcc--cceeeeccchhhcchhhccceeeeccCcHHHHHHHHhhcccceec
Confidence            111112236789999999999999999999999  999999999863  4579999999999999999998 99999999


Q ss_pred             eeeEEeecCC
Q 022058          282 QPIRVSPSKT  291 (303)
Q Consensus       282 ~~l~v~~a~~  291 (303)
                      |+|.+.|++.
T Consensus       683 RrLVLEwA~~  692 (725)
T KOG0110|consen  683 RRLVLEWAKS  692 (725)
T ss_pred             hhhheehhcc
Confidence            9999999975

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

Probab=99.96  E-value=1.4e-28  Score=219.51  Aligned_cols=166  Identities=25%  Similarity=0.367  Sum_probs=144.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCc-ccCC--eeEEE
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGT-MLGY--YPVRV  187 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~-~~~g--~~i~v  187 (303)
                      .+.-.+|||.||..++|.|||++|++||.|.+|.|++|+.+  ++|||||.|.+.++|.+|+. ||.+ .+.|  .+|.|
T Consensus        32 ~~~vKlfVgqIprt~sE~dlr~lFe~yg~V~einl~kDk~t~~s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqv  111 (510)
T KOG0144|consen   32 GSAVKLFVGQIPRTASEKDLRELFEKYGNVYEINLIKDKSTGQSKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQV  111 (510)
T ss_pred             chhhhheeccCCccccHHHHHHHHHHhCceeEEEeecccccCcccceEEEEeccHHHHHHHHHHhhcccccCCCCcceee
Confidence            34566999999999999999999999999999999999987  89999999999999999998 7654 4544  89999


Q ss_pred             eecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHH
Q 022058          188 LPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAE  266 (303)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e  266 (303)
                      ++++...             ++....++|||+-|+..+||.+++.+|.+|  |.|++|.|++|. +.++|||||+|.+.+
T Consensus       112 k~Ad~E~-------------er~~~e~KLFvg~lsK~~te~evr~iFs~f--G~Ied~~ilrd~~~~sRGcaFV~fstke  176 (510)
T KOG0144|consen  112 KYADGER-------------ERIVEERKLFVGMLSKQCTENEVREIFSRF--GHIEDCYILRDPDGLSRGCAFVKFSTKE  176 (510)
T ss_pred             cccchhh-------------hccccchhhhhhhccccccHHHHHHHHHhh--CccchhhheecccccccceeEEEEehHH
Confidence            9886432             111234789999999999999999999999  999999999996 899999999999999


Q ss_pred             HHHHHHH-hCCc-eeCC--eeeEEeecCCCCC
Q 022058          267 SAILALN-CSGM-VLGS--QPIRVSPSKTPVR  294 (303)
Q Consensus       267 ~A~~Ai~-l~g~-~~~g--~~l~v~~a~~~~~  294 (303)
                      .|..||+ |||. .+.|  ..|.|+||.+...
T Consensus       177 ~A~~Aika~ng~~tmeGcs~PLVVkFADtqkd  208 (510)
T KOG0144|consen  177 MAVAAIKALNGTQTMEGCSQPLVVKFADTQKD  208 (510)
T ss_pred             HHHHHHHhhccceeeccCCCceEEEecccCCC
Confidence            9999999 9985 4554  6999999986643

>TIGR01659 sex-lethal sex-lethal family splicing factor

Probab=99.95  E-value=7.2e-28  Score=219.85  Aligned_cols=158  Identities=20%  Similarity=0.328  Sum_probs=132.5

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcc
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFN   96 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~   96 (303)
                      +.+.+|||+|||+++|+++|+++|++||+|++|+|+.|..++.++   ||+|     .+     ++    +|++|+..|+
T Consensus       105 ~~~~~LfVgnLp~~~te~~L~~lF~~~G~V~~v~i~~d~~tg~srGyaFVeF-----~~-----~e----~A~~Ai~~Ln  170 (346)
T TIGR01659       105 NSGTNLIVNYLPQDMTDRELYALFRTIGPINTCRIMRDYKTGYSFGYAFVDF-----GS-----EA----DSQRAIKNLN  170 (346)
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccCcEEEEEE-----cc-----HH----HHHHHHHHcC
Confidence            345579999999999999999999999999999999998766554   9999     88     88    9999999998


Q ss_pred             c----CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHH
Q 022058           97 Q----GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGA  169 (303)
Q Consensus        97 ~----g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A  169 (303)
                      +    +++ .+....  ........++|||+|||+++|+++|+++|+.||.|..|.|+.+..+  ++|||||+|.+.++|
T Consensus       171 G~~l~gr~i~V~~a~--p~~~~~~~~~lfV~nLp~~vtee~L~~~F~~fG~V~~v~i~~d~~tg~~kG~aFV~F~~~e~A  248 (346)
T TIGR01659       171 GITVRNKRLKVSYAR--PGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGQIVQKNILRDKLTGTPRGVAFVRFNKREEA  248 (346)
T ss_pred             CCccCCceeeeeccc--ccccccccceeEEeCCCCcccHHHHHHHHHhcCCEEEEEEeecCCCCccceEEEEEECCHHHH
Confidence            7    222 222111  1112234678999999999999999999999999999999998754  789999999999999


Q ss_pred             HHHHH-hCCcccCC--eeEEEeecCCC
Q 022058          170 RAALN-LGGTMLGY--YPVRVLPSKTA  193 (303)
Q Consensus       170 ~~Ai~-l~g~~~~g--~~i~v~~~~~~  193 (303)
                      ++||+ ||+..+.+  ++|.|.+++..
T Consensus       249 ~~Ai~~lng~~~~g~~~~l~V~~a~~~  275 (346)
T TIGR01659       249 QEAISALNNVIPEGGSQPLTVRLAEEH  275 (346)
T ss_pred             HHHHHHhCCCccCCCceeEEEEECCcc
Confidence            99999 99998875  79999998654

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).

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

Probab=99.94  E-value=3.1e-26  Score=219.55  Aligned_cols=186  Identities=19%  Similarity=0.239  Sum_probs=148.8

Q ss_pred             chHHhhhhccc-------CCCCCCchhh-hhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-Cce
Q 022058           87 NNRRRRNNFNQ-------GRKRLSGRAF-RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLR  157 (303)
Q Consensus        87 ~A~~a~~~~~~-------g~~~~~~~~~-~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G  157 (303)
                      +|.+|+.++++       |......++. +....+...++|||+|||+++++++|+++|+.||.|.+|+|++|..+ ++|
T Consensus        21 ~a~~a~~~~~gy~~~~~~g~r~~g~Pp~~~~~~~p~~~~~lFVgnLp~~~tEd~L~~~F~~~G~I~~vrl~~D~sG~sRG  100 (578)
T TIGR01648        21 AALKALLERTGYTLVQENGQRKYGGPPPGWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPIYELRLMMDFSGQNRG  100 (578)
T ss_pred             HHHHHHHHhhCccccccCCcccCCCCCCcccCCCCCCCCEEEeCCCCCCCCHHHHHHHHHhhCCEEEEEEEECCCCCccc
Confidence            57778777766       2222222221 22233446789999999999999999999999999999999998554 899


Q ss_pred             EEEEEecCHHHHHHHHH-hCCcccC-CeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhh
Q 022058          158 FAFVEFADEHGARAALN-LGGTMLG-YYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFE  235 (303)
Q Consensus       158 ~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~  235 (303)
                      ||||+|.+.++|++||+ ||+..+. |+.|.|.++.                    ..++|||+|||..+++++|.++|+
T Consensus       101 faFV~F~~~e~A~~Ai~~lng~~i~~Gr~l~V~~S~--------------------~~~rLFVgNLP~~~TeeeL~eeFs  160 (578)
T TIGR01648       101 YAFVTFCGKEEAKEAVKLLNNYEIRPGRLLGVCISV--------------------DNCRLFVGGIPKNKKREEILEEFS  160 (578)
T ss_pred             eEEEEeCCHHHHHHHHHHcCCCeecCCccccccccc--------------------cCceeEeecCCcchhhHHHHHHhh
Confidence            99999999999999999 9999885 7887777642                    237899999999999999999999


Q ss_pred             hhcCcceeEEEEecC---CCCcccEEEEEEcCHHHHHHHHH-hC-C-ceeCCeeeEEeecCCCC
Q 022058          236 AACGGEVTRLRLLGD---HVHSTRIAFVEFAVAESAILALN-CS-G-MVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       236 ~~~~G~i~~v~i~~d---~~~~~g~afV~f~~~e~A~~Ai~-l~-g-~~~~g~~l~v~~a~~~~  293 (303)
                      +++ ..+..+.+...   .++++|||||+|.+.++|..|+. |+ + ..+.|+.|.|.|+.+..
T Consensus       161 kv~-egvv~vIv~~~~~~kgKnRGFAFVeF~s~edAa~AirkL~~gki~l~Gr~I~VdwA~p~~  223 (578)
T TIGR01648       161 KVT-EGVVDVIVYHSAADKKKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHVIAVDWAEPEE  223 (578)
T ss_pred             ccc-CCceEEEEeccccccCccCceEEEEcCCHHHHHHHHHHhhccceEecCceEEEEeecccc
Confidence            983 24555554432   35789999999999999999997 64 3 46889999999998654

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.

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

Probab=99.94  E-value=8.5e-27  Score=196.05  Aligned_cols=166  Identities=26%  Similarity=0.445  Sum_probs=149.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .+.+++|.|.-||..+|+++||.+|...|+|++|++++|+-+  |.|||||.|-++++|++|+. |||..+..+.|+|.+
T Consensus        38 ~~skTNLIvNYLPQ~MTqdE~rSLF~SiGeiEScKLvRDKitGqSLGYGFVNYv~p~DAe~AintlNGLrLQ~KTIKVSy  117 (360)
T KOG0145|consen   38 DESKTNLIVNYLPQNMTQDELRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYVRPKDAEKAINTLNGLRLQNKTIKVSY  117 (360)
T ss_pred             CcccceeeeeecccccCHHHHHHHhhcccceeeeeeeeccccccccccceeeecChHHHHHHHhhhcceeeccceEEEEe
Confidence            345677999999999999999999999999999999999876  89999999999999999998 999999999999999


Q ss_pred             cCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHH
Q 022058          190 SKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAES  267 (303)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~  267 (303)
                      +++           +....   ....|||.+||...|..+|.++|++|  |.|..-+|+.|.  |.++|.|||.|...++
T Consensus       118 ARP-----------Ss~~I---k~aNLYvSGlPktMtqkelE~iFs~f--GrIItSRiL~dqvtg~srGVgFiRFDKr~E  181 (360)
T KOG0145|consen  118 ARP-----------SSDSI---KDANLYVSGLPKTMTQKELEQIFSPF--GRIITSRILVDQVTGLSRGVGFIRFDKRIE  181 (360)
T ss_pred             ccC-----------Chhhh---cccceEEecCCccchHHHHHHHHHHh--hhhhhhhhhhhcccceecceeEEEecchhH
Confidence            853           33332   33789999999999999999999999  999999999886  7899999999999999


Q ss_pred             HHHHHH-hCCceeCC--eeeEEeecCCCCC
Q 022058          268 AILALN-CSGMVLGS--QPIRVSPSKTPVR  294 (303)
Q Consensus       268 A~~Ai~-l~g~~~~g--~~l~v~~a~~~~~  294 (303)
                      |..||. |||..-.|  -.|.|+|++.|..
T Consensus       182 Ae~AIk~lNG~~P~g~tepItVKFannPsq  211 (360)
T KOG0145|consen  182 AEEAIKGLNGQKPSGCTEPITVKFANNPSQ  211 (360)
T ss_pred             HHHHHHhccCCCCCCCCCCeEEEecCCccc
Confidence            999999 99988765  4899999987753

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

Probab=99.94  E-value=7.2e-26  Score=218.94  Aligned_cols=172  Identities=19%  Similarity=0.270  Sum_probs=138.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC------------CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSC------------GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGY  182 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~------------G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g  182 (303)
                      ..++|||||||+.+|+++|+++|..+            +.|..+.+..    .+|||||+|.+.++|..||.|||..+.|
T Consensus       174 ~~r~lyVgnLp~~~t~~~l~~~F~~~~~~~~~~~~~~~~~v~~~~~~~----~kg~afVeF~~~e~A~~Al~l~g~~~~g  249 (509)
T TIGR01642       174 QARRLYVGGIPPEFVEEAVVDFFNDLMIATGYHKAEDGKHVSSVNINK----EKNFAFLEFRTVEEATFAMALDSIIYSN  249 (509)
T ss_pred             cccEEEEeCCCCCCCHHHHHHHHHHHHHhcCCCCCCCCCceEEEEECC----CCCEEEEEeCCHHHHhhhhcCCCeEeeC
Confidence            57889999999999999999999964            3455555432    4689999999999999999999999999


Q ss_pred             eeEEEeecCCCCCCCCC----CC-CC-----C-----cccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEE
Q 022058          183 YPVRVLPSKTAILPVNP----TF-LP-----R-----SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRL  247 (303)
Q Consensus       183 ~~i~v~~~~~~~~~~~~----~~-~~-----~-----~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i  247 (303)
                      ++|.|............    .. .+     .     ..........+|||+|||..+++++|+++|+.|  |.|..+.|
T Consensus       250 ~~l~v~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~~~~  327 (509)
T TIGR01642       250 VFLKIRRPHDYIPVPQITPEVSQKNPDDNAKNVEKLVNSTTVLDSKDRIYIGNLPLYLGEDQIKELLESF--GDLKAFNL  327 (509)
T ss_pred             ceeEecCccccCCccccCCCCCCCCCcccccccccccccccCCCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEE
Confidence            99999865432210000    00 00     0     000112235789999999999999999999999  99999999


Q ss_pred             ecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          248 LGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       248 ~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      +.+.  |.++|||||+|.+.++|..|+. |||..|+|+.|.|.++...
T Consensus       328 ~~~~~~g~~~g~afv~f~~~~~a~~A~~~l~g~~~~~~~l~v~~a~~~  375 (509)
T TIGR01642       328 IKDIATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVG  375 (509)
T ss_pred             EecCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECccC
Confidence            9884  7899999999999999999998 9999999999999998543

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

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

Probab=99.94  E-value=7.9e-27  Score=186.77  Aligned_cols=165  Identities=25%  Similarity=0.348  Sum_probs=146.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ...+||||||+..++++.|+++|-+.|+|.++++++|..+  .+||||++|.++++|+-|++ ||...+-|++|+|..+.
T Consensus         8 qd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef~~eedadYAikiln~VkLYgrpIrv~kas   87 (203)
T KOG0131|consen    8 QDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEFRTEEDADYAIKILNMVKLYGRPIRVNKAS   87 (203)
T ss_pred             CCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEEechhhhHHHHHHHHHHHhcCceeEEEecc
Confidence            5688999999999999999999999999999999999876  69999999999999999999 99999999999999874


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEE-EEecCC--CCcccEEEEEEcCHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRL-RLLGDH--VHSTRIAFVEFAVAESA  268 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v-~i~~d~--~~~~g~afV~f~~~e~A  268 (303)
                      .-.             .....+..|||+||.+.+++..|++.|+.|  |.+.+. +|++|+  |.++|+|||.|.+.+.+
T Consensus        88 ~~~-------------~nl~vganlfvgNLd~~vDe~~L~dtFsaf--G~l~~~P~i~rd~~tg~~~~~g~i~~~sfeas  152 (203)
T KOG0131|consen   88 AHQ-------------KNLDVGANLFVGNLDPEVDEKLLYDTFSAF--GVLISPPKIMRDPDTGNPKGFGFINYASFEAS  152 (203)
T ss_pred             ccc-------------ccccccccccccccCcchhHHHHHHHHHhc--cccccCCcccccccCCCCCCCeEEechhHHHH
Confidence            111             111233789999999999999999999999  988874 788885  68999999999999999


Q ss_pred             HHHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          269 ILALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       269 ~~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      .+|+. |||..++++++.|+++.....
T Consensus       153 d~ai~s~ngq~l~nr~itv~ya~k~~~  179 (203)
T KOG0131|consen  153 DAAIGSMNGQYLCNRPITVSYAFKKDT  179 (203)
T ss_pred             HHHHHHhccchhcCCceEEEEEEecCC
Confidence            99999 999999999999999865543

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

Probab=99.94  E-value=2.7e-25  Score=199.41  Aligned_cols=167  Identities=22%  Similarity=0.299  Sum_probs=146.7

Q ss_pred             hhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccC-Ce
Q 022058          108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLG-YY  183 (303)
Q Consensus       108 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~  183 (303)
                      +....+...+.||||.||.++.|++|.-+|+..|+|.+++|+.|+.+  +||||||+|.+.++|++||+ ||+.+|. |+
T Consensus        75 weg~~p~~G~EVfvGkIPrD~~EdeLvplfEkiG~I~elRLMmD~~sG~nRGYAFVtf~~Ke~Aq~Aik~lnn~Eir~GK  154 (506)
T KOG0117|consen   75 WEGPPPPRGCEVFVGKIPRDVFEDELVPLFEKIGKIYELRLMMDPFSGDNRGYAFVTFCTKEEAQEAIKELNNYEIRPGK  154 (506)
T ss_pred             ccCCCCCCCceEEecCCCccccchhhHHHHHhccceeeEEEeecccCCCCcceEEEEeecHHHHHHHHHHhhCccccCCC
Confidence            44445567889999999999999999999999999999999999654  89999999999999999999 9999996 99


Q ss_pred             eEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEE
Q 022058          184 PVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFV  260 (303)
Q Consensus       184 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV  260 (303)
                      .|.|.-+.                    ..+.|||+|+|.++++++|.+.|++.. -.|++|.|..++   .+.+|||||
T Consensus       155 ~igvc~Sv--------------------an~RLFiG~IPK~k~keeIlee~~kVt-eGVvdVivy~~p~dk~KNRGFaFv  213 (506)
T KOG0117|consen  155 LLGVCVSV--------------------ANCRLFIGNIPKTKKKEEILEEMKKVT-EGVVDVIVYPSPDDKTKNRGFAFV  213 (506)
T ss_pred             EeEEEEee--------------------ecceeEeccCCccccHHHHHHHHHhhC-CCeeEEEEecCccccccccceEEE
Confidence            99998763                    237899999999999999999999983 367888887764   679999999


Q ss_pred             EEcCHHHHHHHHH--hCC-ceeCCeeeEEeecCCCCCC
Q 022058          261 EFAVAESAILALN--CSG-MVLGSQPIRVSPSKTPVRP  295 (303)
Q Consensus       261 ~f~~~e~A~~Ai~--l~g-~~~~g~~l~v~~a~~~~~~  295 (303)
                      +|.++.+|..|.+  |+| .++-|+.+.|.||.|...+
T Consensus       214 eYe~H~~Aa~aRrKl~~g~~klwgn~~tVdWAep~~e~  251 (506)
T KOG0117|consen  214 EYESHRAAAMARRKLMPGKIKLWGNAITVDWAEPEEEP  251 (506)
T ss_pred             EeecchhHHHHHhhccCCceeecCCcceeeccCcccCC
Confidence            9999999999997  555 5789999999999987654

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

Probab=99.93  E-value=2e-25  Score=188.84  Aligned_cols=153  Identities=21%  Similarity=0.292  Sum_probs=132.9

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      -+||+.|...++-++||+.|.+||+|.+++|++|..+..++   ||.|     ..     .+    +|+.||..|||   
T Consensus        64 hvfvgdls~eI~~e~lr~aF~pFGevS~akvirD~~T~KsKGYgFVSf-----~~-----k~----dAEnAI~~MnGqWl  129 (321)
T KOG0148|consen   64 HVFVGDLSPEIDNEKLREAFAPFGEVSDAKVIRDMNTGKSKGYGFVSF-----PN-----KE----DAENAIQQMNGQWL  129 (321)
T ss_pred             eEEehhcchhcchHHHHHHhccccccccceEeecccCCcccceeEEec-----cc-----hH----HHHHHHHHhCCeee
Confidence            38999999999999999999999999999999999977766   9999     77     77    99999999998   


Q ss_pred             CCC--CCCchhhhhc--------------cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEE
Q 022058           98 GRK--RLSGRAFRAQ--------------REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFV  161 (303)
Q Consensus        98 g~~--~~~~~~~~~~--------------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV  161 (303)
                      |++  +..|..++..              +....+++||||||+.-+++++||+.|+.||+|.+|++.++.    ||+||
T Consensus       130 G~R~IRTNWATRKp~e~n~~~ltfdeV~NQssp~NtsVY~G~I~~~lte~~mr~~Fs~fG~I~EVRvFk~q----GYaFV  205 (321)
T KOG0148|consen  130 GRRTIRTNWATRKPSEMNGKPLTFDEVYNQSSPDNTSVYVGNIASGLTEDLMRQTFSPFGPIQEVRVFKDQ----GYAFV  205 (321)
T ss_pred             ccceeeccccccCccccCCCCccHHHHhccCCCCCceEEeCCcCccccHHHHHHhcccCCcceEEEEeccc----ceEEE
Confidence            555  3333222211              123468899999999999999999999999999999999875    79999


Q ss_pred             EecCHHHHHHHHH-hCCcccCCeeEEEeecCCCC
Q 022058          162 EFADEHGARAALN-LGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       162 ~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~  194 (303)
                      .|++.|+|.+||. +|+.+|.|..+++.|.+...
T Consensus       206 rF~tkEaAahAIv~mNntei~G~~VkCsWGKe~~  239 (321)
T KOG0148|consen  206 RFETKEAAAHAIVQMNNTEIGGQLVRCSWGKEGD  239 (321)
T ss_pred             EecchhhHHHHHHHhcCceeCceEEEEeccccCC
Confidence            9999999999998 99999999999999986543

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

Probab=99.93  E-value=2.1e-25  Score=188.31  Aligned_cols=182  Identities=23%  Similarity=0.381  Sum_probs=152.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcc-cCC--eeEEE
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTM-LGY--YPVRV  187 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~-~~g--~~i~v  187 (303)
                      ..+++.||||.|...-.|+|++.+|..||.|++|.+.+...+ +|||+||.|.+..+|..||. |||.. +-|  ..|.|
T Consensus        16 g~~drklfvgml~kqq~e~dvrrlf~pfG~~~e~tvlrg~dg~sKGCAFVKf~s~~eAqaAI~aLHgSqTmpGASSSLVV   95 (371)
T KOG0146|consen   16 GGDDRKLFVGMLNKQQSEDDVRRLFQPFGNIEECTVLRGPDGNSKGCAFVKFSSHAEAQAAINALHGSQTMPGASSSLVV   95 (371)
T ss_pred             CccchhhhhhhhcccccHHHHHHHhcccCCcceeEEecCCCCCCCCceEEEeccchHHHHHHHHhcccccCCCCccceEE
Confidence            336789999999999999999999999999999999998876 99999999999999999998 99854 444  78899


Q ss_pred             eecCCCCC------------------------------------------------------------------------
Q 022058          188 LPSKTAIL------------------------------------------------------------------------  195 (303)
Q Consensus       188 ~~~~~~~~------------------------------------------------------------------------  195 (303)
                      +++++.+.                                                                        
T Consensus        96 K~ADTdkER~lRRMQQma~qlGm~~Pl~l~~g~~~ay~qalmQqQa~~~at~~~~~L~p~~~~~~~~mQ~~aA~~angl~  175 (371)
T KOG0146|consen   96 KFADTDKERTLRRMQQMAGQLGMFNPLALPFGAYGAYAQALMQQQAALLATVAGPYLSPMAAFAAAQMQQMAALNANGLA  175 (371)
T ss_pred             EeccchHHHHHHHHHHHHHHhcccCccccccchhHHHHHHHHHHHHHHHHhhcccccChhhhhHHHHHHHHHHHhhcccc
Confidence            98865432                                                                        


Q ss_pred             --CCCCC-------------------------CCC---C-----------------------------------------
Q 022058          196 --PVNPT-------------------------FLP---R-----------------------------------------  204 (303)
Q Consensus       196 --~~~~~-------------------------~~~---~-----------------------------------------  204 (303)
                        +..|.                         +.+   .                                         
T Consensus       176 A~Pv~p~s~~~~pp~~~a~~~~~~~A~~g~ng~~~l~~q~~gqpa~~~vy~ng~~pypaQsp~va~~lq~a~~g~~~Y~A  255 (371)
T KOG0146|consen  176 AAPVTPASGGSTPPGIGATAVPGIPAPIGVNGFTGLPPQPNGQPAAEAVYANGLHPYPAQSPTVADPLQQAYAGVQQYAA  255 (371)
T ss_pred             cCCcCccccCCCCCcccccccCCcccccccccccCCCCCCCCCcchhHHhhcCCccCCCCCccccchhhhhhhhHHHHhh
Confidence              00000                         000   0                                         


Q ss_pred             ---------------------cccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEE
Q 022058          205 ---------------------SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVE  261 (303)
Q Consensus       205 ---------------------~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~  261 (303)
                                           ......+.+++|||..||..+.+.+|.++|-+|  |.|++.+|..|.  +.||+||||.
T Consensus       256 aypaays~v~~~~pq~p~~~~qqqreGPeGCNlFIYHLPQEFgDaEliQmF~PF--GhivSaKVFvDRATNQSKCFGFVS  333 (371)
T KOG0146|consen  256 AYPAAYSPISQAFPQPPPLLPQQQREGPEGCNLFIYHLPQEFGDAELIQMFLPF--GHIVSAKVFVDRATNQSKCFGFVS  333 (371)
T ss_pred             hcchhhhhhhhcCCCCcchhhhhhhcCCCcceEEEEeCchhhccHHHHHHhccc--cceeeeeeeehhccccccceeeEe
Confidence                                 000123457899999999999999999999999  999999999886  7899999999


Q ss_pred             EcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCCC
Q 022058          262 FAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRPR  296 (303)
Q Consensus       262 f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~r  296 (303)
                      |.++.+|+.||+ |||++|+.++|+|.+.+|....|
T Consensus       334 fDNp~SaQaAIqAMNGFQIGMKRLKVQLKRPkdanR  369 (371)
T KOG0146|consen  334 FDNPASAQAAIQAMNGFQIGMKRLKVQLKRPKDANR  369 (371)
T ss_pred             cCCchhHHHHHHHhcchhhhhhhhhhhhcCccccCC
Confidence            999999999999 99999999999999998877655

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

Probab=99.92  E-value=1.5e-24  Score=198.68  Aligned_cols=176  Identities=22%  Similarity=0.260  Sum_probs=148.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..+|||++||++++.++|.++|+.+|+|..|.++.+.+.  ++|||||+|+-.+++++|+. .++..+.||.|.|..+..
T Consensus         5 g~TlfV~~lp~~~~~~qL~e~FS~vGPik~~~vVt~~gs~~~RGfgfVtFam~ED~qrA~~e~~~~kf~Gr~l~v~~A~~   84 (678)
T KOG0127|consen    5 GATLFVSRLPFSSTGEQLEEFFSYVGPIKHAVVVTNKGSSEKRGFGFVTFAMEEDVQRALAETEQSKFEGRILNVDPAKK   84 (678)
T ss_pred             CceEEEecCCCccchhHHHHhhhcccCcceeEEecCCCcccccCccceeeehHhHHHHHHHHhhcCcccceecccccccc
Confidence            489999999999999999999999999999999998886  79999999999999999998 999999999999998755


Q ss_pred             CCCCC-----CCC-----CCCCcc--cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEE
Q 022058          193 AILPV-----NPT-----FLPRSE--DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAF  259 (303)
Q Consensus       193 ~~~~~-----~~~-----~~~~~~--~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~af  259 (303)
                      ...+.     .+.     ......  .....+-..|.|+|||+.+.+.+|+.+|+.|  |.|..|.|++.. |+--||||
T Consensus        85 R~r~e~~~~~e~~~veK~~~q~~~~k~~v~~~k~rLIIRNLPf~~k~~dLk~vFs~~--G~V~Ei~IP~k~dgklcGFaF  162 (678)
T KOG0127|consen   85 RARSEEVEKGENKAVEKPIEQKRPTKAKVDLPKWRLIIRNLPFKCKKPDLKNVFSNF--GKVVEIVIPRKKDGKLCGFAF  162 (678)
T ss_pred             cccchhcccccchhhhcccccCCcchhhccCccceEEeecCCcccCcHHHHHHHhhc--ceEEEEEcccCCCCCccceEE
Confidence            43211     000     000000  0012235789999999999999999999999  999999999875 44449999


Q ss_pred             EEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCC
Q 022058          260 VEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       260 V~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~  293 (303)
                      |+|....+|..|++ +||..|+||.|-|.||-+..
T Consensus       163 V~fk~~~dA~~Al~~~N~~~i~gR~VAVDWAV~Kd  197 (678)
T KOG0127|consen  163 VQFKEKKDAEKALEFFNGNKIDGRPVAVDWAVDKD  197 (678)
T ss_pred             EEEeeHHHHHHHHHhccCceecCceeEEeeecccc
Confidence            99999999999999 99999999999999997543

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

Probab=99.92  E-value=5e-24  Score=186.93  Aligned_cols=250  Identities=17%  Similarity=0.255  Sum_probs=192.3

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      .|+|+-+.|+..|+.||..|.+||+|.+|.+..|..+.+.+   ||+|     .-     +|    .|+-|.++||+   
T Consensus       115 RvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEY-----Ev-----PE----aAqLAlEqMNg~ml  180 (544)
T KOG0124|consen  115 RVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEY-----EV-----PE----AAQLALEQMNGQML  180 (544)
T ss_pred             heeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEE-----eC-----cH----HHHHHHHHhccccc
Confidence            58999999999999999999999999999999999755444   9999     88     88    99999999998   


Q ss_pred             -CCC-CCCchhhhhc---------cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEec
Q 022058           98 -GRK-RLSGRAFRAQ---------REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFA  164 (303)
Q Consensus        98 -g~~-~~~~~~~~~~---------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~  164 (303)
                       ||. ++..+....+         .+...-..|||..+.++++++||+..|+.||+|.+|.+.+++.+  ++|||||+|.
T Consensus       181 GGRNiKVgrPsNmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAFG~I~~C~LAr~pt~~~HkGyGfiEy~  260 (544)
T KOG0124|consen  181 GGRNIKVGRPSNMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAFGEIVKCQLARAPTGRGHKGYGFIEYN  260 (544)
T ss_pred             cCccccccCCCCCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhhcceeeEEeeccCCCCCccceeeEEec
Confidence             443 3332222111         11223456999999999999999999999999999999998865  8999999999


Q ss_pred             CHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCC---------------------------------------------C
Q 022058          165 DEHGARAALN-LGGTMLGYYPVRVLPSKTAILPV---------------------------------------------N  198 (303)
Q Consensus       165 ~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~---------------------------------------------~  198 (303)
                      +..+...||. ||-..++|..|+|..+-+.....                                             +
T Consensus       261 n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~aLl~Pat~s~~P~aaaVAaAAaTAKi~A~eAvAg~avlg~~G~~~~vS  340 (544)
T KOG0124|consen  261 NLQSQSEAIASMNLFDLGGQYLRVGKCVTPPDALLQPATVSAIPAAAAVAAAAATAKIMAAEAVAGSAVLGTVGAPGLVS  340 (544)
T ss_pred             cccchHHHhhhcchhhcccceEecccccCCCchhcCCCCcccCchHHHHHHHHHHHHHHHHHHhccCCcccccCCccccC
Confidence            9999999998 99999999999998753321100                                             0


Q ss_pred             -------------------------------CCCCCCc--------------------------cc--------------
Q 022058          199 -------------------------------PTFLPRS--------------------------ED--------------  207 (303)
Q Consensus       199 -------------------------------~~~~~~~--------------------------~~--------------  207 (303)
                                                     ++..|..                          +.              
T Consensus       341 pA~~aa~p~~~l~qa~~a~~~pgvi~~vtP~~P~iP~~i~p~g~v~P~LA~ppT~g~L~kkkeKe~eelqpkl~~~~~L~  420 (544)
T KOG0124|consen  341 PAPRAAQPLGTLPQAVMAAQAPGVITGVTPARPPIPVTIPPVGVVNPILASPPTLGLLEKKKEKEEEELQPKLERPEMLS  420 (544)
T ss_pred             ccccccCCCCCccccchhccCCceeccCCCCCCCCCccCCCcceechhhcCCCchhhcchhhhhhHhhhcccccCHHHhh
Confidence                                           0000000                          00              


Q ss_pred             --------------------ccccccceEEEcCC--CCCCC---HHHHHHHhhhhcCcceeEEEEecCCCCc------cc
Q 022058          208 --------------------EREMCSRTVYCTNI--DKKVP---QAEVKQFFEAACGGEVTRLRLLGDHVHS------TR  256 (303)
Q Consensus       208 --------------------~~~~~~~~l~V~nL--~~~~t---~~~L~~~F~~~~~G~i~~v~i~~d~~~~------~g  256 (303)
                                          -+...++.+.++|+  |.+++   +.+|++.|.+|  |.|.+|.|...+...      --
T Consensus       421 ~QE~msI~G~sARhlvMqkLmR~~~S~VivLRNMV~P~DiDe~LegEi~EECgKf--G~V~rViI~nekq~e~edaeiiV  498 (544)
T KOG0124|consen  421 EQEHMSISGSSARHLVMQKLMRKQESTVIVLRNMVDPKDIDEDLEGEITEECGKF--GAVNRVIIYNEKQGEEEDAEIIV  498 (544)
T ss_pred             hhhCccccCccHHHHHHHHHhccccCcEEEEeccCChhhhhhHHHHHHHHHHhcc--cceeEEEEEecccccccchhhhh
Confidence                                01223456778887  44554   46899999999  999999998764211      22


Q ss_pred             EEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          257 IAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       257 ~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      -.||+|+...++.+|++ |||+.|+|+++.....
T Consensus       499 KIFVefS~~~e~~rak~ALdGRfFgGr~VvAE~Y  532 (544)
T KOG0124|consen  499 KIFVEFSIASETHRAKQALDGRFFGGRKVVAEVY  532 (544)
T ss_pred             eeeeeechhhHHHHHHHhhccceecCceeehhhh
Confidence            58999999999999999 9999999999876654

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

Probab=99.91  E-value=1.6e-24  Score=185.02  Aligned_cols=147  Identities=26%  Similarity=0.434  Sum_probs=135.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAIL  195 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~  195 (303)
                      ..|||||||..+++++|+.+|++||.|.+|.|+++      ||||+.++...|..||. ||+..|.|..|.|+.++.+  
T Consensus         3 ~KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKN------YgFVHiEdktaaedairNLhgYtLhg~nInVeaSksK--   74 (346)
T KOG0109|consen    3 VKLFIGNLPREATEQELRSLFEQYGKVLECDIVKN------YGFVHIEDKTAAEDAIRNLHGYTLHGVNINVEASKSK--   74 (346)
T ss_pred             cchhccCCCcccchHHHHHHHHhhCceEeeeeecc------cceEEeecccccHHHHhhcccceecceEEEEEecccc--
Confidence            35899999999999999999999999999999863      89999999999999999 9999999999999987543  


Q ss_pred             CCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h
Q 022058          196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C  274 (303)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l  274 (303)
                                    +....+|+|+|+.+.++.++|+..|++|  |.|..|.|++|      |+||.|.-.++|..|+. |
T Consensus        75 --------------sk~stkl~vgNis~tctn~ElRa~fe~y--gpviecdivkd------y~fvh~d~~eda~~air~l  132 (346)
T KOG0109|consen   75 --------------SKASTKLHVGNISPTCTNQELRAKFEKY--GPVIECDIVKD------YAFVHFDRAEDAVEAIRGL  132 (346)
T ss_pred             --------------CCCccccccCCCCccccCHHHhhhhccc--CCceeeeeecc------eeEEEEeeccchHHHHhcc
Confidence                          1244789999999999999999999999  99999999987      89999999999999998 9


Q ss_pred             CCceeCCeeeEEeecCCCC
Q 022058          275 SGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       275 ~g~~~~g~~l~v~~a~~~~  293 (303)
                      ||.++.|++++|..+....
T Consensus       133 ~~~~~~gk~m~vq~stsrl  151 (346)
T KOG0109|consen  133 DNTEFQGKRMHVQLSTSRL  151 (346)
T ss_pred             cccccccceeeeeeecccc
Confidence            9999999999999987544

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

Probab=99.91  E-value=2.4e-24  Score=188.91  Aligned_cols=169  Identities=25%  Similarity=0.407  Sum_probs=149.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      .-|.||||.|.+++.|+.||..|..||+|.+|.+.+|+-+  ++||+||+|+-++.|+.|++ |||..++||.|+|....
T Consensus       112 iMcRvYVGSIsfEl~EDtiR~AF~PFGPIKSInMSWDp~T~kHKgFAFVEYEvPEaAqLAlEqMNg~mlGGRNiKVgrPs  191 (544)
T KOG0124|consen  112 IMCRVYVGSISFELREDTIRRAFDPFGPIKSINMSWDPATGKHKGFAFVEYEVPEAAQLALEQMNGQMLGGRNIKVGRPS  191 (544)
T ss_pred             HhHheeeeeeEEEechHHHHhhccCCCCcceeecccccccccccceEEEEEeCcHHHHHHHHHhccccccCccccccCCC
Confidence            4678999999999999999999999999999999999976  89999999999999999999 99999999999998532


Q ss_pred             CCCCCCCCCCCCCccc------ccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEc
Q 022058          192 TAILPVNPTFLPRSED------EREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFA  263 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~------~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~  263 (303)
                               ..+...+      +.......|||..++++++++||+..|+-|  |+|.+|.+.+++  +..+||||++|.
T Consensus       192 ---------NmpQAQpiID~vqeeAk~fnRiYVaSvHpDLSe~DiKSVFEAF--G~I~~C~LAr~pt~~~HkGyGfiEy~  260 (544)
T KOG0124|consen  192 ---------NMPQAQPIIDMVQEEAKKFNRIYVASVHPDLSETDIKSVFEAF--GEIVKCQLARAPTGRGHKGYGFIEYN  260 (544)
T ss_pred             ---------CCcccchHHHHHHHHHHhhheEEeeecCCCccHHHHHHHHHhh--cceeeEEeeccCCCCCccceeeEEec
Confidence                     1122111      112345789999999999999999999999  999999999996  578999999999


Q ss_pred             CHHHHHHHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          264 VAESAILALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       264 ~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      +..+...|+. ||-+.++|+.|+|..+-+|+.
T Consensus       261 n~qs~~eAiasMNlFDLGGQyLRVGk~vTPP~  292 (544)
T KOG0124|consen  261 NLQSQSEAIASMNLFDLGGQYLRVGKCVTPPD  292 (544)
T ss_pred             cccchHHHhhhcchhhcccceEecccccCCCc
Confidence            9999999998 999999999999998866543

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

Probab=99.91  E-value=7.3e-24  Score=194.96  Aligned_cols=247  Identities=16%  Similarity=0.193  Sum_probs=174.8

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      ++|+--|.-..+..+|.++|+.+|+|.+|+++.|+....++   ||+|     ..     .+    ....|+ .+.|   
T Consensus       181 tvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef-----~D-----~~----sVp~ai-aLsGqrl  245 (549)
T KOG0147|consen  181 TVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEF-----CD-----EQ----SVPLAI-ALSGQRL  245 (549)
T ss_pred             HHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEE-----ec-----cc----chhhHh-hhcCCcc
Confidence            46777777778899999999999999999999999877776   9999     44     22    122222 2222   


Q ss_pred             -CCCCCCchhh-----------hhc-cC-CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEE
Q 022058           98 -GRKRLSGRAF-----------RAQ-RE-DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFV  161 (303)
Q Consensus        98 -g~~~~~~~~~-----------~~~-~~-~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV  161 (303)
                       |.+.+..+..           ..+ .. ...-..||||||.+++++++|+.+|+.||.|+.|.++.|..+  ++|||||
T Consensus       246 lg~pv~vq~sEaeknr~a~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepfg~Ie~v~l~~d~~tG~skgfGfi  325 (549)
T KOG0147|consen  246 LGVPVIVQLSEAEKNRAANASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPFGKIENVQLTKDSETGRSKGFGFI  325 (549)
T ss_pred             cCceeEecccHHHHHHHHhccccccccccccchhhhhhcccccCchHHHHhhhccCcccceeeeeccccccccccCcceE
Confidence             3221100000           000 00 001112999999999999999999999999999999999744  8999999


Q ss_pred             EecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCC--C----------CCCCCc-----------------------
Q 022058          162 EFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVN--P----------TFLPRS-----------------------  205 (303)
Q Consensus       162 ~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~--~----------~~~~~~-----------------------  205 (303)
                      +|.+.++|.+|+. |||.++-|+.|+|...........  .          ...+..                       
T Consensus       326 ~f~~~~~ar~a~e~lngfelAGr~ikV~~v~~r~~~~~a~~~~~d~D~~d~~gl~~~~~g~~Ql~~kla~~~~~~~~s~~  405 (549)
T KOG0147|consen  326 TFVNKEDARKALEQLNGFELAGRLIKVSVVTERVDTKEAAVTQFDFDEDDRQGLSLGSGGRNQLMAKLAEGKGRSLPSTA  405 (549)
T ss_pred             EEecHHHHHHHHHHhccceecCceEEEEEeeeecccccccccccccchhhccccccccccHHHHHHHHhccCCccccchh
Confidence            9999999999998 999999999999976422111000  0          000000                       


Q ss_pred             -----------------------ccccc-------cccceEEEcCC--CCCCC--------HHHHHHHhhhhcCcceeEE
Q 022058          206 -----------------------EDERE-------MCSRTVYCTNI--DKKVP--------QAEVKQFFEAACGGEVTRL  245 (303)
Q Consensus       206 -----------------------~~~~~-------~~~~~l~V~nL--~~~~t--------~~~L~~~F~~~~~G~i~~v  245 (303)
                                             .....       .+..++.+.|+  |.+.|        .+|+.+.+.+|  |.|..|
T Consensus       406 ~~~l~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~i~t~C~lL~nMFdpstete~n~d~eI~edV~Eec~k~--g~v~hi  483 (549)
T KOG0147|consen  406 ISALLLLAKLASAAQFNGVVRVRSVDPADASPAFDIPTQCLLLSNMFDPSTETEPNWDQEIREDVIEECGKH--GKVCHI  483 (549)
T ss_pred             hhHHHhccccchHHhhcCCcCccccCccccccccCCccHHHHHhhcCCcccccCcchhhHHHHHHHHHHHhc--CCeeEE
Confidence                                   00001       22334555554  22222        37888999999  999999


Q ss_pred             EEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          246 RLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       246 ~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      .|.+..   -|+.||.|.+.++|..|+. |||.+|.|+.|+..|-.
T Consensus       484 ~vd~ns---~g~VYvrc~s~~~A~~a~~alhgrWF~gr~Ita~~~~  526 (549)
T KOG0147|consen  484 FVDKNS---AGCVYVRCPSAEAAGTAVKALHGRWFAGRMITAKYLP  526 (549)
T ss_pred             EEccCC---CceEEEecCcHHHHHHHHHHHhhhhhccceeEEEEee
Confidence            886553   2799999999999999999 99999999999998753

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

Probab=99.89  E-value=3.2e-23  Score=166.14  Aligned_cols=159  Identities=19%  Similarity=0.328  Sum_probs=134.7

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCC-Cc--eeeeecchhhhhhchhhhccccchHHhhhhcc
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHT-DH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFN   96 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~-~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~   96 (303)
                      |..++|||+||+..+|++-|.+||-+.|||+++++|+|+-+.. .+  |++|     .+     .|    +|..|++-||
T Consensus         7 nqd~tiyvgnld~kvs~~~l~EL~iqagpVv~i~iPkDrv~~~~qGygF~Ef-----~~-----ee----dadYAikiln   72 (203)
T KOG0131|consen    7 NQDATLYVGNLDEKVSEELLYELFIQAGPVVNLHIPKDRVTQKHQGYGFAEF-----RT-----EE----DADYAIKILN   72 (203)
T ss_pred             CCCceEEEecCCHHHHHHHHHHHHHhcCceeeeecchhhhcccccceeEEEE-----ec-----hh----hhHHHHHHHH
Confidence            4556899999999999999999999999999999999997653 33  9999     88     88    9999999998


Q ss_pred             c----CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEE-EEeeCCCC--CceEEEEEecCHHH
Q 022058           97 Q----GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHS--VLRFAFVEFADEHG  168 (303)
Q Consensus        97 ~----g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~-~i~~~~~~--~~G~~fV~f~~~~~  168 (303)
                      .    |++ ++.... ..+........|||+||.+++++..|.++|+.||.+.+. .+++++.+  ++|||||.|.+.+.
T Consensus        73 ~VkLYgrpIrv~kas-~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~l~~~P~i~rd~~tg~~~~~g~i~~~sfea  151 (203)
T KOG0131|consen   73 MVKLYGRPIRVNKAS-AHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGVLISPPKIMRDPDTGNPKGFGFINYASFEA  151 (203)
T ss_pred             HHHhcCceeEEEecc-cccccccccccccccccCcchhHHHHHHHHHhccccccCCcccccccCCCCCCCeEEechhHHH
Confidence            7    666 322222 223334456889999999999999999999999998764 77787774  78999999999999


Q ss_pred             HHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          169 ARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       169 A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      +.+|+. +||+.+..+++.|.++...
T Consensus       152 sd~ai~s~ngq~l~nr~itv~ya~k~  177 (203)
T KOG0131|consen  152 SDAAIGSMNGQYLCNRPITVSYAFKK  177 (203)
T ss_pred             HHHHHHHhccchhcCCceEEEEEEec
Confidence            999999 9999999999999997544

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

Probab=99.86  E-value=4.5e-22  Score=170.09  Aligned_cols=145  Identities=19%  Similarity=0.237  Sum_probs=124.7

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhcccCCC-CC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK-RL  102 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~-~~  102 (303)
                      +|||+|||-..++.+|+.||++||+|.+|.|+++..     ||..     ++     ..    +|+.+|.+|++-+- .+
T Consensus         4 KLFIGNLp~~~~~~elr~lFe~ygkVlECDIvKNYg-----FVHi-----Ed-----kt----aaedairNLhgYtLhg~   64 (346)
T KOG0109|consen    4 KLFIGNLPREATEQELRSLFEQYGKVLECDIVKNYG-----FVHI-----ED-----KT----AAEDAIRNLHGYTLHGV   64 (346)
T ss_pred             chhccCCCcccchHHHHHHHHhhCceEeeeeecccc-----eEEe-----ec-----cc----ccHHHHhhcccceecce
Confidence            799999999999999999999999999999998865     8888     66     55    88899999998332 22


Q ss_pred             CchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       103 ~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      ......+......+++|+||||.+.++.++|+..|++||+|.+|.|++      +|+||+|...++|..|+. ||+.++.
T Consensus        65 nInVeaSksKsk~stkl~vgNis~tctn~ElRa~fe~ygpviecdivk------dy~fvh~d~~eda~~air~l~~~~~~  138 (346)
T KOG0109|consen   65 NINVEASKSKSKASTKLHVGNISPTCTNQELRAKFEKYGPVIECDIVK------DYAFVHFDRAEDAVEAIRGLDNTEFQ  138 (346)
T ss_pred             EEEEEeccccCCCccccccCCCCccccCHHHhhhhcccCCceeeeeec------ceeEEEEeeccchHHHHhcccccccc
Confidence            222333333355678899999999999999999999999999999985      599999999999999998 9999999


Q ss_pred             CeeEEEeecCCC
Q 022058          182 YYPVRVLPSKTA  193 (303)
Q Consensus       182 g~~i~v~~~~~~  193 (303)
                      |+++.|+.+...
T Consensus       139 gk~m~vq~stsr  150 (346)
T KOG0109|consen  139 GKRMHVQLSTSR  150 (346)
T ss_pred             cceeeeeeeccc
Confidence            999999987544

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

Probab=99.85  E-value=9e-21  Score=179.06  Aligned_cols=169  Identities=22%  Similarity=0.314  Sum_probs=134.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~  194 (303)
                      .+.|+|+|||..+..++|..+|..||+|..+.++  +.+ . -++|+|.+..+|.+|+. |....+...++.+.|+....
T Consensus       385 ~~vil~kNlpa~t~~~elt~~F~~fG~i~rvllp--~~G-~-~aiv~fl~p~eAr~Afrklaysr~k~~plyle~aP~dv  460 (725)
T KOG0110|consen  385 DTVILVKNLPAGTLSEELTEAFLRFGEIGRVLLP--PGG-T-GAIVEFLNPLEARKAFRKLAYSRFKSAPLYLEWAPEDV  460 (725)
T ss_pred             cceeeeccCccccccHHHHHHhhcccccceeecC--ccc-c-eeeeeecCccchHHHHHHhchhhhccCccccccChhhh
Confidence            4669999999999999999999999999999665  321 1 39999999999999999 99999999999988874432


Q ss_pred             CCCCCC--------CCC-----------C------ccc-----------ccccccceEEEcCCCCCCCHHHHHHHhhhhc
Q 022058          195 LPVNPT--------FLP-----------R------SED-----------EREMCSRTVYCTNIDKKVPQAEVKQFFEAAC  238 (303)
Q Consensus       195 ~~~~~~--------~~~-----------~------~~~-----------~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~  238 (303)
                      ....|.        ..+           .      +.+           .......+|||.||++.++.++|..+|... 
T Consensus       461 f~~~pka~~~~~e~~~~~ee~~~Er~s~~d~~v~eD~d~te~ss~a~~a~~~~~~t~lfvkNlnf~Tt~e~l~~~F~k~-  539 (725)
T KOG0110|consen  461 FTEDPKADDLSAESRSKMEENPSERVSAEDGQVEEDKDPTEESSLARVAEDEETETKLFVKNLNFDTTLEDLEDLFSKQ-  539 (725)
T ss_pred             ccCCccccccccccccccccCcceecccccccccccCCccccccchhhhhccccchhhhhhcCCcccchhHHHHHHHhc-
Confidence            220000        000           0      000           000011239999999999999999999998 


Q ss_pred             CcceeEEEEecCC-C----CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          239 GGEVTRLRLLGDH-V----HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       239 ~G~i~~v~i~~d~-~----~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                       |.|.++.|...+ +    .|+|||||+|.+.++|+.|++ |+|..+.|+.|.|+++.
T Consensus       540 -G~VlS~~I~kkkd~~~k~lSmGfgFVEF~~~e~A~~a~k~lqgtvldGH~l~lk~S~  596 (725)
T KOG0110|consen  540 -GTVLSIEISKKKDPANKYLSMGFGFVEFAKPESAQAALKALQGTVLDGHKLELKISE  596 (725)
T ss_pred             -CeEEEEEEeccccccccccccceeEEEecCHHHHHHHHHHhcCceecCceEEEEecc
Confidence             999999887654 2    378999999999999999999 99999999999999997

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

Probab=99.85  E-value=4.8e-21  Score=170.54  Aligned_cols=169  Identities=21%  Similarity=0.315  Sum_probs=147.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||++|+|+++++.|++.|.+||+|.+|.+++|+.+  ++||+||+|.+.+...+++...-+.|.|+.|.+..+.+
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f~~~~~v~~vl~~~~h~~dgr~ve~k~av~   84 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTFATPEGVDAVLNARTHKLDGRSVEPKRAVS   84 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceecCCCcchheeecccccccCCccccceeccC
Confidence            6789999999999999999999999999999999999886  89999999999999999998666789999999887643


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                      .....        ........+.|||++||..+++++++++|++|  |.|..+.++.|.  .+++||+||+|.+.+++.+
T Consensus        85 r~~~~--------~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~--g~v~~~~~~~d~~~~~~rgFgfv~~~~e~sVdk  154 (311)
T KOG4205|consen   85 REDQT--------KVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQF--GKVADVVIMYDKTTSRPRGFGFVTFDSEDSVDK  154 (311)
T ss_pred             ccccc--------ccccccceeEEEecCcCCCCchHHHhhhhhcc--ceeEeeEEeecccccccccceeeEeccccccce
Confidence            22111        11111245789999999999999999999999  999999999996  5789999999999999999


Q ss_pred             HHHhCCceeCCeeeEEeecCCCC
Q 022058          271 ALNCSGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       271 Ai~l~g~~~~g~~l~v~~a~~~~  293 (303)
                      ++...-+.|.|+.+.|..|.|..
T Consensus       155 v~~~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  155 VTLQKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             ecccceeeecCceeeEeeccchh
Confidence            99988899999999999987654

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

Probab=99.84  E-value=1.1e-21  Score=180.61  Aligned_cols=175  Identities=27%  Similarity=0.365  Sum_probs=147.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..+++|+-.|+-..++.+|.++|+.+|.|..|+++.|..+  ++|.|||+|.+.+.+..||.|.|+.+.|.+|.|.....
T Consensus       178 d~Rtvf~~qla~r~~pRdL~efFs~~gkVrdVriI~Dr~s~rskgi~Yvef~D~~sVp~aiaLsGqrllg~pv~vq~sEa  257 (549)
T KOG0147|consen  178 DQRTVFCMQLARRNPPRDLEEFFSIVGKVRDVRIIGDRNSRRSKGIAYVEFCDEQSVPLAIALSGQRLLGVPVIVQLSEA  257 (549)
T ss_pred             hHHHHHHHHHhhcCCchhHHHHHHhhcCcceeEeeccccchhhcceeEEEEecccchhhHhhhcCCcccCceeEecccHH
Confidence            4677999999999999999999999999999999999876  89999999999999999999999999999999998754


Q ss_pred             CCCCCCCCCCCCcc-cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC--CCCcccEEEEEEcCHHHHH
Q 022058          193 AILPVNPTFLPRSE-DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD--HVHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       193 ~~~~~~~~~~~~~~-~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d--~~~~~g~afV~f~~~e~A~  269 (303)
                      ...... ...+... .....+-..|||+||++++++++|+.+|++|  |.|..|.+.+|  .|.++||||++|.+.++|.
T Consensus       258 eknr~a-~~s~a~~~k~~~~p~~rl~vgnLHfNite~~lr~ifepf--g~Ie~v~l~~d~~tG~skgfGfi~f~~~~~ar  334 (549)
T KOG0147|consen  258 EKNRAA-NASPALQGKGFTGPMRRLYVGNLHFNITEDMLRGIFEPF--GKIENVQLTKDSETGRSKGFGFITFVNKEDAR  334 (549)
T ss_pred             HHHHHH-hccccccccccccchhhhhhcccccCchHHHHhhhccCc--ccceeeeeccccccccccCcceEEEecHHHHH
Confidence            332100 0001101 1111122339999999999999999999999  99999999999  4899999999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeecCCC
Q 022058          270 LALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       270 ~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      +|+. |||++|.|+.|+|....-.
T Consensus       335 ~a~e~lngfelAGr~ikV~~v~~r  358 (549)
T KOG0147|consen  335 KALEQLNGFELAGRLIKVSVVTER  358 (549)
T ss_pred             HHHHHhccceecCceEEEEEeeee
Confidence            9987 9999999999999876433

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

Probab=99.84  E-value=2e-19  Score=161.28  Aligned_cols=152  Identities=20%  Similarity=0.235  Sum_probs=118.8

Q ss_pred             CCcccccchhhhHHHHHHHH-hccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           24 NLETKKSESEFTVQKLVDMF-TKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F-~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      .+||.|+||++.+++|++|| ++.|+|+-|.+.-|..++.+.  -|+|     ..     +|    .+++|.+.||.   
T Consensus        46 ~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEF-----k~-----~E----~~qKa~E~lnk~~~  111 (608)
T KOG4212|consen   46 SVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEF-----KD-----PE----NVQKALEKLNKYEV  111 (608)
T ss_pred             eEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEe-----eC-----HH----HHHHHHHHhhhccc
Confidence            39999999999999999999 579999999999999988877  9999     77     77    67777666644   


Q ss_pred             -CCC----------------------------------------------------------CCCchhh---hh------
Q 022058           98 -GRK----------------------------------------------------------RLSGRAF---RA------  109 (303)
Q Consensus        98 -g~~----------------------------------------------------------~~~~~~~---~~------  109 (303)
                       |++                                                          +.+.+..   .+      
T Consensus       112 ~GR~l~vKEd~d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~  191 (608)
T KOG4212|consen  112 NGRELVVKEDHDEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNS  191 (608)
T ss_pred             cCceEEEeccCchhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccc
Confidence             110                                                          0000000   00      


Q ss_pred             ------------cc-----CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHH
Q 022058          110 ------------QR-----EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARA  171 (303)
Q Consensus       110 ------------~~-----~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~  171 (303)
                                  .+     .+.....+||+||.+.+....|++.|.-.|.|+.+.+-.|+.+ ++||+.++|.++-+|-.
T Consensus       192 ~~~~lfgl~~~Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmAGkv~~vdf~idKeG~s~G~~vi~y~hpveavq  271 (608)
T KOG4212|consen  192 SNYNLFGLSASFLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMAGKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQ  271 (608)
T ss_pred             hhhhcccchhhhhhhccCCCCCccceeeeeccccccchHHHHHHhccceeeeeeceeeccccccCCeeEEEecchHHHHH
Confidence                        00     1222445999999999999999999999999999999888877 89999999999999999


Q ss_pred             HHH-hCCcccCCeeEEEee
Q 022058          172 ALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       172 Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ||. ++++-+..++..+..
T Consensus       272 aIsml~~~g~~~~~~~~Rl  290 (608)
T KOG4212|consen  272 AISMLDRQGLFDRRMTVRL  290 (608)
T ss_pred             HHHhhccCCCccccceeec
Confidence            998 887666666666654

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

Probab=99.81  E-value=1.4e-18  Score=154.83  Aligned_cols=249  Identities=21%  Similarity=0.247  Sum_probs=170.9

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhh---------------------
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAI---------------------   82 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~---------------------   82 (303)
                      -|-++|||+++||+||..|+.+||.|+.+.+.+.++.   .|++|     ++     .+                     
T Consensus        30 V~HlRnlp~e~tE~elI~Lg~pFG~vtn~~~lkGknQ---Aflem-----~d-----~~sAvtmv~~y~~~~p~lr~~~~   96 (492)
T KOG1190|consen   30 VVHLRNLPWEVTEEELISLGLPFGKVTNLLMLKGKNQ---AFLEM-----AD-----EESAVTMVNYYTSVTPVLRGQPI   96 (492)
T ss_pred             eeEeccCCccccHHHHHHhcccccceeeeeeeccchh---hhhhh-----cc-----hhhhhheeecccccCccccCcce
Confidence            4779999999999999999999999999998876652   15555     22     11                     


Q ss_pred             ------------cccc---chHHhhhhccc---CCCCCCchhhhhccCCC--CCCEEEEcCCCCCCCHHHHHHHhhcCCc
Q 022058           83 ------------DNFN---NNRRRRNNFNQ---GRKRLSGRAFRAQREDS--VRRTVYVSDIDQNITEERLAGLFSSCGQ  142 (303)
Q Consensus        83 ------------~~~~---~A~~a~~~~~~---g~~~~~~~~~~~~~~~~--~~~~l~V~nlp~~~t~~~l~~~F~~~G~  142 (303)
                                  +..+   -++.+...+..   .-...+.........+.  .--.++|+|+-+.++-+-|..+|+.||.
T Consensus        97 yiq~sn~~~lkt~s~p~q~r~~~vy~~~s~~q~~~~~~s~~~~~~G~~~~~n~vLr~iie~m~ypVslDVLHqvFS~fG~  176 (492)
T KOG1190|consen   97 YIQYSNHSELKTDSQPNQIRGQAVYQAVSSVQEIVLPLSASAVVVGNEDGPNPVLRTIIENMFYPVSLDVLHQVFSKFGF  176 (492)
T ss_pred             eehhhhHHHHhccCchhhhhhhhHHhhhhcccccccccccccccccccCCCceeEEEEeccceeeeEHHHHHHHHhhcce
Confidence                        0000   01111111111   00011110000011111  1223788999999999999999999999


Q ss_pred             eeEEEEeeCCCCCceE-EEEEecCHHHHHHHHH-hCCcccC--CeeEEEeecCCCCC-----------------CCC---
Q 022058          143 VVDCRVCGDPHSVLRF-AFVEFADEHGARAALN-LGGTMLG--YYPVRVLPSKTAIL-----------------PVN---  198 (303)
Q Consensus       143 i~~~~i~~~~~~~~G~-~fV~f~~~~~A~~Ai~-l~g~~~~--g~~i~v~~~~~~~~-----------------~~~---  198 (303)
                      |..|.-.....   || |.|+|.+.+.|..|.. |+|+-|-  .+.|++.+++-...                 +.+   
T Consensus       177 VlKIiTF~Knn---~FQALvQy~d~~sAq~AK~aLdGqnIyngcCtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~  253 (492)
T KOG1190|consen  177 VLKIITFTKNN---GFQALVQYTDAVSAQAAKLALDGQNIYNGCCTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQ  253 (492)
T ss_pred             eEEEEEEeccc---chhhhhhccchhhHHHHHHhccCCcccCceeEEEeehhhcccceeeccccccccccCCCCCCCccc
Confidence            98875554333   44 9999999999999998 9998873  48888888642211                 111   


Q ss_pred             --------------------CCCCCCc-------ccccccc--cceEEEcCCCC-CCCHHHHHHHhhhhcCcceeEEEEe
Q 022058          199 --------------------PTFLPRS-------EDEREMC--SRTVYCTNIDK-KVPQAEVKQFFEAACGGEVTRLRLL  248 (303)
Q Consensus       199 --------------------~~~~~~~-------~~~~~~~--~~~l~V~nL~~-~~t~~~L~~~F~~~~~G~i~~v~i~  248 (303)
                                          |...+..       ....+.+  ...|.|.||.+ .+|.+-|.-+|.-|  |.|.+|+|+
T Consensus       254 p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n~vllvsnln~~~VT~d~LftlFgvY--GdVqRVkil  331 (492)
T KOG1190|consen  254 PSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSANVVLLVSNLNEEAVTPDVLFTLFGVY--GDVQRVKIL  331 (492)
T ss_pred             cccchhhhccccccccccCCcccCCccchhhcccccccccCCCceEEEEecCchhccchhHHHHHHhhh--cceEEEEee
Confidence                                0000000       0000111  36678888876 59999999999999  999999999


Q ss_pred             cCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCC
Q 022058          249 GDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       249 ~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~  293 (303)
                      ..++   -.|+|+|.+...|+-|++ |+|..+.|+.|+|.++|-+.
T Consensus       332 ~nkk---d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  332 YNKK---DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             ecCC---cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            8864   369999999999999999 99999999999999997653

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

Probab=99.80  E-value=2.1e-18  Score=138.79  Aligned_cols=158  Identities=20%  Similarity=0.264  Sum_probs=127.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..+.|||||||.++-+.+|+++|-+||.|..|.+... .+..+||||+|++..+|+.||. -+|..++|+.|+|+++...
T Consensus         5 ~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r-~g~ppfafVeFEd~RDAeDAiygRdGYdydg~rLRVEfprgg   83 (241)
T KOG0105|consen    5 NSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNR-PGPPPFAFVEFEDPRDAEDAIYGRDGYDYDGCRLRVEFPRGG   83 (241)
T ss_pred             ccceEEecCCCcchhhccHHHHHhhhcceEEEEeccC-CCCCCeeEEEecCccchhhhhhcccccccCcceEEEEeccCC
Confidence            5789999999999999999999999999999987532 3356899999999999999999 9999999999999997644


Q ss_pred             CCCCCCC--CCC----------CcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEE
Q 022058          194 ILPVNPT--FLP----------RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVE  261 (303)
Q Consensus       194 ~~~~~~~--~~~----------~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~  261 (303)
                      -......  +..          ............+.|.+||++-+++||++++.+.  |.|....+.+|.     ++.|+
T Consensus        84 r~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmRea--GdvCfadv~rDg-----~GvV~  156 (241)
T KOG0105|consen   84 RSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREA--GDVCFADVQRDG-----VGVVE  156 (241)
T ss_pred             CcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhh--CCeeeeeeeccc-----ceeee
Confidence            2110000  000          0000111123678999999999999999999998  999999999984     89999


Q ss_pred             EcCHHHHHHHHH-hCCceeC
Q 022058          262 FAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       262 f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      |...|+...|+. |+...+.
T Consensus       157 ~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  157 YLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             eeehhhHHHHHHhhcccccc
Confidence            999999999997 8766553

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

Probab=99.77  E-value=1.1e-18  Score=155.47  Aligned_cols=160  Identities=17%  Similarity=0.153  Sum_probs=125.9

Q ss_pred             CCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc
Q 022058           21 KNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ   97 (303)
Q Consensus        21 ~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~   97 (303)
                      .+++|||+.|.|++|++.|++.|++||+|.+|.+++|+.+++++   ||+|     +.     ++    ...+++.....
T Consensus         5 ~~~KlfiGgisw~ttee~Lr~yf~~~Gev~d~~vm~d~~t~rsrgFgfv~f-----~~-----~~----~v~~vl~~~~h   70 (311)
T KOG4205|consen    5 ESGKLFIGGLSWETTEESLREYFSQFGEVTDCVVMRDPSTGRSRGFGFVTF-----AT-----PE----GVDAVLNARTH   70 (311)
T ss_pred             CCcceeecCcCccccHHHHHHHhcccCceeeEEEeccCCCCCcccccceec-----CC-----Cc----chheeeccccc
Confidence            56799999999999999999999999999999999999988777   9999     54     33    22222222211


Q ss_pred             ---CCCCCCchhhhhccCC-----CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHH
Q 022058           98 ---GRKRLSGRAFRAQRED-----SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEH  167 (303)
Q Consensus        98 ---g~~~~~~~~~~~~~~~-----~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~  167 (303)
                         |+.....+........     .....|||++||.+++++++++.|.+||.|..+.++.|..+  ++||+||.|.+++
T Consensus        71 ~~dgr~ve~k~av~r~~~~~~~~~~~tkkiFvGG~~~~~~e~~~r~yfe~~g~v~~~~~~~d~~~~~~rgFgfv~~~~e~  150 (311)
T KOG4205|consen   71 KLDGRSVEPKRAVSREDQTKVGRHLRTKKIFVGGLPPDTTEEDFKDYFEQFGKVADVVIMYDKTTSRPRGFGFVTFDSED  150 (311)
T ss_pred             ccCCccccceeccCcccccccccccceeEEEecCcCCCCchHHHhhhhhccceeEeeEEeecccccccccceeeEecccc
Confidence               3331111111111111     12457999999999999999999999999999999999876  7999999999999


Q ss_pred             HHHHHHHhCCcccCCeeEEEeecCCCC
Q 022058          168 GARAALNLGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       168 ~A~~Ai~l~g~~~~g~~i~v~~~~~~~  194 (303)
                      .+++++....+.|.|+.+.|..+.+..
T Consensus       151 sVdkv~~~~f~~~~gk~vevkrA~pk~  177 (311)
T KOG4205|consen  151 SVDKVTLQKFHDFNGKKVEVKRAIPKE  177 (311)
T ss_pred             ccceecccceeeecCceeeEeeccchh
Confidence            999999988889999999999886543

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

Probab=99.76  E-value=2.5e-17  Score=150.28  Aligned_cols=170  Identities=22%  Similarity=0.256  Sum_probs=133.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ......|.+.+|||++|+++|.++|+.++ |+++.+.+......|-|||+|.+.+++++|++.+...+..|-|.|-.+..
T Consensus         7 ~~~~~~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~~Gr~sGeA~Ve~~seedv~~AlkkdR~~mg~RYIEVf~~~~   85 (510)
T KOG4211|consen    7 GSTAFEVRLRGLPWSATEKEILDFFSNCG-IENLEIPRRNGRPSGEAYVEFTSEEDVEKALKKDRESMGHRYIEVFTAGG   85 (510)
T ss_pred             CCcceEEEecCCCccccHHHHHHHHhcCc-eeEEEEeccCCCcCcceEEEeechHHHHHHHHhhHHHhCCceEEEEccCC
Confidence            33456689999999999999999999995 78877777666678999999999999999999999999999999987754


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE-EEEecCC-CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR-LRLLGDH-VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~-v~i~~d~-~~~~g~afV~f~~~e~A~~  270 (303)
                      .....  .+.+ ...........|.+++||+.||++||.++|+..  --|.. +.++.|+ ++++|-|||+|++.+.|++
T Consensus        86 ~e~d~--~~~~-~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL--~Iv~~gi~l~~d~rgR~tGEAfVqF~sqe~ae~  160 (510)
T KOG4211|consen   86 AEADW--VMRP-GGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGL--EIVPDGILLPMDQRGRPTGEAFVQFESQESAEI  160 (510)
T ss_pred             ccccc--cccC-CCCCCCCCCceEEecCCCccCcHHHHHHHhcCC--cccccceeeeccCCCCcccceEEEecCHHHHHH
Confidence            43211  0111 111112355789999999999999999999987  33334 3455564 7899999999999999999


Q ss_pred             HHHhCCceeCCeeeEEee
Q 022058          271 ALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       271 Ai~l~g~~~~g~~l~v~~  288 (303)
                      |+.-|...|+-+-|.|-.
T Consensus       161 Al~rhre~iGhRYIEvF~  178 (510)
T KOG4211|consen  161 ALGRHRENIGHRYIEVFR  178 (510)
T ss_pred             HHHHHHHhhccceEEeeh
Confidence            998777777777777653

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

Probab=99.75  E-value=1.2e-16  Score=142.51  Aligned_cols=246  Identities=20%  Similarity=0.234  Sum_probs=176.2

Q ss_pred             CcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc-------
Q 022058           25 LETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-------   97 (303)
Q Consensus        25 ~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-------   97 (303)
                      ++|.|+-|-+|-+-|..+|++||.|..|.--. +++..-.-|+|     .+     ++    .|+.|...++|       
T Consensus       153 ~iie~m~ypVslDVLHqvFS~fG~VlKIiTF~-Knn~FQALvQy-----~d-----~~----sAq~AK~aLdGqnIyngc  217 (492)
T KOG1190|consen  153 TIIENMFYPVSLDVLHQVFSKFGFVLKIITFT-KNNGFQALVQY-----TD-----AV----SAQAAKLALDGQNIYNGC  217 (492)
T ss_pred             EEeccceeeeEHHHHHHHHhhcceeEEEEEEe-cccchhhhhhc-----cc-----hh----hHHHHHHhccCCcccCce
Confidence            67999999999999999999999998864422 22222227888     55     55    56666655554       


Q ss_pred             -------------------CCC-CCCchhhhh---------------------------------------ccCCC--CC
Q 022058           98 -------------------GRK-RLSGRAFRA---------------------------------------QREDS--VR  116 (303)
Q Consensus        98 -------------------g~~-~~~~~~~~~---------------------------------------~~~~~--~~  116 (303)
                                         .+. ....+....                                       .+-..  ..
T Consensus       218 CtLrId~Sklt~LnvKynndkSRDyTnp~LP~gd~~p~l~~~~~aa~~~~~~~~g~p~aip~~~~~a~~a~~~~~~~~~n  297 (492)
T KOG1190|consen  218 CTLRIDFSKLTDLNVKYNNDKSRDYTNPDLPVGDGQPSLDQLMAAAFGSVPAVHGAPLAIPSGAAGANAADGKIESPSAN  297 (492)
T ss_pred             eEEEeehhhcccceeeccccccccccCCCCCCCccccccchhhhccccccccccCCcccCCccchhhcccccccccCCCc
Confidence                               000 000000000                                       00001  13


Q ss_pred             CEEEEcCCC-CCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCC
Q 022058          117 RTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       117 ~~l~V~nlp-~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~  194 (303)
                      ..|-|.||. ..+|.+.|..+|.-||+|..|.|+.++.   --|.|+|.+...|+-|+. |+|..+.|++|+|.+++-..
T Consensus       298 ~vllvsnln~~~VT~d~LftlFgvYGdVqRVkil~nkk---d~ALIQmsd~~qAqLA~~hL~g~~l~gk~lrvt~SKH~~  374 (492)
T KOG1190|consen  298 VVLLVSNLNEEAVTPDVLFTLFGVYGDVQRVKILYNKK---DNALIQMSDGQQAQLAMEHLEGHKLYGKKLRVTLSKHTN  374 (492)
T ss_pred             eEEEEecCchhccchhHHHHHHhhhcceEEEEeeecCC---cceeeeecchhHHHHHHHHhhcceecCceEEEeeccCcc
Confidence            568888886 5799999999999999999999998765   359999999999999999 99999999999999986543


Q ss_pred             CCCCC--------------CCCCCcc-------cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCC
Q 022058          195 LPVNP--------------TFLPRSE-------DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVH  253 (303)
Q Consensus       195 ~~~~~--------------~~~~~~~-------~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~  253 (303)
                      .....              ...++-.       ..--+++.+|.+.|+|.++++++|+.+|...  |...+......  +
T Consensus       375 vqlp~egq~d~glT~dy~~spLhrfkkpgsKN~~ni~PpsatlHlsnip~svsee~lk~~f~~~--g~~vkafkff~--k  450 (492)
T KOG1190|consen  375 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNYQNIFPPSATLHLSNIPPSVSEEDLKNLFQEP--GGQVKAFKFFQ--K  450 (492)
T ss_pred             ccCCCCCCccccccccCCCCchhhccCcccccccccCCchhheeeccCCcccchhHHHHhhhcC--CceEEeeeecC--C
Confidence            21110              0000000       0012456789999999999999999999998  76655433221  1


Q ss_pred             cccEEEEEEcCHHHHHHHHH-hCCceeCC-eeeEEeecCCC
Q 022058          254 STRIAFVEFAVAESAILALN-CSGMVLGS-QPIRVSPSKTP  292 (303)
Q Consensus       254 ~~g~afV~f~~~e~A~~Ai~-l~g~~~~g-~~l~v~~a~~~  292 (303)
                      .+.++++++.+.|+|..|+. |+.+.+++ ..|+|+|++..
T Consensus       451 d~kmal~q~~sveeA~~ali~~hnh~lgen~hlRvSFSks~  491 (492)
T KOG1190|consen  451 DRKMALPQLESVEEAIQALIDLHNHYLGENHHLRVSFSKST  491 (492)
T ss_pred             CcceeecccCChhHhhhhccccccccCCCCceEEEEeeccc
Confidence            22499999999999999998 99999975 59999999864

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

Probab=99.75  E-value=5.9e-17  Score=134.98  Aligned_cols=170  Identities=25%  Similarity=0.370  Sum_probs=137.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAG----LFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~----~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ...+|||.||+..+..++|+.    +|++||.|.+|...+.. ..+|-|||.|.+.+.|..|+. |+|..+-|++++|.+
T Consensus         8 pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~-KmRGQA~VvFk~~~~As~A~r~l~gfpFygK~mriqy   86 (221)
T KOG4206|consen    8 PNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTP-KMRGQAFVVFKETEAASAALRALQGFPFYGKPMRIQY   86 (221)
T ss_pred             CCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCC-CccCceEEEecChhHHHHHHHHhcCCcccCchhheec
Confidence            344999999999999999888    99999999999887543 268999999999999999998 999999999999999


Q ss_pred             cCCCCCCC---CCCCCCCc---------------------------------ccccccccceEEEcCCCCCCCHHHHHHH
Q 022058          190 SKTAILPV---NPTFLPRS---------------------------------EDEREMCSRTVYCTNIDKKVPQAEVKQF  233 (303)
Q Consensus       190 ~~~~~~~~---~~~~~~~~---------------------------------~~~~~~~~~~l~V~nL~~~~t~~~L~~~  233 (303)
                      +.....-.   .+.+..+.                                 ......+...+|+.|||..++.+.|..+
T Consensus        87 A~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~niP~es~~e~l~~l  166 (221)
T KOG4206|consen   87 AKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLTNIPSESESEMLSDL  166 (221)
T ss_pred             ccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEecCCcchhHHHHHHH
Confidence            86542100   00000000                                 0112445678999999999999999999


Q ss_pred             hhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC-CeeeEEeecC
Q 022058          234 FEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG-SQPIRVSPSK  290 (303)
Q Consensus       234 F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~-g~~l~v~~a~  290 (303)
                      |++|  .....++++....   +.|||+|.+...|..|.+ ++|..+. .+.++|.+++
T Consensus       167 f~qf--~g~keir~i~~~~---~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  167 FEQF--PGFKEIRLIPPRS---GIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             HhhC--cccceeEeccCCC---ceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            9999  8899998887642   499999999999999998 9998886 8889998875

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

Probab=99.75  E-value=8.2e-17  Score=146.96  Aligned_cols=246  Identities=17%  Similarity=0.172  Sum_probs=173.6

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhc--ccCC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNF--NQGR   99 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~--~~g~   99 (303)
                      -|.++.|||++|++||.++|+.|+ |.++.+++. +++.+.  ||+|     .+     .+    +++.|++.-  ..|.
T Consensus        12 ~vr~rGLPwsat~~ei~~Ff~~~~-I~~~~~~r~-~Gr~sGeA~Ve~-----~s-----ee----dv~~AlkkdR~~mg~   75 (510)
T KOG4211|consen   12 EVRLRGLPWSATEKEILDFFSNCG-IENLEIPRR-NGRPSGEAYVEF-----TS-----EE----DVEKALKKDRESMGH   75 (510)
T ss_pred             EEEecCCCccccHHHHHHHHhcCc-eeEEEEecc-CCCcCcceEEEe-----ec-----hH----HHHHHHHhhHHHhCC
Confidence            477999999999999999999997 677777664 345555  9999     77     66    666665432  1122


Q ss_pred             C----------CCCchhhhhc--cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeE-EEEeeCCCC-CceEEEEEecC
Q 022058          100 K----------RLSGRAFRAQ--REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD-CRVCGDPHS-VLRFAFVEFAD  165 (303)
Q Consensus       100 ~----------~~~~~~~~~~--~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-~~i~~~~~~-~~G~~fV~f~~  165 (303)
                      +          ...+ .++..  ........|.+++||+.||++||.++|+..-.+.. +.++.+... +.|-|||+|++
T Consensus        76 RYIEVf~~~~~e~d~-~~~~~g~~s~~~d~vVRLRGLPfscte~dI~~FFaGL~Iv~~gi~l~~d~rgR~tGEAfVqF~s  154 (510)
T KOG4211|consen   76 RYIEVFTAGGAEADW-VMRPGGPNSSANDGVVRLRGLPFSCTEEDIVEFFAGLEIVPDGILLPMDQRGRPTGEAFVQFES  154 (510)
T ss_pred             ceEEEEccCCccccc-cccCCCCCCCCCCceEEecCCCccCcHHHHHHHhcCCcccccceeeeccCCCCcccceEEEecC
Confidence            2          1111 11111  11235667999999999999999999997766655 556666665 78999999999


Q ss_pred             HHHHHHHHHhCCcccCCeeEEEeecCCCC-----------CCC-CCCCC-------------------------------
Q 022058          166 EHGARAALNLGGTMLGYYPVRVLPSKTAI-----------LPV-NPTFL-------------------------------  202 (303)
Q Consensus       166 ~~~A~~Ai~l~g~~~~g~~i~v~~~~~~~-----------~~~-~~~~~-------------------------------  202 (303)
                      .+.|++|+..|...|+-|-|.|..+....           ... .|...                               
T Consensus       155 qe~ae~Al~rhre~iGhRYIEvF~Ss~~e~~~~~~~~~~~~~rpGpy~~~~a~Rg~~d~~~~~~~~~~~~r~g~~~~g~~  234 (510)
T KOG4211|consen  155 QESAEIALGRHRENIGHRYIEVFRSSRAEVKRAAGPGDGRVGRPGPYDRPGAPRGGYDYGQGRDPGRNATRYGAGGEGYY  234 (510)
T ss_pred             HHHHHHHHHHHHHhhccceEEeehhHHHHHHhhccccccccCCCCccccccCCccccccccccCCCccccccccccCCcc
Confidence            99999999988889999999987652110           000 00000                               


Q ss_pred             ---------C---------------------Ccccc-----c-ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEE
Q 022058          203 ---------P---------------------RSEDE-----R-EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLR  246 (303)
Q Consensus       203 ---------~---------------------~~~~~-----~-~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~  246 (303)
                               .                     .....     . ......+.-++||+..++.++..+|+..   ....|.
T Consensus       235 g~~~~~~~~d~~~~gs~~~~~~~~~~~~~g~~~~g~~g~~~~~~~~g~fv~MRGlpy~a~~~di~nfFspl---~p~~v~  311 (510)
T KOG4211|consen  235 GFSRYPSLQDYGNFGSYGGGRDPNYPVSSGPHRQGGAGDYGNGGPGGHFVHMRGLPYDATENDIANFFSPL---NPYRVH  311 (510)
T ss_pred             ccccCccccccccccccccccccccCCCCCcccCCCcccccCCCCCCceeeecCCCccCCCcchhhhcCCC---CceeEE
Confidence                     0                     00000     0 0112457778999999999999999986   555777


Q ss_pred             EecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          247 LLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       247 i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      |--.+ |+.+|-|.|+|.+.++|..|+.-++..+..+-|.+-.-
T Consensus       312 i~ig~dGr~TGEAdveF~t~edav~Amskd~anm~hrYVElFln  355 (510)
T KOG4211|consen  312 IEIGPDGRATGEADVEFATGEDAVGAMGKDGANMGHRYVELFLN  355 (510)
T ss_pred             EEeCCCCccCCcceeecccchhhHhhhccCCcccCcceeeeccc
Confidence            76664 88999999999999999999986777777776665543

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

Probab=99.73  E-value=9.4e-17  Score=144.30  Aligned_cols=178  Identities=23%  Similarity=0.266  Sum_probs=144.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhh-cCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFS-SCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..+.+||.|||+++.|++|+++|. ..|+|+.|.++.|..+ ++|||.|+|+++|.+++|++ ||..++.||+|.|+...
T Consensus        43 r~R~vfItNIpyd~rWqdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~~~GR~l~vKEd~  122 (608)
T KOG4212|consen   43 RDRSVFITNIPYDYRWQDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYEVNGRELVVKEDH  122 (608)
T ss_pred             ccceEEEecCcchhhhHhHHHHHHHhcCceEeeeeecccCCCcCCceEEEeeCHHHHHHHHHHhhhccccCceEEEeccC
Confidence            456799999999999999999997 7799999999999886 89999999999999999999 99999999999998754


Q ss_pred             CCCCC-----------------------------------CCCCCCCCccc-----------------------------
Q 022058          192 TAILP-----------------------------------VNPTFLPRSED-----------------------------  207 (303)
Q Consensus       192 ~~~~~-----------------------------------~~~~~~~~~~~-----------------------------  207 (303)
                      .....                                   ....+.+++.+                             
T Consensus       123 d~q~~~~~~~~r~g~~~f~~~~~~q~G~~~l~~~g~ggG~~~Rg~~~~D~Dr~sr~~~t~t~~~~~~~~~~~~lfgl~~~  202 (608)
T KOG4212|consen  123 DEQRDQYGRIVRDGGGGFGGGGGVQGGNGGLNGGGGGGGDRDRGFSRRDDDRLSRRNNTNTMSNDYNNSSNYNLFGLSAS  202 (608)
T ss_pred             chhhhhhhheeeccCcccccCcceecccccccccCCCCccccCCCCcccccccccccCccccccccccchhhhcccchhh
Confidence            31110                                   00001111100                             


Q ss_pred             -------ccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCce
Q 022058          208 -------EREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMV  278 (303)
Q Consensus       208 -------~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~  278 (303)
                             -..+....+||.||...+....|++.|.-.  |.|.++.+--|+ |.++|++.++|.++-+|..||. |++.-
T Consensus       203 Flr~~h~f~pPl~~k~fvanl~~~vg~~kL~qvfgmA--Gkv~~vdf~idKeG~s~G~~vi~y~hpveavqaIsml~~~g  280 (608)
T KOG4212|consen  203 FLRSLHIFSPPLHNKVFVANLDYKVGNKKLKQVFGMA--GKVQSVDFSIDKEGNSRGFAVIEYDHPVEAVQAISMLDRQG  280 (608)
T ss_pred             hhhhccCCCCCccceeeeeccccccchHHHHHHhccc--eeeeeeceeeccccccCCeeEEEecchHHHHHHHHhhccCC
Confidence                   012234578999999999999999999998  999999998886 8999999999999999999998 88877


Q ss_pred             eCCeeeEEeecCCCCC
Q 022058          279 LGSQPIRVSPSKTPVR  294 (303)
Q Consensus       279 ~~g~~l~v~~a~~~~~  294 (303)
                      +..++..+....-+.+
T Consensus       281 ~~~~~~~~Rl~~~~Dr  296 (608)
T KOG4212|consen  281 LFDRRMTVRLDRIPDR  296 (608)
T ss_pred             Cccccceeeccccccc
Confidence            7788888877654444

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

Probab=99.70  E-value=1.1e-16  Score=128.79  Aligned_cols=79  Identities=28%  Similarity=0.476  Sum_probs=74.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|++||.|.+|.++.|..+  ++|||||+|.+.++|++|++ ||+..|.|++|+|.++.
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~a~  112 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNPAN  112 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEeCC
Confidence            5778999999999999999999999999999999998765  79999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus       113 ~~  114 (144)
T PLN03134        113 DR  114 (144)
T ss_pred             cC
Confidence            54

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

Probab=99.70  E-value=1.8e-16  Score=127.57  Aligned_cols=80  Identities=23%  Similarity=0.356  Sum_probs=74.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.++.|+.|.  ++++|||||+|.+.++|+.|++ ||+..|+|+.|+|.+
T Consensus        33 ~~~~lfVgnL~~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~~kGfaFV~F~~~e~A~~Al~~lng~~i~Gr~l~V~~  110 (144)
T PLN03134         33 MSTKLFIGGLSWGTDDASLRDAFAHF--GDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAISEMDGKELNGRHIRVNP  110 (144)
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            35789999999999999999999999  999999999885  6899999999999999999998 999999999999999


Q ss_pred             cCCCC
Q 022058          289 SKTPV  293 (303)
Q Consensus       289 a~~~~  293 (303)
                      +.+..
T Consensus       111 a~~~~  115 (144)
T PLN03134        111 ANDRP  115 (144)
T ss_pred             CCcCC
Confidence            97554

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

Probab=99.68  E-value=3.1e-15  Score=131.24  Aligned_cols=175  Identities=19%  Similarity=0.278  Sum_probs=136.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCcee--------EEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVV--------DCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGY  182 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g  182 (303)
                      +..++.|||.|||.++|-+++.++|+.||.|.        .|++.++..+ .+|=|.+.|-..+++..|++ |++..+.|
T Consensus       131 ~~~Nt~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y~K~ESVeLA~~ilDe~~~rg  210 (382)
T KOG1548|consen  131 PKVNTSVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCYIKRESVELAIKILDEDELRG  210 (382)
T ss_pred             cccCceEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEeecccHHHHHHHHhCcccccC
Confidence            44577799999999999999999999999874        5788887776 79999999999999999999 99999999


Q ss_pred             eeEEEeecCCCCCCC-CCC----------------------CCCCc-ccccccccceEEEcCCC----CCCC-------H
Q 022058          183 YPVRVLPSKTAILPV-NPT----------------------FLPRS-EDEREMCSRTVYCTNID----KKVP-------Q  227 (303)
Q Consensus       183 ~~i~v~~~~~~~~~~-~~~----------------------~~~~~-~~~~~~~~~~l~V~nL~----~~~t-------~  227 (303)
                      +.|+|..++-..... .+.                      +.+.. ...+....++|.++|+=    ...+       .
T Consensus       211 ~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~~~~l~~dlk  290 (382)
T KOG1548|consen  211 KKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEKNPDLLNDLK  290 (382)
T ss_pred             cEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhccCHHHHHHHH
Confidence            999999875432110 000                      11111 11223345788888872    1222       4


Q ss_pred             HHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          228 AEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       228 ~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      ++|++-+++|  |.|.+|.|.-.  .+.|.+-|.|.+.++|..||+ |+|++|+||.|+.+.+.-
T Consensus       291 edl~eec~K~--G~v~~vvv~d~--hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~DG  351 (382)
T KOG1548|consen  291 EDLTEECEKF--GQVRKVVVYDR--HPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWDG  351 (382)
T ss_pred             HHHHHHHHHh--CCcceEEEecc--CCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeCC
Confidence            6788889998  99999988643  345799999999999999999 999999999999987643

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

Probab=99.67  E-value=1.5e-16  Score=133.84  Aligned_cols=159  Identities=26%  Similarity=0.318  Sum_probs=128.4

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAIL  195 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~  195 (303)
                      ..+|||+||+...+.+|..+|..||.|..+.+.      .||+||+|++..+|..|+. +|+.++.|-.+.|.|+.....
T Consensus         2 ~rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk------~gf~fv~fed~rda~Dav~~l~~~~l~~e~~vve~~r~~~~   75 (216)
T KOG0106|consen    2 PRVYIGRLPYRARERDVERFFKGYGKIPDADMK------NGFGFVEFEDPRDADDAVHDLDGKELCGERLVVEHARGKRR   75 (216)
T ss_pred             CceeecccCCccchhHHHHHHhhccccccceee------cccceeccCchhhhhcccchhcCceecceeeeeeccccccc
Confidence            358999999999999999999999999998885      3799999999999999998 999999998899999875422


Q ss_pred             CCCCCC---C---CCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHH
Q 022058          196 PVNPTF---L---PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       196 ~~~~~~---~---~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~  269 (303)
                      ....+.   .   .+...........+.|.|++..+.+++|.++|+++  |.+....+.      .+++||+|++.++|.
T Consensus        76 ~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~--g~~~~~~~~------~~~~~v~Fs~~~da~  147 (216)
T KOG0106|consen   76 GRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPA--GEVTYVDAR------RNFAFVEFSEQEDAK  147 (216)
T ss_pred             ccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhccc--CCCchhhhh------ccccceeehhhhhhh
Confidence            111111   0   11111112344678899999999999999999999  999655552      238999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeec
Q 022058          270 LALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       270 ~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      +|+. |+|..+.++.|++...
T Consensus       148 ra~~~l~~~~~~~~~l~~~~~  168 (216)
T KOG0106|consen  148 RALEKLDGKKLNGRRISVEKN  168 (216)
T ss_pred             hcchhccchhhcCceeeeccc
Confidence            9999 9999999999999543

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

Probab=99.67  E-value=1.8e-15  Score=125.37  Aligned_cols=164  Identities=20%  Similarity=0.243  Sum_probs=124.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC---CceEEEEEecCHHHHHHHHH-hCCcccC---Cee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS---VLRFAFVEFADEHGARAALN-LGGTMLG---YYP  184 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~---~~G~~fV~f~~~~~A~~Ai~-l~g~~~~---g~~  184 (303)
                      .+..-++|||.+||.++...+|+.+|..|--.+.+.+.....+   .+.+|||+|.+..+|.+|+. |||..++   +..
T Consensus        30 ~~~~VRTLFVSGLP~DvKpREiynLFR~f~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~st  109 (284)
T KOG1457|consen   30 EPGAVRTLFVSGLPNDVKPREIYNLFRRFHGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGST  109 (284)
T ss_pred             cccccceeeeccCCcccCHHHHHHHhccCCCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCce
Confidence            3345789999999999999999999999988888877654332   45799999999999999998 9999996   788


Q ss_pred             EEEeecCCCCCC----CCC-----C--------CCCCc------------------------------------------
Q 022058          185 VRVLPSKTAILP----VNP-----T--------FLPRS------------------------------------------  205 (303)
Q Consensus       185 i~v~~~~~~~~~----~~~-----~--------~~~~~------------------------------------------  205 (303)
                      |+++.++.....    ..+     .        ...+.                                          
T Consensus       110 LhiElAKSNtK~kr~k~sgtP~~s~al~~~~~~~~qr~sa~~qhd~~l~~p~~l~~~~~a~al~~~~~t~~~~l~a~~~~  189 (284)
T KOG1457|consen  110 LHIELAKSNTKRKRRKGSGTPGSSPALVIDNRNKEQRKSADDQHDEGLSDPDELQEPGNADALKENDTTKSEALSAPDSK  189 (284)
T ss_pred             eEeeehhcCcccccCCCCCCCCCCccccccccChhhcccchhhccccccCccccCCccccccCCCccccchhhhhhhhhc
Confidence            888887543210    000     0        00000                                          


Q ss_pred             ----c---------cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHH
Q 022058          206 ----E---------DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL  272 (303)
Q Consensus       206 ----~---------~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai  272 (303)
                          .         ......+.+|||.||.+.++|++|+++|+.|  ......+|....|  .+.||+.|+..+.|..||
T Consensus       190 ~P~a~a~l~ks~q~~~~~~acstlfianl~~~~~ed~l~~~~~~~--~gf~~l~~~~~~g--~~vaf~~~~~~~~at~am  265 (284)
T KOG1457|consen  190 APSANAHLEKSSQGGSGARACSTLFIANLGPNCTEDELKQLLSRY--PGFHILKIRARGG--MPVAFADFEEIEQATDAM  265 (284)
T ss_pred             CCcccchhhhhhcccccchhhhhHhhhccCCCCCHHHHHHHHHhC--CCceEEEEecCCC--cceEeecHHHHHHHHHHH
Confidence                0         0001124689999999999999999999999  7677666654443  358999999999999999


Q ss_pred             H-hCCcee
Q 022058          273 N-CSGMVL  279 (303)
Q Consensus       273 ~-l~g~~~  279 (303)
                      . |.|..|
T Consensus       266 ~~lqg~~~  273 (284)
T KOG1457|consen  266 NHLQGNLL  273 (284)
T ss_pred             HHhhccee
Confidence            8 999876

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

Probab=99.63  E-value=1.6e-15  Score=128.66  Aligned_cols=80  Identities=21%  Similarity=0.404  Sum_probs=74.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .+.|+|||-.||.+..+.+|-.+|-.||.|.+.++..|+-+  ||.||||.|.+..+|+.||. |||..|+-++|+|...
T Consensus       283 PeGCNlFIYHLPQEFgDaEliQmF~PFGhivSaKVFvDRATNQSKCFGFVSfDNp~SaQaAIqAMNGFQIGMKRLKVQLK  362 (371)
T KOG0146|consen  283 PEGCNLFIYHLPQEFGDAELIQMFLPFGHIVSAKVFVDRATNQSKCFGFVSFDNPASAQAAIQAMNGFQIGMKRLKVQLK  362 (371)
T ss_pred             CCcceEEEEeCchhhccHHHHHHhccccceeeeeeeehhccccccceeeEecCCchhHHHHHHHhcchhhhhhhhhhhhc
Confidence            34788999999999999999999999999999999999876  89999999999999999999 9999999999999876


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      +++
T Consensus       363 RPk  365 (371)
T KOG0146|consen  363 RPK  365 (371)
T ss_pred             Ccc
Confidence            543

>PF00076 RRM_1: RNA recognition motif

Probab=99.63  E-value=1.8e-15  Score=106.26  Aligned_cols=68  Identities=32%  Similarity=0.566  Sum_probs=63.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC-CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH-SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVR  186 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~-~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~  186 (303)
                      |||+|||+++++++|+++|+.||.|..+.+..+.. .++|||||+|.+.++|++|+. +||..+.|++|+
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 LYVGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            79999999999999999999999999999999633 379999999999999999999 999999999885

(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 ....

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

Probab=99.60  E-value=3.2e-14  Score=133.06  Aligned_cols=251  Identities=18%  Similarity=0.208  Sum_probs=176.0

Q ss_pred             CCCcccccchhhhHHHHHHHHhcc-----------CC-cceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHH
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKL-----------NP-LAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRR   90 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~-----------G~-v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~   90 (303)
                      -.+.|.+++.+++++.+-.+|..-           |+ +..|.+-..++   ..|++|     .+     .+    +|..
T Consensus       176 ~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~~n---fa~ie~-----~s-----~~----~at~  238 (500)
T KOG0120|consen  176 RRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLEKN---FAFIEF-----RS-----IS----EATE  238 (500)
T ss_pred             hhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeeccccc---ceeEEe-----cC-----CC----chhh
Confidence            368999999999999999999875           43 55555543332   117888     55     44    4544


Q ss_pred             hhhhc---ccCCC-CCC---------------------chhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeE
Q 022058           91 RRNNF---NQGRK-RLS---------------------GRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD  145 (303)
Q Consensus        91 a~~~~---~~g~~-~~~---------------------~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~  145 (303)
                      +....   -.|.+ .+.                     ...............+||++||..+++.+++++...||++..
T Consensus       239 ~~~~~~~~f~g~~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~fg~lk~  318 (500)
T KOG0120|consen  239 AMALDGIIFEGRPLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSFGPLKA  318 (500)
T ss_pred             hhcccchhhCCCCceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhcccchh
Confidence            43211   11222 000                     000111112224556999999999999999999999999999


Q ss_pred             EEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCCC---------CCc-ccccccc
Q 022058          146 CRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFL---------PRS-EDEREMC  212 (303)
Q Consensus       146 ~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~---------~~~-~~~~~~~  212 (303)
                      ..++.+..+  ++||||.+|.+..-...|+. |||+.++++.|.|..+-...........         +.. ......+
T Consensus       319 f~lv~d~~~g~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~g~~~~~~~~~~~~~~~~~i~~~~~q~~g~~  398 (500)
T KOG0120|consen  319 FRLVKDSATGNSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIVGASNANVNFNISQSQVPGIPLLMTQMAGIP  398 (500)
T ss_pred             heeecccccccccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhccchhccccCCccccccccchhhhcccCCCc
Confidence            999998874  89999999999999999999 9999999999999887433211111011         000 0111233


Q ss_pred             cceEEEcCCCC--CC-CH-------HHHHHHhhhhcCcceeEEEEecC-C----CCcccEEEEEEcCHHHHHHHHH-hCC
Q 022058          213 SRTVYCTNIDK--KV-PQ-------AEVKQFFEAACGGEVTRLRLLGD-H----VHSTRIAFVEFAVAESAILALN-CSG  276 (303)
Q Consensus       213 ~~~l~V~nL~~--~~-t~-------~~L~~~F~~~~~G~i~~v~i~~d-~----~~~~g~afV~f~~~e~A~~Ai~-l~g  276 (303)
                      ...|++.|+-.  .+ .+       ++++..|..|  |.|.+|.|+++ .    .-..|..||+|.+.+++++|+. |+|
T Consensus       399 t~Vl~L~n~Vt~deLkdd~EyeeIlEdvr~ec~k~--g~v~~v~ipr~~~~~~~~~G~GkVFVefas~ed~qrA~~~L~G  476 (500)
T KOG0120|consen  399 TEVLCLTNVVTPDELKDDEEYEEILEDVRTECAKF--GAVRSVEIPRPYPDENPVPGTGKVFVEFADTEDSQRAMEELTG  476 (500)
T ss_pred             chhhhhhhcCCHHHhcchHHHHHHHHHHHHHhccc--CceeEEecCCCCCCCCcCCCcccEEEEecChHHHHHHHHHccC
Confidence            45566665421  11 11       5677788899  99999999988 3    2357899999999999999999 999


Q ss_pred             ceeCCeeeEEeecCCC
Q 022058          277 MVLGSQPIRVSPSKTP  292 (303)
Q Consensus       277 ~~~~g~~l~v~~a~~~  292 (303)
                      ..|.||.|..+|..+-
T Consensus       477 rKF~nRtVvtsYydeD  492 (500)
T KOG0120|consen  477 RKFANRTVVASYYDED  492 (500)
T ss_pred             ceeCCcEEEEEecCHH
Confidence            9999999999987543

>PF00076 RRM_1: RNA recognition motif

Probab=99.59  E-value=8.2e-15  Score=102.81  Aligned_cols=68  Identities=29%  Similarity=0.527  Sum_probs=64.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC-CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       216 l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d-~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      |||+|||..+++++|+++|++|  |.|..+.+..+ .+.++|+|||+|.+.++|.+|+. |||..++|+.|+
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 LYVGNLPPDVTEEELRDFFSQF--GKIESIKVMRNSSGKSKGYAFVEFESEEDAEKALEELNGKKINGRKIR   70 (70)
T ss_dssp             EEEESETTTSSHHHHHHHHHTT--STEEEEEEEEETTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             cEEcCCCCcCCHHHHHHHHHHh--hhcccccccccccccccceEEEEEcCHHHHHHHHHHcCCCEECccCcC
Confidence            7999999999999999999999  99999999996 57889999999999999999999 999999999985

(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 ....

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.59  E-value=8.2e-15  Score=126.45  Aligned_cols=78  Identities=28%  Similarity=0.396  Sum_probs=72.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~~  194 (303)
                      .++|||+|||+.+++++|+++|+.||.|.+|.|+.+.. ++|||||+|.+.++|+.||.|||..|.|+.|.|.++....
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~G~I~~V~I~~d~~-~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~~   81 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFSGDIEYVEMQSENE-RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDYQ   81 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCC-CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCCC
Confidence            57899999999999999999999999999999998864 5799999999999999999999999999999999986543

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

Probab=99.58  E-value=6.1e-15  Score=128.50  Aligned_cols=79  Identities=22%  Similarity=0.312  Sum_probs=75.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..+.|+|.|||+..-+.||+.+|.+||.|.+|.|+.+..+|||||||+|++.++|++|.+ |||..+.||.|.|..+...
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kfG~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~ATar  174 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKFGKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNATAR  174 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhhCceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccchh
Confidence            567899999999999999999999999999999999999999999999999999999998 9999999999999988654

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

Probab=99.57  E-value=5.2e-15  Score=112.40  Aligned_cols=77  Identities=32%  Similarity=0.453  Sum_probs=72.5

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..+++||||||++.++|++|.++|+.+|+|..|.|=.|+.+  ..|||||+|.+.++|..|++ ++|..++.++|.+.|.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~cG~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D~D  113 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSKCGDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRIDWD  113 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHhccchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeeecc
Confidence            36899999999999999999999999999999988887765  89999999999999999999 9999999999999985

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

Probab=99.57  E-value=5.3e-14  Score=123.82  Aligned_cols=156  Identities=27%  Similarity=0.388  Sum_probs=116.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC--CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH--SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~--~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .++|||+|||+++++++|+++|..||.|..+.+..+..  .++|||||+|.+.++|..|+. +++..+.|++|.|.+...
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~~~  194 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKFGPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKAQP  194 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhcCceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecccc
Confidence            58999999999999999999999999999999999873  389999999999999999999 999999999999999642


Q ss_pred             --CCCCCCC-----CC---CCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCC--CcccEEEE
Q 022058          193 --AILPVNP-----TF---LPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFV  260 (303)
Q Consensus       193 --~~~~~~~-----~~---~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~--~~~g~afV  260 (303)
                        .......     ..   ..............+++.+++..++..++...|..+  |.+....+.....  ......++
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~  272 (306)
T COG0724         195 ASQPRSELSNNLDASFAKKLSRGKALLLEKSDNLYVGNLPLKTAEEELADLFKSR--GDIVRASLPPSKDGKIPKSRSFV  272 (306)
T ss_pred             ccccccccccccchhhhccccccccccccccceeeccccccccchhHHHHhcccc--ccceeeeccCCCCCccccccccc
Confidence              1100000     00   001111123345789999999999999999999998  9997777666542  23334444


Q ss_pred             EEcCHHHHHHHHH
Q 022058          261 EFAVAESAILALN  273 (303)
Q Consensus       261 ~f~~~e~A~~Ai~  273 (303)
                      .+.....+.....
T Consensus       273 ~~~~~~~~~~~~~  285 (306)
T COG0724         273 GNEASKDALESNS  285 (306)
T ss_pred             chhHHHhhhhhhc
Confidence            4444444444443

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

Probab=99.55  E-value=1.5e-14  Score=121.50  Aligned_cols=79  Identities=28%  Similarity=0.365  Sum_probs=75.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ...+|.|.||+.++++++|.++|.+|  |.|.+|.|.+|+  |.++|||||+|.+.++|.+||. |||+-++.-.|.|.|
T Consensus       188 D~~tvRvtNLsed~~E~dL~eLf~~f--g~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvEw  265 (270)
T KOG0122|consen  188 DEATVRVTNLSEDMREDDLEELFRPF--GPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVEW  265 (270)
T ss_pred             ccceeEEecCccccChhHHHHHhhcc--CccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEEe
Confidence            45789999999999999999999999  999999999997  8899999999999999999999 999999999999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      ++|.
T Consensus       266 skP~  269 (270)
T KOG0122|consen  266 SKPS  269 (270)
T ss_pred             cCCC
Confidence            9975

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

Probab=99.55  E-value=1.6e-12  Score=115.21  Aligned_cols=248  Identities=18%  Similarity=0.194  Sum_probs=176.7

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHh-----hhh
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRR-----RNN   94 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a-----~~~   94 (303)
                      +-|--+-|++|-..+++.||.+..+.||+|.-|..+..+..   .-|+|     .+     .+    .|+.+     .++
T Consensus        29 ~~spvvhvr~l~~~v~eadl~eal~~fG~i~yvt~~P~~r~---alvef-----ed-----i~----~akn~Vnfaa~n~   91 (494)
T KOG1456|consen   29 NPSPVVHVRGLHQGVVEADLVEALSNFGPIAYVTCMPHKRQ---ALVEF-----ED-----IE----GAKNCVNFAADNQ   91 (494)
T ss_pred             CCCceEEEeccccccchhHHHHHHhcCCceEEEEeccccce---eeeee-----cc-----cc----chhhheehhccCc
Confidence            44445779999999999999999999999999888764321   17888     54     33    34333     222


Q ss_pred             ccc-CCCCC-----CchhhhhccCC-CCCCEEE--EcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecC
Q 022058           95 FNQ-GRKRL-----SGRAFRAQRED-SVRRTVY--VSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFAD  165 (303)
Q Consensus        95 ~~~-g~~~~-----~~~~~~~~~~~-~~~~~l~--V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~  165 (303)
                      .+. |...+     +..+.....+. ..+..|.  |-|--+.+|-+.|..+....|.|..|.|++...   -.|.|+|++
T Consensus        92 i~i~gq~Al~NyStsq~i~R~g~es~~pN~VLl~TIlNp~YpItvDVly~Icnp~GkVlRIvIfkkng---VQAmVEFds  168 (494)
T KOG1456|consen   92 IYIAGQQALFNYSTSQCIERPGDESATPNKVLLFTILNPQYPITVDVLYTICNPQGKVLRIVIFKKNG---VQAMVEFDS  168 (494)
T ss_pred             ccccCchhhcccchhhhhccCCCCCCCCCeEEEEEeecCccccchhhhhhhcCCCCceEEEEEEeccc---eeeEEeech
Confidence            222 22211     11111111111 1233343  445557899999999999999999999987632   369999999


Q ss_pred             HHHHHHHHH-hCCcccC--CeeEEEeecCCCCC--------------C-----CCCC---CCCCc---------------
Q 022058          166 EHGARAALN-LGGTMLG--YYPVRVLPSKTAIL--------------P-----VNPT---FLPRS---------------  205 (303)
Q Consensus       166 ~~~A~~Ai~-l~g~~~~--g~~i~v~~~~~~~~--------------~-----~~~~---~~~~~---------------  205 (303)
                      .+.|++|.. |||..|-  -.+|+|+++++...              +     .++.   +.+..               
T Consensus       169 v~~AqrAk~alNGADIYsGCCTLKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~  248 (494)
T KOG1456|consen  169 VEVAQRAKAALNGADIYSGCCTLKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGG  248 (494)
T ss_pred             hHHHHHHHhhcccccccccceeEEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCC
Confidence            999999999 9999883  58999999876422              0     0000   00000               


Q ss_pred             ------------------------cc-------ccccccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCCCC
Q 022058          206 ------------------------ED-------EREMCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDHVH  253 (303)
Q Consensus       206 ------------------------~~-------~~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~~~  253 (303)
                                              .+       ....++..+-|.+|+.. .+-+.|..+|+.|  |.|++|++++.+- 
T Consensus       249 h~~y~sg~~~~p~~~~P~r~~~~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClY--GNV~rvkFmkTk~-  325 (494)
T KOG1456|consen  249 HSGYYSGDRHGPPHPPPSRYRDGYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLY--GNVERVKFMKTKP-  325 (494)
T ss_pred             CCCCcccccCCCCCCCCCCCccccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhc--CceeeEEEeeccc-
Confidence                                    00       11223567889999874 7889999999999  9999999998752 


Q ss_pred             cccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          254 STRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       254 ~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                        |.|+|++.+..+.++|+. ||+..+-|.+|.|.+++..
T Consensus       326 --gtamVemgd~~aver~v~hLnn~~lfG~kl~v~~SkQ~  363 (494)
T KOG1456|consen  326 --GTAMVEMGDAYAVERAVTHLNNIPLFGGKLNVCVSKQN  363 (494)
T ss_pred             --ceeEEEcCcHHHHHHHHHHhccCccccceEEEeecccc
Confidence              489999999999999998 9999999999999998754

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.54  E-value=3.4e-14  Score=100.08  Aligned_cols=68  Identities=37%  Similarity=0.565  Sum_probs=61.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVR  186 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~  186 (303)
                      |||+|||+++++++|+++|+.||.|..+.+..++.+ ++|+|||+|.+.++|.+|+. +++..++|+.|+
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRFGPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTSSBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhcCCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            799999999999999999999999999999997655 68999999999999999999 888999999874

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 ....

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

Probab=99.53  E-value=3.6e-14  Score=119.25  Aligned_cols=81  Identities=28%  Similarity=0.393  Sum_probs=76.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ...+..+|.|.|||.++++++|+++|..||.|..+.+.+|+.+  ++|||||+|.+.++|.+||. |||.-+..--|+|+
T Consensus       185 ~R~D~~tvRvtNLsed~~E~dL~eLf~~fg~i~rvylardK~TG~~kGFAFVtF~sRddA~rAI~~LnG~gyd~LILrvE  264 (270)
T KOG0122|consen  185 ERDDEATVRVTNLSEDMREDDLEELFRPFGPITRVYLARDKETGLSKGFAFVTFESRDDAARAIADLNGYGYDNLILRVE  264 (270)
T ss_pred             cCCccceeEEecCccccChhHHHHHhhccCccceeEEEEccccCcccceEEEEEecHHHHHHHHHHccCcccceEEEEEE
Confidence            3346788999999999999999999999999999999999987  89999999999999999999 99999999999999


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      |+++
T Consensus       265 wskP  268 (270)
T KOG0122|consen  265 WSKP  268 (270)
T ss_pred             ecCC
Confidence            9875

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

Probab=99.53  E-value=2.2e-12  Score=114.36  Aligned_cols=245  Identities=17%  Similarity=0.156  Sum_probs=179.2

Q ss_pred             ccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc---------
Q 022058           27 TKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---------   97 (303)
Q Consensus        27 ~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---------   97 (303)
                      |=|--|.+|.+-|..+.-.+|+|.+|.|.+.  +.-...|+|     .+     -+    .|++|...|||         
T Consensus       127 IlNp~YpItvDVly~Icnp~GkVlRIvIfkk--ngVQAmVEF-----ds-----v~----~AqrAk~alNGADIYsGCCT  190 (494)
T KOG1456|consen  127 ILNPQYPITVDVLYTICNPQGKVLRIVIFKK--NGVQAMVEF-----DS-----VE----VAQRAKAALNGADIYSGCCT  190 (494)
T ss_pred             eecCccccchhhhhhhcCCCCceEEEEEEec--cceeeEEee-----ch-----hH----HHHHHHhhccccccccccee
Confidence            7788899999999999999999999999764  333339999     66     55    78888888887         


Q ss_pred             ----------------------------------CCC---CC-----------C---------------------chhhh
Q 022058           98 ----------------------------------GRK---RL-----------S---------------------GRAFR  108 (303)
Q Consensus        98 ----------------------------------g~~---~~-----------~---------------------~~~~~  108 (303)
                                                        |+.   +.           +                     .|...
T Consensus       191 LKIeyAkP~rlnV~knd~DtwDyTlp~~~~~~~~g~~~~~r~~~p~~~~~~pss~~G~h~~y~sg~~~~p~~~~P~r~~~  270 (494)
T KOG1456|consen  191 LKIEYAKPTRLNVQKNDKDTWDYTLPDLRGPYDPGRNHYDRQRQPAPLGYHPSSRGGGHSGYYSGDRHGPPHPPPSRYRD  270 (494)
T ss_pred             EEEEecCcceeeeeecCCccccccCCCCCCCCCCCCCCCccccCCCccCCChhhcCCCCCCCcccccCCCCCCCCCCCcc
Confidence                                              000   00           0                     00000


Q ss_pred             hc---------cCCCCCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCC
Q 022058          109 AQ---------REDSVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG  177 (303)
Q Consensus       109 ~~---------~~~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g  177 (303)
                      ..         ......+.++|-+|.. .++-+.|-.+|..||.|+.|++++.+.   |-|.|++.+..+.++|+. ||+
T Consensus       271 ~~~~~~g~a~p~g~~~g~VmMVyGLdh~k~N~drlFNl~ClYGNV~rvkFmkTk~---gtamVemgd~~aver~v~hLnn  347 (494)
T KOG1456|consen  271 GYRDGRGYASPGGGAPGCVMMVYGLDHGKMNCDRLFNLFCLYGNVERVKFMKTKP---GTAMVEMGDAYAVERAVTHLNN  347 (494)
T ss_pred             ccccCCCCCCCCCCCCCcEEEEEeccccccchhhhhhhhhhcCceeeEEEeeccc---ceeEEEcCcHHHHHHHHHHhcc
Confidence            00         0011355699999985 577888999999999999999998664   789999999999999999 999


Q ss_pred             cccCCeeEEEeecCCCCCC-C--------CCCCCCCc-----------cc---ccccccceEEEcCCCCCCCHHHHHHHh
Q 022058          178 TMLGYYPVRVLPSKTAILP-V--------NPTFLPRS-----------ED---EREMCSRTVYCTNIDKKVPQAEVKQFF  234 (303)
Q Consensus       178 ~~~~g~~i~v~~~~~~~~~-~--------~~~~~~~~-----------~~---~~~~~~~~l~V~nL~~~~t~~~L~~~F  234 (303)
                      ..+.|.+|.|..++..... .        +++|....           ..   .-..+++.|...|.|..+||+.|..+|
T Consensus       348 ~~lfG~kl~v~~SkQ~~v~~~~pflLpDgSpSfKdys~SkNnRFssp~qAsKNrIq~Ps~vLHffNaP~~vtEe~l~~i~  427 (494)
T KOG1456|consen  348 IPLFGGKLNVCVSKQNFVSPVQPFLLPDGSPSFKDYSGSKNNRFSSPEQASKNRIQPPSNVLHFFNAPLGVTEEQLIGIC  427 (494)
T ss_pred             CccccceEEEeeccccccccCCceecCCCCcchhhcccccccccCChhHhhcccccCCcceeEEecCCCccCHHHHHHHh
Confidence            9999999999988654321 1        11111100           00   013467889999999999999999999


Q ss_pred             hhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCe------eeEEeecCC
Q 022058          235 EAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQ------PIRVSPSKT  291 (303)
Q Consensus       235 ~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~------~l~v~~a~~  291 (303)
                      .... -...+++|...+......|.++|++.++|..|+. +|...+.+.      .|++.|+.+
T Consensus       428 nek~-v~~~svkvFp~kserSssGllEfe~~s~Aveal~~~NH~pi~~p~gs~PfilKlcfsts  490 (494)
T KOG1456|consen  428 NEKD-VPPTSVKVFPLKSERSSSGLLEFENKSDAVEALMKLNHYPIEGPNGSFPFILKLCFSTS  490 (494)
T ss_pred             hhcC-CCcceEEeecccccccccceeeeehHHHHHHHHHHhccccccCCCCCCCeeeeeeeccc
Confidence            9861 2456778877653223368999999999999998 898888643      566666653

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

Probab=99.51  E-value=5.5e-14  Score=122.63  Aligned_cols=80  Identities=20%  Similarity=0.293  Sum_probs=75.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..+.|+|.|+|+...+-||+.+|++|  |.|.+|+|+.....|||||||+|.+.+||++|.. |||..+.||+|.|.-+.
T Consensus        95 ~pkRLhVSNIPFrFRdpDL~aMF~kf--G~VldVEIIfNERGSKGFGFVTmen~~dadRARa~LHgt~VEGRkIEVn~AT  172 (376)
T KOG0125|consen   95 TPKRLHVSNIPFRFRDPDLRAMFEKF--GKVLDVEIIFNERGSKGFGFVTMENPADADRARAELHGTVVEGRKIEVNNAT  172 (376)
T ss_pred             CCceeEeecCCccccCccHHHHHHhh--CceeeEEEEeccCCCCccceEEecChhhHHHHHHHhhcceeeceEEEEeccc
Confidence            45889999999999999999999999  9999999999877799999999999999999998 99999999999999886


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      +..
T Consensus       173 arV  175 (376)
T KOG0125|consen  173 ARV  175 (376)
T ss_pred             hhh
Confidence            554

>PLN03120 nucleic acid binding protein; Provisional

Probab=99.51  E-value=1.2e-13  Score=119.36  Aligned_cols=77  Identities=26%  Similarity=0.470  Sum_probs=71.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCCC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~~  292 (303)
                      .++|||+|||+.+++++|+++|+.|  |.|.+|.|+++.. ++|||||+|.+.++|..|+.|||..|.|+.|.|.++...
T Consensus         4 ~rtVfVgNLs~~tTE~dLrefFS~~--G~I~~V~I~~d~~-~~GfAFVtF~d~eaAe~AllLnG~~l~gr~V~Vt~a~~~   80 (260)
T PLN03120          4 VRTVKVSNVSLKATERDIKEFFSFS--GDIEYVEMQSENE-RSQIAYVTFKDPQGAETALLLSGATIVDQSVTITPAEDY   80 (260)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeecCC-CCCEEEEEeCcHHHHHHHHHhcCCeeCCceEEEEeccCC
Confidence            4799999999999999999999998  9999999998863 568999999999999999999999999999999998643

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.50  E-value=1.9e-13  Score=116.23  Aligned_cols=79  Identities=20%  Similarity=0.232  Sum_probs=72.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~~  194 (303)
                      ...+|||+||++.+|+++|+++|+.||+|.+|.|+++.. .+|||||+|.++++|+.|+.|+|..|.+++|.|.......
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~G~I~~V~I~~D~e-t~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~~y~   82 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHCGAIEHVEIIRSGE-YACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWGQYE   82 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhcCCeEEEEEecCCC-cceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCcccc
Confidence            357899999999999999999999999999999998854 4689999999999999999999999999999999875443

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

Probab=99.48  E-value=6.6e-14  Score=117.23  Aligned_cols=77  Identities=18%  Similarity=0.271  Sum_probs=69.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      -++||||+|+|.+..+.|+++|++||+|++..|+.|+.+  |||||||+|.+.++|.+|++=-.-.|+||+-.|..+.-
T Consensus        12 ~TKifVggL~w~T~~~~l~~yFeqfGeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA~l   90 (247)
T KOG0149|consen   12 FTKIFVGGLAWETHKETLRRYFEQFGEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLASL   90 (247)
T ss_pred             EEEEEEcCcccccchHHHHHHHHHhCceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchhhh
Confidence            456999999999999999999999999999999999987  89999999999999999999334488999999987643

>PF14259 RRM_6: RNA recognition motif (a

Probab=99.48  E-value=2.4e-13  Score=95.64  Aligned_cols=68  Identities=31%  Similarity=0.552  Sum_probs=61.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       216 l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      |||+|||+.+++++|+++|+.+  |.|..+.+..++ +.++|+|||+|.+.++|.+|++ ++|..++|+.|.
T Consensus         1 v~i~nlp~~~~~~~l~~~f~~~--g~v~~v~~~~~~~~~~~~~a~v~f~~~~~a~~al~~~~~~~~~g~~l~   70 (70)
T PF14259_consen    1 VYISNLPPSTTEEDLRNFFSRF--GPVEKVRLIKNKDGQSRGFAFVEFSSEEDAKRALELLNGKEIDGRKLR   70 (70)
T ss_dssp             EEEESSTTT--HHHHHHHCTTS--SBEEEEEEEESTTSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEE
T ss_pred             CEEeCCCCCCCHHHHHHHHHhc--CCcceEEEEeeeccccCCEEEEEeCCHHHHHHHHHHCCCcEECCEEcC
Confidence            7999999999999999999999  999999999875 7789999999999999999999 888999999884

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 ....

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

Probab=99.44  E-value=9e-13  Score=106.45  Aligned_cols=142  Identities=14%  Similarity=0.147  Sum_probs=104.9

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc-eeeeecchhhhhhchhhhccccchHHhhhhccc-
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH-HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-   97 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~-~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-   97 (303)
                      +.+..|+|+|||.++-+.||.+||-+||.|.+|.|..-. +.... ||+|     +.     +-    +|..||..-++ 
T Consensus         4 r~~~~iyvGNLP~diRekeieDlFyKyg~i~~ieLK~r~-g~ppfafVeF-----Ed-----~R----DAeDAiygRdGY   68 (241)
T KOG0105|consen    4 RNSRRIYVGNLPGDIREKEIEDLFYKYGRIREIELKNRP-GPPPFAFVEF-----ED-----PR----DAEDAIYGRDGY   68 (241)
T ss_pred             cccceEEecCCCcchhhccHHHHHhhhcceEEEEeccCC-CCCCeeEEEe-----cC-----cc----chhhhhhccccc
Confidence            456789999999999999999999999999999985433 32333 9999     66     66    78888765543 


Q ss_pred             --------------CCCCCCchh-----------hhhccCCC---CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEe
Q 022058           98 --------------GRKRLSGRA-----------FRAQREDS---VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC  149 (303)
Q Consensus        98 --------------g~~~~~~~~-----------~~~~~~~~---~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~  149 (303)
                                    |+..-..+-           ....+.+.   ..-.|.|.+||++-++++|+++..+-|.|-...+.
T Consensus        69 dydg~rLRVEfprggr~s~~~~G~y~gggrgGgg~gg~rgppsrrSe~RVvVsGLp~SgSWQDLKDHmReaGdvCfadv~  148 (241)
T KOG0105|consen   69 DYDGCRLRVEFPRGGRSSSDRRGSYSGGGRGGGGGGGRRGPPSRRSEYRVVVSGLPPSGSWQDLKDHMREAGDVCFADVQ  148 (241)
T ss_pred             ccCcceEEEEeccCCCcccccccccCCCCCCCCCCCcccCCcccccceeEEEecCCCCCchHHHHHHHHhhCCeeeeeee
Confidence                          111000000           00001111   23349999999999999999999999999777776


Q ss_pred             eCCCCCceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          150 GDPHSVLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       150 ~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      +|     |++.|+|-..++.+-|+. |..+.+.
T Consensus       149 rD-----g~GvV~~~r~eDMkYAvr~ld~~~~~  176 (241)
T KOG0105|consen  149 RD-----GVGVVEYLRKEDMKYAVRKLDDQKFR  176 (241)
T ss_pred             cc-----cceeeeeeehhhHHHHHHhhcccccc
Confidence            65     589999999999999998 8776664

>PLN03213 repressor of silencing 3; Provisional

Probab=99.44  E-value=3.7e-13  Score=123.08  Aligned_cols=77  Identities=16%  Similarity=0.242  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCH--HHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADE--HGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~--~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ...+||||||++.+++++|+.+|..||.|.+|.|++..  .||||||+|.+.  .++.+||. |||..+.|+.|+|..++
T Consensus         9 ~gMRIYVGNLSydVTEDDLravFSeFGsVkdVEIpRET--GRGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVNKAK   86 (759)
T PLN03213          9 GGVRLHVGGLGESVGRDDLLKIFSPMGTVDAVEFVRTK--GRSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLEKAK   86 (759)
T ss_pred             cceEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeccc--CCceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEeecc
Confidence            45679999999999999999999999999999999543  499999999987  78999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        87 P~   88 (759)
T PLN03213         87 EH   88 (759)
T ss_pred             HH
Confidence            53

>smart00362 RRM_2 RNA recognition motif

Probab=99.44  E-value=9.4e-13  Score=91.80  Aligned_cols=71  Identities=39%  Similarity=0.618  Sum_probs=65.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      +|||+|||..+++++|+++|..||.|..+.+..+...++|+|||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            489999999999999999999999999999998774578999999999999999998 99999999998873

>PLN03121 nucleic acid binding protein; Provisional

Probab=99.43  E-value=1e-12  Score=111.74  Aligned_cols=76  Identities=21%  Similarity=0.270  Sum_probs=70.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      .+.+|||+||++.+|+++|+++|+.+  |.|.+|+|++|. ..+|+|||+|.+.++|..|+.|+|..|.++.|.|..+.
T Consensus         4 ~g~TV~V~NLS~~tTE~dLrefFS~~--G~I~~V~I~~D~-et~gfAfVtF~d~~aaetAllLnGa~l~d~~I~It~~~   79 (243)
T PLN03121          4 GGYTAEVTNLSPKATEKDVYDFFSHC--GAIEHVEIIRSG-EYACTAYVTFKDAYALETAVLLSGATIVDQRVCITRWG   79 (243)
T ss_pred             CceEEEEecCCCCCCHHHHHHHHHhc--CCeEEEEEecCC-CcceEEEEEECCHHHHHHHHhcCCCeeCCceEEEEeCc
Confidence            45899999999999999999999997  999999999984 45689999999999999999999999999999999864

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

Probab=99.43  E-value=3.7e-13  Score=107.83  Aligned_cols=76  Identities=32%  Similarity=0.427  Sum_probs=70.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..+.||||||+..+++.+|...|..||+|.+|-|...+   .|||||+|++..+|+.|+. |+|..|.|..|.|+.+...
T Consensus         9 ~~~kVYVGnL~~~a~k~eLE~~F~~yG~lrsvWvArnP---PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G~   85 (195)
T KOG0107|consen    9 GNTKVYVGNLGSRATKRELERAFSKYGPLRSVWVARNP---PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTGR   85 (195)
T ss_pred             CCceEEeccCCCCcchHHHHHHHHhcCcceeEEEeecC---CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecCC
Confidence            47889999999999999999999999999999998755   4899999999999999998 9999999999999997543

>smart00362 RRM_2 RNA recognition motif

Probab=99.43  E-value=1.2e-12  Score=91.18  Aligned_cols=71  Identities=31%  Similarity=0.550  Sum_probs=66.6

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      +|+|+|||..+++++|+++|.+|  |.|..+.+..+++.++|+|||+|.+.++|..|+. ++|..+.|+.|+|+
T Consensus         1 ~v~i~~l~~~~~~~~l~~~~~~~--g~v~~~~~~~~~~~~~~~~~v~f~~~~~a~~a~~~~~~~~~~~~~i~v~   72 (72)
T smart00362        1 TLFVGNLPPDVTEEDLKELFSKF--GPIESVKIPKDTGKSKGFAFVEFESEEDAEKAIEALNGTKLGGRPLRVE   72 (72)
T ss_pred             CEEEcCCCCcCCHHHHHHHHHhc--CCEEEEEEecCCCCCCceEEEEeCCHHHHHHHHHHhCCcEECCEEEeeC
Confidence            48999999999999999999999  9999999998877788999999999999999998 99999999999874

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

Probab=99.43  E-value=2.6e-12  Score=107.36  Aligned_cols=155  Identities=15%  Similarity=0.180  Sum_probs=116.4

Q ss_pred             cCCCCCcccccchhhhHHHHHH----HHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhc
Q 022058           20 NKNNNLETKKSESEFTVQKLVD----MFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNF   95 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~----~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~   95 (303)
                      |-+++|+|.||......++|+.    ||++||+|.+|...+...-+.-.||-|     .+     .+    .|-.|...+
T Consensus         7 ~pn~TlYInnLnekI~~~elkrsL~~LFsqfG~ildI~a~kt~KmRGQA~VvF-----k~-----~~----~As~A~r~l   72 (221)
T KOG4206|consen    7 NPNGTLYINNLNEKIKKDELKRSLYLLFSQFGKILDISAFKTPKMRGQAFVVF-----KE-----TE----AASAALRAL   72 (221)
T ss_pred             CCCceEeehhccccccHHHHHHHHHHHHHhhCCeEEEEecCCCCccCceEEEe-----cC-----hh----HHHHHHHHh
Confidence            4456999999999999999999    999999999999876544322229999     55     44    555666666


Q ss_pred             cc----CCC-----------CCCchh-------------------hhh-------------------ccCCCCCCEEEEc
Q 022058           96 NQ----GRK-----------RLSGRA-------------------FRA-------------------QREDSVRRTVYVS  122 (303)
Q Consensus        96 ~~----g~~-----------~~~~~~-------------------~~~-------------------~~~~~~~~~l~V~  122 (303)
                      +|    |++           .+..+.                   ...                   .........+|+.
T Consensus        73 ~gfpFygK~mriqyA~s~sdii~~~~~~~v~~~~k~~~~~~~~~~~~~~~ng~~~~~~~~~~p~p~~~~~~ppn~ilf~~  152 (221)
T KOG4206|consen   73 QGFPFYGKPMRIQYAKSDSDIIAQAPGTFVEKEKKINGEILARIKQPLDTNGHFYNMNRMNLPPPFLAQMAPPNNILFLT  152 (221)
T ss_pred             cCCcccCchhheecccCccchhhccCceeccccCccccccccccCCcccccccccccccccCCCCccccCCCCceEEEEe
Confidence            66    322           000000                   000                   0011245669999


Q ss_pred             CCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEeecC
Q 022058          123 DIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG-YYPVRVLPSK  191 (303)
Q Consensus       123 nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~i~v~~~~  191 (303)
                      |||.+++.+.|..+|.+|.-...++++...   .+.|||+|.+...|..|.. +.+..+. ...|.|.+++
T Consensus       153 niP~es~~e~l~~lf~qf~g~keir~i~~~---~~iAfve~~~d~~a~~a~~~lq~~~it~~~~m~i~~a~  220 (221)
T KOG4206|consen  153 NIPSESESEMLSDLFEQFPGFKEIRLIPPR---SGIAFVEFLSDRQASAAQQALQGFKITKKNTMQITFAK  220 (221)
T ss_pred             cCCcchhHHHHHHHHhhCcccceeEeccCC---CceeEEecchhhhhHHHhhhhccceeccCceEEecccC
Confidence            999999999999999999999999998654   3799999999999999998 9988887 7888887753

>PLN03213 repressor of silencing 3; Provisional

Probab=99.41  E-value=8.3e-13  Score=120.80  Aligned_cols=79  Identities=14%  Similarity=0.261  Sum_probs=72.8

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCH--HHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA--ESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~--e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ....+|||+||++.+++++|+..|.+|  |.|.+|.|++..|  +|||||+|.+.  .++.+||. |||..+.|+.|+|.
T Consensus         8 ~~gMRIYVGNLSydVTEDDLravFSeF--GsVkdVEIpRETG--RGFAFVEMssdddaEeeKAISaLNGAEWKGR~LKVN   83 (759)
T PLN03213          8 GGGVRLHVGGLGESVGRDDLLKIFSPM--GTVDAVEFVRTKG--RSFAYIDFSPSSTNSLTKLFSTYNGCVWKGGRLRLE   83 (759)
T ss_pred             CcceEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEecccC--CceEEEEecCCcHHHHHHHHHHhcCCeecCceeEEe
Confidence            345789999999999999999999999  9999999998777  89999999987  67899998 99999999999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      .|+|..
T Consensus        84 KAKP~Y   89 (759)
T PLN03213         84 KAKEHY   89 (759)
T ss_pred             eccHHH
Confidence            998753

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

Probab=99.40  E-value=9.6e-13  Score=110.30  Aligned_cols=83  Identities=18%  Similarity=0.300  Sum_probs=73.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||++|+..+..+.|+++|++|  |+|+.+.|+.|+  |+|+|||||+|.+.++|.+|.+--+..|+||+-.|.+|
T Consensus        11 ~~TKifVggL~w~T~~~~l~~yFeqf--GeI~eavvitd~~t~rskGyGfVTf~d~~aa~rAc~dp~piIdGR~aNcnlA   88 (247)
T KOG0149|consen   11 TFTKIFVGGLAWETHKETLRRYFEQF--GEIVEAVVITDKNTGRSKGYGFVTFRDAEAATRACKDPNPIIDGRKANCNLA   88 (247)
T ss_pred             eEEEEEEcCcccccchHHHHHHHHHh--CceEEEEEEeccCCccccceeeEEeecHHHHHHHhcCCCCcccccccccchh
Confidence            34789999999999999999999999  999999999996  89999999999999999999985567899999998887


Q ss_pred             CCCCCCC
Q 022058          290 KTPVRPR  296 (303)
Q Consensus       290 ~~~~~~r  296 (303)
                      -.--++|
T Consensus        89 ~lg~~pR   95 (247)
T KOG0149|consen   89 SLGGKPR   95 (247)
T ss_pred             hhcCccC
Confidence            5433333

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

Probab=99.40  E-value=9.4e-12  Score=114.90  Aligned_cols=173  Identities=19%  Similarity=0.257  Sum_probs=119.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-----Cce---EEEEEecCHHHHHHHHH-hCCcccCCe
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-----VLR---FAFVEFADEHGARAALN-LGGTMLGYY  183 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-----~~G---~~fV~f~~~~~A~~Ai~-l~g~~~~g~  183 (303)
                      +..++.||||+||++++|+.|...|..||.+. +.++...+.     .+|   |+|+.|+++.++..-+. +.- .-...
T Consensus       256 ~~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~k~~~~~~~ppkGs~~YvflvFe~E~sV~~Ll~aC~~-~~~~~  333 (520)
T KOG0129|consen  256 PRYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPGKANSRGRAPPKGSYGYVFLVFEDERSVQSLLSACSE-GEGNY  333 (520)
T ss_pred             cccccceeecCCCccccHHHHHhhcccccceE-eecCCCccccccCCCCCcccEEEEEecchHHHHHHHHHHhh-cccce
Confidence            34577899999999999999999999999864 566532221     466   99999999999988885 321 11112


Q ss_pred             eEEEeecCCCCCCC-CCCCCCC------cccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCc
Q 022058          184 PVRVLPSKTAILPV-NPTFLPR------SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHS  254 (303)
Q Consensus       184 ~i~v~~~~~~~~~~-~~~~~~~------~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~  254 (303)
                      .+.|.......... -.+|...      .....-.+.+||||++||-.++.++|-.+|+..+ |.|..+-|-.|+  +.+
T Consensus       334 yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~ly-GgV~yaGIDtD~k~KYP  412 (520)
T KOG0129|consen  334 YFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLF-GGVLYVGIDTDPKLKYP  412 (520)
T ss_pred             EEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhc-CceEEEEeccCcccCCC
Confidence            22222211111000 0001000      1112233569999999999999999999999544 999999999995  679


Q ss_pred             ccEEEEEEcCHHHHHHHHH-----hCCceeCCeeeEEeec
Q 022058          255 TRIAFVEFAVAESAILALN-----CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       255 ~g~afV~f~~~e~A~~Ai~-----l~g~~~~g~~l~v~~a  289 (303)
                      +|-|=|+|.+..+-.+||.     |+...+. ++|.|++.
T Consensus       413 kGaGRVtFsnqqsYi~AIsarFvql~h~d~~-KRVEIkPY  451 (520)
T KOG0129|consen  413 KGAGRVTFSNQQAYIKAISARFVQLDHTDID-KRVEIKPY  451 (520)
T ss_pred             CCcceeeecccHHHHHHHhhheEEEeccccc-eeeeecce
Confidence            9999999999999999996     2333333 46676654

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

Probab=99.40  E-value=6.1e-14  Score=112.86  Aligned_cols=78  Identities=23%  Similarity=0.374  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ++.-|||||||+.+||.||--.|++||+|..|.+++|..+  |+||||+.|++..+...|+. |||..|.||.|+|....
T Consensus        34 dsA~Iyiggl~~~LtEgDil~VFSqyGe~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv~  113 (219)
T KOG0126|consen   34 DSAYIYIGGLPYELTEGDILCVFSQYGEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHVS  113 (219)
T ss_pred             cceEEEECCCcccccCCcEEEEeeccCceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeecc
Confidence            5778999999999999999999999999999999999987  89999999999999999998 99999999999999864


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      .
T Consensus       114 ~  114 (219)
T KOG0126|consen  114 N  114 (219)
T ss_pred             c
Confidence            3

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

Probab=99.37  E-value=1.8e-12  Score=115.29  Aligned_cols=253  Identities=17%  Similarity=0.154  Sum_probs=161.0

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcccCCC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK  100 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~  100 (303)
                      -+..+.|||-.++.++-.+|.-.--..--+.+.....+.+.   -|.|     .+     +|... -|.+.-+.+.+++.
T Consensus        62 vvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf-----~d-----~e~Rd-lalkRhkhh~g~ry  130 (508)
T KOG1365|consen   62 VVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRF-----VD-----PEGRD-LALKRHKHHMGTRY  130 (508)
T ss_pred             EEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEe-----cC-----chhhh-hhhHhhhhhccCCc
Confidence            37789999999999999999754322222222222222211   7777     55     33111 23333333333222


Q ss_pred             ----------CCCchhhhhcc-CC----CCCCEEEEcCCCCCCCHHHHHHHhhc---C-CceeEEEEeeCCCC-CceEEE
Q 022058          101 ----------RLSGRAFRAQR-ED----SVRRTVYVSDIDQNITEERLAGLFSS---C-GQVVDCRVCGDPHS-VLRFAF  160 (303)
Q Consensus       101 ----------~~~~~~~~~~~-~~----~~~~~l~V~nlp~~~t~~~l~~~F~~---~-G~i~~~~i~~~~~~-~~G~~f  160 (303)
                                .+......+.. .+    ...--|..++||+++++.++.++|..   . |..+.+-+++.+++ ..|-||
T Consensus       131 ievYka~ge~f~~iagg~s~e~~~flsk~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAF  210 (508)
T KOG1365|consen  131 IEVYKATGEEFLKIAGGTSNEAAPFLSKENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAF  210 (508)
T ss_pred             eeeeccCchhheEecCCccccCCCCCCcccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceE
Confidence                      00000000000 00    11233778999999999999999952   2 35567777776555 789999


Q ss_pred             EEecCHHHHHHHHHhCCcccCCeeEEEeecCCCCC----------CCCC----CCC---CCcccccccccceEEEcCCCC
Q 022058          161 VEFADEHGARAALNLGGTMLGYYPVRVLPSKTAIL----------PVNP----TFL---PRSEDEREMCSRTVYCTNIDK  223 (303)
Q Consensus       161 V~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~~~----------~~~~----~~~---~~~~~~~~~~~~~l~V~nL~~  223 (303)
                      |.|..+++|+.|+.-|...++-|.|.+..+.....          +..+    ...   +...-.......+|.+++||+
T Consensus       211 vlfa~ee~aq~aL~khrq~iGqRYIElFRSTaaEvqqvlnr~~s~pLi~~~~sp~~p~~p~~~~p~~~~kdcvRLRGLPy  290 (508)
T KOG1365|consen  211 VLFACEEDAQFALRKHRQNIGQRYIELFRSTAAEVQQVLNREVSEPLIPGLTSPLLPGGPARLVPPTRSKDCVRLRGLPY  290 (508)
T ss_pred             EEecCHHHHHHHHHHHHHHHhHHHHHHHHHhHHHHHHHHHhhccccccCCCCCCCCCCCccccCCCCCCCCeeEecCCCh
Confidence            99999999999999888888888887766533210          1110    011   111112222357899999999


Q ss_pred             CCCHHHHHHHhhhhcCcceeE--EEEecC-CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          224 KVPQAEVKQFFEAACGGEVTR--LRLLGD-HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       224 ~~t~~~L~~~F~~~~~G~i~~--v~i~~d-~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..+.++|.++|..|. -.|..  |.++.. +|++.|-|||+|.+.|+|..|.+ .+.+...+|.|.|-.
T Consensus       291 ~AtvEdIL~FlgdFa-~~i~f~gVHmv~N~qGrPSGeAFIqm~nae~a~aaaqk~hk~~mk~RYiEvfp  358 (508)
T KOG1365|consen  291 EATVEDILDFLGDFA-TDIRFQGVHMVLNGQGRPSGEAFIQMRNAERARAAAQKCHKKLMKSRYIEVFP  358 (508)
T ss_pred             hhhHHHHHHHHHHHh-hhcccceeEEEEcCCCCcChhhhhhhhhhHHHHHHHHHHHHhhcccceEEEee
Confidence            999999999999983 23433  655544 68999999999999999999887 666666677777654

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

Probab=99.37  E-value=9.4e-13  Score=108.11  Aligned_cols=77  Identities=26%  Similarity=0.389  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      .-.+|.|-||.+-++.++|+.+|++||.|-+|.|+.|..+  ++|||||.|....+|+.|++ |+|..++|+.|.|+.++
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~ar   91 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQMAR   91 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHhCcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehhhh
Confidence            5677999999999999999999999999999999999987  89999999999999999999 99999999999998764

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

Probab=99.36  E-value=3.4e-12  Score=93.61  Aligned_cols=79  Identities=25%  Similarity=0.357  Sum_probs=71.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ++...+-|||.|||+++|.++..++|..||.|..|+|=..+. .+|-|||.|++..+|.+|+. |+|.-+.++.+.|.+.
T Consensus        14 ppevnriLyirNLp~~ITseemydlFGkyg~IrQIRiG~~k~-TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyy   92 (124)
T KOG0114|consen   14 PPEVNRILYIRNLPFKITSEEMYDLFGKYGTIRQIRIGNTKE-TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYY   92 (124)
T ss_pred             ChhhheeEEEecCCccccHHHHHHHhhcccceEEEEecCccC-cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEec
Confidence            344678899999999999999999999999999999965544 48999999999999999999 9999999999999886


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      .
T Consensus        93 q   93 (124)
T KOG0114|consen   93 Q   93 (124)
T ss_pred             C
Confidence            4

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

Probab=99.36  E-value=1.6e-12  Score=99.75  Aligned_cols=79  Identities=20%  Similarity=0.299  Sum_probs=73.8

Q ss_pred             cccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          209 REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       209 ~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      ++..+..|||.++.+..++++|.+.|..|  |.|..+.+-.|.  |-.+|||+|+|.+.++|++|+. |||..|.|+.|.
T Consensus        68 rSVEGwIi~VtgvHeEatEedi~d~F~dy--GeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~  145 (170)
T KOG0130|consen   68 RSVEGWIIFVTGVHEEATEEDIHDKFADY--GEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVS  145 (170)
T ss_pred             cceeeEEEEEeccCcchhHHHHHHHHhhc--ccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCcee
Confidence            34567899999999999999999999999  999999998885  7889999999999999999998 999999999999


Q ss_pred             Eeec
Q 022058          286 VSPS  289 (303)
Q Consensus       286 v~~a  289 (303)
                      |.|+
T Consensus       146 VDw~  149 (170)
T KOG0130|consen  146 VDWC  149 (170)
T ss_pred             EEEE
Confidence            9986

>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=99.35  E-value=8.1e-12  Score=87.48  Aligned_cols=72  Identities=43%  Similarity=0.647  Sum_probs=66.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      +|+|+|||+.+++++|+++|+.+|.|..+.+..++.+ ++|+|||+|.+.++|..|+. +++..+.|+.+.|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            4899999999999999999999999999999987765 68999999999999999999 999999999998864

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).

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

Probab=99.35  E-value=2.3e-12  Score=103.28  Aligned_cols=76  Identities=24%  Similarity=0.320  Sum_probs=69.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      .+.|||+||+..+++.+|..+|..|  |.|..|.|...+   -|||||+|+++.+|..|+. |||..|.|.+|.|.+++-
T Consensus        10 ~~kVYVGnL~~~a~k~eLE~~F~~y--G~lrsvWvArnP---PGfAFVEFed~RDA~DAvr~LDG~~~cG~r~rVE~S~G   84 (195)
T KOG0107|consen   10 NTKVYVGNLGSRATKRELERAFSKY--GPLRSVWVARNP---PGFAFVEFEDPRDAEDAVRYLDGKDICGSRIRVELSTG   84 (195)
T ss_pred             CceEEeccCCCCcchHHHHHHHHhc--CcceeEEEeecC---CCceEEeccCcccHHHHHhhcCCccccCceEEEEeecC
Confidence            4789999999999999999999999  999999998864   3699999999999999998 999999999999999865


Q ss_pred             CC
Q 022058          292 PV  293 (303)
Q Consensus       292 ~~  293 (303)
                      ..
T Consensus        85 ~~   86 (195)
T KOG0107|consen   85 RP   86 (195)
T ss_pred             Cc
Confidence            43

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

Probab=99.35  E-value=4.7e-12  Score=92.89  Aligned_cols=77  Identities=21%  Similarity=0.271  Sum_probs=70.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      .+.|||+|||+++|.++..++|.+|  |.|.+++|-..++ .+|.|||.|++..+|.+|+. |+|+.+.++.|.|.+..+
T Consensus        18 nriLyirNLp~~ITseemydlFGky--g~IrQIRiG~~k~-TrGTAFVVYedi~dAk~A~dhlsg~n~~~ryl~vlyyq~   94 (124)
T KOG0114|consen   18 NRILYIRNLPFKITSEEMYDLFGKY--GTIRQIRIGNTKE-TRGTAFVVYEDIFDAKKACDHLSGYNVDNRYLVVLYYQP   94 (124)
T ss_pred             heeEEEecCCccccHHHHHHHhhcc--cceEEEEecCccC-cCceEEEEehHhhhHHHHHHHhcccccCCceEEEEecCH
Confidence            4789999999999999999999999  9999999977653 56899999999999999998 999999999999999875


Q ss_pred             C
Q 022058          292 P  292 (303)
Q Consensus       292 ~  292 (303)
                      .
T Consensus        95 ~   95 (124)
T KOG0114|consen   95 E   95 (124)
T ss_pred             H
Confidence            4

>smart00360 RRM RNA recognition motif

Probab=99.35  E-value=5.2e-12  Score=87.62  Aligned_cols=68  Identities=38%  Similarity=0.594  Sum_probs=62.5

Q ss_pred             EcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          121 VSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       121 V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      |+|||..+++++|+++|+.||.|..+.+..++.+  ++|+|||+|.+.++|.+|+. +++..+.|+.|.|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            6899999999999999999999999999987643  78999999999999999998 99999999998873

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

Probab=99.34  E-value=6.5e-13  Score=109.99  Aligned_cols=79  Identities=25%  Similarity=0.351  Sum_probs=75.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      -++|||++|...+++.-|...|=+|  |.|.+|.++.|.  ++.+|||||+|...|+|.+||. ||+.+|.||.|+|.++
T Consensus        10 KrtlYVGGladeVtekvLhaAFIPF--GDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen   10 KRTLYVGGLADEVTEKVLHAAFIPF--GDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ceeEEeccchHHHHHHHHHhccccc--cchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            3799999999999999999999999  999999999995  6899999999999999999998 9999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      +|+.
T Consensus        88 kP~k   91 (298)
T KOG0111|consen   88 KPEK   91 (298)
T ss_pred             CCcc
Confidence            9864

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

Probab=99.34  E-value=1.2e-12  Score=108.37  Aligned_cols=82  Identities=29%  Similarity=0.410  Sum_probs=76.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..+++||||+|..++++.-|...|-+||.|.+|.++.|-.+  ++|||||+|.-.++|.+||. ||+.++-||.|+|.++
T Consensus         8 ~~KrtlYVGGladeVtekvLhaAFIPFGDI~dIqiPlDyesqkHRgFgFVefe~aEDAaaAiDNMnesEL~GrtirVN~A   87 (298)
T KOG0111|consen    8 NQKRTLYVGGLADEVTEKVLHAAFIPFGDIKDIQIPLDYESQKHRGFGFVEFEEAEDAAAAIDNMNESELFGRTIRVNLA   87 (298)
T ss_pred             ccceeEEeccchHHHHHHHHHhccccccchhhcccccchhcccccceeEEEeeccchhHHHhhcCchhhhcceeEEEeec
Confidence            46889999999999999999999999999999999998765  89999999999999999999 9999999999999999


Q ss_pred             CCCCC
Q 022058          191 KTAIL  195 (303)
Q Consensus       191 ~~~~~  195 (303)
                      ++...
T Consensus        88 kP~ki   92 (298)
T KOG0111|consen   88 KPEKI   92 (298)
T ss_pred             CCccc
Confidence            77643

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

Probab=99.33  E-value=5.5e-12  Score=108.95  Aligned_cols=79  Identities=20%  Similarity=0.349  Sum_probs=73.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..-+||||+-|+++++|..|+..|+.||+|..|.|+.|..+  ++|||||+|+++.+...|.+ .+|..|+|+.|.|..-
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~YG~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VDvE  178 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKYGPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVDVE  178 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhcCcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEEec
Confidence            45789999999999999999999999999999999999776  89999999999999999999 9999999999999875


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ..
T Consensus       179 Rg  180 (335)
T KOG0113|consen  179 RG  180 (335)
T ss_pred             cc
Confidence            43

>smart00360 RRM RNA recognition motif

Probab=99.32  E-value=9.1e-12  Score=86.36  Aligned_cols=68  Identities=32%  Similarity=0.538  Sum_probs=63.0

Q ss_pred             EcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          218 CTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       218 V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      |+|||..+++++|+++|++|  |.|..+.+..++  +.++|+|||+|.+.++|..|+. |++..+.|+.|+|.
T Consensus         1 i~~l~~~~~~~~l~~~f~~~--g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~a~~a~~~~~~~~~~~~~~~v~   71 (71)
T smart00360        1 VGNLPPDVTEEELRELFSKF--GKIESVRLVRDKDTGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKVK   71 (71)
T ss_pred             CCCCCcccCHHHHHHHHHhh--CCEeEEEEEeCCCCCCCCceEEEEeCCHHHHHHHHHHcCCCeeCCcEEEeC
Confidence            57999999999999999999  999999999874  6789999999999999999998 99999999999874

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

Probab=99.31  E-value=3e-13  Score=108.90  Aligned_cols=76  Identities=24%  Similarity=0.408  Sum_probs=71.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      +.-|||+|||+.+||.||...|++|  |.|++|.+++|+  |+|+||||+.|.+..+..-|+. |||..|.||.|+|...
T Consensus        35 sA~Iyiggl~~~LtEgDil~VFSqy--Ge~vdinLiRDk~TGKSKGFaFLcYEDQRSTILAVDN~NGiki~gRtirVDHv  112 (219)
T KOG0126|consen   35 SAYIYIGGLPYELTEGDILCVFSQY--GEIVDINLIRDKKTGKSKGFAFLCYEDQRSTILAVDNLNGIKILGRTIRVDHV  112 (219)
T ss_pred             ceEEEECCCcccccCCcEEEEeecc--CceEEEEEEecCCCCcccceEEEEecCccceEEEEeccCCceecceeEEeeec
Confidence            3679999999999999999999999  999999999996  8999999999999999999997 9999999999999875


Q ss_pred             C
Q 022058          290 K  290 (303)
Q Consensus       290 ~  290 (303)
                      -
T Consensus       113 ~  113 (219)
T KOG0126|consen  113 S  113 (219)
T ss_pred             c
Confidence            3

>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability

Probab=99.31  E-value=2.2e-11  Score=85.27  Aligned_cols=72  Identities=33%  Similarity=0.572  Sum_probs=66.8

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +|+|+|||..+++++|+++|+.+  |.|..+.+..+. +.++|+|||+|.+.++|..|++ +++..+.|+.++|.+
T Consensus         1 ~i~i~~l~~~~~~~~i~~~~~~~--g~i~~~~~~~~~~~~~~~~~~v~f~s~~~a~~a~~~~~~~~~~~~~~~v~~   74 (74)
T cd00590           1 TLFVGNLPPDVTEEDLRELFSKF--GKVESVRIVRDKDTKSKGFAFVEFEDEEDAEKALEALNGKELGGRPLRVEF   74 (74)
T ss_pred             CEEEeCCCCccCHHHHHHHHHhc--CCEEEEEEeeCCCCCcceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEeC
Confidence            48999999999999999999999  999999999875 4678999999999999999998 999999999999875

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).

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

Probab=99.31  E-value=5e-12  Score=103.88  Aligned_cols=77  Identities=25%  Similarity=0.368  Sum_probs=72.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .-.+|.|-||-+.++.++|+.+|++|  |.|-+|.|++|.  +.++|||||.|....+|+.|+. |+|..|+|+.|.|.+
T Consensus        12 gm~SLkVdNLTyRTspd~LrrvFekY--G~vgDVyIPrdr~Tr~sRgFaFVrf~~k~daedA~damDG~~ldgRelrVq~   89 (256)
T KOG4207|consen   12 GMTSLKVDNLTYRTSPDDLRRVFEKY--GRVGDVYIPRDRYTRQSRGFAFVRFHDKRDAEDALDAMDGAVLDGRELRVQM   89 (256)
T ss_pred             cceeEEecceeccCCHHHHHHHHHHh--CcccceecccccccccccceeEEEeeecchHHHHHHhhcceeeccceeeehh
Confidence            34789999999999999999999999  999999999996  6799999999999999999999 999999999999988


Q ss_pred             cC
Q 022058          289 SK  290 (303)
Q Consensus       289 a~  290 (303)
                      |+
T Consensus        90 ar   91 (256)
T KOG4207|consen   90 AR   91 (256)
T ss_pred             hh
Confidence            75

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

Probab=99.30  E-value=6.1e-12  Score=96.63  Aligned_cols=75  Identities=25%  Similarity=0.348  Sum_probs=71.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      -|||.++....++++|.+.|..||+|..+.+-.|..+  .+||++|+|++.++|++|+. +||..+.|..|.|.|.-.
T Consensus        74 Ii~VtgvHeEatEedi~d~F~dyGeiKNihLNLDRRtGy~KGYaLvEYet~keAq~A~~~~Ng~~ll~q~v~VDw~Fv  151 (170)
T KOG0130|consen   74 IIFVTGVHEEATEEDIHDKFADYGEIKNIHLNLDRRTGYVKGYALVEYETLKEAQAAIDALNGAELLGQNVSVDWCFV  151 (170)
T ss_pred             EEEEeccCcchhHHHHHHHHhhcccccceeeccccccccccceeeeehHhHHHHHHHHHhccchhhhCCceeEEEEEe
Confidence            3999999999999999999999999999999999887  79999999999999999998 999999999999999743

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

Probab=99.29  E-value=7.8e-12  Score=95.25  Aligned_cols=78  Identities=28%  Similarity=0.422  Sum_probs=71.3

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ..+.+|||+||++.++|++|+++|+. | |+|..|.+-.|.  .++=|||||+|-+.++|..|+. ++|..++.+.|.+.
T Consensus        34 r~S~tvyVgNlSfyttEEqiyELFs~-c-G~irriiMGLdr~kktpCGFCFVeyy~~~dA~~AlryisgtrLddr~ir~D  111 (153)
T KOG0121|consen   34 RKSCTVYVGNLSFYTTEEQIYELFSK-C-GDIRRIIMGLDRFKKTPCGFCFVEYYSRDDAEDALRYISGTRLDDRPIRID  111 (153)
T ss_pred             hhcceEEEeeeeeeecHHHHHHHHHh-c-cchheeEeccccCCcCccceEEEEEecchhHHHHHHHhccCcccccceeee
Confidence            35689999999999999999999999 5 999999887775  4678999999999999999999 99999999999999


Q ss_pred             ecC
Q 022058          288 PSK  290 (303)
Q Consensus       288 ~a~  290 (303)
                      |.-
T Consensus       112 ~D~  114 (153)
T KOG0121|consen  112 WDA  114 (153)
T ss_pred             ccc
Confidence            863

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

Probab=99.28  E-value=4.9e-12  Score=106.62  Aligned_cols=141  Identities=16%  Similarity=0.241  Sum_probs=110.6

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc----CC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ----GR   99 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~----g~   99 (303)
                      .++|++|||...+.+|..+|..||.|-+|.+.....     ||+|     ..     ..    +|..|+..+++    |.
T Consensus         3 rv~vg~~~~~~~~~d~E~~f~~yg~~~d~~mk~gf~-----fv~f-----ed-----~r----da~Dav~~l~~~~l~~e   63 (216)
T KOG0106|consen    3 RVYIGRLPYRARERDVERFFKGYGKIPDADMKNGFG-----FVEF-----ED-----PR----DADDAVHDLDGKELCGE   63 (216)
T ss_pred             ceeecccCCccchhHHHHHHhhccccccceeecccc-----eecc-----Cc-----hh----hhhcccchhcCceecce
Confidence            589999999999999999999999999999976543     7888     55     55    78888888776    11


Q ss_pred             C----------------CCCchhh-hh--ccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEE
Q 022058          100 K----------------RLSGRAF-RA--QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAF  160 (303)
Q Consensus       100 ~----------------~~~~~~~-~~--~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~f  160 (303)
                      .                .-..+.. ..  .......+.+.|.+++..+.+++|.+.|..+|.+....+      ..+++|
T Consensus        64 ~~vve~~r~~~~~~g~~~~g~r~~~~~~~~~p~~s~~r~~~~~~~~r~~~qdl~d~~~~~g~~~~~~~------~~~~~~  137 (216)
T KOG0106|consen   64 RLVVEHARGKRRGRGRPRGGDRRSDSRRYRPPSRTHFRLIVRNLSLRVSWQDLKDHFRPAGEVTYVDA------RRNFAF  137 (216)
T ss_pred             eeeeecccccccccCCCCCCCccchhhccCCcccccceeeeccchhhhhHHHHhhhhcccCCCchhhh------hccccc
Confidence            1                0000001 11  112235677999999999999999999999999855444      346999


Q ss_pred             EEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          161 VEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       161 V~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      |+|++.++|.+|+. +++..+.++.|.+..
T Consensus       138 v~Fs~~~da~ra~~~l~~~~~~~~~l~~~~  167 (216)
T KOG0106|consen  138 VEFSEQEDAKRALEKLDGKKLNGRRISVEK  167 (216)
T ss_pred             eeehhhhhhhhcchhccchhhcCceeeecc
Confidence            99999999999998 999999999999943

>PF13893 RRM_5: RNA recognition motif

Probab=99.28  E-value=2.5e-11  Score=81.55  Aligned_cols=55  Identities=31%  Similarity=0.555  Sum_probs=50.4

Q ss_pred             HHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          230 VKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       230 L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      |+++|++|  |.|.++.+.+..   +++|||+|.+.++|..|+. |||..+.|++|+|.||
T Consensus         1 L~~~f~~f--G~V~~i~~~~~~---~~~a~V~f~~~~~A~~a~~~l~~~~~~g~~l~V~~a   56 (56)
T PF13893_consen    1 LYKLFSKF--GEVKKIKIFKKK---RGFAFVEFASVEDAQKAIEQLNGRQFNGRPLKVSYA   56 (56)
T ss_dssp             HHHHHTTT--S-EEEEEEETTS---TTEEEEEESSHHHHHHHHHHHTTSEETTEEEEEEEE
T ss_pred             ChHHhCCc--ccEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            68899999  999999998876   4699999999999999998 9999999999999986

(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 ....

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

Probab=99.27  E-value=2.4e-11  Score=105.02  Aligned_cols=78  Identities=21%  Similarity=0.389  Sum_probs=73.8

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      .+-+||||.-|+..++|+.|+..|+.|  |.|..+.|+.|.  |+++|||||+|++.-+...|.+ .+|..|+|+.|.|.
T Consensus        99 DPy~TLFv~RLnydT~EskLrreF~~Y--G~IkrirlV~d~vTgkskGYAFIeye~erdm~~AYK~adG~~Idgrri~VD  176 (335)
T KOG0113|consen   99 DPYKTLFVARLNYDTSESKLRREFEKY--GPIKRIRLVRDKVTGKSKGYAFIEYEHERDMKAAYKDADGIKIDGRRILVD  176 (335)
T ss_pred             CccceeeeeeccccccHHHHHHHHHhc--CcceeEEEeeecccCCccceEEEEeccHHHHHHHHHhccCceecCcEEEEE
Confidence            456899999999999999999999999  999999999996  8999999999999999999998 99999999999999


Q ss_pred             ecC
Q 022058          288 PSK  290 (303)
Q Consensus       288 ~a~  290 (303)
                      +-.
T Consensus       177 vER  179 (335)
T KOG0113|consen  177 VER  179 (335)
T ss_pred             ecc
Confidence            864

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=99.26  E-value=1.3e-12  Score=126.43  Aligned_cols=224  Identities=17%  Similarity=0.107  Sum_probs=162.6

Q ss_pred             CCcccccchhhhHH-HHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc--
Q 022058           24 NLETKKSESEFTVQ-KLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ--   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~-~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~--   97 (303)
                      .+.+.|+.+..... .++.-|..+|.|..|+++......+..   ++.+     ..     ..    .++.+. ...+  
T Consensus       573 e~~s~~v~p~~~~ke~~~~~~k~~~~vekv~~p~~g~k~h~q~~~~~~~-----s~-----~~----~~esat-~pa~~~  637 (881)
T KOG0128|consen  573 EKESTNVYPEQQKKEIQRRQFKGEGNVEKVNGPKRGFKAHEQPQQQKVQ-----SK-----HG----SAESAT-VPAGGA  637 (881)
T ss_pred             hhcccCCCcchhhHHhhHHHhhcccccccccCccccccccccchhhhhh-----cc-----cc----chhhcc-cccccc
Confidence            45566777766666 578899999999999999843322222   6666     22     11    222211 1111  


Q ss_pred             --CCC---CCCchhhhhcc------CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEee--CCCCCceEEEEEec
Q 022058           98 --GRK---RLSGRAFRAQR------EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCG--DPHSVLRFAFVEFA  164 (303)
Q Consensus        98 --g~~---~~~~~~~~~~~------~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~--~~~~~~G~~fV~f~  164 (303)
                        ++.   ....+......      +.....++||.||++.+.+.+|...|..+|.+..+++.-  +....+|+||+.|.
T Consensus       638 ~a~~~~av~~ad~~~~~~~~kvs~n~~R~~~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F~  717 (881)
T KOG0128|consen  638 LANRSAAVGLADAEEKEENFKVSPNEIRDLIKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEFL  717 (881)
T ss_pred             cCCccccCCCCCchhhhhccCcCchHHHHHHHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEee
Confidence              111   11111111110      011234599999999999999999999999988887762  33337899999999


Q ss_pred             CHHHHHHHHHhCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE
Q 022058          165 DEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR  244 (303)
Q Consensus       165 ~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~  244 (303)
                      ..+++.+|+.++...+.|                              -..++|.|+|+..|.+.|+.++..+  |.+.+
T Consensus       718 ~~~~~~aaV~f~d~~~~g------------------------------K~~v~i~g~pf~gt~e~~k~l~~~~--gn~~~  765 (881)
T KOG0128|consen  718 KPEHAGAAVAFRDSCFFG------------------------------KISVAISGPPFQGTKEELKSLASKT--GNVTS  765 (881)
T ss_pred             cCCchhhhhhhhhhhhhh------------------------------hhhhheeCCCCCCchHHHHhhcccc--CCccc
Confidence            999999999944333333                              1468999999999999999999999  99999


Q ss_pred             EEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          245 LRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       245 v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      ..++... |+++|.++|.|.+..++.++.. +++..+..+.+.|..++|+..
T Consensus       766 ~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~~~~rE~~~~v~vsnp~~~  817 (881)
T KOG0128|consen  766 LRLVTVRAGKPKGKARVDYNTEADASRKVASVDVAGKRENNGEVQVSNPERD  817 (881)
T ss_pred             cchhhhhccccccceeccCCCcchhhhhcccchhhhhhhcCccccccCCccc
Confidence            9988775 8999999999999999999997 888888888888888777443

>PF13893 RRM_5: RNA recognition motif

Probab=99.26  E-value=2.6e-11  Score=81.49  Aligned_cols=55  Identities=35%  Similarity=0.501  Sum_probs=50.1

Q ss_pred             HHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          133 LAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       133 l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      |+++|++||+|.++.+..+.   +|+|||+|.+.++|..|+. |||..+.|++|+|.|+
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            68899999999999998765   5899999999999999998 9999999999999985

(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 ....

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

Probab=99.26  E-value=1.4e-11  Score=114.69  Aligned_cols=77  Identities=31%  Similarity=0.459  Sum_probs=73.5

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      +.|||||||+++++++|.++|+..|.|.+++++.|+.+  ++||||++|.+.++|..|++ |||.++.||+|+|.|+...
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~~~   98 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGVGPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYASNR   98 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhccCccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccccc
Confidence            88999999999999999999999999999999999886  79999999999999999999 9999999999999997543

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

Probab=99.24  E-value=5.4e-11  Score=104.55  Aligned_cols=77  Identities=32%  Similarity=0.547  Sum_probs=73.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..+|||+|||..+++++|.++|.+|  |.|..+.+..|.  +.++|+|||+|.+.++|..|+. |+|..|.|+.|.|.++
T Consensus       115 ~~~l~v~nL~~~~~~~~l~~~F~~~--g~~~~~~~~~d~~~~~~~g~~~v~f~~~~~~~~a~~~~~~~~~~~~~~~v~~~  192 (306)
T COG0724         115 NNTLFVGNLPYDVTEEDLRELFKKF--GPVKRVRLVRDRETGKSRGFAFVEFESEESAEKAIEELNGKELEGRPLRVQKA  192 (306)
T ss_pred             CceEEEeCCCCCCCHHHHHHHHHhc--CceeEEEeeeccccCccCceEEEEecCHHHHHHHHHHcCCCeECCceeEeecc
Confidence            5899999999999999999999999  999999999985  8999999999999999999999 9999999999999997


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      .+
T Consensus       193 ~~  194 (306)
T COG0724         193 QP  194 (306)
T ss_pred             cc
Confidence            64

>smart00361 RRM_1 RNA recognition motif

Probab=99.21  E-value=6.3e-11  Score=83.44  Aligned_cols=59  Identities=19%  Similarity=0.350  Sum_probs=51.9

Q ss_pred             HHHHHHHhh----hhcCcceeEEE-EecCC----CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          227 QAEVKQFFE----AACGGEVTRLR-LLGDH----VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       227 ~~~L~~~F~----~~~~G~i~~v~-i~~d~----~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      +++|+++|+    .|  |.|.++. |..++    ++++|+|||+|.+.++|.+|+. |||..+.|+.|+++
T Consensus         2 ~~~l~~~~~~~~~~f--G~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~~   70 (70)
T smart00361        2 DEDFEREFSEEEEYF--GEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKAE   70 (70)
T ss_pred             chhHHHHHHHHHHhc--CCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEeC
Confidence            578888888    99  9999985 55543    7789999999999999999998 99999999999863

>smart00361 RRM_1 RNA recognition motif

Probab=99.19  E-value=9.8e-11  Score=82.46  Aligned_cols=58  Identities=21%  Similarity=0.270  Sum_probs=51.3

Q ss_pred             HHHHHHHhh----cCCceeEEE-EeeCC----CCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          130 EERLAGLFS----SCGQVVDCR-VCGDP----HSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       130 ~~~l~~~F~----~~G~i~~~~-i~~~~----~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      +++|+++|+    .||.|.++. ++.++    ..++|||||+|.+.++|.+|+. |||..+.|+.|.+
T Consensus         2 ~~~l~~~~~~~~~~fG~v~~v~~v~~~~~~~~~~~rG~~fV~f~~~~dA~~A~~~l~g~~~~gr~l~~   69 (70)
T smart00361        2 DEDFEREFSEEEEYFGEVGKINKIYIDNVGYENHKRGNVYITFERSEDAARAIVDLNGRYFDGRTVKA   69 (70)
T ss_pred             chhHHHHHHHHHHhcCCeeEEEEEEeCCCCCCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEe
Confidence            678999998    999999995 65554    3379999999999999999999 9999999999986

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

Probab=99.16  E-value=5.5e-11  Score=110.84  Aligned_cols=78  Identities=23%  Similarity=0.354  Sum_probs=73.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..+||+|+|+++++++|..+|+..  |.|.+++++.|.  |+++||||++|.+.++|..|+. |||.++.|+.|+|.|+.
T Consensus        19 ~~v~vgnip~~~se~~l~~~~~~~--g~v~s~~~v~D~~tG~~~G~~f~~~~~~~~~~~a~~~lNg~~~~gr~l~v~~~~   96 (435)
T KOG0108|consen   19 SSVFVGNIPYEGSEEQLLSIFSGV--GPVLSFRLVYDRETGKPKGFGFCEFTDEETAERAIRNLNGAEFNGRKLRVNYAS   96 (435)
T ss_pred             cceEecCCCCcccHHHHHHHHhcc--CccceeeecccccCCCcCceeeEecCchhhHHHHHHhcCCcccCCceEEeeccc
Confidence            789999999999999999999998  999999999995  8999999999999999999998 99999999999999986


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      ...
T Consensus        97 ~~~   99 (435)
T KOG0108|consen   97 NRK   99 (435)
T ss_pred             ccc
Confidence            443

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

Probab=99.15  E-value=1.1e-10  Score=109.56  Aligned_cols=170  Identities=22%  Similarity=0.350  Sum_probs=133.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcC-----------C-ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCe
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSC-----------G-QVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYY  183 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~-----------G-~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~  183 (303)
                      .+.++|+++|+.++++.+-.+|..-           | .+..+.+-..    +.|+|++|.+.++|..|+.+++..+.|+
T Consensus       175 ~~r~~v~~~~~~~~e~~~~~f~~~~~~~~gl~~~~~g~~~~s~~~n~~----~nfa~ie~~s~~~at~~~~~~~~~f~g~  250 (500)
T KOG0120|consen  175 ARRLYVGNIPFTSNEESMMSFFNSRMHASGLNQAPDGPSFVSVQLNLE----KNFAFIEFRSISEATEAMALDGIIFEGR  250 (500)
T ss_pred             hhhhcccccCCccCcHhhhhhhhhhhhhcccccCCCCCceeeeeeccc----ccceeEEecCCCchhhhhcccchhhCCC
Confidence            5569999999999999998888732           2 3566666443    4599999999999999999999999999


Q ss_pred             eEEEeecCCCCCCCC----CC----CCCCcc-cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--C
Q 022058          184 PVRVLPSKTAILPVN----PT----FLPRSE-DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--V  252 (303)
Q Consensus       184 ~i~v~~~~~~~~~~~----~~----~~~~~~-~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~  252 (303)
                      ++.+...........    +.    +..... .........+||++||..++++++.++.+.|  |.+..-.++.|.  |
T Consensus       251 ~~~~~r~~d~~~~p~~~~~~~~~~~~~~~~~~t~~~~~~~ki~v~~lp~~l~~~q~~Ell~~f--g~lk~f~lv~d~~~g  328 (500)
T KOG0120|consen  251 PLKIRRPHDYQPVPGITLSPSQLGKVGLLPASTDVPDSPNKIFVGGLPLYLTEDQVKELLDSF--GPLKAFRLVKDSATG  328 (500)
T ss_pred             CceecccccccCCccchhhhccccccCCcccccCcccccchhhhccCcCccCHHHHHHHHHhc--ccchhheeecccccc
Confidence            998876433322111    00    000000 0112234679999999999999999999999  999998888885  6


Q ss_pred             CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          253 HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       253 ~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      .++||||.+|-++.....|+. |||..++++.|.|..|-+
T Consensus       329 ~skg~af~ey~dpsvtd~A~agLnGm~lgd~~lvvq~A~~  368 (500)
T KOG0120|consen  329 NSKGFAFCEYCDPSVTDQAIAGLNGMQLGDKKLVVQRAIV  368 (500)
T ss_pred             cccceeeeeeeCCcchhhhhcccchhhhcCceeEeehhhc
Confidence            899999999999999999998 999999999999998754

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

Probab=99.06  E-value=3.5e-09  Score=93.52  Aligned_cols=152  Identities=13%  Similarity=0.097  Sum_probs=105.2

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcce--------eeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhh
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAK--------EFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRN   93 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~--------v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~   93 (303)
                      .|+|.|||-++|.+++.++|++||-|.+        |+|-++..++..+  -+.|     ..     .+    ...-|+.
T Consensus       136 ~VYVsgLP~DiT~dE~~~~~sKcGiI~~d~~t~epk~KlYrd~~G~lKGDaLc~y-----~K-----~E----SVeLA~~  201 (382)
T KOG1548|consen  136 SVYVSGLPLDITVDEFAEVMSKCGIIMRDPQTGEPKVKLYRDNQGKLKGDALCCY-----IK-----RE----SVELAIK  201 (382)
T ss_pred             eEEecCCCCcccHHHHHHHHHhcceEeccCCCCCeeEEEEecCCCCccCceEEEe-----ec-----cc----HHHHHHH
Confidence            5999999999999999999999998854        6888888877766  5555     22     22    2223433


Q ss_pred             hccc------------------------CCCC----------------CCchhhh-hccCCCCCCEEEEcCCC----CCC
Q 022058           94 NFNQ------------------------GRKR----------------LSGRAFR-AQREDSVRRTVYVSDID----QNI  128 (303)
Q Consensus        94 ~~~~------------------------g~~~----------------~~~~~~~-~~~~~~~~~~l~V~nlp----~~~  128 (303)
                      .|++                        ++..                +.++... ........++|.+.|+-    ...
T Consensus       202 ilDe~~~rg~~~rVerAkfq~Kge~~~~~k~k~k~~~~kk~~k~q~k~~dw~pd~~~~sk~r~~~tVi~kn~Ftp~~~~~  281 (382)
T KOG1548|consen  202 ILDEDELRGKKLRVERAKFQMKGEYDASKKEKGKCKDKKKLKKQQQKLLDWRPDRDDPSKARADRTVILKNMFTPEDFEK  281 (382)
T ss_pred             HhCcccccCcEEEEehhhhhhccCcCcccccccccccHHHHHHHHHhhcccCCCccccccccCCcEEEeeecCCHHHhcc
Confidence            3332                        1110                0011111 00112246789999984    223


Q ss_pred             C-------HHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          129 T-------EERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       129 t-------~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +       .++|++-.+.||.|.+|.|.-  +.+.|.+-|.|.+.++|..||+ |+|..+.||.|......
T Consensus       282 ~~~l~~dlkedl~eec~K~G~v~~vvv~d--~hPdGvvtV~f~n~eeA~~ciq~m~GR~fdgRql~A~i~D  350 (382)
T KOG1548|consen  282 NPDLLNDLKEDLTEECEKFGQVRKVVVYD--RHPDGVVTVSFRNNEEADQCIQTMDGRWFDGRQLTASIWD  350 (382)
T ss_pred             CHHHHHHHHHHHHHHHHHhCCcceEEEec--cCCCceeEEEeCChHHHHHHHHHhcCeeecceEEEEEEeC
Confidence            3       334556678999999998863  2357999999999999999999 99999999999987754

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=99.05  E-value=1.4e-10  Score=113.01  Aligned_cols=160  Identities=17%  Similarity=0.293  Sum_probs=134.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC-CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH-SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~-~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++||+|||+..+++.+|+..|..+|.|.+|.|-+... +-.-|+||.|.+.+.+..|.. +.+..|....+++.+...
T Consensus       371 atrTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~~n~dmtp~ak~e~s~~~I~~g~~r~glG~~  450 (975)
T KOG0112|consen  371 ATRTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSLLNTDMTPSAKFEESGPLIGNGTHRIGLGQP  450 (975)
T ss_pred             hhhhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhhhccccCcccchhhcCCccccCccccccccc
Confidence            577899999999999999999999999999999976533 345699999999999999997 888887655555554321


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL  272 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai  272 (303)
                                      .....+.+++++|+..+....|.+.|..|  |.|..|.+-...    -|++|+|.+...|+.|+
T Consensus       451 ----------------kst~ttr~~sgglg~w~p~~~l~r~fd~f--Gpir~Idy~hgq----~yayi~yes~~~aq~a~  508 (975)
T KOG0112|consen  451 ----------------KSTPTTRLQSGGLGPWSPVSRLNREFDRF--GPIRIIDYRHGQ----PYAYIQYESPPAAQAAT  508 (975)
T ss_pred             ----------------ccccceeeccCCCCCCChHHHHHHHhhcc--CcceeeecccCC----cceeeecccCccchhhH
Confidence                            22345789999999999999999999999  999998775543    39999999999999999


Q ss_pred             H-hCCceeCC--eeeEEeecCCCCCCC
Q 022058          273 N-CSGMVLGS--QPIRVSPSKTPVRPR  296 (303)
Q Consensus       273 ~-l~g~~~~g--~~l~v~~a~~~~~~r  296 (303)
                      . |-|..|+|  ++|.|.|+.++.+..
T Consensus       509 ~~~rgap~G~P~~r~rvdla~~~~~~P  535 (975)
T KOG0112|consen  509 HDMRGAPLGGPPRRLRVDLASPPGATP  535 (975)
T ss_pred             HHHhcCcCCCCCcccccccccCCCCCh
Confidence            8 99999975  789999998876544

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

Probab=99.04  E-value=2.1e-10  Score=97.29  Aligned_cols=162  Identities=20%  Similarity=0.294  Sum_probs=125.1

Q ss_pred             EEEEcCCCCCCCHHH-H--HHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          118 TVYVSDIDQNITEER-L--AGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~-l--~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..+++++-..+..+- |  ...|+.+-......++.+..+ -++++|+.|.....-.++-. -+++.++-++|+..-...
T Consensus        98 ~p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~k~s~a~~k~~~~~~~Kki~~~~VR~a~gts  177 (290)
T KOG0226|consen   98 RPFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESFKASDALLKAETEKEKKKIGKPPVRLAAGTS  177 (290)
T ss_pred             cccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCcchhhhhhhhccccccccccCcceeeccccc
Confidence            356666655554443 3  677887777777777776544 68999999998888777776 777777777766654432


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                      .        ......+-......||++.|...++++-|-..|.+|  ......++++|+  |+++||+||.|.+..++..
T Consensus       178 w--------edPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kf--psf~~akviRdkRTgKSkgygfVSf~~pad~~r  247 (290)
T KOG0226|consen  178 W--------EDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKF--PSFQKAKVIRDKRTGKSKGYGFVSFRDPADYVR  247 (290)
T ss_pred             c--------CCcccccCccccceeecccccccccHHHHHHHHHhc--cchhhccccccccccccccceeeeecCHHHHHH
Confidence            2        111112223345789999999999999999999999  888999999996  8999999999999999999


Q ss_pred             HHH-hCCceeCCeeeEEeec
Q 022058          271 ALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       271 Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      |+. |||..++.+.|++.-+
T Consensus       248 Amrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  248 AMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             HHHhhcccccccchhHhhhh
Confidence            998 9999999999987654

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=99.02  E-value=4e-10  Score=100.38  Aligned_cols=180  Identities=24%  Similarity=0.254  Sum_probs=135.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC--CCceEEEEEecCHHHHHHHHHhCCc-ccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH--SVLRFAFVEFADEHGARAALNLGGT-MLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~--~~~G~~fV~f~~~~~A~~Ai~l~g~-~~~g~~i~v~~~~  191 (303)
                      ..++.|++++.+.+.+.+...++..+|....+.+.....  .++|++++.|...+.+..|+.+.+. ...++.+......
T Consensus        87 ~~~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f~~ks~~~~~l~~s~~~~~~~~~~~~dl~~  166 (285)
T KOG4210|consen   87 SSSTFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHFAGKSQFFAALEESGSKVLDGNKGEKDLNT  166 (285)
T ss_pred             ccccccccccccchhhccccccchhhcCcccchhhhhccccccccceeeccccHHHHHHHHHhhhccccccccccCcccc
Confidence            467899999999999998999999999887776665433  3899999999999999999996664 4445554443322


Q ss_pred             CCCCCCCCCCCCCcccccccccceEE-EcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVY-CTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESA  268 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~-V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A  268 (303)
                      .-....   ..+....... ...++| |.+|++.+++++|+.+|...  |.|..++++.++  +.++|+|+|.|.+..++
T Consensus       167 ~~~~~~---~n~~~~~~~~-~s~~~~~~~~~~f~~~~d~~~~~~~~~--~~i~~~r~~~~~~s~~~kg~a~~~~~~~~~~  240 (285)
T KOG4210|consen  167 RRGLRP---KNKLSRLSSG-PSDTIFFVGELDFSLTRDDLKEHFVSS--GEITSVRLPTDEESGDSKGFAYVDFSAGNSK  240 (285)
T ss_pred             cccccc---cchhcccccC-ccccceeecccccccchHHHhhhccCc--CcceeeccCCCCCccchhhhhhhhhhhchhH
Confidence            111000   0001011112 234455 99999999999999999997  999999999886  68999999999999999


Q ss_pred             HHHHHhCCceeCCeeeEEeecCCCCCCCCCCC
Q 022058          269 ILALNCSGMVLGSQPIRVSPSKTPVRPRVTRP  300 (303)
Q Consensus       269 ~~Ai~l~g~~~~g~~l~v~~a~~~~~~r~~r~  300 (303)
                      ..++..+...+.++.+.+.+..+....-..+.
T Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  272 (285)
T KOG4210|consen  241 KLALNDQTRSIGGRPLRLEEDEPRPKSDGGLF  272 (285)
T ss_pred             HHHhhcccCcccCcccccccCCCCcccccccc
Confidence            88887777889999999999987654434443

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

Probab=99.00  E-value=1.5e-09  Score=95.86  Aligned_cols=76  Identities=21%  Similarity=0.403  Sum_probs=70.0

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH--hCCceeCCeeeEEe
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN--CSGMVLGSQPIRVS  287 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~--l~g~~~~g~~l~v~  287 (303)
                      ....++|||++|-..+++.+|+++|.+|  |+|.++.+....+    +|||+|.+.++|+.|..  +|...+.|++|+|.
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqy--Geirsi~~~~~~~----CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~  298 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQY--GEIRSIRILPRKG----CAFVTFTTREAAEKAAEKSFNKLVINGFRLKIK  298 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhc--CCeeeEEeecccc----cceeeehhhHHHHHHHHhhcceeeecceEEEEE
Confidence            4456899999999999999999999999  9999999998875    99999999999999886  78888999999999


Q ss_pred             ecCC
Q 022058          288 PSKT  291 (303)
Q Consensus       288 ~a~~  291 (303)
                      |+.+
T Consensus       299 Wg~~  302 (377)
T KOG0153|consen  299 WGRP  302 (377)
T ss_pred             eCCC
Confidence            9987

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

Probab=98.99  E-value=9e-11  Score=97.38  Aligned_cols=132  Identities=23%  Similarity=0.368  Sum_probs=111.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|+...++++.|.++|-+-|+|..+.|+.+..+..-||||.|+++-++.-|++ +||..+.++++.|.+- 
T Consensus         6 ae~drtl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f~~E~sv~~a~~L~ng~~l~~~e~q~~~r-   84 (267)
T KOG4454|consen    6 AEMDRTLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFFPNENSVQLAGQLENGDDLEEDEEQRTLR-   84 (267)
T ss_pred             cchhhHHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeecccccchhhhhhhcccchhccchhhcccc-
Confidence            34678999999999999999999999999999999998887743499999999999999999 9999999998887652 


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcC----CCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTN----IDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAE  266 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~n----L~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e  266 (303)
                                                .++    |...++++.+...|+.-  |.+..+++.++. |+.+-++|+.+...-
T Consensus        85 --------------------------~G~shapld~r~~~ei~~~v~s~a--~p~~~~R~~~~~d~rnrn~~~~~~qr~~  136 (267)
T KOG4454|consen   85 --------------------------CGNSHAPLDERVTEEILYEVFSQA--GPIEGVRIPTDNDGRNRNFGFVTYQRLC  136 (267)
T ss_pred             --------------------------cCCCcchhhhhcchhhheeeeccc--CCCCCccccccccCCccCccchhhhhhh
Confidence                                      222    55667889899999998  999999999885 778889999987655


Q ss_pred             HHHHHHH
Q 022058          267 SAILALN  273 (303)
Q Consensus       267 ~A~~Ai~  273 (303)
                      +.-.++.
T Consensus       137 ~~P~~~~  143 (267)
T KOG4454|consen  137 AVPFALD  143 (267)
T ss_pred             cCcHHhh
Confidence            5555554

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

Probab=98.97  E-value=3e-10  Score=94.29  Aligned_cols=141  Identities=23%  Similarity=0.237  Sum_probs=115.8

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc-eeeeecchhhhhhchhhhccccchHHhhhhcccCCCCC
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH-HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRL  102 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~-~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~~~  102 (303)
                      +|||.|+...+|++-|.++|-+-|||+.|.|++++++.... ||+|     ..     +.    ...-|++-+|+.+.. 
T Consensus        11 tl~v~n~~~~v~eelL~ElfiqaGPV~kv~ip~~~d~~~kFa~v~f-----~~-----E~----sv~~a~~L~ng~~l~-   75 (267)
T KOG4454|consen   11 TLLVQNMYSGVSEELLSELFIQAGPVYKVGIPSGQDQEQKFAYVFF-----PN-----EN----SVQLAGQLENGDDLE-   75 (267)
T ss_pred             HHHHHhhhhhhhHHHHHHHhhccCceEEEeCCCCccCCCceeeeec-----cc-----cc----chhhhhhhcccchhc-
Confidence            89999999999999999999999999999999999988886 9999     44     33    456778888873321 


Q ss_pred             CchhhhhccCCCCCCEEEEcC----CCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hC
Q 022058          103 SGRAFRAQREDSVRRTVYVSD----IDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LG  176 (303)
Q Consensus       103 ~~~~~~~~~~~~~~~~l~V~n----lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~  176 (303)
                               ......+++.|+    |...++++.+...|+.-|++..+++.++.++ ++-++|+.+...-....++. ..
T Consensus        76 ---------~~e~q~~~r~G~shapld~r~~~ei~~~v~s~a~p~~~~R~~~~~d~rnrn~~~~~~qr~~~~P~~~~~y~  146 (267)
T KOG4454|consen   76 ---------EDEEQRTLRCGNSHAPLDERVTEEILYEVFSQAGPIEGVRIPTDNDGRNRNFGFVTYQRLCAVPFALDLYQ  146 (267)
T ss_pred             ---------cchhhcccccCCCcchhhhhcchhhheeeecccCCCCCccccccccCCccCccchhhhhhhcCcHHhhhhc
Confidence                     222456788888    8889999999999999999999999988775 77899999999888888887 77


Q ss_pred             CcccCCeeEEEe
Q 022058          177 GTMLGYYPVRVL  188 (303)
Q Consensus       177 g~~~~g~~i~v~  188 (303)
                      +...--+++.+.
T Consensus       147 ~l~~~~~~~~~g  158 (267)
T KOG4454|consen  147 GLELFQKKVTIG  158 (267)
T ss_pred             ccCcCCCCcccc
Confidence            666655554443

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.91  E-value=2e-08  Score=95.77  Aligned_cols=74  Identities=19%  Similarity=0.255  Sum_probs=64.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcce-eEEEEecC-CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEV-TRLRLLGD-HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i-~~v~i~~d-~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+.|-+.|+|++++-+||.++|..|  -.+ .+|.+.+. +|..+|-|.|-|.+.++|..|.. |+++.|.++.|.|..
T Consensus       867 p~V~~~~n~Pf~v~l~dI~~FF~dY--~~~p~sI~~r~nd~G~pTGe~mvAfes~~eAr~A~~dl~~~~i~nr~V~l~i  943 (944)
T KOG4307|consen  867 PRVLSCNNFPFDVTLEDIVEFFNDY--EPDPNSIRIRRNDDGVPTGECMVAFESQEEARRASMDLDGQKIRNRVVSLRI  943 (944)
T ss_pred             CeEEEecCCCccccHHHHHHHhccc--ccCCCceeEeecCCCCcccceeEeecCHHHHHhhhhccccCcccceeEEEEe
Confidence            3578899999999999999999998  333 34666654 58999999999999999999998 999999999998864

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

Probab=98.90  E-value=3e-09  Score=102.47  Aligned_cols=74  Identities=24%  Similarity=0.368  Sum_probs=68.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ++|||||+|+..+++++|..+|+.||+|.+|.++.    ++|||||.+...++|.+|+. |....+.++.|+|.|+...
T Consensus       421 SrTLwvG~i~k~v~e~dL~~~feefGeiqSi~li~----~R~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa~g~  495 (894)
T KOG0132|consen  421 SRTLWVGGIPKNVTEQDLANLFEEFGEIQSIILIP----PRGCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWAVGK  495 (894)
T ss_pred             eeeeeeccccchhhHHHHHHHHHhcccceeEeecc----CCceeEEEEeehhHHHHHHHHHhcccccceeeEEeeeccC
Confidence            78899999999999999999999999999999864    46899999999999999998 9999999999999998543

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

Probab=98.90  E-value=2.3e-09  Score=94.80  Aligned_cols=83  Identities=17%  Similarity=0.293  Sum_probs=76.0

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      .++...|||--|.+-+++++|.-+|+.|  |.|.+|.|++|.  |.+-.||||+|.+.+++.+|.- |++..|++++|+|
T Consensus       236 ~PPeNVLFVCKLNPVTtDeDLeiIFSrF--G~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHV  313 (479)
T KOG0415|consen  236 KPPENVLFVCKLNPVTTDEDLEIIFSRF--GKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHV  313 (479)
T ss_pred             CCCcceEEEEecCCcccccchhhHHhhc--ccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEe
Confidence            3466889999999999999999999999  999999999995  7788999999999999999996 9999999999999


Q ss_pred             eecCCCCC
Q 022058          287 SPSKTPVR  294 (303)
Q Consensus       287 ~~a~~~~~  294 (303)
                      .|+....+
T Consensus       314 DFSQSVsk  321 (479)
T KOG0415|consen  314 DFSQSVSK  321 (479)
T ss_pred             ehhhhhhh
Confidence            99876554

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

Probab=98.87  E-value=6.7e-09  Score=91.82  Aligned_cols=76  Identities=17%  Similarity=0.377  Sum_probs=68.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH--hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN--LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~--l~g~~~~g~~i~v~~~  190 (303)
                      +...++|||++|-..+++.+|+++|-+||+|.++++....    |+|||+|.+.++|+.|.+  +|...|.|++|.|.|+
T Consensus       225 D~~I~tLyIg~l~d~v~e~dIrdhFyqyGeirsi~~~~~~----~CAFv~ftTR~aAE~Aae~~~n~lvI~G~Rl~i~Wg  300 (377)
T KOG0153|consen  225 DTSIKTLYIGGLNDEVLEQDIRDHFYQYGEIRSIRILPRK----GCAFVTFTTREAAEKAAEKSFNKLVINGFRLKIKWG  300 (377)
T ss_pred             ccceeEEEecccccchhHHHHHHHHhhcCCeeeEEeeccc----ccceeeehhhHHHHHHHHhhcceeeecceEEEEEeC
Confidence            3357789999998899999999999999999999997644    699999999999999996  8888889999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      .+
T Consensus       301 ~~  302 (377)
T KOG0153|consen  301 RP  302 (377)
T ss_pred             CC
Confidence            76

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

Probab=98.87  E-value=6.6e-09  Score=85.84  Aligned_cols=80  Identities=26%  Similarity=0.342  Sum_probs=70.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ....++|..+|..+.+.++..+|.+|. |.|..+++.+..  |.|+|||||+|.+.+.|..|-. ||++-+.++.|.|.+
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~-g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~v  126 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFG-GTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHV  126 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcC-CeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEE
Confidence            346789999999999999999999984 677778887775  8999999999999999999998 999999999999998


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      -.|-
T Consensus       127 mppe  130 (214)
T KOG4208|consen  127 MPPE  130 (214)
T ss_pred             eCch
Confidence            7554

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

Probab=98.82  E-value=2e-08  Score=89.77  Aligned_cols=162  Identities=20%  Similarity=0.240  Sum_probs=113.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEee-CCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCG-DPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~-~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      +...+..++|||..++.+|-.+|....-..-.+.+. ...+ ..|.+.|.|.+.+.-+.|++-+...+++|.|.|-.+..
T Consensus        59 ~~vvvRaRglpwq~Sd~~ia~ff~gl~ia~gg~aKOG~~qgrRnge~lvrf~d~e~RdlalkRhkhh~g~ryievYka~g  138 (508)
T KOG1365|consen   59 DNVVVRARGLPWQSSDQDIARFFKGLNIANGGRALCLNAQGRRNGEALVRFVDPEGRDLALKRHKHHMGTRYIEVYKATG  138 (508)
T ss_pred             cceEEEecCCCCCcccCCHHHHHhhhhccccceeeeehhhhccccceEEEecCchhhhhhhHhhhhhccCCceeeeccCc
Confidence            445577899999999999999998442221111111 1122 45899999999999999999888899999999977643


Q ss_pred             CCC-CC-------CCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhc--CcceeEEEEecC-CCCcccEEEEE
Q 022058          193 AIL-PV-------NPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAAC--GGEVTRLRLLGD-HVHSTRIAFVE  261 (303)
Q Consensus       193 ~~~-~~-------~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~--~G~i~~v~i~~d-~~~~~g~afV~  261 (303)
                      ... ..       .+.|.++      ...-.|..++||+++++.|+..+|.+.|  .|..+.|-++.. .|+.+|-|||.
T Consensus       139 e~f~~iagg~s~e~~~flsk------~~qvivRmRGLPfdat~~dVv~FF~~~cpv~~g~egvLFV~rpdgrpTGdAFvl  212 (508)
T KOG1365|consen  139 EEFLKIAGGTSNEAAPFLSK------ENQVIVRMRGLPFDATALDVVEFFGPPCPVTGGTEGVLFVTRPDGRPTGDAFVL  212 (508)
T ss_pred             hhheEecCCccccCCCCCCc------ccceEEEecCCCCCcchHHHHHhcCCCCcccCCccceEEEECCCCCcccceEEE
Confidence            311 00       0111111      1234678899999999999999997655  145556655554 68999999999


Q ss_pred             EcCHHHHHHHHHhCCceeCCe
Q 022058          262 FAVAESAILALNCSGMVLGSQ  282 (303)
Q Consensus       262 f~~~e~A~~Ai~l~g~~~~g~  282 (303)
                      |...++|+.|+.-|-..++-|
T Consensus       213 fa~ee~aq~aL~khrq~iGqR  233 (508)
T KOG1365|consen  213 FACEEDAQFALRKHRQNIGQR  233 (508)
T ss_pred             ecCHHHHHHHHHHHHHHHhHH
Confidence            999999999996444444433

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

Probab=98.82  E-value=6.5e-09  Score=92.05  Aligned_cols=78  Identities=24%  Similarity=0.471  Sum_probs=72.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +...|||.-|.+-++.++|.-+|+.||.|.+|.+++|..+  +.-||||+|++.+++++|.- |++..|.++.|.|.+++
T Consensus       238 PeNVLFVCKLNPVTtDeDLeiIFSrFG~i~sceVIRD~ktgdsLqyaFiEFen~escE~AyFKMdNvLIDDrRIHVDFSQ  317 (479)
T KOG0415|consen  238 PENVLFVCKLNPVTTDEDLEIIFSRFGKIVSCEVIRDRKTGDSLQYAFIEFENKESCEQAYFKMDNVLIDDRRIHVDFSQ  317 (479)
T ss_pred             CcceEEEEecCCcccccchhhHHhhcccceeeeEEecccccchhheeeeeecchhhHHHHHhhhcceeeccceEEeehhh
Confidence            4567999999999999999999999999999999999887  78899999999999999996 99999999999999874


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      .
T Consensus       318 S  318 (479)
T KOG0415|consen  318 S  318 (479)
T ss_pred             h
Confidence            3

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

Probab=98.81  E-value=2.4e-08  Score=83.33  Aligned_cols=88  Identities=16%  Similarity=0.260  Sum_probs=74.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC-CC--CcccEEEEEEcCHHHHHHHHH-hCCceeC---Ceee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-HV--HSTRIAFVEFAVAESAILALN-CSGMVLG---SQPI  284 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d-~~--~~~g~afV~f~~~e~A~~Ai~-l~g~~~~---g~~l  284 (303)
                      ..+||||.+||.++...+|..+|.+|  ..-+.+.|... ++  -++-+|||+|.+..+|..|++ |||..|+   +..|
T Consensus        33 ~VRTLFVSGLP~DvKpREiynLFR~f--~GYEgslLK~Tsk~~~~~~pvaFatF~s~q~A~aamnaLNGvrFDpE~~stL  110 (284)
T KOG1457|consen   33 AVRTLFVSGLPNDVKPREIYNLFRRF--HGYEGSLLKYTSKGDQVCKPVAFATFTSHQFALAAMNALNGVRFDPETGSTL  110 (284)
T ss_pred             ccceeeeccCCcccCHHHHHHHhccC--CCccceeeeeccCCCccccceEEEEecchHHHHHHHHHhcCeeeccccCcee
Confidence            46899999999999999999999998  66666666544 32  356799999999999999999 9999995   7899


Q ss_pred             EEeecCCCCCCCCCCCC
Q 022058          285 RVSPSKTPVRPRVTRPG  301 (303)
Q Consensus       285 ~v~~a~~~~~~r~~r~~  301 (303)
                      ++.++|...+.++.|.+
T Consensus       111 hiElAKSNtK~kr~k~s  127 (284)
T KOG1457|consen  111 HIELAKSNTKRKRRKGS  127 (284)
T ss_pred             EeeehhcCcccccCCCC
Confidence            99999988776666654

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

Probab=98.74  E-value=2.9e-08  Score=92.85  Aligned_cols=84  Identities=14%  Similarity=0.258  Sum_probs=75.0

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCC--CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~--~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ..+++|+|.+|...+...+|+.+|++|  |.|+-++|++...  ..++|+||++.+.++|.+||. ||-.+|+|+.|.|.
T Consensus       403 ~~gRNlWVSGLSstTRAtDLKnlFSKy--GKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVE  480 (940)
T KOG4661|consen  403 TLGRNLWVSGLSSTTRATDLKNLFSKY--GKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVE  480 (940)
T ss_pred             ccccceeeeccccchhhhHHHHHHHHh--cceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeee
Confidence            346789999999999999999999999  9999999998752  358999999999999999998 99999999999999


Q ss_pred             ecCCCCCCC
Q 022058          288 PSKTPVRPR  296 (303)
Q Consensus       288 ~a~~~~~~r  296 (303)
                      .++..+...
T Consensus       481 kaKNEp~Gk  489 (940)
T KOG4661|consen  481 KAKNEPGGK  489 (940)
T ss_pred             ecccCcccc
Confidence            997765443

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]

Probab=98.74  E-value=2.3e-08  Score=97.97  Aligned_cols=149  Identities=14%  Similarity=0.135  Sum_probs=113.3

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      .+||++||+.++++.+|+..|..+|.|.+|.|-+-..+..+.  ||.|     ..     ..    .+-.+.-.+.+   
T Consensus       373 rTLf~Gnl~~kl~eseiR~af~e~gkve~VDiKtP~~~~esa~~f~~~-----~n-----~d----mtp~ak~e~s~~~I  438 (975)
T KOG0112|consen  373 RTLFLGNLDSKLTESEIRPAFDESGKVEEVDIKTPHIKTESAYAFVSL-----LN-----TD----MTPSAKFEESGPLI  438 (975)
T ss_pred             hhhhhcCcccchhhhhhhhhhhhhccccccccccCCCCcccchhhhhh-----hc-----cc----cCcccchhhcCCcc
Confidence            389999999999999999999999999999997764433333  8888     54     33    44444444443   


Q ss_pred             --CCCCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-
Q 022058           98 --GRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-  174 (303)
Q Consensus        98 --g~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-  174 (303)
                        |...+.    .........+.+++++|+.++....|...|..||.|..|.+-.    ...|+||.|++...++.|+. 
T Consensus       439 ~~g~~r~g----lG~~kst~ttr~~sgglg~w~p~~~l~r~fd~fGpir~Idy~h----gq~yayi~yes~~~aq~a~~~  510 (975)
T KOG0112|consen  439 GNGTHRIG----LGQPKSTPTTRLQSGGLGPWSPVSRLNREFDRFGPIRIIDYRH----GQPYAYIQYESPPAAQAATHD  510 (975)
T ss_pred             ccCccccc----ccccccccceeeccCCCCCCChHHHHHHHhhccCcceeeeccc----CCcceeeecccCccchhhHHH
Confidence              211111    1111233567899999999999999999999999998866522    23599999999999999999 


Q ss_pred             hCCcccCC--eeEEEeecCCC
Q 022058          175 LGGTMLGY--YPVRVLPSKTA  193 (303)
Q Consensus       175 l~g~~~~g--~~i~v~~~~~~  193 (303)
                      |-|..++|  +.+.|.++...
T Consensus       511 ~rgap~G~P~~r~rvdla~~~  531 (975)
T KOG0112|consen  511 MRGAPLGGPPRRLRVDLASPP  531 (975)
T ss_pred             HhcCcCCCCCcccccccccCC
Confidence            99999985  88999987654

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

Probab=98.74  E-value=2.4e-08  Score=96.41  Aligned_cols=75  Identities=25%  Similarity=0.449  Sum_probs=69.5

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++||||++|+..+++.||.++|+.|  |.|.+|.+....    |+|||++.+..+|.+|++ |++..+.++.|++.|+
T Consensus       419 V~SrTLwvG~i~k~v~e~dL~~~feef--GeiqSi~li~~R----~cAfI~M~~RqdA~kalqkl~n~kv~~k~Iki~Wa  492 (894)
T KOG0132|consen  419 VCSRTLWVGGIPKNVTEQDLANLFEEF--GEIQSIILIPPR----GCAFIKMVRRQDAEKALQKLSNVKVADKTIKIAWA  492 (894)
T ss_pred             EeeeeeeeccccchhhHHHHHHHHHhc--ccceeEeeccCC----ceeEEEEeehhHHHHHHHHHhcccccceeeEEeee
Confidence            357899999999999999999999999  999999997665    599999999999999998 9999999999999998


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      .-
T Consensus       493 ~g  494 (894)
T KOG0132|consen  493 VG  494 (894)
T ss_pred             cc
Confidence            53

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

Probab=98.73  E-value=2.6e-08  Score=93.12  Aligned_cols=79  Identities=25%  Similarity=0.365  Sum_probs=72.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||.+|+..+-..+|+.+|++||.|.-.+++++-.+  -+.||||++.+.++|.+||. ||.+++.|+.|.|..++
T Consensus       404 ~gRNlWVSGLSstTRAtDLKnlFSKyGKVvGAKVVTNaRsPGaRCYGfVTMSts~eAtkCI~hLHrTELHGrmISVEkaK  483 (940)
T KOG4661|consen  404 LGRNLWVSGLSSTTRATDLKNLFSKYGKVVGAKVVTNARSPGARCYGFVTMSTSAEATKCIEHLHRTELHGRMISVEKAK  483 (940)
T ss_pred             cccceeeeccccchhhhHHHHHHHHhcceeceeeeecCCCCCcceeEEEEecchHHHHHHHHHhhhhhhcceeeeeeecc
Confidence            3677999999999999999999999999999999987765  58899999999999999999 99999999999999876


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus       484 NE  485 (940)
T KOG4661|consen  484 NE  485 (940)
T ss_pred             cC
Confidence            54

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

Probab=98.72  E-value=4.6e-08  Score=80.88  Aligned_cols=78  Identities=23%  Similarity=0.336  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC-CceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSC-GQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~-G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....+++..+|.-+.+..+..+|.++ |.+..+++.++..+  |+|||||+|++++.|.-|-+ ||+..+.++-|.|..-
T Consensus        48 ~~g~~~~~~~p~g~~e~~~~~~~~q~~g~v~r~rlsRnkrTGNSKgYAFVEFEs~eVA~IaAETMNNYLl~e~lL~c~vm  127 (214)
T KOG4208|consen   48 IEGVVYVDHIPHGFFETEILNYFRQFGGTVTRFRLSRNKRTGNSKGYAFVEFESEEVAKIAAETMNNYLLMEHLLECHVM  127 (214)
T ss_pred             CccceeecccccchhHHHHhhhhhhcCCeeEEEEeecccccCCcCceEEEEeccHHHHHHHHHHhhhhhhhhheeeeEEe
Confidence            45669999999999999999999988 78888888888765  89999999999999999998 9999999999999875


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      .+
T Consensus       128 pp  129 (214)
T KOG4208|consen  128 PP  129 (214)
T ss_pred             Cc
Confidence            43

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

Probab=98.65  E-value=1.1e-07  Score=82.12  Aligned_cols=78  Identities=23%  Similarity=0.285  Sum_probs=72.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ....|+|.|||+.++++||+++|..||.+..+.+-+++.+ +.|.|-|.|...++|.+|++ +|+..++|++|.+.....
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i~~  161 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEFGELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEIISS  161 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHhccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEecC
Confidence            4577999999999999999999999999999999999887 89999999999999999999 999999999999887644

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]

Probab=98.65  E-value=2.9e-08  Score=88.54  Aligned_cols=156  Identities=17%  Similarity=0.198  Sum_probs=114.6

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhc----
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNF----   95 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~----   95 (303)
                      -+.|++++.+.+.+.+...+|.++|.+..+.+....+....+   |+.|     +.     .+    .+..++...    
T Consensus        89 ~~~f~g~~s~~~e~~~~~~~~~~~g~~~~~~~S~~~~~~~sk~~~s~~f-----~~-----ks----~~~~~l~~s~~~~  154 (285)
T KOG4210|consen   89 STFFVGELSENIEESEDDNFSSEAGLRVDARSSSLEDSLSSKGGLSVHF-----AG-----KS----QFFAALEESGSKV  154 (285)
T ss_pred             ccccccccccchhhccccccchhhcCcccchhhhhccccccccceeecc-----cc-----HH----HHHHHHHhhhccc
Confidence            368999999999999999999999999999888866544333   8888     65     44    444433221    


Q ss_pred             ccCC---CCCCchhh------hhccCCCCCCEEE-EcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEe
Q 022058           96 NQGR---KRLSGRAF------RAQREDSVRRTVY-VSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEF  163 (303)
Q Consensus        96 ~~g~---~~~~~~~~------~~~~~~~~~~~l~-V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f  163 (303)
                      +.+.   ..+.....      ..........++| |++|+..+++++|+..|..+|.|..++++.++.+  .+|||||.|
T Consensus       155 ~~~~~~~~dl~~~~~~~~~n~~~~~~~~~s~~~~~~~~~~f~~~~d~~~~~~~~~~~i~~~r~~~~~~s~~~kg~a~~~~  234 (285)
T KOG4210|consen  155 LDGNKGEKDLNTRRGLRPKNKLSRLSSGPSDTIFFVGELDFSLTRDDLKEHFVSSGEITSVRLPTDEESGDSKGFAYVDF  234 (285)
T ss_pred             cccccccCcccccccccccchhcccccCccccceeecccccccchHHHhhhccCcCcceeeccCCCCCccchhhhhhhhh
Confidence            1111   11111000      0011122344455 9999999999999999999999999999998776  799999999


Q ss_pred             cCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          164 ADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       164 ~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      .....+..++..+...+.++++.+....+
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  263 (285)
T KOG4210|consen  235 SAGNSKKLALNDQTRSIGGRPLRLEEDEP  263 (285)
T ss_pred             hhchhHHHHhhcccCcccCcccccccCCC
Confidence            99999999997666778899999988653

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

Probab=98.64  E-value=1.3e-07  Score=81.69  Aligned_cols=79  Identities=27%  Similarity=0.377  Sum_probs=72.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ....|+|.|||..++++||+++|..|  |.+..+-|-.++ |.+.|.|-|.|...++|.+|++ +||..++|+.+++...
T Consensus        82 ~~~~v~v~NL~~~V~~~Dl~eLF~~~--~~~~r~~vhy~~~G~s~Gta~v~~~r~~DA~~avk~~~gv~ldG~~mk~~~i  159 (243)
T KOG0533|consen   82 RSTKVNVSNLPYGVIDADLKELFAEF--GELKRVAVHYDRAGRSLGTADVSFNRRDDAERAVKKYNGVALDGRPMKIEII  159 (243)
T ss_pred             CcceeeeecCCcCcchHHHHHHHHHh--ccceEEeeccCCCCCCCccceeeecchHhHHHHHHHhcCcccCCceeeeEEe
Confidence            34789999999999999999999999  999999999996 8999999999999999999998 9999999999998875


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      .++
T Consensus       160 ~~~  162 (243)
T KOG0533|consen  160 SSP  162 (243)
T ss_pred             cCc
Confidence            443

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]

Probab=98.63  E-value=8.6e-09  Score=100.47  Aligned_cols=142  Identities=13%  Similarity=-0.010  Sum_probs=111.8

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCC-CCc--eeeeecchhhhhhchhhhccccchHHhhhhcccCC
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQH-TDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGR   99 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~-~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~   99 (303)
                      .++||+||++.+.+.+|...|..+|.+..+++.-....+ .++  |+.|     ..     ++    .|.+|+.-...  
T Consensus       668 ~~~fvsnl~~~~~~~dl~~~~~~~~~~e~vqi~~h~n~~~~rG~~Y~~F-----~~-----~~----~~~aaV~f~d~--  731 (881)
T KOG0128|consen  668 IKIFVSNLSPKMSEEDLSERFSPSGTIEVVQIVIHKNEKRFRGKAYVEF-----LK-----PE----HAGAAVAFRDS--  731 (881)
T ss_pred             HHHHHhhcchhhcCchhhhhcCccchhhhHHHHHHhhccccccceeeEe-----ec-----CC----chhhhhhhhhh--
Confidence            358999999999999999999999998888776333322 233  9999     77     66    56665542221  


Q ss_pred             CCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCC
Q 022058          100 KRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGG  177 (303)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g  177 (303)
                                  ....+..|+|.|.|+..|.+.|+.+++.+|.+.+.+++..+.+ .+|.+||.|.++.++.+++. .+.
T Consensus       732 ------------~~~gK~~v~i~g~pf~gt~e~~k~l~~~~gn~~~~~~vt~r~gkpkg~a~v~y~~ea~~s~~~~s~d~  799 (881)
T KOG0128|consen  732 ------------CFFGKISVAISGPPFQGTKEELKSLASKTGNVTSLRLVTVRAGKPKGKARVDYNTEADASRKVASVDV  799 (881)
T ss_pred             ------------hhhhhhhhheeCCCCCCchHHHHhhccccCCccccchhhhhccccccceeccCCCcchhhhhcccchh
Confidence                        0001567999999999999999999999999999998887776 89999999999999999997 877


Q ss_pred             cccCCeeEEEeecCC
Q 022058          178 TMLGYYPVRVLPSKT  192 (303)
Q Consensus       178 ~~~~g~~i~v~~~~~  192 (303)
                      ..+.-+.+.|..+.+
T Consensus       800 ~~~rE~~~~v~vsnp  814 (881)
T KOG0128|consen  800 AGKRENNGEVQVSNP  814 (881)
T ss_pred             hhhhhcCccccccCC
Confidence            777666666665433

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

Probab=98.58  E-value=4.1e-07  Score=84.62  Aligned_cols=141  Identities=16%  Similarity=0.154  Sum_probs=96.7

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCC-----Cc---eeeeecchhhhhhchhhhccccchHHh
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHT-----DH---HFSVINNNFADDNKQSAIDNFNNNRRR   91 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~-----~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a   91 (303)
                      ..+.+|||+.||+++||++|...|..||.+. |..+. +.+..     .+   ||..   -|..     +.    ..+..
T Consensus       257 ~~S~KVFvGGlp~dise~~i~~~F~~FGs~~-VdWP~-k~~~~~~~ppkGs~~Yvfl---vFe~-----E~----sV~~L  322 (520)
T KOG0129|consen  257 RYSRKVFVGGLPWDITEAQINASFGQFGSVK-VDWPG-KANSRGRAPPKGSYGYVFL---VFED-----ER----SVQSL  322 (520)
T ss_pred             ccccceeecCCCccccHHHHHhhcccccceE-eecCC-CccccccCCCCCcccEEEE---Eecc-----hH----HHHHH
Confidence            6677899999999999999999999999975 34442 11111     11   4444   1133     21    11222


Q ss_pred             hhhcc--cCCC---------------CCCchhh------hhccCCCCCCEEEEcCCCCCCCHHHHHHHhh-cCCceeEEE
Q 022058           92 RNNFN--QGRK---------------RLSGRAF------RAQREDSVRRTVYVSDIDQNITEERLAGLFS-SCGQVVDCR  147 (303)
Q Consensus        92 ~~~~~--~g~~---------------~~~~~~~------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~  147 (303)
                      +....  .++.               .+.|...      ...+.-+..+|||||+||.-++.++|-.+|. .||-|..+-
T Consensus       323 l~aC~~~~~~~yf~vss~~~k~k~VQIrPW~laDs~fv~d~sq~lDprrTVFVGgvprpl~A~eLA~imd~lyGgV~yaG  402 (520)
T KOG0129|consen  323 LSACSEGEGNYYFKVSSPTIKDKEVQIRPWVLADSDFVLDHNQPIDPRRTVFVGGLPRPLTAEELAMIMEDLFGGVLYVG  402 (520)
T ss_pred             HHHHhhcccceEEEEecCcccccceeEEeeEeccchhhhccCcccCccceEEecCCCCcchHHHHHHHHHHhcCceEEEE
Confidence            22111  1111               1111111      1222334689999999999999999999999 899999999


Q ss_pred             EeeCCC-C-CceEEEEEecCHHHHHHHHH
Q 022058          148 VCGDPH-S-VLRFAFVEFADEHGARAALN  174 (303)
Q Consensus       148 i~~~~~-~-~~G~~fV~f~~~~~A~~Ai~  174 (303)
                      |-.|+. . .+|-|=|+|++..+-.+||.
T Consensus       403 IDtD~k~KYPkGaGRVtFsnqqsYi~AIs  431 (520)
T KOG0129|consen  403 IDTDPKLKYPKGAGRVTFSNQQAYIKAIS  431 (520)
T ss_pred             eccCcccCCCCCcceeeecccHHHHHHHh
Confidence            988854 4 89999999999999999997

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=98.56  E-value=7.1e-09  Score=93.69  Aligned_cols=148  Identities=20%  Similarity=0.243  Sum_probs=116.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCC-cccCCeeEEEeecCCCCC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG-TMLGYYPVRVLPSKTAIL  195 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g-~~~~g~~i~v~~~~~~~~  195 (303)
                      .+|++||.+..+..+|+.+|...-.-.+-.++.    ..||+||.+.+...|.+|++ ++| .++.|.++.|..+-++. 
T Consensus         3 klyignL~p~~~psdl~svfg~ak~~~~g~fl~----k~gyafvd~pdq~wa~kaie~~sgk~elqGkr~e~~~sv~kk-   77 (584)
T KOG2193|consen    3 KLYIGNLSPQVTPSDLESVFGDAKIPGSGQFLV----KSGYAFVDCPDQQWANKAIETLSGKVELQGKRQEVEHSVPKK-   77 (584)
T ss_pred             cccccccCCCCChHHHHHHhccccCCCCcceee----ecceeeccCCchhhhhhhHHhhchhhhhcCceeeccchhhHH-
Confidence            589999999999999999997541111111221    24899999999999999999 777 55779999998763221 


Q ss_pred             CCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEec-CCCCcccEEEEEEcCHHHHHHHHH-
Q 022058          196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLG-DHVHSTRIAFVEFAVAESAILALN-  273 (303)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~-d~~~~~g~afV~f~~~e~A~~Ai~-  273 (303)
                                     ...+.+-|+|+|+...++-|..+...|  |.++.|.... |..  +-..-|+|.+.+.+..||. 
T Consensus        78 ---------------qrsrk~Qirnippql~wevld~Ll~qy--g~ve~~eqvnt~~e--tavvnvty~~~~~~~~ai~k  138 (584)
T KOG2193|consen   78 ---------------QRSRKIQIRNIPPQLQWEVLDSLLAQY--GTVENCEQVNTDSE--TAVVNVTYSAQQQHRQAIHK  138 (584)
T ss_pred             ---------------HHhhhhhHhcCCHHHHHHHHHHHHhcc--CCHhHhhhhccchH--HHHHHHHHHHHHHHHHHHHh
Confidence                           123568899999999999999999999  9999997643 332  2245578999999999998 


Q ss_pred             hCCceeCCeeeEEeec
Q 022058          274 CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       274 l~g~~~~g~~l~v~~a  289 (303)
                      |+|..+....+++.|-
T Consensus       139 l~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen  139 LNGPQLENQHLKVGYI  154 (584)
T ss_pred             hcchHhhhhhhhcccC
Confidence            9999999999999873

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

Probab=98.55  E-value=8.4e-08  Score=89.83  Aligned_cols=166  Identities=16%  Similarity=0.202  Sum_probs=108.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..++|+|-|||.++++++|+.+|+.||+|..++.-..   .+|..||+|-+..+|++|++ |++.+|.|+.|+.......
T Consensus        74 ~~~~L~v~nl~~~Vsn~~L~~~f~~yGeir~ir~t~~---~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k~~~~~~~  150 (549)
T KOG4660|consen   74 NQGTLVVFNLPRSVSNDTLLRIFGAYGEIREIRETPN---KRGIVFVEFYDVRDAERALKALNRREIAGKRIKRPGGARR  150 (549)
T ss_pred             ccceEEEEecCCcCCHHHHHHHHHhhcchhhhhcccc---cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhcCCCcccc
Confidence            5788999999999999999999999999998665433   46899999999999999999 9999999998883221111


Q ss_pred             CC--CCCCCCCCCc------ccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCH
Q 022058          194 IL--PVNPTFLPRS------EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA  265 (303)
Q Consensus       194 ~~--~~~~~~~~~~------~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~  265 (303)
                      ..  ..+..+...-      .....-....++ +.|++..+...+..+|..+  |.+.. +..   +.-...-|+.|.+.
T Consensus       151 ~~~~~~~~~~~~~~~~p~a~s~pgg~~~~~~~-g~l~P~~s~~~~~~~~~~~--~~~~~-~~~---~~~~hq~~~~~~~~  223 (549)
T KOG4660|consen  151 AMGLQSGTSFLNHFGSPLANSPPGGWPRGQLF-GMLSPTRSSILLEHISSVD--GSSPG-RET---PLLNHQRFVEFADN  223 (549)
T ss_pred             cchhcccchhhhhccchhhcCCCCCCcCCcce-eeeccchhhhhhhcchhcc--Ccccc-ccc---cchhhhhhhhhccc
Confidence            00  0000000000      000011112333 3388888876666667666  76665 222   11112577888888


Q ss_pred             HHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          266 ESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       266 e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      .++..+.. + |..+.+..-...++.+
T Consensus       224 ~s~a~~~~~~-G~~~s~~~~v~t~S~~  249 (549)
T KOG4660|consen  224 RSYAFSEPRG-GFLISNSSGVITFSGP  249 (549)
T ss_pred             cchhhcccCC-ceecCCCCceEEecCC
Confidence            88755554 4 7777766655555543

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

Probab=98.54  E-value=2.5e-07  Score=88.70  Aligned_cols=84  Identities=17%  Similarity=0.264  Sum_probs=73.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-----CCcccEEEEEEcCHHHHHHHHH-hCCceeCCee
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-----VHSTRIAFVEFAVAESAILALN-CSGMVLGSQP  283 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-----~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~  283 (303)
                      .+..++|||+||++.++++.|...|..|  |+|..++|+.-.     .+.+.+|||-|.+..+|++|+. |+|..+.+..
T Consensus       171 DP~TTNlyv~Nlnpsv~E~~ll~tfGrf--gPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e  248 (877)
T KOG0151|consen  171 DPQTTNLYVGNLNPSVDENFLLRTFGRF--GPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYE  248 (877)
T ss_pred             CCcccceeeecCCccccHHHHHHHhccc--CcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeee
Confidence            4556899999999999999999999999  999999887542     3456799999999999999998 9999999999


Q ss_pred             eEEeecCCCCCC
Q 022058          284 IRVSPSKTPVRP  295 (303)
Q Consensus       284 l~v~~a~~~~~~  295 (303)
                      +++.|+++.+-+
T Consensus       249 ~K~gWgk~V~ip  260 (877)
T KOG0151|consen  249 MKLGWGKAVPIP  260 (877)
T ss_pred             eeeccccccccC
Confidence            999999654433

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

Probab=98.53  E-value=1.9e-07  Score=86.93  Aligned_cols=77  Identities=17%  Similarity=0.279  Sum_probs=67.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCC--CCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP--HSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~--~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..+|||+|||.+++..+|++.|..||.|+...|....  ..+.+||||+|.+.++++.||.-+-..++++.+.|+.-+.
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~FG~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~~  366 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQFGPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKRP  366 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhcccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEeccc
Confidence            4459999999999999999999999999988887644  2344899999999999999999778889999999987544

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.52  E-value=8.7e-07  Score=65.85  Aligned_cols=76  Identities=21%  Similarity=0.231  Sum_probs=64.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhc--CCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccC----CeeEE
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSS--CGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLG----YYPVR  186 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~--~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~----g~~i~  186 (303)
                      .+||+|+|||...|.++|.+++..  .|...-+.++.|..+  +.|||||.|.+++.|.+..+ ++|..+.    .+...
T Consensus         1 RTTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~   80 (97)
T PF04059_consen    1 RTTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCE   80 (97)
T ss_pred             CeeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEE
Confidence            368999999999999999988863  467788888888765  89999999999999999998 9998885    35556


Q ss_pred             EeecC
Q 022058          187 VLPSK  191 (303)
Q Consensus       187 v~~~~  191 (303)
                      |.+++
T Consensus        81 i~yAr   85 (97)
T PF04059_consen   81 ISYAR   85 (97)
T ss_pred             EehhH
Confidence            66654

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.52  E-value=2.8e-07  Score=88.38  Aligned_cols=79  Identities=20%  Similarity=0.333  Sum_probs=70.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-----CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-----VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ..++|||+||+++++++.|-..|..||+|.+++++....-     .+-||||.|-+..+|++|++ |+|+.+.++.+++.
T Consensus       173 ~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~g  252 (877)
T KOG0151|consen  173 QTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLG  252 (877)
T ss_pred             cccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeec
Confidence            4567999999999999999999999999999999885432     46799999999999999999 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      |+++-
T Consensus       253 Wgk~V  257 (877)
T KOG0151|consen  253 WGKAV  257 (877)
T ss_pred             ccccc
Confidence            98553

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=98.51  E-value=5.3e-08  Score=87.37  Aligned_cols=171  Identities=21%  Similarity=0.238  Sum_probs=126.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-----CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-----VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-----~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ...|.|.||.++.+.++++.+|...|.|..+.|+.....     ....|||.|.+...+..|..|..+.+-++.|.|-+.
T Consensus         7 ~~vIqvanispsat~dqm~tlFg~lGkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p~   86 (479)
T KOG4676|consen    7 LGVIQVANISPSATKDQMQTLFGNLGKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRPY   86 (479)
T ss_pred             CceeeecccCchhhHHHHHHHHhhccccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEec
Confidence            347999999999999999999999999999999885443     357899999999999999998888888888888764


Q ss_pred             CCCCC-------------------CCCC---CC------------------CCCcccc--cccccceEEEcCCCCCCCHH
Q 022058          191 KTAIL-------------------PVNP---TF------------------LPRSEDE--REMCSRTVYCTNIDKKVPQA  228 (303)
Q Consensus       191 ~~~~~-------------------~~~~---~~------------------~~~~~~~--~~~~~~~l~V~nL~~~~t~~  228 (303)
                      -....                   +.+.   .-                  ++.....  -+.-.++++|.+|+..+...
T Consensus        87 ~~~~~p~r~af~~l~~~navprll~pdg~Lp~~~~lt~~nh~p~ailktP~Lp~~~~A~kleeirRt~~v~sl~~~~~l~  166 (479)
T KOG4676|consen   87 GDEVIPDRFAFVELADQNAVPRLLPPDGVLPGDRPLTKINHSPNAILKTPELPPQAAAKKLEEIRRTREVQSLISAAILP  166 (479)
T ss_pred             CCCCCccHHHHHhcCcccccccccCCCCccCCCCccccccCCccceecCCCCChHhhhhhhHHHHhhhhhhcchhhhcch
Confidence            22111                   0000   00                  0000000  01123679999999999999


Q ss_pred             HHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          229 EVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       229 ~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ++...|..+  |.|.+..+.-...  .-+|.+.|....+...|+.++|..+.-+...+..-+
T Consensus       167 e~~e~f~r~--Gev~ya~~ask~~--s~~c~~sf~~qts~~halr~~gre~k~qhsr~ai~k  224 (479)
T KOG4676|consen  167 ESGESFERK--GEVSYAHTASKSR--SSSCSHSFRKQTSSKHALRSHGRERKRQHSRRAIIK  224 (479)
T ss_pred             hhhhhhhhc--chhhhhhhhccCC--CcchhhhHhhhhhHHHHHHhcchhhhhhhhhhhhcC
Confidence            999999999  9999887765432  236789999998889999999988874444443333

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.49  E-value=2.5e-07  Score=80.01  Aligned_cols=81  Identities=27%  Similarity=0.423  Sum_probs=74.0

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ......+||+|+.+.++.+++..+|+. | |.|..+.|+.|.  ++++||+||+|.+.+.+..|+.|||..|.|+.+.|.
T Consensus        98 ~~d~~sv~v~nvd~~~t~~~~e~hf~~-C-g~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt  175 (231)
T KOG4209|consen   98 EVDAPSVWVGNVDFLVTLTKIELHFES-C-GGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVT  175 (231)
T ss_pred             ccCCceEEEeccccccccchhhheeec-c-CCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceee
Confidence            456689999999999999999999999 5 999999999986  679999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022058          288 PSKTP  292 (303)
Q Consensus       288 ~a~~~  292 (303)
                      +.+..
T Consensus       176 ~~r~~  180 (231)
T KOG4209|consen  176 LKRTN  180 (231)
T ss_pred             eeeee
Confidence            87544

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]

Probab=98.48  E-value=3.6e-07  Score=87.43  Aligned_cols=170  Identities=15%  Similarity=0.061  Sum_probs=126.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~  193 (303)
                      .+.+-+.+.+++.+..+++++|..- .|.++.|..+.-.  ..|-++|.|....++++|++-|...+-.|.+.+...-..
T Consensus       311 ~~y~~~~gm~fn~~~nd~rkfF~g~-~~~~~~l~~~~v~~~~tG~~~v~f~~~~~~q~A~~rn~~~~~~R~~q~~P~g~~  389 (944)
T KOG4307|consen  311 KYYNNYKGMEFNNDFNDGRKFFPGR-NAQSTDLSENRVAPPQTGRKTVMFTPQAPFQNAFTRNPSDDVNRPFQTGPPGNL  389 (944)
T ss_pred             hheeeecccccccccchhhhhcCcc-cccccchhhhhcCCCcCCceEEEecCcchHHHHHhcCchhhhhcceeecCCCcc
Confidence            4557778999999999999998643 3455555544433  379999999999999999998888888899988765322


Q ss_pred             CCCC------------------CCCCCCCccc-------ccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE-EEE
Q 022058          194 ILPV------------------NPTFLPRSED-------EREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR-LRL  247 (303)
Q Consensus       194 ~~~~------------------~~~~~~~~~~-------~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~-v~i  247 (303)
                      ....                  .+...++...       .......+|||..||..+++.++.++|...  -.|++ |.|
T Consensus       390 ~~~~a~~~~~~~~~~~~~~~hg~p~~~pr~~~~~gq~vp~P~~ag~~lyv~~lP~~t~~~~~v~~f~~~--~~Ved~I~l  467 (944)
T KOG4307|consen  390 GRNGAPPFQAGVPPPVIQNNHGRPIAPPRAMVRPGQNVPFPGGAGGALYVFQLPVMTPIVPPVNKFMGA--AAVEDFIEL  467 (944)
T ss_pred             ccccCccccccCCCCcccccCCCCCCCcccccCCCCCCCCCCCccceEEeccCCccccccchhhhhhhh--hhhhheeEe
Confidence            1100                  0001111100       112235789999999999999999999987  57777 777


Q ss_pred             ecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          248 LGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       248 ~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+.+ ++-++.|||.|.+.+++..|.. -+.+.++.+.|+|..
T Consensus       468 t~~P~~~~~~~afv~F~~~~a~~~a~~~~~k~y~G~r~irv~s  510 (944)
T KOG4307|consen  468 TRLPTDLLRPAAFVAFIHPTAPLTASSVKTKFYPGHRIIRVDS  510 (944)
T ss_pred             ccCCcccccchhhheeccccccchhhhcccccccCceEEEeec
Confidence            7775 6778899999999999999988 677778888999875

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2

Probab=98.48  E-value=1.2e-06  Score=65.17  Aligned_cols=78  Identities=23%  Similarity=0.227  Sum_probs=68.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeC----CeeeEE
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLG----SQPIRV  286 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~----g~~l~v  286 (303)
                      +||-|+|+|...|.++|.+++...|.|...-+.++.|-  +.+.|||||.|.++++|.+-.+ ++|..+.    .+...|
T Consensus         2 TTvMirNIPn~~t~~~L~~~l~~~~~g~yDF~YLPiDf~~~~N~GYAFVNf~~~~~~~~F~~~f~g~~w~~~~s~Kvc~i   81 (97)
T PF04059_consen    2 TTVMIRNIPNKYTQEMLIQILDEHFKGKYDFFYLPIDFKNKCNLGYAFVNFTSPQAAIRFYKAFNGKKWPNFNSKKVCEI   81 (97)
T ss_pred             eeEEEecCCCCCCHHHHHHHHHHhccCcceEEEeeeeccCCCceEEEEEEcCCHHHHHHHHHHHcCCccccCCCCcEEEE
Confidence            68999999999999999999998776888889999884  5679999999999999999888 9999885    567778


Q ss_pred             eecCC
Q 022058          287 SPSKT  291 (303)
Q Consensus       287 ~~a~~  291 (303)
                      .||+-
T Consensus        82 ~yAri   86 (97)
T PF04059_consen   82 SYARI   86 (97)
T ss_pred             ehhHh
Confidence            88764

It is found C-terminal to the RNA-binding region RNP-1 (IPR000504 from INTERPRO).

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

Probab=98.47  E-value=4.6e-07  Score=84.33  Aligned_cols=82  Identities=18%  Similarity=0.304  Sum_probs=70.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ..+|||+|||.+++.++|.++|..|  |.|....|....  ++..+||||+|.+.+++..|++-+-..+++++|.|.-.+
T Consensus       288 ~~~i~V~nlP~da~~~~l~~~Fk~F--G~Ik~~~I~vr~~~~~~~~fgFV~f~~~~~~~~~i~Asp~~ig~~kl~Veek~  365 (419)
T KOG0116|consen  288 GLGIFVKNLPPDATPAELEEVFKQF--GPIKEGGIQVRSPGGKNPCFGFVEFENAAAVQNAIEASPLEIGGRKLNVEEKR  365 (419)
T ss_pred             ccceEeecCCCCCCHHHHHHHHhhc--ccccccceEEeccCCCcCceEEEEEeecchhhhhhhcCccccCCeeEEEEecc
Confidence            3459999999999999999999999  999988776643  444499999999999999999977888999999999887


Q ss_pred             CCCCCC
Q 022058          291 TPVRPR  296 (303)
Q Consensus       291 ~~~~~r  296 (303)
                      +..+..
T Consensus       366 ~~~~g~  371 (419)
T KOG0116|consen  366 PGFRGN  371 (419)
T ss_pred             cccccc
Confidence            754443

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]

Probab=98.47  E-value=2.5e-07  Score=79.94  Aligned_cols=82  Identities=24%  Similarity=0.337  Sum_probs=74.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      .....+.+||+|+.+.++.+++...|+.||.|..+.++.|...  ++||+||+|.+.+.++.++.||+..+.|+.+.|.+
T Consensus        97 ~~~d~~sv~v~nvd~~~t~~~~e~hf~~Cg~i~~~ti~~d~~~~~~k~~~yvef~~~~~~~~ay~l~gs~i~~~~i~vt~  176 (231)
T KOG4209|consen   97 KEVDAPSVWVGNVDFLVTLTKIELHFESCGGINRVTVPKDKFRGHPKGFAYVEFSSYELVEEAYKLDGSEIPGPAIEVTL  176 (231)
T ss_pred             hccCCceEEEeccccccccchhhheeeccCCccceeeeccccCCCcceeEEEecccHhhhHHHhhcCCcccccccceeee
Confidence            4446788999999999999999999999999999999888765  79999999999999999999999999999999998


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      ....
T Consensus       177 ~r~~  180 (231)
T KOG4209|consen  177 KRTN  180 (231)
T ss_pred             eeee
Confidence            7554

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

Probab=98.41  E-value=4.9e-07  Score=77.06  Aligned_cols=148  Identities=17%  Similarity=0.223  Sum_probs=109.8

Q ss_pred             CcccccchhhhHHH-H--HHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhccc--
Q 022058           25 LETKKSESEFTVQK-L--VDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ--   97 (303)
Q Consensus        25 ~~~~nl~~~~t~~~-L--~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~--   97 (303)
                      .++.|+--++..+- |  ...|+.|-.+....+.++..+....  |+.|     .             +..+......  
T Consensus        99 p~~~~~g~~v~pep~lp~~~~f~~~p~L~ktk~v~~~p~~~~~~~~~~~-----k-------------~s~a~~k~~~~~  160 (290)
T KOG0226|consen   99 PFQSNAGATVNPEPPLPLPVVFSEYPSLVKTKLVRDRPQPIRPEAFESF-----K-------------ASDALLKAETEK  160 (290)
T ss_pred             ccccccccccCCCCCCcchhhhccchhhhhhhhhhcCCCccCcccccCc-----c-------------hhhhhhhhcccc
Confidence            55777766666555 4  7888988888888999888877766  7777     1             1111111111  


Q ss_pred             -----CCC--CCCchhhhhcc----CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEec
Q 022058           98 -----GRK--RLSGRAFRAQR----EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFA  164 (303)
Q Consensus        98 -----g~~--~~~~~~~~~~~----~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~  164 (303)
                           |++  +......+.+.    -+..+..||+|.|.-+++.+.|-..|.+|-.....++++|..+  ++||+||.|.
T Consensus       161 ~~Kki~~~~VR~a~gtswedPsl~ew~~~DfRIfcgdlgNevnd~vl~raf~Kfpsf~~akviRdkRTgKSkgygfVSf~  240 (290)
T KOG0226|consen  161 EKKKIGKPPVRLAAGTSWEDPSLAEWDEDDFRIFCGDLGNEVNDDVLARAFKKFPSFQKAKVIRDKRTGKSKGYGFVSFR  240 (290)
T ss_pred             ccccccCcceeeccccccCCcccccCccccceeecccccccccHHHHHHHHHhccchhhccccccccccccccceeeeec
Confidence                 222  22222222221    2335678999999999999999999999999999999999886  8999999999


Q ss_pred             CHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          165 DEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       165 ~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      +..++..|+. |||.-++.|+|++..+
T Consensus       241 ~pad~~rAmrem~gkyVgsrpiklRkS  267 (290)
T KOG0226|consen  241 DPADYVRAMREMNGKYVGSRPIKLRKS  267 (290)
T ss_pred             CHHHHHHHHHhhcccccccchhHhhhh
Confidence            9999999998 9999999999987654

>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=98.40  E-value=1.8e-06  Score=61.45  Aligned_cols=67  Identities=25%  Similarity=0.334  Sum_probs=47.1

Q ss_pred             ceEEEcCCCCCCCHH----HHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          214 RTVYCTNIDKKVPQA----EVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~----~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..|+|.|||...+..    .|++++.- |||.|..|.    .    +.|+|.|.+.+.|.+|.+ |+|..+.|+.|.|+|
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdN-CGGkVl~v~----~----~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~   73 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDN-CGGKVLSVS----G----GTAILRFPNQEFAERAQKRMEGEDVFGNKISVSF   73 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHT-TT--EEE------T----T-EEEEESSHHHHHHHHHHHTT--SSSS--EEES
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhc-cCCEEEEEe----C----CEEEEEeCCHHHHHHHHHhhcccccccceEEEEE
Confidence            468999999988764    56677777 778888773    1    489999999999999999 999999999999999


Q ss_pred             c
Q 022058          289 S  289 (303)
Q Consensus       289 a  289 (303)
                      .
T Consensus        74 ~   74 (90)
T PF11608_consen   74 S   74 (90)
T ss_dssp             S
T ss_pred             c
Confidence            8

Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures [].; PDB: 2DIU_A.

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

Probab=98.28  E-value=1.1e-06  Score=82.60  Aligned_cols=74  Identities=26%  Similarity=0.368  Sum_probs=65.0

Q ss_pred             cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       207 ~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      .+...+..+|+|-|||.++++++|+.+|+.|  |+|..|+--+.   .+|.+||+|-+.-+|++|++ |++.++.|++|+
T Consensus        69 ~~~~~~~~~L~v~nl~~~Vsn~~L~~~f~~y--Geir~ir~t~~---~~~~~~v~FyDvR~A~~Alk~l~~~~~~~~~~k  143 (549)
T KOG4660|consen   69 SEKDMNQGTLVVFNLPRSVSNDTLLRIFGAY--GEIREIRETPN---KRGIVFVEFYDVRDAERALKALNRREIAGKRIK  143 (549)
T ss_pred             CcccCccceEEEEecCCcCCHHHHHHHHHhh--cchhhhhcccc---cCceEEEEEeehHhHHHHHHHHHHHHhhhhhhc
Confidence            3345567899999999999999999999999  99998655444   34699999999999999999 999999999998

>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=98.08  E-value=1.4e-05  Score=56.94  Aligned_cols=67  Identities=24%  Similarity=0.278  Sum_probs=46.6

Q ss_pred             CEEEEcCCCCCCCHHH----HHHHhhcCC-ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          117 RTVYVSDIDQNITEER----LAGLFSSCG-QVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~----l~~~F~~~G-~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..|+|.|||.+.+...    |+.++..|| .|.+|.        .|.|+|.|.+.+.|.+|.+ |+|..+.|+.|.|.+.
T Consensus         3 s~L~V~NLP~~~d~~~I~~RL~qLsdNCGGkVl~v~--------~~tAilrF~~~~~A~RA~KRmegEdVfG~kI~v~~~   74 (90)
T PF11608_consen    3 SLLYVSNLPTNKDPSSIKNRLRQLSDNCGGKVLSVS--------GGTAILRFPNQEFAERAQKRMEGEDVFGNKISVSFS   74 (90)
T ss_dssp             EEEEEES--TTS-HHHHHHHHHHHHHTTT--EEE----------TT-EEEEESSHHHHHHHHHHHTT--SSSS--EEESS
T ss_pred             cEEEEecCCCCCCHHHHHHHHHHHhhccCCEEEEEe--------CCEEEEEeCCHHHHHHHHHhhcccccccceEEEEEc
Confidence            4599999999998776    556666886 666552        2579999999999999999 9999999999999986


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      .
T Consensus        75 ~   75 (90)
T PF11608_consen   75 P   75 (90)
T ss_dssp             -
T ss_pred             C
Confidence            3

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=97.81  E-value=7.8e-05  Score=56.56  Aligned_cols=68  Identities=16%  Similarity=0.302  Sum_probs=43.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h--C---CceeCCeeeEEe
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C--S---GMVLGSQPIRVS  287 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l--~---g~~~~g~~l~v~  287 (303)
                      ..|.|.+++..++.++|+..|++|  |.|.+|.+.++..    .|+|.|.+.++|+.|+. +  .   +..+.+..+++.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~--g~V~yVD~~~G~~----~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~   75 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQF--GEVAYVDFSRGDT----EGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLE   75 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS----EEEEE--TT-S----EEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhc--CCcceEEecCCCC----EEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEE
Confidence            468888999999999999999999  9999999988754    79999999999999996 4  3   445666665554

It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_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=97.72  E-value=0.00015  Score=55.02  Aligned_cols=54  Identities=20%  Similarity=0.291  Sum_probs=36.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN  174 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~  174 (303)
                      +.|+|.+++..++.++|++.|+.||.|..|.+.....    -|||.|.+.+.|++|+.
T Consensus         2 ~il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~----~g~VRf~~~~~A~~a~~   55 (105)
T PF08777_consen    2 CILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDT----EGYVRFKTPEAAQKALE   55 (105)
T ss_dssp             -EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-S----EEEEEESS---HHHHHH
T ss_pred             eEEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCC----EEEEEECCcchHHHHHH
Confidence            4688999999999999999999999999988866443    69999999999999997

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

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

Probab=97.60  E-value=0.00017  Score=47.56  Aligned_cols=52  Identities=27%  Similarity=0.442  Sum_probs=42.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHH
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL  173 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai  173 (303)
                      +.|-|.+.|++..+..|+ .|..||+|..+.+....    -+.||.|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~~~vl~-~F~~fGeI~~~~~~~~~----~~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLAEEVLE-HFASFGEIVDIYVPEST----NWMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHHHHHHH-HHHhcCCEEEEEcCCCC----cEEEEEECCHHHHHhhC
Confidence            568899998777655554 88899999998886322    38999999999999985

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.56  E-value=9.2e-05  Score=65.75  Aligned_cols=114  Identities=15%  Similarity=0.245  Sum_probs=76.8

Q ss_pred             CCEEEEcCCCCCCCHHH----H--HHHhhcCCceeEEEEeeCCCC---CceE--EEEEecCHHHHHHHHH-hCCcccCCe
Q 022058          116 RRTVYVSDIDQNITEER----L--AGLFSSCGQVVDCRVCGDPHS---VLRF--AFVEFADEHGARAALN-LGGTMLGYY  183 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~----l--~~~F~~~G~i~~~~i~~~~~~---~~G~--~fV~f~~~~~A~~Ai~-l~g~~~~g~  183 (303)
                      +.-+||-+||+.+..++    |  .++|.+||.|..|.+-+.-..   -.+.  .||+|.+.++|.+||. .+|..++||
T Consensus       114 KNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DGr  193 (480)
T COG5175         114 KNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDGR  193 (480)
T ss_pred             cceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccCc
Confidence            34489999998876665    3  579999999999888653311   1233  4999999999999998 999999999


Q ss_pred             eEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCC---CCCHHHHHHHhh
Q 022058          184 PVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDK---KVPQAEVKQFFE  235 (303)
Q Consensus       184 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~---~~t~~~L~~~F~  235 (303)
                      .|+..+..++....   +.....   =+...++|+.--.+   ..+.++|...=.
T Consensus       194 ~lkatYGTTKYCts---YLRn~~---CpNp~CMyLHEpg~e~Ds~tK~el~n~qh  242 (480)
T COG5175         194 VLKATYGTTKYCTS---YLRNAV---CPNPDCMYLHEPGPEKDSLTKDELCNSQH  242 (480)
T ss_pred             eEeeecCchHHHHH---HHcCCC---CCCCCeeeecCCCcccccccHHHHhhhhh
Confidence            99999986654210   111100   01224566643322   467787776533

>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=97.49  E-value=0.00035  Score=52.33  Aligned_cols=73  Identities=15%  Similarity=0.172  Sum_probs=53.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEE-------------EecCCCCcccEEEEEEcCHHHHHHHHHhCCceeC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLR-------------LLGDHVHSTRIAFVEFAVAESAILALNCSGMVLG  280 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~-------------i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~  280 (303)
                      .-|.|.+.|+. ....|.++|++|  |.|....             +...    ..+..|+|.++.+|.+|+.-||..+.
T Consensus         7 ~wVtVFGfp~~-~~~~Vl~~F~~~--G~Ile~~~~~~~~~~~~~~~~~~~----~NWi~I~Y~~~~~A~rAL~~NG~i~~   79 (100)
T PF05172_consen    7 TWVTVFGFPPS-ASNQVLRHFSSF--GTILEHFEVLRSSSGINPYPIPSG----GNWIHITYDNPLSAQRALQKNGTIFS   79 (100)
T ss_dssp             CEEEEE---GG-GHHHHHHHHHCC--S-EECEEGGG----------E-CC----TTEEEEEESSHHHHHHHHTTTTEEET
T ss_pred             eEEEEEccCHH-HHHHHHHHHHhc--ceEEEeecccccccccccccCCCC----CCEEEEECCCHHHHHHHHHhCCeEEc
Confidence            56888899988 456788999998  9998775             2222    24999999999999999999999998


Q ss_pred             Ce-eeEEeecCCCC
Q 022058          281 SQ-PIRVSPSKTPV  293 (303)
Q Consensus       281 g~-~l~v~~a~~~~  293 (303)
                      |. .+-|.+.++..
T Consensus        80 g~~mvGV~~~~~~~   93 (100)
T PF05172_consen   80 GSLMVGVKPCDPAD   93 (100)
T ss_dssp             TCEEEEEEE-HHHH
T ss_pred             CcEEEEEEEcHHhH
Confidence            75 66688875443

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.

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=97.47  E-value=0.00027  Score=60.69  Aligned_cols=83  Identities=25%  Similarity=0.206  Sum_probs=72.6

Q ss_pred             HHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEE
Q 022058          168 GARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLR  246 (303)
Q Consensus       168 ~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~  246 (303)
                      -|..|-. |++....|+.+.|.++..                     ..|||.||...+..+.|.+.|+.|  |.|....
T Consensus         6 ~ae~ak~eLd~~~~~~~~lr~rfa~~---------------------a~l~V~nl~~~~sndll~~~f~~f--g~~e~av   62 (275)
T KOG0115|consen    6 LAEIAKRELDGRFPKGRSLRVRFAMH---------------------AELYVVNLMQGASNDLLEQAFRRF--GPIERAV   62 (275)
T ss_pred             HHHHHHHhcCCCCCCCCceEEEeecc---------------------ceEEEEecchhhhhHHHHHhhhhc--Cccchhe
Confidence            4566665 999999999999999731                     579999999999999999999999  9999977


Q ss_pred             EecC-CCCcccEEEEEEcCHHHHHHHHH
Q 022058          247 LLGD-HVHSTRIAFVEFAVAESAILALN  273 (303)
Q Consensus       247 i~~d-~~~~~g~afV~f~~~e~A~~Ai~  273 (303)
                      +..| .++..+-++|.|...-.|.+|..
T Consensus        63 ~~vD~r~k~t~eg~v~~~~k~~a~~a~r   90 (275)
T KOG0115|consen   63 AKVDDRGKPTREGIVEFAKKPNARKAAR   90 (275)
T ss_pred             eeecccccccccchhhhhcchhHHHHHH
Confidence            7666 58899999999999999988886

>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=97.44  E-value=0.00074  Score=50.57  Aligned_cols=75  Identities=21%  Similarity=0.253  Sum_probs=51.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEE-EeeC-------CC-CCceEEEEEecCHHHHHHHHHhCCcccCCeeE
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCR-VCGD-------PH-SVLRFAFVEFADEHGARAALNLGGTMLGYYPV  185 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~-i~~~-------~~-~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i  185 (303)
                      ..+.|.|-+.|+. ....+-+.|++||+|.+.. +.++       +. .....-.|+|.++.+|.+||..||..+.|.-|
T Consensus         5 ~~~wVtVFGfp~~-~~~~Vl~~F~~~G~Ile~~~~~~~~~~~~~~~~~~~~NWi~I~Y~~~~~A~rAL~~NG~i~~g~~m   83 (100)
T PF05172_consen    5 SETWVTVFGFPPS-ASNQVLRHFSSFGTILEHFEVLRSSSGINPYPIPSGGNWIHITYDNPLSAQRALQKNGTIFSGSLM   83 (100)
T ss_dssp             GCCEEEEE---GG-GHHHHHHHHHCCS-EECEEGGG----------E-CCTTEEEEEESSHHHHHHHHTTTTEEETTCEE
T ss_pred             CCeEEEEEccCHH-HHHHHHHHHHhcceEEEeecccccccccccccCCCCCCEEEEECCCHHHHHHHHHhCCeEEcCcEE
Confidence            4567889899988 5566777899999998774 1111       00 12358999999999999999999999988544


Q ss_pred             -EEeec
Q 022058          186 -RVLPS  190 (303)
Q Consensus       186 -~v~~~  190 (303)
                       -|.+.
T Consensus        84 vGV~~~   89 (100)
T PF05172_consen   84 VGVKPC   89 (100)
T ss_dssp             EEEEE-
T ss_pred             EEEEEc
Confidence             46664

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.

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.38  E-value=0.00016  Score=64.88  Aligned_cols=78  Identities=21%  Similarity=0.321  Sum_probs=68.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCcee--------EEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVV--------DCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYY  183 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~  183 (303)
                      ..-+|||-+||..+++++|.++|.++|.|.        .|.+.+++.+  .||-|.|.|.+...|+.|+. +++..+.+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~gn  144 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFCGN  144 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhccccccCC
Confidence            466799999999999999999999999884        3455566665  79999999999999999999 999999999


Q ss_pred             eEEEeecCC
Q 022058          184 PVRVLPSKT  192 (303)
Q Consensus       184 ~i~v~~~~~  192 (303)
                      +|+|..+..
T Consensus       145 ~ikvs~a~~  153 (351)
T KOG1995|consen  145 TIKVSLAER  153 (351)
T ss_pred             Cchhhhhhh
Confidence            999987643

>COG5175 MOT2 Transcriptional repressor [Transcription]

Probab=97.35  E-value=0.00052  Score=61.10  Aligned_cols=76  Identities=17%  Similarity=0.368  Sum_probs=61.5

Q ss_pred             ceEEEcCCCCCCCHHH----H--HHHhhhhcCcceeEEEEecCC---CCccc--EEEEEEcCHHHHHHHHH-hCCceeCC
Q 022058          214 RTVYCTNIDKKVPQAE----V--KQFFEAACGGEVTRLRLLGDH---VHSTR--IAFVEFAVAESAILALN-CSGMVLGS  281 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~----L--~~~F~~~~~G~i~~v~i~~d~---~~~~g--~afV~f~~~e~A~~Ai~-l~g~~~~g  281 (303)
                      .-+||-+|++.+..++    |  .++|.+|  |.|..+.|-+..   ....+  -.+|+|.+.|+|.+||. .+|..++|
T Consensus       115 NLvYVigi~pkva~Ee~~~vLk~~eyFGQy--GkI~KIvvNkkt~s~nst~~h~gvYITy~~kedAarcIa~vDgs~~DG  192 (480)
T COG5175         115 NLVYVIGIPPKVADEEVAPVLKRHEYFGQY--GKIKKIVVNKKTSSLNSTASHAGVYITYSTKEDAARCIAEVDGSLLDG  192 (480)
T ss_pred             ceeEEecCCCCCCcccccccccchhhhhhc--cceeEEEecccccccccccccceEEEEecchHHHHHHHHHhccccccC
Confidence            4589999999887665    2  3789999  999999887653   11122  35999999999999998 99999999


Q ss_pred             eeeEEeecCC
Q 022058          282 QPIRVSPSKT  291 (303)
Q Consensus       282 ~~l~v~~a~~  291 (303)
                      |.|+..|..+
T Consensus       193 r~lkatYGTT  202 (480)
T COG5175         193 RVLKATYGTT  202 (480)
T ss_pred             ceEeeecCch
Confidence            9999998754

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]

Probab=97.34  E-value=0.00021  Score=64.13  Aligned_cols=79  Identities=19%  Similarity=0.270  Sum_probs=68.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE--------EEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR--------LRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~--------v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      ...+|||-+||..+++.+|..+|.+-  |.|..        +.|-+|.  +.++|-|.|.|.+..+|+.|+. +++..+.
T Consensus        65 ~~~ti~v~g~~d~~~~~~~~~~f~qc--g~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~akaai~~~agkdf~  142 (351)
T KOG1995|consen   65 DNETIFVWGCPDSVCENDNADFFLQC--GVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAAKAAIEWFAGKDFC  142 (351)
T ss_pred             ccccceeeccCccchHHHHHHHHhhc--ceeccCCCCCCcchhccccccccCcCCceeeeecChhhhhhhhhhhcccccc
Confidence            45789999999999999999999994  87753        4555564  6789999999999999999999 9999999


Q ss_pred             CeeeEEeecCCC
Q 022058          281 SQPIRVSPSKTP  292 (303)
Q Consensus       281 g~~l~v~~a~~~  292 (303)
                      +..|+|+++...
T Consensus       143 gn~ikvs~a~~r  154 (351)
T KOG1995|consen  143 GNTIKVSLAERR  154 (351)
T ss_pred             CCCchhhhhhhc
Confidence            999999998543

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.32  E-value=0.00091  Score=63.35  Aligned_cols=74  Identities=20%  Similarity=0.235  Sum_probs=61.3

Q ss_pred             ccceEEEcCCCCCCC------HHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeC-Ce
Q 022058          212 CSRTVYCTNIDKKVP------QAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLG-SQ  282 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t------~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~-g~  282 (303)
                      -...|+|-|+|.--.      ..-|.++|+++  |.|+...++.+. |.++||.|++|.+..+|..|++ |||+.|+ ++
T Consensus        57 ~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~--gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknH  134 (698)
T KOG2314|consen   57 FDSVVVVDGAPVVGPARLEKLKKVLTKVFSKA--GKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNH  134 (698)
T ss_pred             cceEEEECCCcccChhHHHHHHHHHHHHHHhh--ccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccc
Confidence            346788999885321      24567899999  999999999885 7899999999999999999999 9999997 56


Q ss_pred             eeEEe
Q 022058          283 PIRVS  287 (303)
Q Consensus       283 ~l~v~  287 (303)
                      ++.|.
T Consensus       135 tf~v~  139 (698)
T KOG2314|consen  135 TFFVR  139 (698)
T ss_pred             eEEee
Confidence            66665

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=97.31  E-value=0.00076  Score=58.97  Aligned_cols=77  Identities=23%  Similarity=0.259  Sum_probs=60.0

Q ss_pred             ceEEEcCCC--CCCC---HHHHHHHhhhhcCcceeEEEEecCCCC---cccEEEEEEcCHHHHHHHHH-hCCceeCCeee
Q 022058          214 RTVYCTNID--KKVP---QAEVKQFFEAACGGEVTRLRLLGDHVH---STRIAFVEFAVAESAILALN-CSGMVLGSQPI  284 (303)
Q Consensus       214 ~~l~V~nL~--~~~t---~~~L~~~F~~~~~G~i~~v~i~~d~~~---~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l  284 (303)
                      +.|.++|+-  ..++   +++++..+++|  |.|..|.|.-+++.   ..--.||+|...++|.+|+- |||+.|+||.+
T Consensus       282 kvlllrnmVg~gevd~elede~keEceKy--g~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v  359 (378)
T KOG1996|consen  282 KVLLLRNMVGAGEVDEELEDETKEECEKY--GKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVV  359 (378)
T ss_pred             HHHHhhhhcCcccccHHHHHHHHHHHHhh--cceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceee
Confidence            345556542  2333   46888999998  99999988877643   23358999999999999998 99999999999


Q ss_pred             EEeecCCC
Q 022058          285 RVSPSKTP  292 (303)
Q Consensus       285 ~v~~a~~~  292 (303)
                      ...|.+..
T Consensus       360 ~A~Fyn~e  367 (378)
T KOG1996|consen  360 SACFYNLE  367 (378)
T ss_pred             eheeccHH
Confidence            99887543

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

Probab=97.26  E-value=0.00086  Score=44.16  Aligned_cols=52  Identities=15%  Similarity=0.252  Sum_probs=42.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHH
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL  272 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai  272 (303)
                      +.|-|.+.++... +.+..+|..|  |+|..+.+.....    +.+|+|.+..+|++|+
T Consensus         2 ~wI~V~Gf~~~~~-~~vl~~F~~f--GeI~~~~~~~~~~----~~~l~y~~~~~ae~Al   53 (53)
T PF14605_consen    2 TWISVSGFPPDLA-EEVLEHFASF--GEIVDIYVPESTN----WMYLKYKSRKDAEKAL   53 (53)
T ss_pred             cEEEEEeECchHH-HHHHHHHHhc--CCEEEEEcCCCCc----EEEEEECCHHHHHhhC
Confidence            4678888887765 4566689998  9999999984433    8999999999999985

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]

Probab=97.24  E-value=0.0013  Score=62.43  Aligned_cols=76  Identities=25%  Similarity=0.256  Sum_probs=62.3

Q ss_pred             CCCCEEEEcCCCCCCC--HH----HHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccC-Cee
Q 022058          114 SVRRTVYVSDIDQNIT--EE----RLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLG-YYP  184 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t--~~----~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~  184 (303)
                      .....|+|-|+|---.  .+    -|..+|+.+|.|....++.+..+ .+||.|++|.+..+|+.|++ +||..++ .++
T Consensus        56 g~D~vVvv~g~PvV~~~rl~klk~vl~kvfsk~gk~vn~~~P~~e~ggtkG~lf~E~~~~~~A~~aVK~l~G~~ldknHt  135 (698)
T KOG2314|consen   56 GFDSVVVVDGAPVVGPARLEKLKKVLTKVFSKAGKIVNMYYPIDEEGGTKGYLFVEYASMRDAKKAVKSLNGKRLDKNHT  135 (698)
T ss_pred             CcceEEEECCCcccChhHHHHHHHHHHHHHHhhccccceeeccCccCCeeeEEEEEecChhhHHHHHHhcccceecccce
Confidence            3466799999985322  22    36679999999999999987765 89999999999999999999 9999987 677


Q ss_pred             EEEee
Q 022058          185 VRVLP  189 (303)
Q Consensus       185 i~v~~  189 (303)
                      +.|..
T Consensus       136 f~v~~  140 (698)
T KOG2314|consen  136 FFVRL  140 (698)
T ss_pred             EEeeh
Confidence            77754

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=97.22  E-value=0.0018  Score=51.49  Aligned_cols=56  Identities=29%  Similarity=0.489  Sum_probs=47.4

Q ss_pred             HHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCC
Q 022058          228 AEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       228 ~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      .+|.+.|..|  |.+.-+++.-+      .-+|+|.+-++|.+|+.|+|.+++|+.|+|++..|
T Consensus        51 ~~ll~~~~~~--GevvLvRfv~~------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKtp  106 (146)
T PF08952_consen   51 DELLQKFAQY--GEVVLVRFVGD------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKTP  106 (146)
T ss_dssp             HHHHHHHHCC--S-ECEEEEETT------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE---
T ss_pred             HHHHHHHHhC--CceEEEEEeCC------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCCc
Confidence            4788889998  99998888766      48999999999999999999999999999998654

; PDB: 1UFW_A 2DNR_A.

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=96.77  E-value=0.0014  Score=62.57  Aligned_cols=76  Identities=12%  Similarity=0.169  Sum_probs=62.0

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee---CCeeeE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL---GSQPIR  285 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~---~g~~l~  285 (303)
                      ...+..|+|.||---+|..+|+.+..+-| |.|+..  ..|+  -+..|||.|.+.++|...+. |||..+   +++.|.
T Consensus       441 ~~~SnvlhI~nLvRPFTlgQLkelL~rtg-g~Vee~--WmDk--IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~  515 (718)
T KOG2416|consen  441 KEPSNVLHIDNLVRPFTLGQLKELLGRTG-GNVEEF--WMDK--IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLI  515 (718)
T ss_pred             CCccceEeeecccccchHHHHHHHHhhcc-CchHHH--HHHH--hhcceeEecccHHHHHHHHHHHhccccCCCCCceeE
Confidence            44568899999999999999999999875 777766  3332  22379999999999999998 999887   578898


Q ss_pred             EeecC
Q 022058          286 VSPSK  290 (303)
Q Consensus       286 v~~a~  290 (303)
                      +.|+.
T Consensus       516 adf~~  520 (718)
T KOG2416|consen  516 ADFVR  520 (718)
T ss_pred             eeecc
Confidence            88863

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.75  E-value=0.00078  Score=57.89  Aligned_cols=69  Identities=25%  Similarity=0.300  Sum_probs=58.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC----------Cc----eEEEEEecCHHHHHHHHH-hCCccc
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS----------VL----RFAFVEFADEHGARAALN-LGGTML  180 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~----------~~----G~~fV~f~~~~~A~~Ai~-l~g~~~  180 (303)
                      ...||+++||+.++..-|+++|+.||.|-.|.+-.....          ++    .-|.|+|.+...|..+.. ||+..|
T Consensus        74 ~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF~~KrvAK~iAe~Lnn~~I  153 (278)
T KOG3152|consen   74 TGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEFISKRVAKRIAELLNNTPI  153 (278)
T ss_pred             ceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHHHHHHHHHHHHHHhCCCcc
Confidence            356999999999999999999999999999988664321          11    138899999999999888 999999


Q ss_pred             CCee
Q 022058          181 GYYP  184 (303)
Q Consensus       181 ~g~~  184 (303)
                      +|+.
T Consensus       154 ggkk  157 (278)
T KOG3152|consen  154 GGKK  157 (278)
T ss_pred             CCCC
Confidence            9865

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function

Probab=96.74  E-value=0.0074  Score=48.01  Aligned_cols=54  Identities=31%  Similarity=0.432  Sum_probs=46.0

Q ss_pred             HHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          132 RLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       132 ~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      +|-+.|..||.+.-+++.-+      .-+|+|.+-++|.+|+.++|..+.|+.|.|....
T Consensus        52 ~ll~~~~~~GevvLvRfv~~------~mwVTF~dg~sALaals~dg~~v~g~~l~i~LKt  105 (146)
T PF08952_consen   52 ELLQKFAQYGEVVLVRFVGD------TMWVTFRDGQSALAALSLDGIQVNGRTLKIRLKT  105 (146)
T ss_dssp             HHHHHHHCCS-ECEEEEETT------CEEEEESSCHHHHHHHHGCCSEETTEEEEEEE--
T ss_pred             HHHHHHHhCCceEEEEEeCC------eEEEEECccHHHHHHHccCCcEECCEEEEEEeCC
Confidence            57778889999998888753      4899999999999999999999999999998754

; PDB: 1UFW_A 2DNR_A.

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]

Probab=96.62  E-value=0.00017  Score=65.90  Aligned_cols=142  Identities=17%  Similarity=0.250  Sum_probs=99.4

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCC--CCCCc-eeeeecchhhhhhchhhhccccchHHhhhhccc--
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYH--QHTDH-HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ--   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~--~~~~~-~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~--   97 (303)
                      ++++++||....+..+|+.+|...      .++-...  -++.. ||.+     ..     ..    -|-+++..+++  
T Consensus         2 nklyignL~p~~~psdl~svfg~a------k~~~~g~fl~k~gyafvd~-----pd-----q~----wa~kaie~~sgk~   61 (584)
T KOG2193|consen    2 NKLYIGNLSPQVTPSDLESVFGDA------KIPGSGQFLVKSGYAFVDC-----PD-----QQ----WANKAIETLSGKV   61 (584)
T ss_pred             CcccccccCCCCChHHHHHHhccc------cCCCCcceeeecceeeccC-----Cc-----hh----hhhhhHHhhchhh
Confidence            378999999999999999999864      1111110  01111 6666     33     33    56688888877  


Q ss_pred             ---CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEe-eCCCCCceEEEEEecCHHHHHHH
Q 022058           98 ---GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC-GDPHSVLRFAFVEFADEHGARAA  172 (303)
Q Consensus        98 ---g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~-~~~~~~~G~~fV~f~~~~~A~~A  172 (303)
                         |++ .+.......    ..++.+.|.|+|+...++.|..+...||.++.|... .+..+  -.-=|+|...+.+..|
T Consensus        62 elqGkr~e~~~sv~kk----qrsrk~Qirnippql~wevld~Ll~qyg~ve~~eqvnt~~et--avvnvty~~~~~~~~a  135 (584)
T KOG2193|consen   62 ELQGKRQEVEHSVPKK----QRSRKIQIRNIPPQLQWEVLDSLLAQYGTVENCEQVNTDSET--AVVNVTYSAQQQHRQA  135 (584)
T ss_pred             hhcCceeeccchhhHH----HHhhhhhHhcCCHHHHHHHHHHHHhccCCHhHhhhhccchHH--HHHHHHHHHHHHHHHH
Confidence               433 111111111    134569999999999999999999999999998653 33332  2344678999999999


Q ss_pred             HH-hCCcccCCeeEEEeec
Q 022058          173 LN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       173 i~-l~g~~~~g~~i~v~~~  190 (303)
                      |. ++|..+....++|.+-
T Consensus       136 i~kl~g~Q~en~~~k~~Yi  154 (584)
T KOG2193|consen  136 IHKLNGPQLENQHLKVGYI  154 (584)
T ss_pred             HHhhcchHhhhhhhhcccC
Confidence            98 9999999988888874

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.61  E-value=0.0012  Score=56.85  Aligned_cols=61  Identities=25%  Similarity=0.286  Sum_probs=51.0

Q ss_pred             HHHHHHhh-hhcCcceeEEEEecCCC-CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          228 AEVKQFFE-AACGGEVTRLRLLGDHV-HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       228 ~~L~~~F~-~~~~G~i~~v~i~~d~~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ++|...|+ +|  |.|+.+.|...-+ .-.|-++|.|...++|++|++ |||.++.|++|+..++.
T Consensus        83 Ed~f~E~~~ky--gEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   83 EDVFTELEDKY--GEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HHHHHHHHHHh--hhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            45556666 77  9999987766533 457789999999999999999 99999999999999873

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]

Probab=96.51  E-value=0.00095  Score=57.38  Aligned_cols=66  Identities=6%  Similarity=0.084  Sum_probs=54.4

Q ss_pred             cccCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCC---------CCCc------eeeeecchhhhhhchhhh
Q 022058           18 NNNKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQ---------HTDH------HFSVINNNFADDNKQSAI   82 (303)
Q Consensus        18 ~~~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~---------~~~~------~v~f~~~~~~~~~~~~~~   82 (303)
                      ++.+.|=||++|+|+.+...-||++|+.||+|-.|.|-+..+.         +..+      ||+|     .+     ..
T Consensus        70 kkrk~GVvylS~IPp~m~~~rlReil~~yGeVGRvylqpE~~s~~~~r~~~~~n~~~~y~EGWvEF-----~~-----Kr  139 (278)
T KOG3152|consen   70 KKRKTGVVYLSNIPPYMDPVRLREILSQYGEVGRVYLQPEDDSKRAARKRKGGNYKKLYSEGWVEF-----IS-----KR  139 (278)
T ss_pred             hhccceEEEeccCCCccCHHHHHHHHHhccccceEEecchhhHHHHHHhhcCCCccccchhHHHHH-----HH-----HH
Confidence            4457788999999999999999999999999999999876654         2211      8888     77     66


Q ss_pred             ccccchHHhhhhccc
Q 022058           83 DNFNNNRRRRNNFNQ   97 (303)
Q Consensus        83 ~~~~~A~~a~~~~~~   97 (303)
                          .|++....||+
T Consensus       140 ----vAK~iAe~Lnn  150 (278)
T KOG3152|consen  140 ----VAKRIAELLNN  150 (278)
T ss_pred             ----HHHHHHHHhCC
Confidence                78888888887

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.49  E-value=0.0034  Score=57.70  Aligned_cols=69  Identities=25%  Similarity=0.454  Sum_probs=57.4

Q ss_pred             hhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeC---CCC------------CceEEEEEecCHHHHHHH
Q 022058          108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD---PHS------------VLRFAFVEFADEHGARAA  172 (303)
Q Consensus       108 ~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~---~~~------------~~G~~fV~f~~~~~A~~A  172 (303)
                      ....+.-.+++|.+-|||.+-.-+-|.++|..+|.|.+|+|+..   +..            .+-+|+|+|...+.|.+|
T Consensus       223 ~~~~eel~srtivaenLP~Dh~~enl~kiFg~~G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA  302 (484)
T KOG1855|consen  223 EFDEEELPSRTIVAENLPLDHSYENLSKIFGTVGSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKA  302 (484)
T ss_pred             CccccccccceEEEecCCcchHHHHHHHHhhcccceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHH
Confidence            33334457899999999999999999999999999999999875   211            146899999999999999


Q ss_pred             HH-hC
Q 022058          173 LN-LG  176 (303)
Q Consensus       173 i~-l~  176 (303)
                      .+ +|
T Consensus       303 ~e~~~  307 (484)
T KOG1855|consen  303 RELLN  307 (484)
T ss_pred             HHhhc
Confidence            99 54

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]

Probab=96.48  E-value=0.0014  Score=56.52  Aligned_cols=53  Identities=25%  Similarity=0.401  Sum_probs=46.3

Q ss_pred             cCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          139 SCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       139 ~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +||+|+++.+..+..- -.|=.||.|..+++|++|+. ||+.++.|++|...++.
T Consensus        92 kygEiee~~Vc~Nl~~hl~GNVYV~f~~Ee~ae~a~~~lnnRw~~G~pi~ae~~p  146 (260)
T KOG2202|consen   92 KYGEIEELNVCDNLGDHLVGNVYVKFRSEEDAEAALEDLNNRWYNGRPIHAELSP  146 (260)
T ss_pred             HhhhhhhhhhhcccchhhhhhhhhhcccHHHHHHHHHHHcCccccCCcceeeecC
Confidence            8999999877655443 57889999999999999999 99999999999998863

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=96.45  E-value=0.013  Score=41.84  Aligned_cols=54  Identities=22%  Similarity=0.343  Sum_probs=41.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG  176 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~  176 (303)
                      ....+|. .|..+...||.++|+.||.|. |..+-|.     -|||...+.+.|..++. +.
T Consensus         9 dHVFhlt-FPkeWK~~DI~qlFspfG~I~-VsWi~dT-----SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen    9 DHVFHLT-FPKEWKTSDIYQLFSPFGQIY-VSWINDT-----SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CCEEEEE---TT--HHHHHHHCCCCCCEE-EEEECTT-----EEEEEECCCHHHHHHHHHHT
T ss_pred             ceEEEEe-CchHhhhhhHHHHhccCCcEE-EEEEcCC-----cEEEEeecHHHHHHHHHHhc
Confidence            3445666 999999999999999999975 6676554     49999999999999998 54

; 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.

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.45  E-value=0.0025  Score=57.06  Aligned_cols=74  Identities=16%  Similarity=0.243  Sum_probs=60.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCC--ceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      +-.+|||||-|.+|.+||.+.....|  .+.++++..++..  |||||+|...+...+++-++ |-..+|.|..-.|..
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~~  158 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQSTGLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVLS  158 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhhhHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeeec
Confidence            33599999999999999998888766  5667777665543  89999999999999999999 888888886555543

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]

Probab=96.44  E-value=0.0034  Score=56.24  Aligned_cols=74  Identities=11%  Similarity=0.173  Sum_probs=60.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCc--ceeEEEEecC--CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGG--EVTRLRLLGD--HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G--~i~~v~i~~d--~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ..++||+||-..+|++||.+.....  |  .+.++++.-.  .|+++|||+|...+..+..+.++ |-.++|+|+.-.|.
T Consensus        80 k~~~YvGNL~W~TTD~DL~~A~~S~--G~~~~~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~MeiLP~k~iHGQ~P~V~  157 (498)
T KOG4849|consen   80 KYCCYVGNLLWYTTDADLLKALQST--GLAQFADMKFFENRTNGQSKGYALLVLNSDAAVKQTMEILPTKTIHGQSPTVL  157 (498)
T ss_pred             eEEEEecceeEEeccHHHHHHHHhh--hHHHHhhhhhhhcccCCcccceEEEEecchHHHHHHHHhcccceecCCCCeee
Confidence            4689999999999999999998886  6  4455665554  38999999999999988899998 89999998765554


Q ss_pred             e
Q 022058          288 P  288 (303)
Q Consensus       288 ~  288 (303)
                      .
T Consensus       158 ~  158 (498)
T KOG4849|consen  158 S  158 (498)
T ss_pred             c
Confidence            3

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]

Probab=96.32  E-value=0.0081  Score=54.72  Aligned_cols=78  Identities=19%  Similarity=0.343  Sum_probs=64.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCC-----CcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-----HSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~-----~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      ..|-|.||.+.++.++++.+|.-.  |.|..+.|.+..+     ...-.|||.|.+..++..|..|-++.+-++.|.|-+
T Consensus         8 ~vIqvanispsat~dqm~tlFg~l--GkI~elrlyp~~~d~~~pv~sRtcyVkf~d~~sv~vaQhLtntvfvdraliv~p   85 (479)
T KOG4676|consen    8 GVIQVANISPSATKDQMQTLFGNL--GKIPELRLYPNVDDSKIPVISRTCYVKFLDSQSVTVAQHLTNTVFVDRALIVRP   85 (479)
T ss_pred             ceeeecccCchhhHHHHHHHHhhc--cccccccccCCCCCccCcceeeeEEEeccCCcceeHHhhhccceeeeeeEEEEe
Confidence            478999999999999999999999  9999999988532     234589999999999999999888888787777765


Q ss_pred             c-CCCC
Q 022058          289 S-KTPV  293 (303)
Q Consensus       289 a-~~~~  293 (303)
                      + .+++
T Consensus        86 ~~~~~~   91 (479)
T KOG4676|consen   86 YGDEVI   91 (479)
T ss_pred             cCCCCC
Confidence            4 4443

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]

Probab=96.12  E-value=0.0068  Score=55.84  Aligned_cols=66  Identities=21%  Similarity=0.283  Sum_probs=55.1

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC---C----CC--------cccEEEEEEcCHHHHHHHHH-
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD---H----VH--------STRIAFVEFAVAESAILALN-  273 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d---~----~~--------~~g~afV~f~~~e~A~~Ai~-  273 (303)
                      +.+.++|.+.|||.+-.-+.|.++|..+  |.|..|+|..-   +    +.        .+-+|+|+|...+.|.+|.+ 
T Consensus       228 el~srtivaenLP~Dh~~enl~kiFg~~--G~IksIRIckPgaip~d~r~~~~~~~~~~tk~~AlvEye~~~~A~KA~e~  305 (484)
T KOG1855|consen  228 ELPSRTIVAENLPLDHSYENLSKIFGTV--GSIKSIRICKPGAIPEDVRGFPKKYFELQTKECALVEYEEVEAARKAREL  305 (484)
T ss_pred             ccccceEEEecCCcchHHHHHHHHhhcc--cceeeeeecCCCCCCcccccCCccchhhhhhhhhhhhhhhhHHHHHHHHh
Confidence            3467999999999998889999999998  99999998864   1    11        25589999999999999999 


Q ss_pred             hCCc
Q 022058          274 CSGM  277 (303)
Q Consensus       274 l~g~  277 (303)
                      |+..
T Consensus       306 ~~~e  309 (484)
T KOG1855|consen  306 LNPE  309 (484)
T ss_pred             hchh
Confidence            6443

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=95.83  E-value=0.072  Score=36.09  Aligned_cols=54  Identities=22%  Similarity=0.303  Sum_probs=45.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcC-cceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACG-GEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN  273 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~-G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~  273 (303)
                      ..|+|+++. .++.++|+.+|..|++ ....+|..+.|.     .|-|.|.+.+.|.+|+.
T Consensus         6 eavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDt-----ScNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    6 EAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDT-----SCNVVFKDEETAARALV   60 (62)
T ss_pred             ceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCC-----cEEEEECCHHHHHHHHH
Confidence            579999987 4777889999999841 356788888887     69999999999999986

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]

Probab=95.37  E-value=0.051  Score=47.86  Aligned_cols=62  Identities=23%  Similarity=0.186  Sum_probs=51.1

Q ss_pred             HHHHHHHhhcCCceeEEEEeeCCCC---CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          130 EERLAGLFSSCGQVVDCRVCGDPHS---VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       130 ~~~l~~~F~~~G~i~~~~i~~~~~~---~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ++++++-..+||.|..|.|.-.+..   -.---||+|+..++|.+|+- |||..|+||.+...+..
T Consensus       300 ede~keEceKyg~V~~viifeip~~p~deavRiFveF~r~e~aiKA~VdlnGRyFGGr~v~A~Fyn  365 (378)
T KOG1996|consen  300 EDETKEECEKYGKVGNVIIFEIPSQPEDEAVRIFVEFERVESAIKAVVDLNGRYFGGRVVSACFYN  365 (378)
T ss_pred             HHHHHHHHHhhcceeeEEEEecCCCccchhheeeeeeccHHHHHHHHHhcCCceecceeeeheecc
Confidence            3456777889999999988877653   12348999999999999997 99999999999887753

>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []

Probab=95.28  E-value=0.16  Score=38.71  Aligned_cols=66  Identities=14%  Similarity=0.120  Sum_probs=51.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      ..+.+...|..++.++|..+.+.+. ..|..++|++|....+-.+.++|.+.++|..-.. .||+.|.
T Consensus        14 ~~~~l~vp~~~~~~d~l~~f~~~~~-~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   14 TLCCLAVPPYMTPSDFLLFFGAPFR-EDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             eEEEEEeCcccccHHHHHHhhhccc-ccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            3444455555666777877777764 6788899999975567789999999999999887 9999874

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>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=94.76  E-value=0.33  Score=37.05  Aligned_cols=63  Identities=11%  Similarity=0.115  Sum_probs=49.9

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcC-CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          119 VYVSDIDQNITEERLAGLFSSC-GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~-G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      +.+...|+.++-++|..+.+.+ ..|..++|++|...++-.+.+.|.+.++|+.... +||+.+.
T Consensus        16 ~~l~vp~~~~~~d~l~~f~~~~~~~i~~~riird~~pnrymVLikF~~~~~Ad~Fy~~fNGk~Fn   80 (110)
T PF07576_consen   16 CCLAVPPYMTPSDFLLFFGAPFREDIEHIRIIRDGTPNRYMVLIKFRDQESADEFYEEFNGKPFN   80 (110)
T ss_pred             EEEEeCcccccHHHHHHhhhcccccEEEEEEeeCCCCceEEEEEEECCHHHHHHHHHHhCCCccC
Confidence            4445555666677777666655 4678889998877788899999999999999998 9998886

These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=94.73  E-value=0.21  Score=46.71  Aligned_cols=68  Identities=18%  Similarity=0.275  Sum_probs=60.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcC-CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSC-GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~-G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      ..++.|+|-.+|-.++-.||-.+...+ -.|.++++++|...++-...|.|.+.++|....+ +||..+.
T Consensus        72 ~~~~mLcilaVP~~mt~~Dll~F~~~~~~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   72 SSSTMLCILAVPAYMTSHDLLRFCASFIKQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CCCcEEEEEeccccccHHHHHHHHHHHhhhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            347889999999999999998888755 4689999999777788889999999999999998 9999986

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=94.47  E-value=0.081  Score=50.50  Aligned_cols=69  Identities=20%  Similarity=0.386  Sum_probs=56.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhh--cCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFS--SCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG--GTMLGYYPVRVL  188 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~--~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~--g~~~~g~~i~v~  188 (303)
                      ..|.|.++-||.++..++++.||+  .|..+.+|.+-.+.+     =||+|++..+|+.|.+ |.  -.+|.|++|...
T Consensus       174 kRcIvilREIpettp~e~Vk~lf~~encPk~iscefa~N~n-----WyITfesd~DAQqAykylreevk~fqgKpImAR  247 (684)
T KOG2591|consen  174 KRCIVILREIPETTPIEVVKALFKGENCPKVISCEFAHNDN-----WYITFESDTDAQQAYKYLREEVKTFQGKPIMAR  247 (684)
T ss_pred             ceeEEEEeecCCCChHHHHHHHhccCCCCCceeeeeeecCc-----eEEEeecchhHHHHHHHHHHHHHhhcCcchhhh
Confidence            456678899999999999999998  588999999987665     7999999999999997 43  355677776543

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]

Probab=94.35  E-value=0.034  Score=53.36  Aligned_cols=73  Identities=14%  Similarity=0.149  Sum_probs=59.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhh-cCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc---CCeeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFS-SCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML---GYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~-~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~---~g~~i~v~~  189 (303)
                      .+..|+|.||-.-+|.-+|+.++. .+|.|++. +| |+  -+..|||.|.+.++|.+-+. |||..+   +++.|.+.|
T Consensus       443 ~SnvlhI~nLvRPFTlgQLkelL~rtgg~Vee~-Wm-Dk--IKShCyV~yss~eEA~atr~AlhnV~WP~sNPK~L~adf  518 (718)
T KOG2416|consen  443 PSNVLHIDNLVRPFTLGQLKELLGRTGGNVEEF-WM-DK--IKSHCYVSYSSVEEAAATREALHNVQWPPSNPKHLIADF  518 (718)
T ss_pred             ccceEeeecccccchHHHHHHHHhhccCchHHH-HH-HH--hhcceeEecccHHHHHHHHHHHhccccCCCCCceeEeee
Confidence            355699999999999999999998 67777776 33 22  24579999999999999998 999777   368888888


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      ..
T Consensus       519 ~~  520 (718)
T KOG2416|consen  519 VR  520 (718)
T ss_pred             cc
Confidence            64

>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=94.32  E-value=0.19  Score=42.02  Aligned_cols=62  Identities=21%  Similarity=0.187  Sum_probs=46.8

Q ss_pred             CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC--CceeCCeeeEEeecCCCC
Q 022058          226 PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS--GMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       226 t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~--g~~~~g~~l~v~~a~~~~  293 (303)
                      ..+.|+++|..+  +.+....+++.=+    -..|.|.+.++|..|.. |+  +..+.|..+++-|+.+..
T Consensus         8 ~~~~l~~l~~~~--~~~~~~~~L~sFr----Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~~~   72 (184)
T PF04847_consen    8 NLAELEELFSTY--DPPVQFSPLKSFR----RIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQPTP   72 (184)
T ss_dssp             -HHHHHHHHHTT---SS-EEEEETTTT----EEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----SS
T ss_pred             hHHHHHHHHHhc--CCceEEEEcCCCC----EEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccccc
Confidence            357899999999  9888888887743    69999999999999998 99  999999999999985443

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.

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons

Probab=94.25  E-value=0.067  Score=44.46  Aligned_cols=76  Identities=17%  Similarity=0.149  Sum_probs=48.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhc-CCce---eEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcccCC---
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSS-CGQV---VDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTMLGY---  182 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i---~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g---  182 (303)
                      ....|.|++||+++|++++.+.++. ++.-   ..+.-......    .-.-|||.|.+.+++..... ++|..+.+   
T Consensus         6 ~~~KvVIR~LPP~LteeeF~~~i~~~l~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~kg   85 (176)
T PF03467_consen    6 EGTKVVIRRLPPNLTEEEFWEQISPWLPDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSKG   85 (176)
T ss_dssp             ---EEEEEEE-TTS-HHHHCCCCSS--SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TTS
T ss_pred             cCceEEEeCCCCCCCHHHHHHHhhhhcccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCCC
Confidence            4568999999999999999997776 6665   33332222211    23569999999999999998 99977742   


Q ss_pred             --eeEEEeec
Q 022058          183 --YPVRVLPS  190 (303)
Q Consensus       183 --~~i~v~~~  190 (303)
                        .+-.|.++
T Consensus        86 ~~~~~~VE~A   95 (176)
T PF03467_consen   86 NEYPAVVEFA   95 (176)
T ss_dssp             -EEEEEEEE-
T ss_pred             CCcceeEEEc
Confidence              34455554

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.

>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi)

Probab=94.21  E-value=0.066  Score=39.02  Aligned_cols=74  Identities=23%  Similarity=0.214  Sum_probs=47.5

Q ss_pred             EEEEecCHHHHHHHHH--hCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhh
Q 022058          159 AFVEFADEHGARAALN--LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEA  236 (303)
Q Consensus       159 ~fV~f~~~~~A~~Ai~--l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~  236 (303)
                      |.|+|.+..-|++.++  -+...+++..+.|.-+.-...     ...+-+-......++|.|.|||...++++|++..+-
T Consensus         1 AlITF~e~~VA~~i~~~~~~~v~l~~~~~~V~v~P~~~~-----~~~k~qv~~~vs~rtVlvsgip~~l~ee~l~D~LeI   75 (88)
T PF07292_consen    1 ALITFEEEGVAQRILKKKKHPVPLEDCCVRVKVSPVTLG-----HLQKFQVFSGVSKRTVLVSGIPDVLDEEELRDKLEI   75 (88)
T ss_pred             CEEEeCcHHHHHHHHhCCEEEEEECCEEEEEEEEeEecC-----CceEEEEEEcccCCEEEEeCCCCCCChhhheeeEEE
Confidence            6899999999999998  444555666665554311000     000111112345688999999999999998877554


Q ss_pred             h
Q 022058          237 A  237 (303)
Q Consensus       237 ~  237 (303)
                      +
T Consensus        76 h   76 (88)
T PF07292_consen   76 H   76 (88)
T ss_pred             E
Confidence            3

This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=94.21  E-value=0.14  Score=40.44  Aligned_cols=71  Identities=18%  Similarity=0.169  Sum_probs=53.1

Q ss_pred             CCCEEEEcCCCCCC----CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQNI----TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~----t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .-.+|.|.=|..++    +...+-..++.||+|.+|.+....     -|.|.|.+..+|-+|+. ++. ...|..+.+.|
T Consensus        85 PMsTIVVRWlkknm~~~edl~sV~~~Ls~fGpI~SVT~cGrq-----savVvF~d~~SAC~Av~Af~s-~~pgtm~qCsW  158 (166)
T PF15023_consen   85 PMSTIVVRWLKKNMQPTEDLKSVIQRLSVFGPIQSVTLCGRQ-----SAVVVFKDITSACKAVSAFQS-RAPGTMFQCSW  158 (166)
T ss_pred             CceeEEeehhhhcCChHHHHHHHHHHHHhcCCcceeeecCCc-----eEEEEehhhHHHHHHHHhhcC-CCCCceEEeec
Confidence            45567776555444    344566677899999999886433     49999999999999998 544 66788899988


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      ..
T Consensus       159 qq  160 (166)
T PF15023_consen  159 QQ  160 (166)
T ss_pred             cc
Confidence            53

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function

Probab=94.20  E-value=0.3  Score=33.09  Aligned_cols=53  Identities=23%  Similarity=0.293  Sum_probs=43.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcC---CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSC---GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN  174 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~---G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~  174 (303)
                      ...|+|.+++ +++.++|+.+|..|   .....|.++-|..     |=|.|.+.+.|.+|+.
T Consensus         5 peavhirGvd-~lsT~dI~~y~~~y~~~~~~~~IEWIdDtS-----cNvvf~d~~~A~~AL~   60 (62)
T PF10309_consen    5 PEAVHIRGVD-ELSTDDIKAYFSEYFDEEGPFRIEWIDDTS-----CNVVFKDEETAARALV   60 (62)
T ss_pred             eceEEEEcCC-CCCHHHHHHHHHHhcccCCCceEEEecCCc-----EEEEECCHHHHHHHHH
Confidence            3468999985 58889999999988   1345788887664     8999999999999986

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]

Probab=94.04  E-value=0.068  Score=46.27  Aligned_cols=74  Identities=28%  Similarity=0.337  Sum_probs=61.9

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hC--C--cccCCeeEEEeec
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LG--G--TMLGYYPVRVLPS  190 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~--g--~~~~g~~i~v~~~  190 (303)
                      ..|+|.||+.-++.+.|..-|+.||+|+...++.|... ..|-++|.|...-.|.+|.. ++  +  ....+++.-|.+.
T Consensus        32 a~l~V~nl~~~~sndll~~~f~~fg~~e~av~~vD~r~k~t~eg~v~~~~k~~a~~a~rr~~~~g~~~~~~~~p~~VeP~  111 (275)
T KOG0115|consen   32 AELYVVNLMQGASNDLLEQAFRRFGPIERAVAKVDDRGKPTREGIVEFAKKPNARKAARRCREGGFGGTTGGRPVGVEPM  111 (275)
T ss_pred             ceEEEEecchhhhhHHHHHhhhhcCccchheeeecccccccccchhhhhcchhHHHHHHHhccCccccCCCCCccCCChh
Confidence            77999999999999999999999999998888877665 77889999999999999997 42  2  3334677777654

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)

Probab=94.03  E-value=0.2  Score=35.92  Aligned_cols=53  Identities=21%  Similarity=0.337  Sum_probs=39.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS  275 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~  275 (303)
                      ...+|. .|..+...||.++|++|  |.|. |..+.|.     .|||...+.+.|..|+. ++
T Consensus        10 HVFhlt-FPkeWK~~DI~qlFspf--G~I~-VsWi~dT-----SAfV~l~~r~~~~~v~~~~~   63 (87)
T PF08675_consen   10 HVFHLT-FPKEWKTSDIYQLFSPF--GQIY-VSWINDT-----SAFVALHNRDQAKVVMNTLK   63 (87)
T ss_dssp             CEEEEE---TT--HHHHHHHCCCC--CCEE-EEEECTT-----EEEEEECCCHHHHHHHHHHT
T ss_pred             eEEEEe-CchHhhhhhHHHHhccC--CcEE-EEEEcCC-----cEEEEeecHHHHHHHHHHhc
Confidence            445555 99999999999999999  8775 4455554     79999999999999887 53

; 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.

>PF15023 DUF4523: Protein of unknown function (DUF4523)

Probab=93.59  E-value=0.23  Score=39.30  Aligned_cols=73  Identities=21%  Similarity=0.127  Sum_probs=53.8

Q ss_pred             ccccceEEEcCCCCC----CCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeee
Q 022058          210 EMCSRTVYCTNIDKK----VPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPI  284 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~----~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l  284 (303)
                      +++-.+|.|+=|..+    -+-..+....+.|  |+|.+|.+.-.+     .|.|.|.+..+|.+|+. ++. ...|..+
T Consensus        83 epPMsTIVVRWlkknm~~~edl~sV~~~Ls~f--GpI~SVT~cGrq-----savVvF~d~~SAC~Av~Af~s-~~pgtm~  154 (166)
T PF15023_consen   83 EPPMSTIVVRWLKKNMQPTEDLKSVIQRLSVF--GPIQSVTLCGRQ-----SAVVVFKDITSACKAVSAFQS-RAPGTMF  154 (166)
T ss_pred             CCCceeEEeehhhhcCChHHHHHHHHHHHHhc--CCcceeeecCCc-----eEEEEehhhHHHHHHHHhhcC-CCCCceE
Confidence            345567777655444    3334555667789  999999886443     79999999999999998 654 6678888


Q ss_pred             EEeecC
Q 022058          285 RVSPSK  290 (303)
Q Consensus       285 ~v~~a~  290 (303)
                      +++|-.
T Consensus       155 qCsWqq  160 (166)
T PF15023_consen  155 QCSWQQ  160 (166)
T ss_pred             Eeeccc
Confidence            888854

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.57  E-value=0.045  Score=51.22  Aligned_cols=65  Identities=20%  Similarity=0.203  Sum_probs=55.4

Q ss_pred             CCCCC-CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCC
Q 022058          221 IDKKV-PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       221 L~~~~-t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      .|+.. +-.+|..+|.+|  |.|..|.|-....    .|.|+|.+..+|-.|-..++..|.++.|+|-|-++
T Consensus       380 ~~~glnt~a~ln~hfA~f--G~i~n~qv~~~~~----~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  380 SPFGLNTIADLNPHFAQF--GEIENIQVDYSSL----HAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cCCCCchHhhhhhhhhhc--CccccccccCchh----hheeeeeccccccchhccccceecCceeEEEEecC
Confidence            34443 458899999999  9999999866532    69999999999988888899999999999999887

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]

Probab=93.25  E-value=0.046  Score=51.12  Aligned_cols=73  Identities=16%  Similarity=0.175  Sum_probs=61.1

Q ss_pred             CCEEEEcCCCCCC-CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNI-TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~-t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      .+.|-+.-.|+.+ +..+|...|.+||.|..|.+-....    .|.|+|.+..+|-.|-..++..|++|.|+|.|-.+
T Consensus       372 hs~l~lek~~~glnt~a~ln~hfA~fG~i~n~qv~~~~~----~a~vTF~t~aeag~a~~s~~avlnnr~iKl~whnp  445 (526)
T KOG2135|consen  372 HSPLALEKSPFGLNTIADLNPHFAQFGEIENIQVDYSSL----HAVVTFKTRAEAGEAYASHGAVLNNRFIKLFWHNP  445 (526)
T ss_pred             cchhhhhccCCCCchHhhhhhhhhhcCccccccccCchh----hheeeeeccccccchhccccceecCceeEEEEecC
Confidence            4456666666654 5778999999999999999866533    59999999999999999999999999999999765

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=93.20  E-value=0.17  Score=44.91  Aligned_cols=69  Identities=23%  Similarity=0.331  Sum_probs=53.1

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCee-EEEee
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYP-VRVLP  189 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~-i~v~~  189 (303)
                      ...|-|-++|+.-. ..|..+|+.||.|.+.....+-    -+-+|.|.+.-+|++||..||+.|+|-. |-|..
T Consensus       197 D~WVTVfGFppg~~-s~vL~~F~~cG~Vvkhv~~~ng----NwMhirYssr~~A~KALskng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  197 DTWVTVFGFPPGQV-SIVLNLFSRCGEVVKHVTPSNG----NWMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKP  266 (350)
T ss_pred             cceEEEeccCccch-hHHHHHHHhhCeeeeeecCCCC----ceEEEEecchhHHHHhhhhcCeeeccceEEeeee
Confidence            45688888887654 3566789999999887665322    3899999999999999999999998743 44444

>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=92.96  E-value=0.13  Score=42.84  Aligned_cols=77  Identities=12%  Similarity=0.073  Sum_probs=48.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhh-hcCcce---eEEEEecC-C--C-CcccEEEEEEcCHHHHHHHHH-hCCceeC---
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEA-ACGGEV---TRLRLLGD-H--V-HSTRIAFVEFAVAESAILALN-CSGMVLG---  280 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~-~~~G~i---~~v~i~~d-~--~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~---  280 (303)
                      ...|.|++||+++|++++++.+.+ +  +.-   .++.-..+ .  . ..-.-|+|.|.+.+++..-.. ++|+.|.   
T Consensus         7 ~~KvVIR~LPP~LteeeF~~~i~~~l--~~~~~w~y~~g~~~~~~~~~~~~SRaYi~F~~~~~~~~F~~~~~g~~F~D~k   84 (176)
T PF03467_consen    7 GTKVVIRRLPPNLTEEEFWEQISPWL--PDEWDWYYFQGKYGKKSFKPPTYSRAYINFKNPEDLLEFRDRFDGHVFVDSK   84 (176)
T ss_dssp             --EEEEEEE-TTS-HHHHCCCCSS----SSE---EEEEEEES-SSSTTS--EEEEEEESSCHHHHHHHHHCTTEEEE-TT
T ss_pred             CceEEEeCCCCCCCHHHHHHHhhhhc--ccccceEEEecCCCCccCCCCcceEEEEEeCCHHHHHHHHHhcCCcEEECCC
Confidence            368999999999999999997777 5  544   23321122 1  1 224469999999999888887 9998873   


Q ss_pred             C--eeeEEeecCC
Q 022058          281 S--QPIRVSPSKT  291 (303)
Q Consensus       281 g--~~l~v~~a~~  291 (303)
                      |  ..-.|.+|--
T Consensus        85 g~~~~~~VE~Apy   97 (176)
T PF03467_consen   85 GNEYPAVVEFAPY   97 (176)
T ss_dssp             S-EEEEEEEE-SS
T ss_pred             CCCcceeEEEcch
Confidence            2  2455666643

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.

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]

Probab=92.74  E-value=0.34  Score=45.26  Aligned_cols=67  Identities=10%  Similarity=0.212  Sum_probs=58.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      +..|+|-.+|..++-.||..++..++ -.|.+++|++|.--.+=..++.|.+.++|..-.+ +||..|.
T Consensus        74 ~~mLcilaVP~~mt~~Dll~F~~~~~-~~I~~irivRd~~pnrymvLIkFr~q~da~~Fy~efNGk~Fn  141 (493)
T KOG0804|consen   74 STMLCILAVPAYMTSHDLLRFCASFI-KQISDIRIVRDGMPNRYMVLIKFRDQADADTFYEEFNGKQFN  141 (493)
T ss_pred             CcEEEEEeccccccHHHHHHHHHHHh-hhhheeEEeecCCCceEEEEEEeccchhHHHHHHHcCCCcCC
Confidence            58899999999999999999999986 7899999999753344579999999999999998 9999884

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.37  E-value=0.056  Score=48.58  Aligned_cols=79  Identities=16%  Similarity=0.286  Sum_probs=61.5

Q ss_pred             ceEEEcCCCCCCCHHHHH---HHhhhhcCcceeEEEEecCC----C-CcccEEEEEEcCHHHHHHHHH-hCCceeCCeee
Q 022058          214 RTVYCTNIDKKVPQAEVK---QFFEAACGGEVTRLRLLGDH----V-HSTRIAFVEFAVAESAILALN-CSGMVLGSQPI  284 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~---~~F~~~~~G~i~~v~i~~d~----~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l  284 (303)
                      .-+||-+|+..+..+.+.   ..|.+|  |.|..|.+..+.    + .....++|+|...++|..||. .+|..++|+.|
T Consensus        78 nlvyvvgl~~~~ade~~l~~~eyfgqy--gki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~l  155 (327)
T KOG2068|consen   78 NLVYVVGLPLDLADESVLERTEYFGQY--GKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRAL  155 (327)
T ss_pred             hhhhhhCCCccccchhhhhCccccccc--ccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhh
Confidence            346777888776554443   568898  999999888865    1 123459999999999999999 99999999999


Q ss_pred             EEeecCCCCC
Q 022058          285 RVSPSKTPVR  294 (303)
Q Consensus       285 ~v~~a~~~~~  294 (303)
                      +..++.++-.
T Consensus       156 ka~~gttkyc  165 (327)
T KOG2068|consen  156 KASLGTTKYC  165 (327)
T ss_pred             HHhhCCCcch
Confidence            9988876543

>KOG2068 consensus MOT2 transcription factor [Transcription]

Probab=92.33  E-value=0.068  Score=48.04  Aligned_cols=79  Identities=18%  Similarity=0.306  Sum_probs=61.4

Q ss_pred             CCEEEEcCCCCCCCHHH-HH--HHhhcCCceeEEEEeeCCC--C---CceEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 022058          116 RRTVYVSDIDQNITEER-LA--GLFSSCGQVVDCRVCGDPH--S---VLRFAFVEFADEHGARAALN-LGGTMLGYYPVR  186 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~-l~--~~F~~~G~i~~~~i~~~~~--~---~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~  186 (303)
                      +.-+||-+|+..+..+. |+  +.|.+||.|.++.+..+..  .   ..--+||+|...++|..||. .+|..+.|+.++
T Consensus        77 knlvyvvgl~~~~ade~~l~~~eyfgqygki~ki~~~~~~S~~s~~~~~~s~yITy~~~eda~rci~~v~g~~~dg~~lk  156 (327)
T KOG2068|consen   77 KNLVYVVGLPLDLADESVLERTEYFGQYGKINKIVKNKDPSSSSSSGGTCSVYITYEEEEDADRCIDDVDGFVDDGRALK  156 (327)
T ss_pred             hhhhhhhCCCccccchhhhhCcccccccccceEEeecCCcccccCCCCCCcccccccchHhhhhHHHHhhhHHhhhhhhH
Confidence            34488888987765554 43  4888999999999988662  1   11239999999999999999 999999999988


Q ss_pred             EeecCCCC
Q 022058          187 VLPSKTAI  194 (303)
Q Consensus       187 v~~~~~~~  194 (303)
                      ..+..++.
T Consensus       157 a~~gttky  164 (327)
T KOG2068|consen  157 ASLGTTKY  164 (327)
T ss_pred             HhhCCCcc
Confidence            87765543

>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=92.12  E-value=0.57  Score=39.19  Aligned_cols=60  Identities=23%  Similarity=0.168  Sum_probs=44.9

Q ss_pred             CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEeecCC
Q 022058          129 TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG--GTMLGYYPVRVLPSKT  192 (303)
Q Consensus       129 t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~--g~~~~g~~i~v~~~~~  192 (303)
                      ..+.|+++|..|+.+.....++.-.    -..|.|.+.+.|.+|.. ++  +..+.|..++|.++..
T Consensus         8 ~~~~l~~l~~~~~~~~~~~~L~sFr----Ri~v~f~~~~~A~~~r~~l~~~~~~~~g~~l~~yf~~~   70 (184)
T PF04847_consen    8 NLAELEELFSTYDPPVQFSPLKSFR----RIRVVFESPESAQRARQLLHWDGTSFNGKRLRVYFGQP   70 (184)
T ss_dssp             -HHHHHHHHHTT-SS-EEEEETTTT----EEEEE-SSTTHHHHHHHTST--TSEETTEE-EEE----
T ss_pred             hHHHHHHHHHhcCCceEEEEcCCCC----EEEEEeCCHHHHHHHHHHhcccccccCCCceEEEEccc
Confidence            4578999999999998887776443    59999999999999998 99  8999999999988743

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.

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]

Probab=91.13  E-value=0.93  Score=40.34  Aligned_cols=68  Identities=19%  Similarity=0.211  Sum_probs=52.6

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCe-eeEEee
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQ-PIRVSP  288 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~-~l~v~~  288 (303)
                      .=|-|.++|+.-. .-|..+|+++  |.|++..-....+    +-+|.|.+.-+|++||.-||+.|+|. .|-|..
T Consensus       198 ~WVTVfGFppg~~-s~vL~~F~~c--G~Vvkhv~~~ngN----wMhirYssr~~A~KALskng~ii~g~vmiGVkp  266 (350)
T KOG4285|consen  198 TWVTVFGFPPGQV-SIVLNLFSRC--GEVVKHVTPSNGN----WMHIRYSSRTHAQKALSKNGTIIDGDVMIGVKP  266 (350)
T ss_pred             ceEEEeccCccch-hHHHHHHHhh--CeeeeeecCCCCc----eEEEEecchhHHHHhhhhcCeeeccceEEeeee
Confidence            3456668887653 5688899997  9998876653333    99999999999999999999999875 445665

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=90.90  E-value=0.17  Score=50.71  Aligned_cols=70  Identities=31%  Similarity=0.346  Sum_probs=59.5

Q ss_pred             EEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee--CCeeeEEeecCCC
Q 022058          217 YCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL--GSQPIRVSPSKTP  292 (303)
Q Consensus       217 ~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~--~g~~l~v~~a~~~  292 (303)
                      ++.|.+-..+-.-|.-+|..|  |.|.++..+++-+    .|.|+|.+.+.|..|+. |+|+++  -|-..+|.+|++.
T Consensus       302 ~~~nn~v~~tSssL~~l~s~y--g~v~s~wtlr~~N----~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  302 SLENNAVNLTSSSLATLCSDY--GSVASAWTLRDLN----MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhcccccchHHHHHHHHHhh--cchhhheeccccc----chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            444455566778899999999  9999999998865    89999999999999999 999986  4778999998764

>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=89.64  E-value=1.6  Score=29.96  Aligned_cols=54  Identities=13%  Similarity=0.142  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          224 KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       224 ~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      .++-++++.-+..|     ...+|..|+-    --||.|.+..+|.+|.. .||..+.+.++.+
T Consensus        11 ~~~v~d~K~~Lr~y-----~~~~I~~d~t----GfYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKY-----RWDRIRDDRT----GFYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcC-----CcceEEecCC----EEEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            46778999999998     3444555541    27999999999999999 8999988877654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2318 consensus Uncharacterized conserved protein [Function unknown]

Probab=88.71  E-value=2.1  Score=41.42  Aligned_cols=78  Identities=17%  Similarity=0.284  Sum_probs=62.0

Q ss_pred             cccceEEEcCCCCC-CCHHHHHHHhhhhc--CcceeEEEEecCC-CC----------c----------------------
Q 022058          211 MCSRTVYCTNIDKK-VPQAEVKQFFEAAC--GGEVTRLRLLGDH-VH----------S----------------------  254 (303)
Q Consensus       211 ~~~~~l~V~nL~~~-~t~~~L~~~F~~~~--~G~i~~v~i~~d~-~~----------~----------------------  254 (303)
                      ...+.|-|-||... +...+|.-+|+.|+  +|.|.+|.|.+.. |+          +                      
T Consensus       172 ~~T~RLAVvNMDWd~v~AkDL~v~~nSFlP~gGsilSV~IYpSeFGkeRM~eEeV~GP~~el~~~~e~~~~s~sD~ee~~  251 (650)
T KOG2318|consen  172 EETKRLAVVNMDWDRVKAKDLFVLFNSFLPKGGSILSVKIYPSEFGKERMKEEEVHGPPKELFKPVEEYKESESDDEEEE  251 (650)
T ss_pred             cccceeeEeccccccccHHHHHHHHHhhcCCCCceeEEEechhhhhHHHhhhhcccCChhhhccccccCcccccchhhhh
Confidence            34678999999985 78899999999988  5799999998742 21          1                      


Q ss_pred             -------c---------cEEEEEEcCHHHHHHHHH-hCCceeC--CeeeEEee
Q 022058          255 -------T---------RIAFVEFAVAESAILALN-CSGMVLG--SQPIRVSP  288 (303)
Q Consensus       255 -------~---------g~afV~f~~~e~A~~Ai~-l~g~~~~--g~~l~v~~  288 (303)
                             +         -||.|+|.+.+.|.+... .+|.+|.  +..|-+.|
T Consensus       252 ~~~~~kLR~Yq~~rLkYYyAVvecDsi~tA~~vYe~CDG~EfEsS~~~~DLRF  304 (650)
T KOG2318|consen  252 DVDREKLRQYQLNRLKYYYAVVECDSIETAKAVYEECDGIEFESSANKLDLRF  304 (650)
T ss_pred             hHHHHHHHHHHhhhheeEEEEEEecCchHHHHHHHhcCcceeccccceeeeee
Confidence                   1         279999999999999998 9999996  45555555

>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=88.63  E-value=2.2  Score=29.28  Aligned_cols=54  Identities=19%  Similarity=0.278  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          127 NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       127 ~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      .++-++++..+..|+-.   +|..+..   | -||.|.+..+|++|.. .+|..+.+..|.+
T Consensus        11 ~~~v~d~K~~Lr~y~~~---~I~~d~t---G-fYIvF~~~~Ea~rC~~~~~~~~~f~y~m~M   65 (66)
T PF11767_consen   11 GVTVEDFKKRLRKYRWD---RIRDDRT---G-FYIVFNDSKEAERCFRAEDGTLFFTYRMQM   65 (66)
T ss_pred             CccHHHHHHHHhcCCcc---eEEecCC---E-EEEEECChHHHHHHHHhcCCCEEEEEEEEe
Confidence            57889999999999753   2333443   5 6999999999999999 9998888777654

This entry represents a domain of unknown function which is associated with the SET domain and found in histone lysine methyltransferases [].

>KOG2591 consensus c-Mpl binding protein, contains La domain [Signal transduction mechanisms]

Probab=88.24  E-value=1.8  Score=41.71  Aligned_cols=67  Identities=19%  Similarity=0.280  Sum_probs=52.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhh-hcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC--CceeCCeeeEE
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEA-ACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS--GMVLGSQPIRV  286 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~-~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~--g~~~~g~~l~v  286 (303)
                      +.+.++-||.++..++++.+|.. -| ..+.+|.+....+     =||+|.+..||++|.+ |.  -.+|-|+.|..
T Consensus       176 cIvilREIpettp~e~Vk~lf~~enc-Pk~iscefa~N~n-----WyITfesd~DAQqAykylreevk~fqgKpImA  246 (684)
T KOG2591|consen  176 CIVILREIPETTPIEVVKALFKGENC-PKVISCEFAHNDN-----WYITFESDTDAQQAYKYLREEVKTFQGKPIMA  246 (684)
T ss_pred             eEEEEeecCCCChHHHHHHHhccCCC-CCceeeeeeecCc-----eEEEeecchhHHHHHHHHHHHHHhhcCcchhh
Confidence            66778999999999999999985 34 6888998877664     7999999999999987 53  24555665543

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=87.42  E-value=0.5  Score=46.25  Aligned_cols=118  Identities=19%  Similarity=0.171  Sum_probs=81.0

Q ss_pred             hhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCee
Q 022058          106 AFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYP  184 (303)
Q Consensus       106 ~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~  184 (303)
                      +..........-++||+|+...+..+-++.+...+|-|.++....       |||..|..+....+|+. ++...++|..
T Consensus        30 ~qp~~~~~~~~~~vfv~~~~~~~s~~~~~~il~~~g~v~s~kr~~-------fgf~~f~~~~~~~ra~r~~t~~~~~~~k  102 (668)
T KOG2253|consen   30 IQPVFQPLPPRDTVFVGNISYLVSQEFWKSILAKSGFVPSWKRDK-------FGFCEFLKHIGDLRASRLLTELNIDDQK  102 (668)
T ss_pred             CcccccCCCCCceeEecchhhhhhHHHHHHHHhhCCcchhhhhhh-------hcccchhhHHHHHHHHHHhcccCCCcch
Confidence            333333444677899999999999999999999999998876643       99999999999999998 8888888877


Q ss_pred             EEEeecCCCCCC----------CCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhh
Q 022058          185 VRVLPSKTAILP----------VNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEA  236 (303)
Q Consensus       185 i~v~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~  236 (303)
                      +.+.........          ....+.|.+.      .+-.+|.|+|..+.+......+.-
T Consensus       103 l~~~~d~q~~~n~~k~~~~~~~~~~~f~p~~s------rr~e~i~~k~~~l~~~~~~~~~~i  158 (668)
T KOG2253|consen  103 LIENVDEQTIENADKEKSIANKESHKFVPSSS------RRQESIQNKPLSLDEQIHKKSLQI  158 (668)
T ss_pred             hhccchhhhhcCccccccchhhhhcccCCchh------HHHHHhhccccchhHHHHHHHHhc
Confidence            776653221110          0111222211      355667777776666555555443

>PF14111 DUF4283: Domain of unknown function (DUF4283)

Probab=87.03  E-value=1.2  Score=35.56  Aligned_cols=109  Identities=13%  Similarity=-0.027  Sum_probs=71.5

Q ss_pred             CCCHHHHHHHhh----cCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCCCCCCCCCCC
Q 022058          127 NITEERLAGLFS----SCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFL  202 (303)
Q Consensus       127 ~~t~~~l~~~F~----~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~~~~~~~~~~  202 (303)
                      ..+-..|...+.    ..|.+.-..+      ..++..+.|.+.+++.+++......+.+..+.+..-.+..       .
T Consensus        28 ~~~~~~l~~~l~~~W~~~~~~~i~~l------~~~~fl~~F~~~~d~~~vl~~~p~~~~~~~~~l~~W~~~~-------~   94 (153)
T PF14111_consen   28 PISLSALEQELAKIWKLKGGVKIRDL------GDNLFLFQFESEEDRQRVLKGGPWNFNGHFLILQRWSPDF-------N   94 (153)
T ss_pred             CCCHHHHHHHHHHHhCCCCcEEEEEe------CCCeEEEEEEeccceeEEEecccccccccchhhhhhcccc-------c
Confidence            455666655554    3444332222      2368999999999999999877777888888877643221       1


Q ss_pred             CCcccccccccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCC
Q 022058          203 PRSEDEREMCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDH  251 (303)
Q Consensus       203 ~~~~~~~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~  251 (303)
                      +..... .....=|.|.|||.. .+++-|+.+-+..  |.+..+......
T Consensus        95 ~~~~~~-~~~~vWVri~glP~~~~~~~~~~~i~~~i--G~~i~vD~~t~~  141 (153)
T PF14111_consen   95 PSEVKF-EHIPVWVRIYGLPLHLWSEEILKAIGSKI--GEPIEVDENTLK  141 (153)
T ss_pred             ccccce-eccchhhhhccCCHHHhhhHHHHHHHHhc--CCeEEEEcCCCC
Confidence            111110 011133677899987 7888899999998  999998876554

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]

Probab=86.66  E-value=0.55  Score=47.26  Aligned_cols=71  Identities=31%  Similarity=0.328  Sum_probs=60.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC--CeeEEEeecCCC
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG--YYPVRVLPSKTA  193 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~--g~~i~v~~~~~~  193 (303)
                      .++.|.+-..+...|.-+++.||.|.+...+++-+    .|.|.|.+.+.|..|+. ++|.++.  |-+.+|.+++..
T Consensus       301 ~~~~nn~v~~tSssL~~l~s~yg~v~s~wtlr~~N----~alvs~~s~~sai~a~dAl~gkevs~~g~Ps~V~~ak~~  374 (1007)
T KOG4574|consen  301 QSLENNAVNLTSSSLATLCSDYGSVASAWTLRDLN----MALVSFSSVESAILALDALQGKEVSVTGAPSRVSFAKTL  374 (1007)
T ss_pred             hhhhcccccchHHHHHHHHHhhcchhhheeccccc----chhhhhHHHHHHHHhhhhhcCCcccccCCceeEEecccc
Confidence            44555566677778999999999999999988876    69999999999999998 9998875  888999888654

>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=85.65  E-value=4.4  Score=28.32  Aligned_cols=59  Identities=17%  Similarity=0.325  Sum_probs=33.6

Q ss_pred             CCCHHHHHHHhhhhcC---cceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          224 KVPQAEVKQFFEAACG---GEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       224 ~~t~~~L~~~F~~~~~---G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .++..+|..++...++   ..|-.+.|...      |+||+-... .|..++. |++..+.|+.|.|+.|
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 GLTPRDIVGAICNEAGIPGRDIGRIDIFDN------FSFVEVPEE-VAEKVLEALNGKKIKGKKVRVERA   74 (74)
T ss_dssp             T--HHHHHHHHHTCTTB-GGGEEEEEE-SS-------EEEEE-TT--HHHHHHHHTT--SSS----EEE-
T ss_pred             CCCHHHHHHHHHhccCCCHHhEEEEEEeee------EEEEEECHH-HHHHHHHHhcCCCCCCeeEEEEEC
Confidence            5778888888887620   13445666654      899998765 6677777 9999999999999865

; PDB: 2G0C_A 3MOJ_B.

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]

Probab=85.26  E-value=0.89  Score=44.58  Aligned_cols=69  Identities=20%  Similarity=0.169  Sum_probs=57.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      +..++||+|+...+..+-++.+... | |.|.++....       |||..|..+.....|+. ++-..++|+.|.+...
T Consensus        39 ~~~~vfv~~~~~~~s~~~~~~il~~-~-g~v~s~kr~~-------fgf~~f~~~~~~~ra~r~~t~~~~~~~kl~~~~d  108 (668)
T KOG2253|consen   39 PRDTVFVGNISYLVSQEFWKSILAK-S-GFVPSWKRDK-------FGFCEFLKHIGDLRASRLLTELNIDDQKLIENVD  108 (668)
T ss_pred             CCceeEecchhhhhhHHHHHHHHhh-C-Ccchhhhhhh-------hcccchhhHHHHHHHHHHhcccCCCcchhhccch
Confidence            4578999999999998888888777 6 9887765543       89999999999999998 8888888888776653

>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=84.60  E-value=29  Score=31.03  Aligned_cols=172  Identities=13%  Similarity=0.123  Sum_probs=101.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC---------CCceEEEEEecCHHHHHHHHH-----hC--Cc
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH---------SVLRFAFVEFADEHGARAALN-----LG--GT  178 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~---------~~~G~~fV~f~~~~~A~~Ai~-----l~--g~  178 (303)
                      ..|.|.+.|+..+++--.+-..|-.||+|++|.++.+..         +..-...+-|-+.+.+.....     |.  .+
T Consensus        14 rTRSLLfeNv~~sidLh~Fl~~fv~~~pIESiYL~~~~~~~~d~~~~d~~~~SilLSFlsr~~CLdFYNnvLQrLsEfK~   93 (309)
T PF10567_consen   14 RTRSLLFENVNNSIDLHSFLTKFVKFGPIESIYLIKSNDKPSDDYNDDKNNQSILLSFLSREICLDFYNNVLQRLSEFKT   93 (309)
T ss_pred             eeHHHHHhhccccccHHHHHHHhhccCceeEEEEecCCCcccccccccccceEEEEeeechHHHHHHHHHHHHHHHHHHH
Confidence            467799999999999999999999999999999998661         124568888888777655432     22  13


Q ss_pred             ccCCeeEEEeecCCCCCC----CC-CCCC-----CC-c-ccccccccceEEEcCCCCCCCHHH-HHHHh---hhhcCc--
Q 022058          179 MLGYYPVRVLPSKTAILP----VN-PTFL-----PR-S-EDEREMCSRTVYCTNIDKKVPQAE-VKQFF---EAACGG--  240 (303)
Q Consensus       179 ~~~g~~i~v~~~~~~~~~----~~-~~~~-----~~-~-~~~~~~~~~~l~V~nL~~~~t~~~-L~~~F---~~~~~G--  240 (303)
                      .+....|.+.+..-....    .. ..+.     +. . +-...+..+.|.|. +...+.+++ +.+.+   ..-  +  
T Consensus        94 ~L~S~~L~lsFV~l~y~~~~~~~~~~~~~~~~~~~~L~~~i~~~gATRSl~Ie-F~~~~~~~dl~~~kL~fL~~~--~n~  170 (309)
T PF10567_consen   94 KLKSESLTLSFVSLNYQKKTDPNDEEADFSDYLVASLQYNIINRGATRSLAIE-FKDPVDKDDLIEKKLPFLKNS--NNK  170 (309)
T ss_pred             hcCCcceeEEEEEEeccccccccccccchhhHHhhhhhheeecCCcceEEEEE-ecCccchhHHHHHhhhhhccC--CCc
Confidence            344566666654321110    00 0000     00 0 00112234566663 233343333 22222   111  2  


Q ss_pred             --ceeEEEEecCCC----CcccEEEEEEcCHHHHHHHHH-h--CCceeC-CeeeEEeec
Q 022058          241 --EVTRLRLLGDHV----HSTRIAFVEFAVAESAILALN-C--SGMVLG-SQPIRVSPS  289 (303)
Q Consensus       241 --~i~~v~i~~d~~----~~~g~afV~f~~~e~A~~Ai~-l--~g~~~~-g~~l~v~~a  289 (303)
                        -+++|.|+....    =++.||.++|-+...|...+. |  ++...+ .+..-|...
T Consensus       171 RYVlEsIDlVna~~~~~~Fp~~YaILtFlnIsMAiEV~dYlk~~~~~~~Iskc~fVs~~  229 (309)
T PF10567_consen  171 RYVLESIDLVNADEPSKHFPKNYAILTFLNISMAIEVLDYLKSNSKKLGISKCFFVSVQ  229 (309)
T ss_pred             eEEEEEEEEeccCcccccCCcceEEEeehhHHhHHHHHHHHHhcccccCcceEEEEecc
Confidence              467788886532    257799999999999988886 4  444443 344445443

It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, co-purifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in P39935 from SWISSPROT and P39936 from SWISSPROT.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	303
1fnx_H	174	Solution Structure Of The Huc Rbd1-Rbd2 Complexed W		3e-07
1fxl_A	167	Crystal Structure Of Hud And Au-Rich Element Of The		5e-07
1cvj_A	190	X-Ray Crystal Structure Of The Poly(A)-Binding Prot		1e-06
4f02_A	213	Crystal Structure Of The Pabp-Binding Site Of Eif4g		1e-06
2jwn_A	124	Solution Nmr Structure Of The Protease-Resistent Do		2e-05
2qfj_A	216	Crystal Structure Of First Two Rrm Domains Of Fir B		3e-05
3b4d_A	96	Crystal Structure Of Human Pabpn1 Rrm Length = 96		4e-05
3ucg_A	89	Crystal Structure Of A Rna Binding Domain Of Hypoth		5e-05
4ed5_A	177	Crystal Structure Of The Two N-Terminal Rrm Domains		7e-05
4egl_A	177	Crystal Structure Of Two Tandem Rna Recognition Mot		7e-05
2kxf_A	199	Solution Structure Of The First Two Rrm Domains Of		2e-04
3md3_A	166	Crystal Structure Of The First Two Rrm Domains Of Y		3e-04
2x1a_A	97	Structure Of Rna15 Rrm With Rna Bound (G) Length =		3e-04
2x1f_A	96	Structure Of Rna15 Rrm With Bound Rna (Gu) Length =		4e-04
2km8_B	84	Interdomain Rrm Packing Contributes To Rna Recognit		5e-04
2cq4_A	114	Solution Structure Of Rna Binding Domain In Rna Bin		5e-04

>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The Au-Rich Element Length = 174

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 81/188 (43%), Gaps = 30/188 (15%)
Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL 173
           +  + V+ + QN+T++    LF S G +  C++  D  +   L + FV ++D + A  A+
Sbjct: 4   KTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAI 63
Query: 174 N-LGGTMLGYYPVRVL---PSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAE 229
           N L G  L    ++V    PS  +I   N                 +Y + + K + Q E
Sbjct: 64  NTLNGLKLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMSQKE 106
Query: 230 VKQFFEAACGGEVTRLRLLGDHVH--STRIAFVEF---AVAESAILALNCSGMVLGSQPI 284
           ++Q F     G +   R+L D     S  + F+ F     AE AI  LN    +  ++PI
Sbjct: 107 MEQLFSQY--GRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPI 164
Query: 285 RVSPSKTP 292
            V  +  P
Sbjct: 165 TVKFANNP 172

>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos Rna Length = 167

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 78/182 (42%), Gaps = 30/182 (16%)
Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL 173
           +  + V+ + QN+T+E    LF S G++  C++  D  +   L + FV + D   A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
Query: 174 N-LGGTMLGYYPVRV---LPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAE 229
           N L G  L    ++V    PS  +I   N                 +Y + + K + Q E
Sbjct: 62  NTLNGLRLQTKTIKVSYARPSSASIRDAN-----------------LYVSGLPKTMTQKE 104
Query: 230 VKQFFEAACGGEVTRLRLLGDHVH--STRIAFVEF---AVAESAILALNCSGMVLGSQPI 284
           ++Q F     G +   R+L D V   S  + F+ F     AE AI  LN       ++PI
Sbjct: 105 LEQLFSQY--GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPI 162
Query: 285 RV 286
            V
Sbjct: 163 TV 164

>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In Complex With Polyadenylate Rna Length = 190

Iteration: 1
 Score = 50.4 bits (119), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 78/178 (43%), Gaps = 18/178 (10%)
Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD--PHSVLRFAFVEFADEHGARAALN- 174
           ++YV D+  ++TE  L   FS  G ++  RVC D      L +A+V F     A  AL+ 
Sbjct: 12  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           +   ++   PVR++ S+            R    R+     ++  N+DK +    +   F
Sbjct: 72  MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSIDNKALYDTF 119
Query: 235 EAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL-NCSGMVLGSQPIRVSPSKT 291
            A   G +   +++ D   S    FV F   E+A  A+   +GM+L  + + V   K+
Sbjct: 120 SAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 175

>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In Complex With Rrm1-2 Of Pabp And Poly(A) Length = 213

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 78/178 (43%), Gaps = 18/178 (10%)
Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD--PHSVLRFAFVEFADEHGARAALN- 174
           ++YV D+  ++TE  L   FS  G ++  RVC D      L +A+V F     A  AL+ 
Sbjct: 17  SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           +   ++   PVR++ S+            R    R+     ++  N+DK +    +   F
Sbjct: 77  MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSIDNKALYDTF 124
Query: 235 EAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL-NCSGMVLGSQPIRVSPSKT 291
            A   G +   +++ D   S    FV F   E+A  A+   +GM+L  + + V   K+
Sbjct: 125 SAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS 180

>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of Xenopus Laevis Epabp2 Length = 124

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 51/93 (54%), Gaps = 2/93 (2%)
Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEH 167
           ++++  +R+VYV ++D   T + L   FSSCG +    +  D  S     +A++EFA+ +
Sbjct: 30  EKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERN 89
Query: 168 GARAALNLGGTMLGYYPVRVLPSKTAILPVNPT 200
              AA+ +  T+     ++VLP +T +  ++ T
Sbjct: 90  SVDAAVAMDETVFRGRTIKVLPKRTNMPGISST 122

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 90/204 (44%), Gaps = 15/204 (7%)
Query: 104 GRAFRAQREDS--VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FA 159
           GR   AQR+ +  +   VYV  I   + E+ +   F+  G +    +  D  ++    FA
Sbjct: 14  GRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFA 73
Query: 160 FVEFADEHGARAAL-NLGGTMLGYYPVRV-LPSKTAILPVNPTFLPRSEDEREMCSRTVY 217
           FVE+     A+ AL  +   MLG   ++V  PS   I    P     +E+ R      +Y
Sbjct: 74  FVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSN--IGQAQPIIDQLAEEARAF--NRIY 129
Query: 218 CTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR--IAFVEFAVAESAILALNCS 275
             ++ + +   ++K  FEA   G++    L  D          F+E+  A+S+  A++  
Sbjct: 130 VASVHQDLSDDDIKSVFEAF--GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Query: 276 GMV-LGSQPIRVSPSKTPVRPRVT 298
            +  LG Q +RV  + TP  P +T
Sbjct: 188 NLFDLGGQYLRVGKAVTPPMPLLT 211

>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm Length = 96

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN 174
           R++YV ++D   T E L   F  CG V    +  D  S     FA++EF+D+   R +L 
Sbjct: 6   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 175 LGGTMLGYYPVRVLPSKT 192
           L  ++     ++V+P +T
Sbjct: 66  LDESLFRGRQIKVIPKRT 83

>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens At 1.95 A Resolution Length = 89

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN 174
           R++YV ++D   T E L   F  CG V    +  D  S     FA++EF+D+   R +L 
Sbjct: 7   RSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 175 LGGTMLGYYPVRVLPSKT 192
           L  ++     ++V+P +T
Sbjct: 67  LDESLFRGRQIKVIPKRT 84

>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur Complexed With Rna Length = 177

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 82/180 (45%), Gaps = 26/180 (14%)
Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP---HSVLRFAFVEFADEHGARAA 172
           R  + V+ + QN+T++ L  LFSS G+V   ++  D    HS L + FV +     A  A
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHS-LGYGFVNYVTAKDAERA 60
Query: 173 LN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVK 231
           +N L G  L    ++V  ++           P SE  ++     +Y + + + + Q +V+
Sbjct: 61  INTLNGLRLQSKTIKVSYAR-----------PSSEVIKDA---NLYISGLPRTMTQKDVE 106
Query: 232 QFFEAACGGEVTRLRLLGDHVH--STRIAFVEF---AVAESAILALNCSGMVLGSQPIRV 286
             F  +  G +   R+L D     S  +AF+ F   + AE AI + N       S+PI V
Sbjct: 107 DMF--SRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 164

>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of Human Antigen R Length = 177

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 81/180 (45%), Gaps = 26/180 (14%)
Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP---HSVLRFAFVEFADEHGARAA 172
           R  + V+ + QN+T++ L  LFSS G+V   ++  D    HS L + FV +     A  A
Sbjct: 2   RTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHS-LGYGFVNYVTAKDAERA 60
Query: 173 LN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVK 231
           +N L G  L    ++V  ++           P SE  ++     +Y + + + + Q +V+
Sbjct: 61  INTLNGLRLQSKTIKVSYAR-----------PSSEVIKDA---NLYISGLPRTMTQKDVE 106
Query: 232 QFFEAACGGEVTRLRLLGDHVH--STRIAFVEF---AVAESAILALNCSGMVLGSQPIRV 286
             F     G +   R+L D     S  +AF+ F   + AE AI + N       S+PI V
Sbjct: 107 DMFSRF--GRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSEPITV 164

>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fbp-Interacting Repressor (Fir) Length = 199

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/196 (25%), Positives = 86/196 (43%), Gaps = 13/196 (6%)
Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEH 167
           QR  ++   VYV  I   + E+ +   F+  G +    +  D  ++    FAFVE+    
Sbjct: 7   QRALAIMCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPE 66
Query: 168 GARAAL-NLGGTMLGYYPVRV-LPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKV 225
            A+ AL  +   MLG   ++V  PS   I    P     +E+ R      +Y  ++ + +
Sbjct: 67  AAQLALEQMNSVMLGGRNIKVGRPSN--IGQAQPIIDQLAEEARAF--NRIYVASVHQDL 122
Query: 226 PQAEVKQFFEAACGGEVTRLRLLGDHVHSTR--IAFVEFAVAESAILALNCSGMV-LGSQ 282
              ++K  FEA   G++    L  D          F+E+  A+S+  A++   +  LG Q
Sbjct: 123 SDDDIKSVFEAF--GKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQ 180
Query: 283 PIRVSPSKTPVRPRVT 298
            +RV  + TP  P +T
Sbjct: 181 YLRVGKAVTPPMPLLT 196

>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast Poly Binding Protein (Pub1) Length = 166

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 42/176 (23%), Positives = 74/176 (42%), Gaps = 19/176 (10%)
Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV-LRFAFVEFADEHGARAALN- 174
           R +YV ++D+ ITE+ L   F   G + + ++  D ++  + +AFVE+   H A  AL  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTV--YCTNIDKKVPQAEVKQ 232
           L G  +          +  I+ +N  F  +     +  +  V     N+D +  +   K 
Sbjct: 61  LNGKQI----------ENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKD 110
Query: 233 FFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNC-SGMVLGSQPIRVS 287
            F +   G V      G    S    FV F   + A  A++   G  L  +P+R++
Sbjct: 111 -FPSYLSGHVMWDMQTG---SSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162

>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G) Length = 97

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFAD-EHGARAAL 173
           R VY+  I  + TEE++  L S+ G V++ ++  DP +     +AF+EF D E  A A  
Sbjct: 4   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
Query: 174 NLGGTMLG 181
           NL G  LG
Sbjct: 64  NLNGYQLG 71

>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu) Length = 96

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFAD-EHGARAAL 173
           R VY+  I  + TEE++  L S+ G V++ ++  DP +     +AF+EF D E  A A  
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
Query: 174 NLGGTMLG 181
           NL G  LG
Sbjct: 63  NLNGYQLG 70

>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In The Rna15, Hrp1, Anchor Rna 3' Processing Ternary Complex Length = 84

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFAD-EHGARAAL 173
           R VY+  I  + TEE++  L S+ G V++ ++  DP +     +AF+EF D E  A A  
Sbjct: 5   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
Query: 174 NLGGTMLG 181
           NL G  LG
Sbjct: 65  NLNGYQLG 72

>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding Motif Protein 23 Length = 114

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/89 (32%), Positives = 48/89 (53%), Gaps = 6/89 (6%)
Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEF 262
           S +ER+  +RTV+C  +  ++   +++ FF A   G+V  +R++ D     S  IA+VEF
Sbjct: 19  SPEERD--ARTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSRRSKGIAYVEF 74
Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSKT 291
              +S  LA+  +G  L   PI V  S+ 
Sbjct: 75  CEIQSVPLAIGLTGQRLLGVPIIVQASQA 103

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	303
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	2e-28
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	5e-24
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-27
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	1e-12
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	3e-26
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	2e-24
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-26
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-10
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	3e-09
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	4e-26
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	2e-13
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	1e-06
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-25
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	2e-12
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	5e-10
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	4e-23
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	8e-11
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-23
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	9e-23
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-08
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	2e-21
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	7e-10
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	1e-20
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-09
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-19
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	4e-08
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	1e-18
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	6e-10
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	2e-04
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-18
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	5e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	5e-18
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-07
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-05
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	6e-18
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-09
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	9e-17
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	2e-14
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	7e-16
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	4e-10
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	2e-15
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	6e-07
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-15
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-14
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	2e-10
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	5e-14
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	1e-10
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-13
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	5e-09
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	4e-13
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	3e-06
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	4e-13
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-07
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	8e-13
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	9e-04
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-12
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	6e-08
1x5o_A	114	RNA binding motif, single-stranded interacting pro	1e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-12
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	1e-08
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-12
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	8e-04
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	2e-12
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	8e-06
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	2e-12
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	5e-07
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	3e-12
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-05
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	3e-12
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-05
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	4e-12
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	4e-12
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	1e-11
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	4e-06
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-11
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	5e-04
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	1e-11
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	3e-04
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	2e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	3e-11
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	8e-05
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	3e-11
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	2e-04
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	3e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-11
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	8e-09
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	3e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	3e-11
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	2e-04
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	4e-11
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	1e-04
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	6e-11
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	1e-08
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	7e-11
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	1e-04
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	8e-11
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	1e-09
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-11
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	8e-04
2div_A	99	TRNA selenocysteine associated protein; structural	9e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	9e-11
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	1e-05
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	9e-11
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	3e-05
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	9e-11
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	1e-05
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-10
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	9e-07
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	2e-10
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	2e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-10
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	2e-04
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	2e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	2e-10
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	9e-08
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	2e-10
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	3e-06
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	2e-10
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	5e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	2e-10
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	9e-07
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	2e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	3e-10
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	5e-06
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	3e-10
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	7e-04
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	3e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	3e-10
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	5e-07
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	3e-10
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	2e-04
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	3e-10
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	4e-06
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	4e-10
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	9e-05
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	4e-10
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	7e-09
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-10
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	4e-04
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	5e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-10
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	5e-05
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	6e-10
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	3e-06
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	7e-10
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	3e-05
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	9e-10
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-04
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	9e-10
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	9e-10
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	1e-09
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	4e-07
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	1e-09
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-05
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-09
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	1e-05
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	1e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	1e-09
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	3e-09
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	1e-09
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	1e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-09
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	2e-06
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	2e-09
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	8e-06
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-09
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	2e-06
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	3e-09
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	2e-05
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	3e-09
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-04
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	3e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	4e-09
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	7e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-09
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	7e-06
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	4e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	5e-09
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	2e-08
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	5e-09
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	2e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	5e-09
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	1e-06
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	3e-06
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	5e-09
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	3e-07
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	5e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-09
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	6e-04
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	6e-09
1x4e_A	85	RNA binding motif, single-stranded interacting pro	7e-09
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	7e-09
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	8e-09
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	8e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	9e-09
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	1e-04
1x5p_A	97	Negative elongation factor E; structure genomics,	1e-08
1x5p_A	97	Negative elongation factor E; structure genomics,	2e-04
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	1e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	1e-08
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	3e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	1e-08
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	3e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	1e-08
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-05
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-08
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	1e-05
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	2e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	3e-08
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	6e-07
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	3e-08
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	9e-06
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	4e-08
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	1e-04
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	6e-08
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	6e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	7e-08
2dis_A	109	Unnamed protein product; structural genomics, RRM	9e-07
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	8e-08
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-06
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	9e-08
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	2e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-07
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	1e-06
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	1e-07
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	2e-04
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	2e-07
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	3e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	2e-07
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	9e-05
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	3e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	3e-07
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	8e-05
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	4e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	6e-07
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	1e-05
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	6e-07
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	7e-07
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	8e-07
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	9e-07
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	9e-07
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	1e-06
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	2e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-06
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	1e-04
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens} Len	2e-06
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	2e-06
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	3e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	3e-06
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-04
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	3e-06
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	2e-04
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	4e-06
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	5e-06
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	6e-06
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	6e-06
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	6e-06
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	7e-06
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	9e-06
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	2e-05
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	2e-05
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	2e-05
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	3e-05
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	3e-05
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-05
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	5e-05
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	6e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-05
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	7e-05
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	7e-05
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	1e-04
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	2e-04
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	2e-04
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	4e-04
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	7e-04

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score =  109 bits (275), Expect = 2e-28
 Identities = 38/220 (17%), Positives = 73/220 (33%), Gaps = 32/220 (14%)

Query: 79  QSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFS 138
           ++AI+ F+              RL  R    Q + +    + V+++  ++T+++   L  
Sbjct: 71  EAAINAFHQ------------SRLRERELSVQLQPT-DALLCVANLPPSLTQQQFEELVR 117

Query: 139 SCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAIL 195
             G +  C +     +     + F E+  +  A  A + L G  LG   + V  +     
Sbjct: 118 PFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPRTLYVHWTD---- 173

Query: 196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAE-VKQFFEAACGGEVTRLRLLGDHV-H 253
                          + SR +    +       + + +   A      T  +L       
Sbjct: 174 -------AGQLTPALLHSRCLCVDRLPPGFNDVDALCRALSAV--HSPTFCQLACGQDGQ 224

Query: 254 STRIAFVEFAVAESAILAL-NCSGMVLGSQPIRVSPSKTP 292
               A +E+  AE A  A     G+ LG   +RVS     
Sbjct: 225 LKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPG 264

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284

 Score = 97.7 bits (244), Expect = 5e-24
 Identities = 34/201 (16%), Positives = 64/201 (31%), Gaps = 31/201 (15%)

Query: 99  RKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRF 158
            + +  R    +R+   RR + +  +  ++T + +  L S    +  C V          
Sbjct: 5   PEEIRKRLEHTERQFRNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKY----KGT 59

Query: 159 AFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVY 217
           AFV   +   A AA+N    + L    + V    T                       + 
Sbjct: 60  AFVTLLNGEQAEAAINAFHQSRLRERELSVQLQPT--------------------DALLC 99

Query: 218 CTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAVAESAILALN-C 274
             N+   + Q + ++       G + R  L+       S    F E+   +SA  A +  
Sbjct: 100 VANLPPSLTQQQFEELVRPF--GSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157

Query: 275 SGMVLGSQPIRVSPSKTPVRP 295
            G  LG + + V  +      
Sbjct: 158 LGKPLGPRTLYVHWTDAGQLT 178

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score =  105 bits (264), Expect = 1e-27
 Identities = 48/216 (22%), Positives = 86/216 (39%), Gaps = 17/216 (7%)

Query: 96  NQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV 155
             G++   G A + Q   ++   VYV  I   + E+ +   F+  G +    +  D  ++
Sbjct: 8   TGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTM 67

Query: 156 --LRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMC 212
               FAFVE+     A+ AL  +   MLG   ++V              +     E    
Sbjct: 68  KHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV---GRPSNIGQAQPIIDQLAEEARA 124

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAES 267
              +Y  ++ + +   ++K  FEA   G++    L  D          F+E+     ++ 
Sbjct: 125 FNRIYVASVHQDLSDDDIKSVFEAF--GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQD 182

Query: 268 AILALNCSGMVLGSQPIRVSPSKTPVRPRVT--RPG 301
           A+ ++N     LG Q +RV  + TP  P +T   PG
Sbjct: 183 AVSSMN--LFDLGGQYLRVGKAVTPPMPLLTPATPG 216

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216

 Score = 65.0 bits (159), Expect = 1e-12
 Identities = 19/117 (16%), Positives = 49/117 (41%), Gaps = 9/117 (7%)

Query: 79  QSAIDNFN----NNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLA 134
           Q A++  N      R  +        +      +   E      +YV+ + Q+++++ + 
Sbjct: 84  QLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143

Query: 135 GLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
            +F + G++    +  DP +  +   + F+E+     ++ A++ +    LG   +RV
Sbjct: 144 SVFEAFGKIKSATLARDPTT-GKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score =  103 bits (260), Expect = 3e-26
 Identities = 37/224 (16%), Positives = 77/224 (34%), Gaps = 29/224 (12%)

Query: 84  NFNNNRRRRNNFNQGRKRLSGR-AFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQ 142
              +++R  +  +     L+ + A  A   +    TV V ++ ++  + ++   F  CG 
Sbjct: 8   ARPDSKRPLDEGSPAAAGLTSKKANEALTRNRELTTVLVKNLPKSYNQNKVYKYFKHCGP 67

Query: 143 VVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFL 202
           ++   V        RFA +EFA   GA AA+     ++G   + V               
Sbjct: 68  IIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHLT----------- 116

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVE 261
                       T++ TN      Q  ++   +         +RL     +++R  A+++
Sbjct: 117 ----------ECTLWMTNFPPSYTQRNIRDLLQ-DINVVALSIRLPSLRFNTSRRFAYID 165

Query: 262 F---AVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGM 302
                 A   +  LN  G+ +    +    S    + + T    
Sbjct: 166 VTSKEDARYCVEKLN--GLKIEGYTLVTKVSNPLEKSKRTDSAT 207

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292

 Score = 99.3 bits (248), Expect = 2e-24
 Identities = 34/195 (17%), Positives = 73/195 (37%), Gaps = 18/195 (9%)

Query: 100 KRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQV-VDCRVCGDPHSVLR- 157
           K +               T+++++   + T+  +  L      V +  R+     +  R 
Sbjct: 103 KVVGQNEIIVSHLTE--CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRR 160

Query: 158 FAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTV 216
           FA+++   +  AR  +  L G  +  Y +    S        P    +  D   +  R +
Sbjct: 161 FAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN-------PLEKSKRTDSATLEGREI 213

Query: 217 YCTNIDKKVPQ-AEVKQFFEAACGGEVTRLRLLGDHV---HSTRIAFVEFAVAESAILAL 272
              N+  ++     +++ FE    G + ++ +         +   AF+ F   +SA  AL
Sbjct: 214 MIRNLSTELLDENLLRESFEGF--GSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERAL 271

Query: 273 NCSGMVLGSQPIRVS 287
             +  +LG++ I VS
Sbjct: 272 QMNRSLLGNREISVS 286

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score =  100 bits (252), Expect = 3e-26
 Identities = 33/180 (18%), Positives = 66/180 (36%), Gaps = 23/180 (12%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGAR 170
           E +    +++ +++ N +   L    S      D  V        R F +V+F       
Sbjct: 9   ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 68

Query: 171 AALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEV 230
            AL L G  +    +++   K              + ++   +RT+   N+   + + E+
Sbjct: 69  KALELTGLKVFGNEIKLEKPK------------GRDSKKVRAARTLLAKNLSFNITEDEL 116

Query: 231 KQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAILALNCSGMVLGSQPIRVS 287
           K+ FE A   E+  +   G    S  IA++EF     AE  +      G  +  + + + 
Sbjct: 117 KEVFEDA--LEIRLVSQDG---KSKGIAYIEFKSEADAEKNLEEKQ--GAEIDGRSVSLY 169

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 57.2 bits (139), Expect = 3e-10
 Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 6/82 (7%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADE 166
           R  ++    RT+   ++  NITE+ L  +F    ++      G      +  A++EF  E
Sbjct: 91  RDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS----KGIAYIEFKSE 146

Query: 167 HGARAALN-LGGTMLGYYPVRV 187
             A   L    G  +    V +
Sbjct: 147 ADAEKNLEEKQGAEIDGRSVSL 168

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175

 Score = 54.5 bits (132), Expect = 3e-09
 Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEF 262
             E         ++  N++     AE+K             L ++     + R   +V+F
Sbjct: 4   MVEGSESTTPFNLFIGNLNPNKSVAELKVAISEL--FAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSK 290
             AE    AL  +G+ +    I++   K
Sbjct: 62  ESAEDLEKALELTGLKVFGNEIKLEKPK 89

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score =  101 bits (254), Expect = 4e-26
 Identities = 47/185 (25%), Positives = 78/185 (42%), Gaps = 22/185 (11%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGA 169
                 ++YV D+  ++TE  L   FS  G ++  RVC D  +   L +A+V F     A
Sbjct: 11  PSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADA 70

Query: 170 RAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQA 228
             AL+ +   ++   PVR++ S+            R    R+     ++  N+DK +   
Sbjct: 71  ERALDTMNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGNIFIKNLDKSIDNK 118

Query: 229 EVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAILALNCSGMVLGSQPIR 285
            +   F A   G +   +++ D   S    FV F     AE AI  +N  GM+L  + + 
Sbjct: 119 ALYDTFSA--FGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN--GMLLNDRKVF 174

Query: 286 VSPSK 290
           V   K
Sbjct: 175 VGRFK 179

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 67.3 bits (165), Expect = 2e-13
 Identities = 27/115 (23%), Positives = 52/115 (45%), Gaps = 20/115 (17%)

Query: 81  AIDNFNNNRRRRNNFNQGRKRLSGRAFR---AQREDSVRR----TVYVSDIDQNITEERL 133
           A+D  N               + G+  R   +QR+ S+R+     +++ ++D++I  + L
Sbjct: 73  ALDTMNF------------DVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKAL 120

Query: 134 AGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
              FS+ G ++ C+V  D +    + FV F  +  A  A+  + G +L    V V
Sbjct: 121 YDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A* Length = 213

 Score = 47.3 bits (113), Expect = 1e-06
 Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 9/91 (9%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVE 261
            +         ++Y  ++   V +A + + F  A  G +  +R+  D +   S   A+V 
Sbjct: 6   MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPA--GPILSIRVCRDMITRRSLGYAYVN 63

Query: 262 F---AVAESAILALNCSGMVLGSQPIRVSPS 289
           F   A AE A+  +N    V+  +P+R+  S
Sbjct: 64  FQQPADAERALDTMN--FDVIKGKPVRIMWS 92

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 99.3 bits (248), Expect = 2e-25
 Identities = 36/189 (19%), Positives = 66/189 (34%), Gaps = 22/189 (11%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-------FAFVEFADEHGA 169
           R +YV +I   ITEE +   F++  ++           +         FAF+EF      
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 170 RAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSR------TVYCTNIDK 223
             A+   G +     +++            +  P       + +        ++   +  
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPN 124

Query: 224 KVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAESAILALNCSGMV 278
            +   +VK+   +   G +    L+ D     S   AF E+    V + AI  LN  GM 
Sbjct: 125 YLNDDQVKELLTSF--GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN--GMQ 180

Query: 279 LGSQPIRVS 287
           LG + + V 
Sbjct: 181 LGDKKLLVQ 189

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 63.5 bits (155), Expect = 2e-12
 Identities = 16/107 (14%), Positives = 42/107 (39%), Gaps = 4/107 (3%)

Query: 84  NFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQV 143
              ++ +     ++               DS  + +++  +   + ++++  L +S G +
Sbjct: 83  RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHK-LFIGGLPNYLNDDQVKELLTSFGPL 141

Query: 144 VDCRVCGDPHS-VLR-FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
               +  D  + + + +AF E+ D +    A+  L G  LG   + V
Sbjct: 142 KAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198

 Score = 57.0 bits (138), Expect = 5e-10
 Identities = 15/96 (15%), Positives = 30/96 (31%), Gaps = 9/96 (9%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-------HSTRIAFVEFAVA 265
           +R +Y  NI   + +  +  FF A     +  L     +             AF+EF   
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQ--MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 266 ESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           +    A+   G++   Q +++               
Sbjct: 62  DETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSEN 97

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 92.3 bits (230), Expect = 4e-23
 Identities = 42/184 (22%), Positives = 81/184 (44%), Gaps = 28/184 (15%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARA 171
           +    + V+ + Q++T+  L  LF + G +  CR+  D  +     +AFV+F  E  ++ 
Sbjct: 1   ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60

Query: 172 ALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEV 230
           A+  L G  +    ++V  ++           P  E  ++     +Y TN+ + +   ++
Sbjct: 61  AIKVLNGITVRNKRLKVSYAR-----------PGGESIKD---TNLYVTNLPRTITDDQL 106

Query: 231 KQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAESAILALNCSGMVL--GSQP 283
              F     G + +  +L D +      +AFV +     A+ AI ALN   ++   GSQP
Sbjct: 107 DTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALN--NVIPEGGSQP 162

Query: 284 IRVS 287
           + V 
Sbjct: 163 LSVR 166

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168

 Score = 58.7 bits (143), Expect = 8e-11
 Identities = 25/114 (21%), Positives = 46/114 (40%), Gaps = 12/114 (10%)

Query: 79  QSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFS 138
           Q AI   N          + ++     A R   E      +YV+++ + IT+++L  +F 
Sbjct: 59  QRAIKVLNGITV------RNKRLKVSYA-RPGGESIKDTNLYVTNLPRTITDDQLDTIFG 111

Query: 139 SCGQVVDCRVCGDPHSVL--RFAFVEFADEHGARAALN-LGGTML--GYYPVRV 187
             G +V   +  D  +      AFV +     A+ A++ L   +   G  P+ V
Sbjct: 112 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSV 165

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 92.2 bits (230), Expect = 5e-23
 Identities = 36/180 (20%), Positives = 77/180 (42%), Gaps = 23/180 (12%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV-LRFAFVEFADEHGARAALN- 174
           R +YV ++D+ ITE+ L   F   G + + ++  D ++  + +AFVE+   H A  AL  
Sbjct: 1   RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60

Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
           L G  +    V++             +  +S+      +  ++  +++  V    ++  F
Sbjct: 61  LNGKQIENNIVKI------------NWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAF 108

Query: 235 EAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAESAILALNCSGMVLGSQPIRVSPS 289
           +           ++ D     S    FV F     A++A+ ++   G  L  +P+R++ +
Sbjct: 109 KDF--PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQ--GQDLNGRPLRINWA 164

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166

 Score = 63.7 bits (156), Expect = 1e-12
 Identities = 21/117 (17%), Positives = 42/117 (35%), Gaps = 22/117 (18%)

Query: 81  AIDNFNNNRRRRNNFNQGRKRLSGRAFR---AQREDSVRR----TVYVSDIDQNITEERL 133
           A+   N             K++     +   A +           ++V D++ N+ +E L
Sbjct: 57  ALQTLNG------------KQIENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETL 104

Query: 134 AGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
              F      +   V  D  +     + FV F  +  A+ A++ + G  L   P+R+
Sbjct: 105 RNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 91.5 bits (228), Expect = 9e-23
 Identities = 35/183 (19%), Positives = 61/183 (33%), Gaps = 30/183 (16%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDC-----RVCGDPHSV--LRFAFVEFADEHGA 169
           R +YV +I   ITEE +   F++  ++                     FAF+EF      
Sbjct: 5   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 64

Query: 170 RAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAE 229
             A+   G +     +++                            ++   +   +   +
Sbjct: 65  TQAMAFDGIIFQGQSLKIRRPH-----------DYQPLPGAH---KLFIGGLPNYLNDDQ 110

Query: 230 VKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAESAILALNCSGMVLGSQPI 284
           VK+   +   G +    L+ D     S   AF E+    V + AI  LN  GM LG + +
Sbjct: 111 VKELLTSF--GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLN--GMQLGDKKL 166

Query: 285 RVS 287
            V 
Sbjct: 167 LVQ 169

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172

 Score = 51.8 bits (125), Expect = 3e-08
 Identities = 15/93 (16%), Positives = 30/93 (32%), Gaps = 9/93 (9%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-------HSTRIAFVEFAVA 265
           +R +Y  NI   + +  +  FF A     +  L     +             AF+EF   
Sbjct: 4   ARRLYVGNIPFGITEEAMMDFFNAQ--MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSV 61

Query: 266 ESAILALNCSGMVLGSQPIRVSPSKTPVRPRVT 298
           +    A+   G++   Q +++            
Sbjct: 62  DETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA 94

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 88.0 bits (219), Expect = 2e-21
 Identities = 49/182 (26%), Positives = 80/182 (43%), Gaps = 28/182 (15%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL 173
           +  + V+ + QN+T+E    LF S G++  C++  D  +   L + FV + D   A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 174 N-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQ 232
           N L G  L    ++V  ++           P S   R+     +Y + + K + Q E++Q
Sbjct: 62  NTLNGLRLQTKTIKVSYAR-----------PSSASIRD---ANLYVSGLPKTMTQKELEQ 107

Query: 233 FFEAACGGEVTRLRLLGDHV--HSTRIAFVEF---AVAESAILALNCSGMVL--GSQPIR 285
            F     G +   R+L D V   S  + F+ F     AE AI  LN  G      ++PI 
Sbjct: 108 LFSQY--GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLN--GQKPSGATEPIT 163

Query: 286 VS 287
           V 
Sbjct: 164 VK 165

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167

 Score = 56.0 bits (136), Expect = 7e-10
 Identities = 26/112 (23%), Positives = 44/112 (39%), Gaps = 12/112 (10%)

Query: 81  AIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSC 140
           AI+  N  R       Q +      A  +         +YVS + + +T++ L  LFS  
Sbjct: 60  AINTLNGLRL------QTKTIKVSYARPSSASIRDAN-LYVSGLPKTMTQKELEQLFSQY 112

Query: 141 GQVVDCRVCGDPHSVL-R-FAFVEFADEHGARAALN-LGGTML--GYYPVRV 187
           G+++  R+  D  + + R   F+ F     A  A+  L G        P+ V
Sbjct: 113 GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITV 164

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 85.7 bits (213), Expect = 1e-20
 Identities = 43/187 (22%), Positives = 76/187 (40%), Gaps = 28/187 (14%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR----FAFVEFADEHGA 169
           S    ++V  + +  +E+ L  LF   G V +  V  D            FV F     A
Sbjct: 1   SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60

Query: 170 RAA---LNLGGTMLGY-YPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKV 225
             A   L+    + G  +P+++ P+              SE    +  R ++   I KK 
Sbjct: 61  LEAQNALHNMKVLPGMHHPIQMKPAD-------------SEKNNAVEDRKLFIGMISKKC 107

Query: 226 PQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEF---AVAESAILALNCS-GMVLG 280
            + +++  F +   G++   R+L      +R  AFV F   A+A++AI A++ +  M   
Sbjct: 108 TENDIRVMFSSF--GQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEGC 165

Query: 281 SQPIRVS 287
           S P+ V 
Sbjct: 166 SSPMVVK 172

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175

 Score = 54.9 bits (133), Expect = 2e-09
 Identities = 21/105 (20%), Positives = 44/105 (41%), Gaps = 7/105 (6%)

Query: 79  QSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRT-VYVSDIDQNITEERLAGLF 137
             A +  +N +            +  +   +++ ++V    +++  I +  TE  +  +F
Sbjct: 61  LEAQNALHNMKV----LPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMF 116

Query: 138 SSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN-LGGTML 180
           SS GQ+ +CR+   P  + R  AFV F     A+ A+  +     
Sbjct: 117 SSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQT 161

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 82.6 bits (204), Expect = 4e-19
 Identities = 41/202 (20%), Positives = 81/202 (40%), Gaps = 32/202 (15%)

Query: 117 RTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-N 174
             + VS+++ + +T + L  LF   G V   ++  +       A V+ AD + A+ A+ +
Sbjct: 4   SVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE---NALVQMADGNQAQLAMSH 60

Query: 175 LGGTMLGYYPVRVLPSKTAILPVN---------------------PTFLPRSEDEREMCS 213
           L G  L   P+R+  SK   + +                           ++       S
Sbjct: 61  LNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPS 120

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
            T++ +NI   V + ++K  F  + GG V   +         ++A ++    E A+ AL 
Sbjct: 121 ATLHLSNIPPSVSEEDLKVLFS-SNGGVVKGFKFF---QKDRKMALIQMGSVEEAVQALI 176

Query: 274 C--SGMVLGSQPIRVSPSKTPV 293
              +  +  +  +RVS SK+ +
Sbjct: 177 DLHNHDLGENHHLRVSFSKSTI 198

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198

 Score = 51.8 bits (124), Expect = 4e-08
 Identities = 26/130 (20%), Positives = 47/130 (36%), Gaps = 6/130 (4%)

Query: 69  INNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVR--RTVYVSDIDQ 126
           I    +             ++    ++         +      ++      T+++S+I  
Sbjct: 71  IRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 130

Query: 127 NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGY-YP 184
           +++EE L  LFSS G VV            + A ++      A  AL  L    LG  + 
Sbjct: 131 SVSEEDLKVLFSSNGGVVKGFKFFQKDR--KMALIQMGSVEEAVQALIDLHNHDLGENHH 188

Query: 185 VRVLPSKTAI 194
           +RV  SK+ I
Sbjct: 189 LRVSFSKSTI 198

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 82.4 bits (204), Expect = 1e-18
 Identities = 38/184 (20%), Positives = 63/184 (34%), Gaps = 32/184 (17%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEH 167
             ++  + R  ++V ++  +ITEE    LF   G+  +  +  D      F F+      
Sbjct: 14  PGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----RGFGFIRLESRT 69

Query: 168 GARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVP 226
            A  A   L GT+L   P+R+                            +   N+   V 
Sbjct: 70  LAEIAKAELDGTILKSRPLRI--------------------RFATHGAALTVKNLSPVVS 109

Query: 227 QAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFA---VAESAILALNCSGMVLGSQ 282
              ++Q F     G V +  ++ D    +T   FVEFA    A  A+      G  L + 
Sbjct: 110 NELLEQAFSQF--GPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCG-DGAFLLTT 166

Query: 283 PIRV 286
             R 
Sbjct: 167 TPRP 170

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 57.8 bits (140), Expect = 6e-10
 Identities = 24/92 (26%), Positives = 32/92 (34%), Gaps = 4/92 (4%)

Query: 100 KRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-F 158
             L  R  R +        + V ++   ++ E L   FS  G V    V  D        
Sbjct: 81  TILKSRPLRIRFATHGAA-LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGK 139

Query: 159 AFVEFADEHGARAALN--LGGTMLGYYPVRVL 188
            FVEFA +  AR AL     G  L     R +
Sbjct: 140 GFVEFAAKPPARKALERCGDGAFLLTTTPRPV 171

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 13/96 (13%)

Query: 195 LPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHS 254
           + +   FL   E         ++  N+   + + + K+ FE    GE + + +  D    
Sbjct: 6   IDIKS-FLKPGEKTYTQ-RCRLFVGNLPTDITEEDFKRLFERY--GEPSEVFINRDR--- 58

Query: 255 TRIAFVEF---AVAESAILALNCSGMVLGSQPIRVS 287
               F+      +AE A   L+  G +L S+P+R+ 
Sbjct: 59  -GFGFIRLESRTLAEIAKAELD--GTILKSRPLRIR 91

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 80.8 bits (199), Expect = 3e-18
 Identities = 45/215 (20%), Positives = 87/215 (40%), Gaps = 32/215 (14%)

Query: 104 GRAFRAQREDSVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
           GR        +    + VS+++   +T + L  LF   G V   ++  +       A V+
Sbjct: 22  GRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKE---NALVQ 78

Query: 163 FADEHGARAAL-NLGGTMLGYYPVRVLPSKTAIL-------------------PVNPTFL 202
            AD + A+ A+ +L G  L   P+R+  SK   +                   P++    
Sbjct: 79  MADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKK 138

Query: 203 PRSEDEREMC--SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFV 260
           P S++ + +   S T++ +NI   V + ++K  F +  G          D     ++A +
Sbjct: 139 PGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR----KMALI 194

Query: 261 EFAVAESAILALNC--SGMVLGSQPIRVSPSKTPV 293
           +    E A+ AL    +  +  +  +RVS SK+ +
Sbjct: 195 QMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 229

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229

 Score = 48.8 bits (116), Expect = 5e-07
 Identities = 23/123 (18%), Positives = 43/123 (34%), Gaps = 6/123 (4%)

Query: 69  INNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVR--RTVYVSDIDQ 126
           I    +             ++    ++         +      ++      T+++S+I  
Sbjct: 102 IRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP 161

Query: 127 NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGY-YP 184
           +++EE L  LFSS G VV            + A ++      A  AL  L    LG  + 
Sbjct: 162 SVSEEDLKVLFSSNGGVVKGFKFFQKDR--KMALIQMGSVEEAVQALIDLHNHDLGENHH 219

Query: 185 VRV 187
           +RV
Sbjct: 220 LRV 222

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 79.7 bits (196), Expect = 5e-18
 Identities = 25/208 (12%), Positives = 61/208 (29%), Gaps = 32/208 (15%)

Query: 116 RRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL- 173
              + V  +D   +  +R+  +F   G V   +           A VE AD +    A+ 
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPG---AAMVEMADGYAVDRAIT 60

Query: 174 NLGGTMLGYYPVRVLPSKTAILPVNPTFL-----------------------PRSEDERE 210
           +L    +    + V  SK   +    ++                          +++  +
Sbjct: 61  HLNNNFMFGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQ 120

Query: 211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAIL 270
             S  ++  N   +V +    +  +       T +++       +    +E+     A+ 
Sbjct: 121 HPSNVLHFFNAPLEVTEENFFEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALE 180

Query: 271 ALNCSGMVLGSQPIRVSPSKTPVRPRVT 298
            L      L    ++      P   ++ 
Sbjct: 181 TL----GFLNHYQMKNPNGPYPYTLKLC 204

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 48.9 bits (116), Expect = 3e-07
 Identities = 12/98 (12%), Positives = 27/98 (27%), Gaps = 2/98 (2%)

Query: 78  KQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLF 137
            QS      +   +  + ++  +  +       R       ++  +    +TEE    + 
Sbjct: 85  GQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEIC 144

Query: 138 SSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL 173
              G      V        R     +E+  +  A   L
Sbjct: 145 DELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETL 182

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205

 Score = 43.5 bits (102), Expect = 3e-05
 Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 5/92 (5%)

Query: 213 SRTVYCTNID-KKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA 271
           S  +    +D  K+    V   F     G V +++ +     +  +   +    + AI  
Sbjct: 4   SPVLMVYGLDQSKMNCDRVFNVFCLY--GNVEKVKFMKSKPGAAMVEMADGYAVDRAITH 61

Query: 272 LNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH 303
           LN     +  Q + V  SK P        G+ 
Sbjct: 62  LN--NNFMFGQKMNVCVSKQPAIMPGQSYGLE 91

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 76.5 bits (189), Expect = 6e-18
 Identities = 24/79 (30%), Positives = 40/79 (50%), Gaps = 1/79 (1%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
             +D   RT+YV ++ +++TE  +  LFS  G    C++  +  S   + FVEF +   A
Sbjct: 9   MEDDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDA 68

Query: 170 RAAL-NLGGTMLGYYPVRV 187
            AAL  + G  +    V+V
Sbjct: 69  AAALAAMNGRKILGKEVKV 87

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 7/83 (8%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV---AESAI 269
            RT+Y  N+ + V +  + Q F     G     +++ +H  +    FVEF     A +A+
Sbjct: 15  PRTLYVGNLSRDVTEVLILQLFSQI--GPCKSCKMITEHTSNDPYCFVEFYEHRDAAAAL 72

Query: 270 LALNCSGMVLGSQPIRVSPSKTP 292
            A+N  G  +  + ++V+ + TP
Sbjct: 73  AAMN--GRKILGKEVKVNWATTP 93

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 73.9 bits (182), Expect = 9e-17
 Identities = 27/102 (26%), Positives = 43/102 (42%), Gaps = 4/102 (3%)

Query: 94  NFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH 153
           + + G+  +         E+   RTV+   +   I    L   FS+ G+V D R+  D +
Sbjct: 3   SGSSGKSPVREPVDNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRN 62

Query: 154 SVLR---FAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT 192
           S  R    A+VEF +      A+ L G  L   P+ V  S+ 
Sbjct: 63  SR-RSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA 103

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 67.3 bits (165), Expect = 2e-14
 Identities = 31/101 (30%), Positives = 53/101 (52%), Gaps = 7/101 (6%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFV 260
             S +ER+  +RTV+C  +  ++   +++ FF A   G+V  +R++ D     S  IA+V
Sbjct: 17  NLSPEERD--ARTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSRRSKGIAYV 72

Query: 261 EFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           EF   +S  LA+  +G  L   PI V  S+   + R++ P 
Sbjct: 73  EFCEIQSVPLAIGLTGQRLLGVPIIVQASQ-AEKNRLSGPS 112

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 72.6 bits (179), Expect = 7e-16
 Identities = 33/175 (18%), Positives = 64/175 (36%), Gaps = 21/175 (12%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL-R-FAFVEFADEHGARAALN 174
             +++  ++ + TE+ L   F   G V D ++  DP +   R F F+ F         + 
Sbjct: 4   CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63

Query: 175 LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFF 234
               + G    +V+  K AI        PR E ++   +  ++   I   V   E ++FF
Sbjct: 64  TQHILDG----KVIDPKRAI--------PRDEQDK---TGKIFVGGIGPDVRPKEFEEFF 108

Query: 235 EAACGGEVTRLRLLGDHVHSTR--IAFVEFAVAESAILALNCSGMVLGSQPIRVS 287
                G +   +L+ D          FV +  A++         +    + I + 
Sbjct: 109 SQW--GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIK 161

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167

 Score = 56.8 bits (138), Expect = 4e-10
 Identities = 11/80 (13%), Positives = 27/80 (33%), Gaps = 3/80 (3%)

Query: 111 REDSVR-RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEH 167
           R++  +   ++V  I  ++  +     FS  G ++D ++  D  +     F FV +    
Sbjct: 81  RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD 140

Query: 168 GARAALNLGGTMLGYYPVRV 187
                            + +
Sbjct: 141 AVDRVCQNKFIDFKDRKIEI 160

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFV 161
           SG +     ++   RTV+V +++  + EE L  LF   G +    +C D     + F FV
Sbjct: 3   SGSSGMFPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFV 62

Query: 162 EFADEHGARAALN-LGGTMLGYYPVRV 187
            F        A+  L G  L   P+ V
Sbjct: 63  CFKHPESVSYAIALLNGIRLYGRPINV 89

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 8/79 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAV---AESA 268
            RTV+  N++ +V +  + + F  A  G +T++ +  D         FV F        A
Sbjct: 16  DRTVFVGNLEARVREEILYELFLQA--GPLTKVTICKDREGKPKSFGFVCFKHPESVSYA 73

Query: 269 ILALNCSGMVLGSQPIRVS 287
           I  LN  G+ L  +PI VS
Sbjct: 74  IALLN--GIRLYGRPINVS 90

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196

 Score = 72.3 bits (178), Expect = 2e-15
 Identities = 37/186 (19%), Positives = 71/186 (38%), Gaps = 20/186 (10%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL-R-FAFVEFADE 166
           + +E    R +++  +    T+E L   F   G + DC V  DP++   R F FV +A  
Sbjct: 6   SPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATV 65

Query: 167 HGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMC---SRTVYCTNIDK 223
               AA+N     +     RV+  K A+         R + +R       + ++   I +
Sbjct: 66  EEVDAAMNARPHKVDG---RVVEPKRAV--------SREDSQRPGAHLTVKKIFVGGIKE 114

Query: 224 KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR--IAFVEFAVAESAILALNCSGMVLGS 281
              +  ++ +FE    G++  + ++ D     +   AFV F   +S    +      +  
Sbjct: 115 DTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNG 172

Query: 282 QPIRVS 287
               V 
Sbjct: 173 HNCEVR 178

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 67.8 bits (166), Expect = 2e-14
 Identities = 25/87 (28%), Positives = 47/87 (54%), Gaps = 2/87 (2%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFAD 165
             ++++  +R+VYV ++D   T + L   FSSCG +    +  D  S     +A++EFA+
Sbjct: 28  AEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE 87

Query: 166 EHGARAALNLGGTMLGYYPVRVLPSKT 192
            +   AA+ +  T+     ++VLP +T
Sbjct: 88  RNSVDAAVAMDETVFRGRTIKVLPKRT 114

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 25/98 (25%), Positives = 45/98 (45%), Gaps = 4/98 (4%)

Query: 196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--H 253
              P     +E+++E+  R+VY  N+D      +++  F +   G + R+ +L D    H
Sbjct: 19  TEGPPQPLSAEEKKEIDKRSVYVGNVDYGSTAQDLEAHFSSC--GSINRITILCDKFSGH 76

Query: 254 STRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT 291
               A++EFA   S   A+     V   + I+V P +T
Sbjct: 77  PKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT 114

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 65.6 bits (161), Expect = 5e-14
 Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGAR 170
           ++  R++YV ++D   T E L   F  CG V    +  D  S     FA++EF+D+   R
Sbjct: 3   EADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVR 62

Query: 171 AALNLGGTMLGYYPVRVLPSKT 192
            +L L  ++     ++V+P +T
Sbjct: 63  TSLALDESLFRGRQIKVIPKRT 84

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89

 Score = 56.0 bits (136), Expect = 1e-10
 Identities = 25/92 (27%), Positives = 42/92 (45%), Gaps = 10/92 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAVAESAIL 270
           +R++Y  N+D      E++  F     G V R+ +L D    H    A++EF+  ES   
Sbjct: 6   ARSIYVGNVDYGATAEELEAHFHGC--GSVNRVTILCDKFSGHPKGFAYIEFSDKESVRT 63

Query: 271 ALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGM 302
           +L     +   + I+V P +T       RPG+
Sbjct: 64  SLALDESLFRGRQIKVIPKRTN------RPGI 89

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 64.4 bits (157), Expect = 2e-13
 Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 1/85 (1%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADE 166
              + D   R+VY+     + T + +       GQV++ ++    H   +   FV F   
Sbjct: 3   WILKNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSI 62

Query: 167 HGARAALNLGGTMLGYYPVRVLPSK 191
             A+  +   G       + +L   
Sbjct: 63  ESAKKFVETPGQKYKETDLLILFKD 87

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 52.0 bits (125), Expect = 5e-09
 Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEF 262
           R   + ++ +R+VY           ++K++ E    G+V  +++      + +   FV F
Sbjct: 2   RWILKNDVKNRSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTLHKAFKGSIFVVF 59

Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSK 290
              ESA   +   G       + +    
Sbjct: 60  DSIESAKKFVETPGQKYKETDLLILFKD 87

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 63.4 bits (155), Expect = 4e-13
 Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 3/88 (3%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAF 160
           S  +     E +   TVYV  +D+ ++E  L  LF   G VV+  +  D  +     + F
Sbjct: 2   SSGSSGPISERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGF 61

Query: 161 VEFADEHGARAAL-NLGGTMLGYYPVRV 187
           VEF  E  A  A+  +    L   P+RV
Sbjct: 62  VEFLSEEDADYAIKIMDMIKLYGKPIRV 89

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 44.2 bits (105), Expect = 3e-06
 Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 10/94 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAV---AES 267
             TVY   +D+KV +  + + F  A  G V    +  D V        FVEF     A+ 
Sbjct: 15  DATVYVGGLDEKVSEPLLWELFLQA--GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72

Query: 268 AILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           AI  ++   + L  +PIRV+ +       ++ P 
Sbjct: 73  AIKIMD--MIKLYGKPIRVNKAS-AHNKNLSGPS 103

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 63.5 bits (155), Expect = 4e-13
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 5/79 (6%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
            +      TVY   I   +T++ +   FS  GQ+++ RV  +      ++FV F+    A
Sbjct: 19  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----KGYSFVRFSTHESA 74

Query: 170 RAAL-NLGGTMLGYYPVRV 187
             A+ ++ GT +  + V+ 
Sbjct: 75  AHAIVSVNGTTIEGHVVKC 93

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 47.7 bits (114), Expect = 2e-07
 Identities = 18/83 (21%), Positives = 34/83 (40%), Gaps = 11/83 (13%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF---AVAESAI 269
           + TVYC  I   +    ++Q F     G++  +R+  +       +FV F     A  AI
Sbjct: 25  NCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPEK----GYSFVRFSTHESAAHAI 78

Query: 270 LALNCSGMVLGSQPIRVSPSKTP 292
           +++N  G  +    ++    K  
Sbjct: 79  VSVN--GTTIEGHVVKCYWGKES 99

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 63.0 bits (154), Expect = 8e-13
 Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 17/118 (14%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG 177
           +++ ++D++I  + L   FS+ G ++ C+V  D +    + FV F  +  A  A+  + G
Sbjct: 8   IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67

Query: 178 TMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSR-----TVYCTNIDKKVPQAEV 230
            +L    V V             F  R E E E+ +R      VY  N      +A  
Sbjct: 68  MLLNDRKVFVGR-----------FKSRKEREAELGARAKEFTNVYIKNFGPGSTRAAA 114

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A Length = 115

 Score = 37.6 bits (88), Expect = 9e-04
 Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 11/92 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAI 269
           S  ++  N+DK +    +   F A   G +   +++ D   S    FV F     AE AI
Sbjct: 5   SGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAI 62

Query: 270 LALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
             +N  GM+L  + + V       + R  R  
Sbjct: 63  EKMN--GMLLNDRKVFVGRF----KSRKEREA 88

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 6/78 (7%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
           ED    T+YV  +   ITE  L   F   G++    V          AF++FA    A  
Sbjct: 8   EDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ----CAFIQFATRQAAEV 63

Query: 172 ALN--LGGTMLGYYPVRV 187
           A        ++    + V
Sbjct: 64  AAEKSFNKLIVNGRRLNV 81

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85

 Score = 48.4 bits (116), Expect = 6e-08
 Identities = 13/77 (16%), Positives = 31/77 (40%), Gaps = 10/77 (12%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF---AVAESAIL 270
            T+Y   +   + + +++  F     GE+  + +    V   + AF++F     AE A  
Sbjct: 13  TTLYVGGLGDTITETDLRNHFYQF--GEIRTITV----VQRQQCAFIQFATRQAAEVAAE 66

Query: 271 ALNCSGMVLGSQPIRVS 287
                 +++  + + V 
Sbjct: 67  KSFN-KLIVNGRRLNVK 82

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 62.3 bits (152), Expect = 1e-12
 Identities = 17/95 (17%), Positives = 35/95 (36%), Gaps = 4/95 (4%)

Query: 99  RKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR- 157
              +  +  + Q +D     +Y+S++  ++ E+ L  +    GQV+  R+  D     R 
Sbjct: 10  ASGVQAQMAKQQEQDPTN--LYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRG 67

Query: 158 FAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK 191
             F          A +    G  +   P    P++
Sbjct: 68  VGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPTE 102

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 14/79 (17%), Positives = 27/79 (34%), Gaps = 5/79 (6%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
           +       T Y+ +I    TE  L  LF + G ++D +   +        F+++     A
Sbjct: 21  RSAPPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHYPEKG----CCFIKYDTHEQA 76

Query: 170 RAAL-NLGGTMLGYYPVRV 187
              +  L         +R 
Sbjct: 77  AVCIVALANFPFQGRNLRT 95

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101

 Score = 50.8 bits (122), Expect = 1e-08
 Identities = 16/100 (16%), Positives = 34/100 (34%), Gaps = 15/100 (15%)

Query: 195 LPVNPTFLPRSEDEREMCS----RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD 250
           + + P   P++ D     +     T Y  NI     +A++   F+    G +   +   +
Sbjct: 5   IGLPPQVNPQAVDHIIRSAPPRVTTAYIGNIPHFATEADLIPLFQNF--GFILDFKHYPE 62

Query: 251 HVHSTRIAFVEF---AVAESAILALNCSGMVLGSQPIRVS 287
                   F+++     A   I+AL         + +R  
Sbjct: 63  K----GCCFIKYDTHEQAAVCIVALA--NFPFQGRNLRTG 96

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 62.9 bits (153), Expect = 2e-12
 Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FA 159
           SG +  +    + +R +YV  + + + ++ L   F   G + D ++  D  +  +   FA
Sbjct: 50  SGGSGGSGGSATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYET-EKHRGFA 108

Query: 160 FVEFADEHGARAAL-NLGGTMLGYYPVRV 187
           FVEF     A AA+ N+  + L    +RV
Sbjct: 109 FVEFELAEDAAAAIDNMNESELFGRTIRV 137

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140

 Score = 37.8 bits (88), Expect = 8e-04
 Identities = 20/80 (25%), Positives = 36/80 (45%), Gaps = 9/80 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAV---AES 267
            R +Y   + ++V    +   F     G++T +++  D+        AFVEF +   A +
Sbjct: 63  KRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 120

Query: 268 AILALNCSGMVLGSQPIRVS 287
           AI  +N     L  + IRV+
Sbjct: 121 AIDNMN--ESELFGRTIRVN 138

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 61.5 bits (150), Expect = 2e-12
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 1/81 (1%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGAR 170
           E +    +++ +++ N +   L    S      D  V        R F +V+F       
Sbjct: 13  ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLE 72

Query: 171 AALNLGGTMLGYYPVRVLPSK 191
            AL L G  +    +++   K
Sbjct: 73  KALELTGLKVFGNEIKLEKPK 93

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 101

 Score = 43.0 bits (102), Expect = 8e-06
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 3/87 (3%)

Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFA 263
            E         ++  N++     AE+K             L ++     + R   +V+F 
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISEL--FAKNDLAVVDVRTGTNRKFGYVDFE 66

Query: 264 VAESAILALNCSGMVLGSQPIRVSPSK 290
            AE    AL  +G+ +    I++   K
Sbjct: 67  SAEDLEKALELTGLKVFGNEIKLEKPK 93

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 5/86 (5%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
           S  +   ++  + R  ++V ++  +ITEE +  LF   G+  +  +  D      F F+ 
Sbjct: 2   SSGSSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK----GFGFIR 57

Query: 163 FADEHGARAALN-LGGTMLGYYPVRV 187
                 A  A   L    L    +RV
Sbjct: 58  LETRTLAEIAKVELDNMPLRGKQLRV 83

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 46.1 bits (110), Expect = 5e-07
 Identities = 15/97 (15%), Positives = 35/97 (36%), Gaps = 11/97 (11%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
               ++       ++  N+   + + E+++ FE    G+   + +  D        F+  
Sbjct: 5   SSGGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKY--GKAGEVFIHKDK----GFGFIRL 58

Query: 263 ---AVAESAILALNCSGMVLGSQPIRVSPSKTPVRPR 296
               +AE A + L+   M L  + +RV  +       
Sbjct: 59  ETRTLAEIAKVELD--NMPLRGKQLRVRFACHSASLT 93

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 3/75 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLG 176
           R+V+VS   + +   +L+  F + G V    +  D      FA VE  D     A L+  
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAFGPVASVVMDKDKG---VFAIVEMGDVGAREAVLSQS 65

Query: 177 GTMLGYYPVRVLPSK 191
              LG + +RV P +
Sbjct: 66  QHSLGGHRLRVRPRE 80

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 41.5 bits (98), Expect = 2e-05
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
           R+V+ +   + V  A++ ++F A   G V  + +  D       A VE     +    L+
Sbjct: 9   RSVFVSGFPRGVDSAQLSEYFLAF--GPVASVVMDKD---KGVFAIVEMGDVGAREAVLS 63

Query: 274 CSGMVLGSQPIRVSPSK 290
            S   LG   +RV P +
Sbjct: 64  QSQHSLGGHRLRVRPRE 80

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 61.3 bits (149), Expect = 3e-12
 Identities = 16/74 (21%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL- 173
           + V  + ++ N+ E  L  +    G+V +  +   P +   L  A V F    GA+  + 
Sbjct: 7   KEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66

Query: 174 NLGGTMLGYYPVRV 187
           NL  T +    +  
Sbjct: 67  NLHLTSVMGNIIHA 80

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110

 Score = 42.4 bits (100), Expect = 1e-05
 Identities = 13/80 (16%), Positives = 25/80 (31%), Gaps = 9/80 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAES 267
            + V    ++  V +  +K        GEV  + +L          +A V F     A+ 
Sbjct: 6   LKEVTFARLNDNVRETFLKDMCRKY--GEVEEVEILLHPRTRKHLGLARVLFTSTRGAKE 63

Query: 268 AILALNCSGMVLGSQPIRVS 287
            +  L+     +    I   
Sbjct: 64  TVKNLH--LTSVMGNIIHAQ 81

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A Length = 115

 Score = 61.2 bits (149), Expect = 4e-12
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FA 159
           S  +   +++ S    V+V D+   IT E +   F+  G++ D RV  D  +  +   + 
Sbjct: 2   SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMAT-GKSKGYG 60

Query: 160 FVEFADEHGARAALN-LGGTMLGYYPVRV 187
           FV F ++  A  A+  +GG  LG   +R 
Sbjct: 61  FVSFFNKWDAENAIQQMGGQWLGGRQIRT 89

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens} Length = 87

 Score = 59.9 bits (146), Expect = 4e-12
 Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 5/73 (6%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAALN- 174
           V+V D+   IT   +A  F+  G++ D RV  D  +  +   + FV F ++  A  A+  
Sbjct: 9   VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMAT-GKSKGYGFVSFFNKWDAENAIQQ 67

Query: 175 LGGTMLGYYPVRV 187
           +GG  LG   +R 
Sbjct: 68  MGGQWLGGRQIRT 80

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 60.6 bits (147), Expect = 1e-11
 Identities = 25/107 (23%), Positives = 43/107 (40%), Gaps = 8/107 (7%)

Query: 89  RRRRNNFNQGRKRLSGRAFRAQREDSVRR-----TVYVSDIDQNITEERLAGLFSSCGQV 143
           +  R++      +   + FR   E+  +      T+YV ++    TEE++  LFS  G +
Sbjct: 7   KALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDI 66

Query: 144 VDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
               +  D        F FVE+     A  A+  + GT L    +R 
Sbjct: 67  KKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRT 113

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156

 Score = 45.2 bits (107), Expect = 4e-06
 Identities = 22/104 (21%), Positives = 43/104 (41%), Gaps = 9/104 (8%)

Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI--AFVEF 262
            +++    S T+Y  N+     + ++ + F  +  G++ ++ +  D +  T     FVE+
Sbjct: 31  EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKS--GDIKKIIMGLDKMKKTACGFCFVEY 88

Query: 263 ---AVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH 303
              A AE+A+  +N  G  L  + IR          R    G  
Sbjct: 89  YSRADAENAMRYIN--GTRLDDRIIRTDWDAGFKEGRQYGRGRS 130

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 59.6 bits (145), Expect = 1e-11
 Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 2/87 (2%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFV 161
           S  +  A +   +  TV+V+++D  +  ++L  +FS  G VV   +  D     R    V
Sbjct: 2   SSGSSGALQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTV 61

Query: 162 EFADEHGARAALN-LGGTMLGYYPVRV 187
            F     A  A++   G +L   P+ V
Sbjct: 62  TFEQSIEAVQAISMFNGQLLFDRPMHV 88

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 38.1 bits (89), Expect = 5e-04
 Identities = 27/92 (29%), Positives = 38/92 (41%), Gaps = 8/92 (8%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAV---AESA 268
             TV+  N+D KV   ++K+ F  A  G V R  +L D    S  I  V F     A  A
Sbjct: 15  GSTVFVANLDYKVGWKKLKEVFSMA--GVVVRADILEDKDGKSRGIGTVTFEQSIEAVQA 72

Query: 269 ILALNCSGMVLGSQPIRVSPSKTPVRPRVTRP 300
           I   N  G +L  +P+ V   +  +      P
Sbjct: 73  ISMFN--GQLLFDRPMHVKMDERALPKGDFFP 102

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 58.7 bits (143), Expect = 1e-11
 Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 5/78 (6%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGAR 170
           + +R +YV  + + + ++ L   F   G + D ++  D  +  +   FAFVEF     A 
Sbjct: 5   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYET-EKHRGFAFVEFELAEDAA 63

Query: 171 AAL-NLGGTMLGYYPVRV 187
           AA+ N+  + L    +RV
Sbjct: 64  AAIDNMNESELFGRTIRV 81

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 11/84 (13%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAV---AE 266
            R +Y   + ++V    +   F     G++T +++  D+  + +    AFVEF +   A 
Sbjct: 7   KRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYE-TEKHRGFAFVEFELAEDAA 63

Query: 267 SAILALNCSGMVLGSQPIRVSPSK 290
           +AI  +N     L  + IRV+ +K
Sbjct: 64  AAIDNMN--ESELFGRTIRVNLAK 85

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 58.4 bits (142), Expect = 2e-11
 Identities = 19/76 (25%), Positives = 35/76 (46%), Gaps = 6/76 (7%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-----FAFVEFADEHGARAA 172
            +++ +++ + TEE L G+FS  G +  C +    +         F FVE+     A+ A
Sbjct: 7   GLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKA 66

Query: 173 LN-LGGTMLGYYPVRV 187
           L  L G  +  + + V
Sbjct: 67  LKQLQGHTVDGHKLEV 82

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 59.9 bits (145), Expect = 3e-11
 Identities = 26/112 (23%), Positives = 36/112 (32%), Gaps = 4/112 (3%)

Query: 77  NKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGL 136
              + +D           F              +    +   VYV ++  N  +  L   
Sbjct: 34  ANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLGNNGNKTELERA 93

Query: 137 FSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
           F   G +    V  +P     FAFVEF D   A  A+  L G  L    VRV
Sbjct: 94  FGYYGPLRSVWVARNPP---GFAFVEFEDPRDAADAVRELDGRTLCGCRVRV 142

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 25/147 (17%), Positives = 42/147 (28%), Gaps = 13/147 (8%)

Query: 154 SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMC 212
           ++      E  D   A                     +         +        R+ C
Sbjct: 11  TLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMHRDSC 70

Query: 213 --SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV---AES 267
                VY  N+     + E+++ F     G +  + +  +       AFVEF     A  
Sbjct: 71  PLDCKVYVGNLGNNGNKTELERAFGYY--GPLRSVWVARN---PPGFAFVEFEDPRDAAD 125

Query: 268 AILALNCSGMVLGSQPIRVSPSKTPVR 294
           A+  L+  G  L    +RV  S    R
Sbjct: 126 AVRELD--GRTLCGCRVRVELSNGEKR 150

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 58.9 bits (143), Expect = 3e-11
 Identities = 17/108 (15%), Positives = 37/108 (34%), Gaps = 2/108 (1%)

Query: 82  IDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCG 141
           + +    ++   + ++ +  L                + VS++D  +++  +  LF+  G
Sbjct: 1   MASMTGGQQMGRDPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFG 60

Query: 142 QVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
            +    V  D        A V F     A  A+    G  L   P+ +
Sbjct: 61  TLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 108

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 17/90 (18%), Positives = 34/90 (37%), Gaps = 10/90 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAV---AESA 268
              +  +N+D  V  A++++ F     G + +  +  D    S   A V F     A  A
Sbjct: 35  GAKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVDYDRSGRSLGTADVHFERRADALKA 92

Query: 269 ILALNCSGMVLGSQPIRVS--PSKTPVRPR 296
           +      G+ L  +P+ +    S+  +   
Sbjct: 93  MKQYK--GVPLDGRPMDIQLVASQIDLEHH 120

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118

 Score = 58.5 bits (142), Expect = 3e-11
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 96  NQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV 155
           +      +  A   Q E      +++  + Q  T+  LA  F   G V+  +V  D  + 
Sbjct: 20  SVALSAAAAAAAGKQIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTS 79

Query: 156 LR--FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
           L   F FV F +   A+ A+  + G  +G   ++V
Sbjct: 80  LSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV 114

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 58.0 bits (141), Expect = 3e-11
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 4/92 (4%)

Query: 99  RKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR- 157
           R        R++   S   T ++ ++  ++TEE +   F     +   R+  +P +  R 
Sbjct: 2   RGSHHHHHHRSRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERL 60

Query: 158 --FAFVEFADEHGARAALNLGGTMLGYYPVRV 187
             F + EF D     +AL+L    LG   +RV
Sbjct: 61  KGFGYAEFEDLDSLLSALSLNEESLGNRRIRV 92

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAVAESAI 269
             T +  N+   V +  +K+FF    G  ++ +RL  +  +  R     + EF   +S +
Sbjct: 19  PYTAFLGNLPYDVTEESIKEFFR---GLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 75

Query: 270 LALNCSGMVLGSQPIRVSPSK 290
            AL+ +   LG++ IRV  + 
Sbjct: 76  SALSLNEESLGNRRIRVDVAD 96

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115

 Score = 58.5 bits (142), Expect = 3e-11
 Identities = 23/98 (23%), Positives = 46/98 (46%), Gaps = 3/98 (3%)

Query: 93  NNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP 152
           ++ + G  + S  A  +Q+E      +++  + Q   ++ L  +F   G VV  +V  D 
Sbjct: 2   SSGSSGLTQQSIGAAGSQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDK 61

Query: 153 HSVLR--FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
            + L   F FV + +   A+AA+  + G  +G   ++V
Sbjct: 62  QTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV 99

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 58.1 bits (141), Expect = 3e-11
 Identities = 19/100 (19%), Positives = 36/100 (36%), Gaps = 2/100 (2%)

Query: 90  RRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC 149
           R +   ++ +  L    F           + VS++D  +++  +  LF+  G +    V 
Sbjct: 3   RPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVH 62

Query: 150 GDPHSVLR-FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
            D        A V F  +  A  A+    G  L   P+ +
Sbjct: 63  YDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNI 102

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAV---AESA 268
              +  +N+D  V  A++++ F     G + +  +  D    S   A V F     A  A
Sbjct: 29  GGKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVHYDRSGRSLGTADVHFERKADALKA 86

Query: 269 ILALNCSGMVLGSQPIRVS 287
           +   N  G+ L  +P+ + 
Sbjct: 87  MKQYN--GVPLDGRPMNIQ 103

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 57.6 bits (140), Expect = 4e-11
 Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 106 AFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVE 162
           +  +    + +R +YV  + + + ++ L   F   G + D ++  D  +  +   FAFVE
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYET-EKHRGFAFVE 60

Query: 163 FADEHGARAAL-NLGGTMLGYYPVRV 187
           F     A AA+ N+  + L    +RV
Sbjct: 61  FELAEDAAAAIDNMNESELFGRTIRV 86

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 24/104 (23%), Positives = 44/104 (42%), Gaps = 10/104 (9%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFV 260
                      R +Y   + ++V    +   F     G++T +++  D+        AFV
Sbjct: 2   SSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETEKHRGFAFV 59

Query: 261 EFAV---AESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           EF +   A +AI  +N     L  + IRV+ +K P+R + + P 
Sbjct: 60  EFELAEDAAAAIDNMN--ESELFGRTIRVNLAK-PMRIKESGPS 100

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 57.3 bits (139), Expect = 6e-11
 Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAAL 173
            T ++ ++  ++TEE +   F     +   R+  +P +  R   F + EF D     +AL
Sbjct: 16  YTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 174 NLGGTMLGYYPVRV 187
           +L    LG   +RV
Sbjct: 75  SLNEESLGNKRIRV 88

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 6/83 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAVAESAI 269
             T +  N+   V +  +K+FF    G  ++ +RL  +  +  R     + EF   +S +
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFR---GLNISAVRLPREPSNPERLKGFGYAEFEDLDSLL 71

Query: 270 LALNCSGMVLGSQPIRVSPSKTP 292
            AL+ +   LG++ IRV  +   
Sbjct: 72  SALSLNEESLGNKRIRVDVADQA 94

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} Length = 83

 Score = 56.7 bits (138), Expect = 7e-11
 Identities = 17/73 (23%), Positives = 33/73 (45%), Gaps = 5/73 (6%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAALN- 174
           ++V D++ N+ +E L   F      +   V  D  +      + FV F  +  A+ A++ 
Sbjct: 4   LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQT-GSSRGYGFVSFTSQDDAQNAMDS 62

Query: 175 LGGTMLGYYPVRV 187
           + G  L   P+R+
Sbjct: 63  MQGQDLNGRPLRI 75

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 57.3 bits (139), Expect = 7e-11
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 2/91 (2%)

Query: 98  GRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR 157
           G   +SG         +    +YV ++  +I  + +  +F   G + D  +         
Sbjct: 4   GSSGMSGGGVIRGPAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGP-P 62

Query: 158 FAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
           FAFVEF D   A  A+    G     Y +RV
Sbjct: 63  FAFVEFEDPRDAEDAVYGRDGYDYDGYRLRV 93

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 18/92 (19%), Positives = 32/92 (34%), Gaps = 9/92 (9%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAI 269
              +Y  N+   +   +++  F     G +  + L          AFVEF     AE A+
Sbjct: 22  DCRIYVGNLPPDIRTKDIEDVFYKY--GAIRDIDLKNRR-GGPPFAFVEFEDPRDAEDAV 78

Query: 270 LALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
              +  G       +RV   ++  R   + P 
Sbjct: 79  YGRD--GYDYDGYRLRVEFPRSG-RGTGSGPS 107

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 56.9 bits (138), Expect = 8e-11
 Identities = 17/87 (19%), Positives = 34/87 (39%), Gaps = 2/87 (2%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADE 166
            +    +   TV +     N+TE+ +    +     V  R+  + H     + FV+F++E
Sbjct: 2   SSGSSGTTCHTVKLRGAPFNVTEKNVMEFLAPLK-PVAIRIVRNAHGNKTGYIFVDFSNE 60

Query: 167 HGARAALNLGGTMLGYYPVRVLPSKTA 193
              + AL      +G   + V   K+ 
Sbjct: 61  EEVKQALKCNREYMGGRYIEVFREKSG 87

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 91

 Score = 53.5 bits (129), Expect = 1e-09
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 4/81 (4%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILA 271
             TV        V +  V +F       +   +R++ +   +     FV+F+  E    A
Sbjct: 10  CHTVKLRGAPFNVTEKNVMEFLA---PLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQA 66

Query: 272 LNCSGMVLGSQPIRVSPSKTP 292
           L C+   +G + I V   K+ 
Sbjct: 67  LKCNREYMGGRYIEVFREKSG 87

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 57.2 bits (139), Expect = 8e-11
 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEH 167
           R  R   V   +YV ++D  I +ERL   FS  G +   +V  +      F FV F+   
Sbjct: 9   RITRYQVVN--LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPE 66

Query: 168 GARAALN-LGGTMLGYYPVRV 187
            A  A+  + G ++   P+ V
Sbjct: 67  EATKAVTEMNGRIVATKPLYV 87

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 37.2 bits (87), Expect = 8e-04
 Identities = 17/104 (16%), Positives = 41/104 (39%), Gaps = 11/104 (10%)

Query: 201 FLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFV 260
                +         +Y  N+D  +    +++ F     G +T  +++ +   S    FV
Sbjct: 3   SGSSGDRITRYQVVNLYVKNLDDGIDDERLRKAFSPF--GTITSAKVMMEGGRSKGFGFV 60

Query: 261 EFAV---AESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
            F+    A  A+  +N  G ++ ++P+ V+ +    + +  R  
Sbjct: 61  CFSSPEEATKAVTEMN--GRIVATKPLYVALA----QRKEERQS 98

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 56.9 bits (138), Expect = 9e-11
 Identities = 17/85 (20%), Positives = 39/85 (45%), Gaps = 5/85 (5%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQ-VVDCRVCGDPHS--VLRFAFVEFAD 165
           +     +  ++++ D++  + E  ++  F++ G+ V+  ++  +  +     + FVEFAD
Sbjct: 2   SSGSSGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFAD 61

Query: 166 EHGARAAL-NLGGTML-GYYPVRVL 188
              A   L  + G  L G  P +  
Sbjct: 62  LATAEKCLHKINGKPLPGATPAKRF 86

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 56.9 bits (138), Expect = 9e-11
 Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
           SG +  ++ + + +R ++VS+I     +  L  +F   G+++D  +  +      F FV 
Sbjct: 3   SGSSGNSESKSTPKR-LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVT 61

Query: 163 FADEHGARAALN-LGGTMLGYYPVRV 187
           F +   A  A   L GT++    + V
Sbjct: 62  FENSADADRAREKLHGTVVEGRKIEV 87

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 18/102 (17%), Positives = 40/102 (39%), Gaps = 8/102 (7%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
                E +   + ++ +NI  +    +++Q F     G++  + ++ +   S    FV F
Sbjct: 5   SSGNSESKSTPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERGSKGFGFVTF 62

Query: 263 AV---AESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
                A+ A   L+  G V+  + I V+ +        + P 
Sbjct: 63  ENSADADRAREKLH--GTVVEGRKIEVNNAT-ARVMTNSGPS 101

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 56.4 bits (137), Expect = 9e-11
 Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 7/80 (8%)

Query: 113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAA 172
            S    +++ ++ +  TE+ +  LF   G+V++C +      +  + FV   D+  A  A
Sbjct: 5   SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDI------IKNYGFVHIEDKTAAEDA 58

Query: 173 L-NLGGTMLGYYPVRVLPSK 191
           + NL    L    + V  SK
Sbjct: 59  IRNLHHYKLHGVNINVEASK 78

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 41.0 bits (97), Expect = 3e-05
 Identities = 18/91 (19%), Positives = 31/91 (34%), Gaps = 13/91 (14%)

Query: 209 REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VA 265
                  ++  N+ ++  + E++  FE    G+V    ++          FV       A
Sbjct: 4   GSSGMVKLFIGNLPREATEQEIRSLFEQY--GKVLECDII------KNYGFVHIEDKTAA 55

Query: 266 ESAILALNCSGMVLGSQPIRVSPSKTPVRPR 296
           E AI  L+     L    I V  SK   +  
Sbjct: 56  EDAIRNLH--HYKLHGVNINVEASKNKSKAS 84

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 57.4 bits (139), Expect = 9e-11
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL 173
           V R +Y+ ++   IT E +  +F   G +   RV   P +  R  A+V + D   A+ A+
Sbjct: 7   VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPET--RGTAYVVYEDIFDAKNAV 64

Query: 174 -NLGGTMLGYYPVRVLPSKT 192
            +L G  +    + VL    
Sbjct: 65  DHLSGFNVSNRYLVVLYYNA 84

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115

 Score = 42.7 bits (101), Expect = 1e-05
 Identities = 17/81 (20%), Positives = 34/81 (41%), Gaps = 6/81 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILA 271
           +R +Y  N+  K+   E+   F     G + ++R+       TR  A+V +     A  A
Sbjct: 8   NRILYIRNLPYKITAEEMYDIFGKY--GPIRQIRVGNT--PETRGTAYVVYEDIFDAKNA 63

Query: 272 L-NCSGMVLGSQPIRVSPSKT 291
           + + SG  + ++ + V     
Sbjct: 64  VDHLSGFNVSNRYLVVLYYNA 84

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 56.9 bits (138), Expect = 1e-10
 Identities = 20/96 (20%), Positives = 35/96 (36%), Gaps = 7/96 (7%)

Query: 97  QGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL 156
            G           Q  +     ++V     ++ E  L  +F   G + + ++        
Sbjct: 12  SGLVPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKILNG----- 66

Query: 157 RFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK 191
            FAFVEF +   A  A+  + G      P+ V+ SK
Sbjct: 67  -FAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 101

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108

 Score = 45.7 bits (109), Expect = 9e-07
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 13/95 (13%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
                E E+ +  ++       V ++E+ + F     G +  +++L         AFVEF
Sbjct: 21  MHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPF--GPMKEVKILNG------FAFVEF 72

Query: 263 AV---AESAILALNCSGMVLGSQPIRVSPSKTPVR 294
                A  AI  ++  G    +QP+ V  SK P +
Sbjct: 73  EEAESAAKAIEEVH--GKSFANQPLEVVYSKLPAK 105

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135

 Score = 57.1 bits (138), Expect = 2e-10
 Identities = 24/105 (22%), Positives = 43/105 (40%), Gaps = 3/105 (2%)

Query: 86  NNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD 145
             +        Q   R S    R   +     ++ V ++    + + L  +F   G+V D
Sbjct: 17  RGSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGD 76

Query: 146 CRVCGDPHS-VLR-FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
             +  D ++   R FAFV F D+  A  A++ + G +L    +RV
Sbjct: 77  VYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 121

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens} Length = 99

 Score = 56.2 bits (136), Expect = 2e-10
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 11/90 (12%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL---R-------F 158
                S   T++V  + +N+T E +A  F   G +   +  G P   L   R        
Sbjct: 6   HHHSHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGE 65

Query: 159 AFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
           A V F D   A+AA+    G      P++V
Sbjct: 66  ATVSFDDPPSAKAAIDWFDGKEFSGNPIKV 95

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 56.1 bits (136), Expect = 2e-10
 Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAAL 173
           R VY+  I  + TEE++  L S+ G V++ ++  DP +  R   +AF+EF D   + +A+
Sbjct: 3   RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQT-GRSKGYAFIEFRDLESSASAV 61

Query: 174 -NLGGTMLGYYPVRV 187
            NL G  LG   ++ 
Sbjct: 62  RNLNGYQLGSRFLKC 76

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAVAESAIL 270
           SR VY  +I     + ++         G V  L+++ D     S   AF+EF   ES+  
Sbjct: 2   SRVVYLGSIPYDQTEEQILDLCSNV--GPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 59

Query: 271 AL-NCSGMVLGSQPIRVSPSK 290
           A+ N +G  LGS+ ++   S 
Sbjct: 60  AVRNLNGYQLGSRFLKCGYSS 80

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 113

 Score = 56.3 bits (136), Expect = 2e-10
 Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 11/89 (12%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR----------FA 159
             EDS    +YV  ++ ++T + LA  F  CG V   +  G P   +            A
Sbjct: 9   PDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDA 68

Query: 160 FVEFADEHGARAALN-LGGTMLGYYPVRV 187
            V + D   A+AA+    G       ++V
Sbjct: 69  TVSYEDPPTAKAAVEWFDGKDFQGSKLKV 97

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 7/73 (9%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL-N 174
           + +YV ++  + +EE +   F++       RV       +R +AFV F++   A  A+  
Sbjct: 16  KILYVRNLMLSTSEEMIEKEFNNIKPGAVERV-----KKIRDYAFVHFSNREDAVEAMKA 70

Query: 175 LGGTMLGYYPVRV 187
           L G +L   P+ V
Sbjct: 71  LNGKVLDGSPIEV 83

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99

 Score = 48.4 bits (116), Expect = 9e-08
 Identities = 25/99 (25%), Positives = 41/99 (41%), Gaps = 8/99 (8%)

Query: 205 SEDEREMCS-RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA 263
           S DE  M S + +Y  N+     +  +++ F     G V R++           AFV F+
Sbjct: 6   SGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVK------KIRDYAFVHFS 59

Query: 264 VAESAILAL-NCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
             E A+ A+   +G VL   PI V+ +K   +       
Sbjct: 60  NREDAVEAMKALNGKVLDGSPIEVTLAKPVDKDSSGPSS 98

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 55.7 bits (135), Expect = 2e-10
 Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 7/72 (9%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NL 175
           + ++V ++   +TEE L   FS  G++   +   D      +AF+ F +  GA  A+  +
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD------YAFIHFDERDGAVKAMEEM 65

Query: 176 GGTMLGYYPVRV 187
            G  L    + +
Sbjct: 66  NGKDLEGENIEI 77

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 13/93 (13%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAIL 270
           + ++  N+   V +  +++ F     G++ R++ L D       AF+ F     A  A+ 
Sbjct: 12  KVLFVRNLANTVTEEILEKAFSQF--GKLERVKKLKD------YAFIHFDERDGAVKAME 63

Query: 271 ALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGMH 303
            +N  G  L  + I +  +K P + R  R    
Sbjct: 64  EMN--GKDLEGENIEIVFAKPPDQKRKERKAQR 94

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 56.4 bits (136), Expect = 2e-10
 Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 2/105 (1%)

Query: 91  RRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVC 149
           R ++                 + +    V +  +    T+E +   FS    V +   + 
Sbjct: 17  RGSHMASMTGGQQMGRGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLP 76

Query: 150 GDPHSVLR-FAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA 193
            DP   +   AFV+FA +  A  AL      +G+  + V  S   
Sbjct: 77  VDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQE 121

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A Length = 126

 Score = 55.7 bits (134), Expect = 5e-10
 Identities = 20/88 (22%), Positives = 27/88 (30%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
             S          V    +     + E+ QFF             +      T  AFV+F
Sbjct: 32  RGSNSADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQF 91

Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSK 290
           A  E A  AL      +G + I V  S 
Sbjct: 92  ASQELAEKALGKHKERIGHRYIEVFKSS 119

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 55.1 bits (133), Expect = 2e-10
 Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 7/78 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC-GDP------HSVLRFAFVEFADEHGA 169
           R +YV +I   ITEE +   F++  ++       G+P      +    FAF+EF      
Sbjct: 7   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 66

Query: 170 RAALNLGGTMLGYYPVRV 187
             A+   G +     +++
Sbjct: 67  TQAMAFDGIIFQGQSLKI 84

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A Length = 87

 Score = 45.1 bits (107), Expect = 9e-07
 Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI------AFVEFAVAE 266
           +R +Y  NI   + +  +  FF A         +  G+ V + +I      AF+EF   +
Sbjct: 6   ARRLYVGNIPFGITEEAMMDFFNA-QMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 64

Query: 267 SAILALNCSGMVLGSQPIRV 286
               A+   G++   Q +++
Sbjct: 65  ETTQAMAFDGIIFQGQSLKI 84

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94

 Score = 55.3 bits (134), Expect = 2e-10
 Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL 173
           + TVYVS++  ++T   L  +FS  G+VV   +  D  +      AF+ F D+  A+   
Sbjct: 16  KSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCT 75

Query: 174 -NLGGTMLGYYPVRV 187
             +    L    ++ 
Sbjct: 76  RAINNKQLFGRVIKA 90

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 55.3 bits (134), Expect = 3e-10
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 7/76 (9%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NL 175
             ++V ++    T + L  LF   G+V++C V      V  +AFV    E  A+AA+  L
Sbjct: 10  WKIFVGNVSAACTSQELRSLFERRGRVIECDV------VKDYAFVHMEKEADAKAAIAQL 63

Query: 176 GGTMLGYYPVRVLPSK 191
            G  +    + V  S 
Sbjct: 64  NGKEVKGKRINVELST 79

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90

 Score = 43.4 bits (103), Expect = 5e-06
 Identities = 21/92 (22%), Positives = 35/92 (38%), Gaps = 13/92 (14%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF---AVAESAI 269
           +  ++  N+       E++  FE    G V    ++ D+      AFV     A A++AI
Sbjct: 9   TWKIFVGNVSAACTSQELRSLFERR--GRVIECDVVKDY------AFVHMEKEADAKAAI 60

Query: 270 LALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
             LN  G  +  + I V  S    +      G
Sbjct: 61  AQLN--GKEVKGKRINVELSTKGQKKSGPSSG 90

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 55.7 bits (135), Expect = 3e-10
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 104 GRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLR-FAFV 161
           G +  +  +     T+ V ++    + + L  +F   G+V D  +  +PH+   R FAFV
Sbjct: 1   GSSGSSGPDVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFV 60

Query: 162 EFADEHGARAALN-LGGTMLGYYPVRV 187
            F D   A+ A   + G  L    +RV
Sbjct: 61  RFHDRRDAQDAEAAMDGAELDGRELRV 87

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103

 Score = 37.6 bits (88), Expect = 7e-04
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 14/96 (14%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR----IAFVEFAV---A 265
             T+   N+  +     +++ FE    G V  + +  +    T+     AFV F     A
Sbjct: 13  MITLKVDNLTYRTSPDSLRRVFEKY--GRVGDVYIPREPH--TKAPRGFAFVRFHDRRDA 68

Query: 266 ESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           + A  A++  G  L  + +RV  ++   R  ++ P 
Sbjct: 69  QDAEAAMD--GAELDGRELRVQVAR-YGRRDLSGPS 101

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 5/96 (5%)

Query: 96  NQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV 155
           +      +  A   Q+  +    +YV  +  NITE+ L G+F   G++   ++  D  + 
Sbjct: 6   HHHSHMAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETG 65

Query: 156 LR---FAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
            R   + F+ F+D   A+ AL  L G  L   P++V
Sbjct: 66  -RSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV 100

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 55.4 bits (134), Expect = 3e-10
 Identities = 20/91 (21%), Positives = 40/91 (43%), Gaps = 3/91 (3%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFV 161
           S   FR       +  +++S +  + T+E L  +  + G V D R+  +     +  A+V
Sbjct: 5   SSGVFRYSTSLE-KHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYV 63

Query: 162 EFADEHGARAAL-NLGGTMLGYYPVRVLPSK 191
           E+ +E  A  A+  + G  +    ++V  S 
Sbjct: 64  EYENESQASQAVMKMDGMTIKENIIKVAISN 94

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100

 Score = 46.5 bits (111), Expect = 5e-07
 Identities = 17/96 (17%), Positives = 41/96 (42%), Gaps = 8/96 (8%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVE 261
                   +    ++ + +     + E+++  +A   G V  LRL+ +     + +A+VE
Sbjct: 7   GVFRYSTSLEKHKLFISGLPFSCTKEELEEICKAH--GTVKDLRLVTNRAGKPKGLAYVE 64

Query: 262 FA---VAESAILALNCSGMVLGSQPIRVSPSKTPVR 294
           +     A  A++ ++  GM +    I+V+ S +   
Sbjct: 65  YENESQASQAVMKMD--GMTIKENIIKVAISNSGPS 98

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 57.2 bits (138), Expect = 3e-10
 Identities = 18/101 (17%), Positives = 34/101 (33%), Gaps = 2/101 (1%)

Query: 89  RRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRV 148
            R +   ++ +  L                + VS++D  +++  +  LF+  G +    V
Sbjct: 61  SRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAV 120

Query: 149 CGDPHSVLR-FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
             D        A V F     A  A+    G  L   P+ +
Sbjct: 121 DYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDI 161

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 16/86 (18%), Positives = 34/86 (39%), Gaps = 4/86 (4%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAVAESAILA 271
              +  +N+D  V  A++++ F     G + +  +  D    S   A V F     A+ A
Sbjct: 88  GAKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVDYDRSGRSLGTADVHFERRADALKA 145

Query: 272 LN-CSGMVLGSQPIRVSPSKTPVRPR 296
           +    G+ L  +P+ +    + +   
Sbjct: 146 MKQYKGVPLDGRPMDIQLVASQIDLE 171

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 55.1 bits (133), Expect = 3e-10
 Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 4/94 (4%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
           S  +  +  +    R + + +I  ++  E L  L    G V  C       S      V 
Sbjct: 2   SSGSSGSVPKRQRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNT-DSETAVVNVT 60

Query: 163 FADEHGARAALN-LGGTMLGYYPVRV--LPSKTA 193
           ++ +  AR AL+ L G  L  + ++V  +P + A
Sbjct: 61  YSSKDQARQALDKLNGFQLENFTLKVAYIPDEMA 94

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96

 Score = 43.6 bits (103), Expect = 4e-06
 Identities = 14/78 (17%), Positives = 26/78 (33%), Gaps = 8/78 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAI 269
            R +   NI   +    +         G V     +      T +  V ++    A  A+
Sbjct: 15  IRKLQIRNIPPHLQWEVLDSLLVQY--GVVESCEQVNTDS-ETAVVNVTYSSKDQARQAL 71

Query: 270 LALNCSGMVLGSQPIRVS 287
             LN  G  L +  ++V+
Sbjct: 72  DKLN--GFQLENFTLKVA 87

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 55.4 bits (134), Expect = 4e-10
 Identities = 18/90 (20%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FA 159
           SG + +  ++ +    + V +I     +  +  LFS+ G++   R+            F 
Sbjct: 3   SGSSGQVPKKQT-TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61

Query: 160 FVEFADEHGARAALN--LGGTMLGYYPVRV 187
           FV+F  +  A+ A N     T L    + +
Sbjct: 62  FVDFITKQDAKKAFNALCHSTHLYGRRLVL 91

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107

 Score = 40.0 bits (94), Expect = 9e-05
 Identities = 17/91 (18%), Positives = 35/91 (38%), Gaps = 7/91 (7%)

Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVE 261
            +  ++  +  +   NI  +  Q E+++ F     GE+  +RL      +       FV+
Sbjct: 7   GQVPKKQTTSKILVRNIPFQANQREIRELFSTF--GELKTVRLPKKMTGTGAHRGFGFVD 64

Query: 262 FAVAESAILALN--CSGMVLGSQPIRVSPSK 290
           F   + A  A N  C    L  + + +  + 
Sbjct: 65  FITKQDAKKAFNALCHSTHLYGRRLVLEWAD 95

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 55.6 bits (134), Expect = 4e-10
 Identities = 19/96 (19%), Positives = 34/96 (35%), Gaps = 2/96 (2%)

Query: 97  QGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSV 155
            G+     +  R++        VY+  +      + +   F     V D   +   P+  
Sbjct: 6   SGKSPSGQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGK 65

Query: 156 LR-FAFVEFADEHGARAALNLGGTMLGYYPVRVLPS 190
                FVEF +E   +AAL      +G   ++V P 
Sbjct: 66  ATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI 101

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 124

 Score = 52.1 bits (125), Expect = 7e-09
 Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAVAESAILA 271
              VY   +  +     V  FF+         + +       +T   FVEF        A
Sbjct: 25  GFCVYLKGLPFEAENKHVIDFFKK-LDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAA 83

Query: 272 LNCSGMVLGSQPIRVSPS 289
           L      +G++ I+V P 
Sbjct: 84  LCRHKQYMGNRFIQVHPI 101

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 55.4 bits (134), Expect = 4e-10
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 13/93 (13%)

Query: 111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP---HSVLR-FAFVEFADE 166
            + +  +TV++ ++  +  EE L  +    G +   RV   P   HS  +  AF +F  +
Sbjct: 10  SDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHS--KGCAFAQFMTQ 67

Query: 167 HGARAA---LNLGGTMLGYY----PVRVLPSKT 192
             A+      +L     G       ++V  + T
Sbjct: 68  EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 11/88 (12%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAES 267
            +TV+  N+     +  + +  +    G++  +R++      HS   AF +F     A+ 
Sbjct: 15  GKTVFIRNLSFDSEEEALGEVLQQF--GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72

Query: 268 AILALN----CSGMVLGSQPIRVSPSKT 291
            + A +      G+ L  + ++V  + T
Sbjct: 73  CLAAASLEAEGGGLKLDGRQLKVDLAVT 100

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens} Length = 116

 Score = 55.5 bits (134), Expect = 5e-10
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 11/89 (12%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR----------FA 159
           ++++S   T++V  + +N+T E +A  F   G +   +  G P   L            A
Sbjct: 1   EQDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEA 60

Query: 160 FVEFADEHGARAAL-NLGGTMLGYYPVRV 187
            V F D   A+AA+    G      P++V
Sbjct: 61  TVSFDDPPSAKAAIDWFDGKEFSGNPIKV 89

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 55.0 bits (133), Expect = 5e-10
 Identities = 20/94 (21%), Positives = 38/94 (40%), Gaps = 5/94 (5%)

Query: 99  RKRLSGRAFRAQREDSVRRT----VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS 154
               SG   R    ++  ++    ++VS+I     +  L  +F   G+++D  +  +   
Sbjct: 8   HHHSSGLVPRGSHMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG 67

Query: 155 VLRFAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
              F FV F +   A  A   L GT++    + V
Sbjct: 68  SKGFGFVTFENSADADRAREKLHGTVVEGRKIEV 101

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 40.8 bits (96), Expect = 5e-05
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 11/97 (11%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA 263
               E +   + ++ +NI  +    +++Q F     G++  + ++ +   S    FV F 
Sbjct: 20  HMNTENKSQPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERGSKGFGFVTFE 77

Query: 264 ---VAESAILALNCSGMVLGSQPIRVSPSKTPVRPRV 297
               A+ A   L+  G V+  + I V+ +      RV
Sbjct: 78  NSADADRAREKLH--GTVVEGRKIEVNNA----TARV 108

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 54.2 bits (131), Expect = 6e-10
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 7/76 (9%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NL 175
             ++V +I    T + L   F   G V++C +      V  +AFV       A  A+  L
Sbjct: 11  TKLHVGNISPTCTNQELRAKFEEYGPVIECDI------VKDYAFVHMERAEDAVEAIRGL 64

Query: 176 GGTMLGYYPVRVLPSK 191
             T      + V  S 
Sbjct: 65  DNTEFQGKRMHVQLST 80

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92

 Score = 43.8 bits (104), Expect = 3e-06
 Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 13/95 (13%)

Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA- 263
           S       S  ++  NI       E++  FE    G V    ++ D+      AFV    
Sbjct: 2   SSGSSGKASTKLHVGNISPTCTNQELRAKFEEY--GPVIECDIVKDY------AFVHMER 53

Query: 264 --VAESAILALNCSGMVLGSQPIRVSPSKTPVRPR 296
              A  AI  L+        + + V  S + +R  
Sbjct: 54  AEDAVEAIRGLD--NTEFQGKRMHVQLSTSRLRTA 86

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 54.6 bits (132), Expect = 7e-10
 Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFV 161
           S  +  ++      R ++V  +++  +EE +  LF   G + +C V   P    +  AFV
Sbjct: 2   SSGSSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFV 61

Query: 162 EFADEHGARAALN 174
           +F+    A+AA++
Sbjct: 62  KFSSHTEAQAAIH 74

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105

 Score = 41.1 bits (97), Expect = 3e-05
 Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 7/95 (7%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVE 261
               + R    R ++   ++K+  + +V + F+    G +    +L      S   AFV+
Sbjct: 5   SSGSESRGGRDRKLFVGMLNKQQSEEDVLRLFQPF--GVIDECTVLRGPDGSSKGCAFVK 62

Query: 262 FAV---AESAILALNCSG-MVLGSQPIRVSPSKTP 292
           F+    A++AI AL+ S  M   S  + V  + T 
Sbjct: 63  FSSHTEAQAAIHALHGSQTMPGASSSLVVKFADTD 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 54.2 bits (131), Expect = 9e-10
 Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 4/95 (4%)

Query: 96  NQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS- 154
           +       G     QR       ++V+ + +  TEE +   F+  G++ +  +  D  + 
Sbjct: 4   DYDSVEQDGDEPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTG 62

Query: 155 VLR-FAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
            L+ +  VE+     A+AA+  L G  L   P+ V
Sbjct: 63  YLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 97

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106

 Score = 39.2 bits (92), Expect = 2e-04
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 7/87 (8%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI---AFV 260
               +R +    ++ T + ++  + ++   F     GE+  + L  D   +  +     V
Sbjct: 14  EPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDR-RTGYLKGYTLV 70

Query: 261 EFAVAESAILAL-NCSGMVLGSQPIRV 286
           E+   + A  A+   +G  L  QPI V
Sbjct: 71  EYETYKEAQAAMEGLNGQDLMGQPISV 97

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95

 Score = 53.7 bits (130), Expect = 9e-10
 Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFA 164
           RA  + +    + V  +    TE  L  +FS  G + D  +  D  S  R   FAFV F 
Sbjct: 9   RANPDPN--CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSR-RSRGFAFVYFE 65

Query: 165 DEHGARAAL-NLGGTMLGYYPVRV 187
           +   A+ A     G  L    +RV
Sbjct: 66  NVDDAKEAKERANGMELDGRRIRV 89

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1 Length = 139

 Score = 55.1 bits (133), Expect = 9e-10
 Identities = 21/109 (19%), Positives = 41/109 (37%), Gaps = 13/109 (11%)

Query: 87  NNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC 146
             +  +    Q +++      +   E  V R + V+ I   + E +L  LF   G +   
Sbjct: 13  YGQTAQLQQLQQQQQQHIPPTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESV 72

Query: 147 RVCGDPHSVLR-------FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
           ++  D     R       + FV+F     A+ A+  L G  +    ++V
Sbjct: 73  KIVCD-----RETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV 116

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 18/103 (17%), Positives = 39/103 (37%), Gaps = 5/103 (4%)

Query: 94  NFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH 153
           + + G +      F +       + +Y+ ++   +TE  L  LF+   +     +     
Sbjct: 3   SGSSGEEIRKIPMFSSYNPGEPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM 62

Query: 154 SVLR---FAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT 192
           +  R    AF+ F ++  A  AL+ + G  L    + +   K 
Sbjct: 63  T-GRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFGKN 104

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115

 Score = 46.9 bits (112), Expect = 4e-07
 Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 8/93 (8%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI---AFVEFAVAESAI 269
           ++ +Y  N+  +V + ++   F      E     +      + R+   AF+ F   E A 
Sbjct: 25  NKVLYLKNLSPRVTERDLVSLFARF--QEKKGPPIQFRM-MTGRMRGQAFITFPNKEIAW 81

Query: 270 LALN-CSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
            AL+  +G  L  + + +   K   + R + P 
Sbjct: 82  QALHLVNGYKLYGKILVIEFGKNK-KQRSSGPS 113

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 14/72 (19%), Positives = 27/72 (37%), Gaps = 1/72 (1%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
             ++V ++  + T + L   F+ CG V+   +  +         V+F     A  A   +
Sbjct: 9   CQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMM 68

Query: 176 GGTMLGYYPVRV 187
            G  L    + V
Sbjct: 69  NGMKLSGREIDV 80

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 7/87 (8%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAI 269
           +  ++  N+        +K  F     G V    +  ++  S     V+F    VAE A 
Sbjct: 8   ACQIFVRNLPFDFTWKMLKDKFNEC--GHVLYADIKMENGKSKGCGVVKFESPEVAERAC 65

Query: 270 LALNCSGMVLGSQPIRVSPSKTPVRPR 296
             +N  GM L  + I V   +    P 
Sbjct: 66  RMMN--GMKLSGREIDVRIDRNASGPS 90

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAF 160
           S  +    R      T+ V+++ ++  E  L  LF   G +    +  D  +     FAF
Sbjct: 2   SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61

Query: 161 VEFADEHGARAALN-LGGTMLGYYPVRV 187
           + F     A  A+  + G    +  + V
Sbjct: 62  ISFHRREDAARAIAGVSGFGYDHLILNV 89

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 20/94 (21%), Positives = 37/94 (39%), Gaps = 10/94 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFA---VAES 267
           + T+  TN+ +   + ++++ F     G ++R+ L  D     S   AF+ F     A  
Sbjct: 15  NATIRVTNLSEDTRETDLQELFRPF--GSISRIYLAKDKTTGQSKGFAFISFHRREDAAR 72

Query: 268 AILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           AI  ++  G       + V  +K P        G
Sbjct: 73  AIAGVS--GFGYDHLILNVEWAK-PSTNSGPSSG 103

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97

 Score = 53.8 bits (130), Expect = 1e-09
 Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 5/72 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
             ++V  +  N +   LA  F   G +              FA++++     A+AA   +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGD----SFAYIQYESLDAAQAACAKM 73

Query: 176 GGTMLGYYPVRV 187
            G  LG    R+
Sbjct: 74  RGFPLGGPDRRL 85

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 54.0 bits (130), Expect = 1e-09
 Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 4/79 (5%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEFAVAESAILA 271
              V    +     + +V+ FF    G  V  + LL DHV  +     V+F   +    A
Sbjct: 16  DLYVSVHGMPFSAMENDVRDFFH---GLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEA 72

Query: 272 LNCSGMVLGSQPIRVSPSK 290
           L  + M++  + + VSP+ 
Sbjct: 73  LKRNRMLMIQRYVEVSPAT 91

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 109

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 15/90 (16%), Positives = 27/90 (30%), Gaps = 2/90 (2%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFV 161
           SG + +    +     V V  +  +  E  +   F    +V    +  D          V
Sbjct: 3   SGSSGKPLPINPDDLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLV 61

Query: 162 EFADEHGARAALNLGGTMLGYYPVRVLPSK 191
           +F        AL     ++    V V P+ 
Sbjct: 62  KFLSPQDTFEALKRNRMLMIQRYVEVSPAT 91

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129

 Score = 54.3 bits (131), Expect = 1e-09
 Identities = 23/105 (21%), Positives = 34/105 (32%), Gaps = 5/105 (4%)

Query: 87  NNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC 146
                 +     +     R    +        + V  +    TE  L  +FS  G + D 
Sbjct: 17  RGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADV 76

Query: 147 RVCGDPHSVLR---FAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
            +  D  S  R   FAFV F +   A+ A     G  L    +RV
Sbjct: 77  SIVYDQQS-RRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV 120

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 53.3 bits (129), Expect = 1e-09
 Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLR-FAFVEFADEHGARAAL-N 174
            +YV  +  NITE+ L G+F   G++ +  +  D  +   + + F+ F+D   AR AL  
Sbjct: 7   GLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66

Query: 175 LGGTMLGYYPVRV 187
           L G  L   P+RV
Sbjct: 67  LNGFELAGRPMRV 79

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 53.4 bits (129), Expect = 2e-09
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 3/73 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLR-FAFVEFADEHGARAALN 174
            T YV ++  N  +  +  +F     +   R+  D  +   + F +VEF +    + AL 
Sbjct: 16  YTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT 74

Query: 175 LGGTMLGYYPVRV 187
             G +LG   +RV
Sbjct: 75  YDGALLGDRSLRV 87

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus} Length = 103

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 8/93 (8%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAVAESAI 269
             T Y  N+     Q ++   F+      +  +RL+ D   + +     +VEF   +S  
Sbjct: 15  PYTAYVGNLPFNTVQGDIDAIFK---DLSIRSVRLVRDK-DTDKFKGFCYVEFDEVDSLK 70

Query: 270 LALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGM 302
            AL   G +LG + +RV  ++   +   + P  
Sbjct: 71  EALTYDGALLGDRSLRVDIAE-GRKQDKSGPSS 102

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 52.9 bits (127), Expect = 2e-09
 Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGAR 170
               +   VYV ++ ++     L       G  V  R+        R AF+ + D   A+
Sbjct: 14  EGAPLAADVYVGNLPRDARVSDLKRALRELG-SVPLRLTWQGPR--RRAFLHYPDSAAAQ 70

Query: 171 AAL-NLGGTMLGYYPVRVLPSKTA 193
            A+  L G  LG   +RV  ++  
Sbjct: 71  QAVSCLQGLRLGTDTLRVALARQQ 94

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97

 Score = 42.9 bits (101), Expect = 8e-06
 Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 12/93 (12%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
           P  E      +  VY  N+ +    +++K+      G    RL   G      R AF+ +
Sbjct: 11  PPGEGAPL--AADVYVGNLPRDARVSDLKRAL-RELGSVPLRLTWQG----PRRRAFLHY 63

Query: 263 ---AVAESAILALNCSGMVLGSQPIRVSPSKTP 292
              A A+ A+  L   G+ LG+  +RV+ ++  
Sbjct: 64  PDSAAAQQAVSCLQ--GLRLGTDTLRVALARQQ 94

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 52.5 bits (127), Expect = 2e-09
 Identities = 14/74 (18%), Positives = 35/74 (47%), Gaps = 4/74 (5%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAAL- 173
            V++  + +N+T++ +  +FS+ G++    +  +         +A+VEF +   A  AL 
Sbjct: 6   KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65

Query: 174 NLGGTMLGYYPVRV 187
           ++ G  +    +  
Sbjct: 66  HMDGGQIDGQEITA 79

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 19/92 (20%), Positives = 37/92 (40%), Gaps = 11/92 (11%)

Query: 211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAV--- 264
           M    V+   + + V +  + + F     G++  + +  + +H       A+VEF     
Sbjct: 2   MKPTKVHIGRLTRNVTKDHIMEIFSTY--GKIKMIDMPVERMHPHLSKGYAYVEFENPDE 59

Query: 265 AESAILALNCSGMVLGSQPIRVSPSKTPVRPR 296
           AE A+  ++  G  +  Q I  +    P  PR
Sbjct: 60  AEKALKHMD--GGQIDGQEITATAVLAP-WPR 88

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 54.5 bits (131), Expect = 3e-09
 Identities = 27/114 (23%), Positives = 47/114 (41%), Gaps = 4/114 (3%)

Query: 78  KQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQRED-SVRRTVYVSDIDQNITEERLAGL 136
           KQ A DN  +     ++  +      G        D     ++ V ++    + + L  +
Sbjct: 31  KQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVEGMTSLKVDNLTYRTSPDTLRRV 90

Query: 137 FSSCGQVVDCRVCGDPHS-VLR-FAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
           F   G+V D  +  D ++   R FAFV F D+  A  A+  + G +L    +RV
Sbjct: 91  FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRV 144

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158

 Score = 43.3 bits (102), Expect = 2e-05
 Identities = 27/156 (17%), Positives = 50/156 (32%), Gaps = 12/156 (7%)

Query: 147 RVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSE 206
           ++  +  ++      E  D   A           G          T    V         
Sbjct: 4   KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHH 63

Query: 207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFA 263
                   ++   N+  +     +++ FE    G V  + +  D  ++      AFV F 
Sbjct: 64  HMDVEGMTSLKVDNLTYRTSPDTLRRVFEKY--GRVGDVYIPRDR-YTKESRGFAFVRFH 120

Query: 264 ---VAESAILALNCSGMVLGSQPIRVSPSKTPVRPR 296
               AE A+ A++  G VL  + +RV  ++   RP 
Sbjct: 121 DKRDAEDAMDAMD--GAVLDGRELRVQMAR-YGRPP 153

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 52.7 bits (127), Expect = 3e-09
 Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 6/73 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL-N 174
           RT+   ++  NITE+ L  +F    ++      G      +  A++EF  E  A   L  
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKS----KGIAYIEFKSEADAEKNLEE 72

Query: 175 LGGTMLGYYPVRV 187
             G  +    V +
Sbjct: 73  KQGAEIDGRSVSL 85

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 14/99 (14%)

Query: 206 EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV- 264
             ++   +RT+   N+   + + E+K+ FE A   E+  +   G    S  IA++EF   
Sbjct: 9   TSKKVRAARTLLAKNLSFNITEDELKEVFEDA--LEIRLVSQDG---KSKGIAYIEFKSE 63

Query: 265 --AESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
             AE  +      G  +  + + +  +      +    G
Sbjct: 64  ADAEKNLEEKQ--GAEIDGRSVSLYYT----GEKGGTRG 96

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 16/72 (22%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL-NL 175
            +++  +++   E+ L  +F   G + +  +  D  S  R FAF+ F +   A+ A  ++
Sbjct: 9   KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68

Query: 176 GGTMLGYYPVRV 187
            G  L    ++V
Sbjct: 69  NGKSLHGKAIKV 80

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.8 bits (127), Expect = 4e-09
 Identities = 15/81 (18%), Positives = 29/81 (35%), Gaps = 2/81 (2%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSVLR-FAFVEFADEHGA 169
            +S +   ++++I  +IT+  +           +   V  D +      A V+F +E  A
Sbjct: 11  VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 70

Query: 170 RAALNLGGTMLGYYPVRVLPS 190
           R +  L    L      V   
Sbjct: 71  RKSERLHRKKLNGREAFVHVV 91

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 52.0 bits (125), Expect = 7e-09
 Identities = 18/102 (17%), Positives = 33/102 (32%), Gaps = 3/102 (2%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-HSTRIAFVEF 262
             E +        + TNI   + + +V QF E     +   + +L D+       A V+F
Sbjct: 6   SGEGDVNSAKVCAHITNIPFSITKMDVLQFLEG-IPVDENAVHVLVDNNGQGLGQALVQF 64

Query: 263 AVAESAILALNCSGMVLGSQPIRVSP-SKTPVRPRVTRPGMH 303
              + A  +       L  +   V   +   +R     P   
Sbjct: 65  KNEDDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQ 106

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 15/73 (20%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 104 GRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFV 161
           G +  +  +D     +++  I +N+ E+ L  LF   G++ +  V  D  + +    AF+
Sbjct: 1   GSSGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFL 60

Query: 162 EFADEHGARAALN 174
            + +   A  A +
Sbjct: 61  TYCERESALKAQS 73

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106

 Score = 43.1 bits (102), Expect = 7e-06
 Identities = 21/99 (21%), Positives = 43/99 (43%), Gaps = 8/99 (8%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFV 260
             S   ++  +  ++   I + + + ++K  FE    G++  L +L D         AF+
Sbjct: 3   SGSSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEF--GKIYELTVLKDRFTGMHKGCAFL 60

Query: 261 EFA---VAESAILALNCSGMVLG-SQPIRVSPSKTPVRP 295
            +     A  A  AL+    + G ++PI+V P+ +  R 
Sbjct: 61  TYCERESALKAQSALHEQKTLPGMNRPIQVKPADSESRG 99

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 52.3 bits (126), Expect = 4e-09
 Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL- 173
           R+V+V +I    TEE+L  +FS  G VV  R+  D  +     + F E+ D+  A +A+ 
Sbjct: 9   RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68

Query: 174 NLGGTMLGYYPVRV 187
           NL G       +RV
Sbjct: 69  NLNGREFSGRALRV 82

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 52.1 bits (125), Expect = 5e-09
 Identities = 19/88 (21%), Positives = 27/88 (30%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
                        V    +     + E+ QFF             +     ST  AFV+F
Sbjct: 5   SSGNSPDTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQF 64

Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSK 290
           A  E A  AL      +G + I +  S 
Sbjct: 65  ASQEIAEKALKKHKERIGHRYIEIFKSS 92

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104

 Score = 50.5 bits (121), Expect = 2e-08
 Identities = 17/79 (21%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSVLR-FAFVEFADEHGARAALN 174
             V +  +    ++E +   FS    V +   +  D        AFV+FA +  A  AL 
Sbjct: 16  GFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALK 75

Query: 175 LGGTMLGYYPVRVLPSKTA 193
                +G+  + +  S  A
Sbjct: 76  KHKERIGHRYIEIFKSSRA 94

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 51.8 bits (125), Expect = 5e-09
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 117 RTVYVSDIDQNITEERL----AGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARA 171
            T+Y++++++ I ++ L      +FS  GQ++D  V        R  AFV F +   A  
Sbjct: 9   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM--RGQAFVIFKEVSSATN 66

Query: 172 AL-NLGGTMLGYYPVRVLPSKT 192
           AL ++ G      P+R+  +KT
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKT 88

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97

 Score = 44.5 bits (106), Expect = 2e-06
 Identities = 21/83 (25%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACG--GEVTRLRLLGDHVHSTRIAFVEFAVAESAIL 270
           + T+Y  N+++K+ + E+K+   A     G++  + +        + AFV F    SA  
Sbjct: 8   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQ-AFVIFKEVSSATN 66

Query: 271 AL-NCSGMVLGSQPIRVSPSKTP 292
           AL +  G     +P+R+  +KT 
Sbjct: 67  ALRSMQGFPFYDKPMRIQYAKTD 89

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 55.3 bits (132), Expect = 5e-09
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 8/82 (9%)

Query: 117 RTVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARA 171
            T+Y++++++ I ++ L      +FS  GQ++D  V        R  AFV F +   A  
Sbjct: 10  HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM--RGQAFVIFKEVSSATN 67

Query: 172 ALN-LGGTMLGYYPVRVLPSKT 192
           AL  + G      P+R+  +KT
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKT 89

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 47.9 bits (113), Expect = 1e-06
 Identities = 18/106 (16%), Positives = 37/106 (34%), Gaps = 5/106 (4%)

Query: 84  NFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQV 143
                        Q          +   E+     ++++++ +   E  L+ LF+     
Sbjct: 175 LAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGF 234

Query: 144 VDCRVCGDPHSVLRFAFVEFADEHGARAALNL--GGTMLGYYPVRV 187
            + R+    H     AFVEF +E  A AA +   G  +     +++
Sbjct: 235 KEVRLVPGRHD---IAFVEFDNEVQAGAARDALQGFKITQNNAMKI 277

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282

 Score = 46.8 bits (110), Expect = 3e-06
 Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 4/94 (4%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACG--GEVTRLRLLGDHVHSTRIAFVEFAVAESAIL 270
           + T+Y  N+++K+ + E+K+   A     G++  + +          AFV F    SA  
Sbjct: 9   NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL-KMRGQAFVIFKEVSSATN 67

Query: 271 ALN-CSGMVLGSQPIRVSPSKTPVRPRVTRPGMH 303
           AL    G     +P+R+  +KT         G  
Sbjct: 68  ALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTF 101

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 52.6 bits (126), Expect = 5e-09
 Identities = 19/81 (23%), Positives = 38/81 (46%), Gaps = 6/81 (7%)

Query: 117 RTVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAA 172
           + V +++I+  + +E+L      L SS G ++D  V     +    A++ FA +  A+A 
Sbjct: 30  QVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSDDN-SGKAYIVFATQESAQAF 88

Query: 173 LN-LGGTMLGYYPVRVLPSKT 192
           +    G      P+ +  S+T
Sbjct: 89  VEAFQGYPFQGNPLVITFSET 109

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127

 Score = 48.0 bits (114), Expect = 3e-07
 Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACG--GEVTRLRLLGDHVHSTRIAFVEFAVAESAIL 270
           S+ V  TNI+ +VP+ +++    A     G++  + +      ++  A++ FA  ESA  
Sbjct: 29  SQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLSD-DNSGKAYIVFATQESAQA 87

Query: 271 ALN-CSGMVLGSQPIRVSPSKTP 292
            +    G      P+ ++ S+TP
Sbjct: 88  FVEAFQGYPFQGNPLVITFSETP 110

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90

 Score = 51.4 bits (124), Expect = 5e-09
 Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALN 174
           R +YV ++  + T E++  LFS  G+V + ++  D  +     F FVE  +E  + A   
Sbjct: 2   RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61

Query: 175 LGGTMLGYYPVRV 187
           L  T      +RV
Sbjct: 62  LDNTDFMGRTIRV 74

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 51.9 bits (125), Expect = 6e-09
 Identities = 20/80 (25%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHG 168
             S    ++V  +  +  E+ L  +FS  GQ+ +  V  D  +  R   F FV F +   
Sbjct: 8   MASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQ-RSRGFGFVTFENIDD 66

Query: 169 ARAALN-LGGTMLGYYPVRV 187
           A+ A+  + G  +    +RV
Sbjct: 67  AKDAMMAMNGKSVDGRQIRV 86

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85

 Score = 51.0 bits (123), Expect = 7e-09
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL--RFAFVEFADEHGARAALN-L 175
           +Y+  +    T++ L  L    G++V  +   D  +     + FV+F     A+ A+  L
Sbjct: 8   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 67

Query: 176 GGTMLGYYPVRV 187
             + +     + 
Sbjct: 68  KASGVQAQMAKQ 79

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 96

 Score = 51.4 bits (124), Expect = 7e-09
 Identities = 19/74 (25%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSVLR--FAFVEFADEHGARAALN 174
            +++ ++D  I E+ L   FS+ G ++   ++  DP +     +AF+ FA    + AA+ 
Sbjct: 7   GIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66

Query: 175 -LGGTMLGYYPVRV 187
            + G  L   P+ V
Sbjct: 67  AMNGQYLCNRPITV 80

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101

 Score = 51.5 bits (124), Expect = 8e-09
 Identities = 22/70 (31%), Positives = 31/70 (44%), Gaps = 4/70 (5%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGG 177
           VYV ++     +  L   FS  G +    +  +P     FAFVEF D   A  A+  L G
Sbjct: 3   VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPG---FAFVEFEDPRDAEDAVRGLDG 59

Query: 178 TMLGYYPVRV 187
            ++    VRV
Sbjct: 60  KVICGSRVRV 69

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99

 Score = 51.4 bits (124), Expect = 8e-09
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLR-FAFVEFADEHGARAALN- 174
            ++V ++    +EE L  LFS+ G + +     D  +   + FAFV F     A  A   
Sbjct: 10  RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69

Query: 175 LGGTMLGYYPVRVLPSK 191
           + G +     + VLPS 
Sbjct: 70  VDGQVFQGRMLHVLPST 86

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 51.5 bits (124), Expect = 9e-09
 Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL-N 174
            ++V+ I +   E+ +   F   G++ +  +  D  +     +A VE+     A AA   
Sbjct: 28  ILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEA 87

Query: 175 LGGTMLGYYPVRV 187
           L G  +    ++V
Sbjct: 88  LNGAEIMGQTIQV 100

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110

 Score = 39.6 bits (93), Expect = 1e-04
 Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 8/94 (8%)

Query: 207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI---AFVEFA 263
            +R +    ++ T+I ++  + E+++ F     GE+  + L  D   +      A VE+ 
Sbjct: 20  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDR-RTGFSKGYALVEYE 76

Query: 264 VAESAILAL-NCSGMVLGSQPIRVSPSKTPVRPR 296
             + A+ A    +G  +  Q I+V        P+
Sbjct: 77  THKQALAAKEALNGAEIMGQTIQVDWCF-VKGPK 109

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 24/86 (27%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
           S  +   +R      T+YV   D  +T   L G FS  G ++D  +  DP      AFV 
Sbjct: 2   SSGSSGERRAPRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSM--DPPR--NCAFVT 55

Query: 163 FADEHGARAAL-NLGGTMLGYYPVRV 187
           +     A  A+  L GT +    ++V
Sbjct: 56  YEKMESADQAVAELNGTQVESVQLKV 81

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97

 Score = 38.8 bits (91), Expect = 2e-04
 Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 13/77 (16%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV---AESAIL 270
            T+Y    D  +    ++  F     G +  L +          AFV +     A+ A+ 
Sbjct: 16  NTLYVYGED--MTPTLLRGAFSPF--GNIIDLSMDPPR----NCAFVTYEKMESADQAVA 67

Query: 271 ALNCSGMVLGSQPIRVS 287
            LN  G  + S  ++V+
Sbjct: 68  ELN--GTQVESVQLKVN 82

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALNLGG 177
           V+V  ID  + E  +   F+  G V + ++  D   V + + FV F ++   +  +    
Sbjct: 12  VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVESQI 71

Query: 178 TMLG 181
              G
Sbjct: 72  NFHG 75

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 50.9 bits (122), Expect = 1e-08
 Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN 174
              V++  +    TE  +   FS     +   +   P   +   A VEFA    A AA+ 
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFSPLN-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMA 73

Query: 175 LGGTMLGYYPVRVLPSKTA 193
                + +  V +  + TA
Sbjct: 74  KDKANMQHRYVELFLNSTA 92

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102

 Score = 49.7 bits (119), Expect = 3e-08
 Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 4/81 (4%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAILA 271
              V+   +  +  + ++  FF         R+ +           A VEFA  E A+ A
Sbjct: 15  GHCVHMRGLPYRATENDIYNFFS---PLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAA 71

Query: 272 LNCSGMVLGSQPIRVSPSKTP 292
           +      +  + + +  + T 
Sbjct: 72  MAKDKANMQHRYVELFLNSTA 92

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 51.8 bits (124), Expect = 1e-08
 Identities = 19/106 (17%), Positives = 33/106 (31%), Gaps = 4/106 (3%)

Query: 89  RRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRV 148
                   Q  +      F  Q        V++  +    TE  +   FS     V   +
Sbjct: 21  MASMTGGQQMGRGSGDSEFTVQSTTG--HCVHMRGLPYKATENDIYNFFSPLN-PVRVHI 77

Query: 149 CGDPHSVLR-FAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA 193
              P   +   A VEFA    A AA++     + +  + +  + T 
Sbjct: 78  EIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTT 123

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A Length = 139

 Score = 50.6 bits (121), Expect = 3e-08
 Identities = 17/95 (17%), Positives = 30/95 (31%), Gaps = 2/95 (2%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
                 +      V+   +  K  + ++  FF       V      G     T  A VEF
Sbjct: 36  DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEI--GPDGRVTGEADVEF 93

Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRV 297
           A  E A+ A++     +  + I +  + T      
Sbjct: 94  ATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNG 128

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 12/73 (16%), Positives = 24/73 (32%), Gaps = 5/73 (6%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN- 174
           +  +   ++        +   FS  G +    +          A VEF +   AR A   
Sbjct: 10  KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLL----PEGGITAIVEFLEPLEARKAFRH 65

Query: 175 LGGTMLGYYPVRV 187
           L  +   + P+ +
Sbjct: 66  LAYSKFHHVPLYL 78

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 41.3 bits (97), Expect = 4e-05
 Identities = 15/85 (17%), Positives = 26/85 (30%), Gaps = 9/85 (10%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA 263
                R      +   N+      AE+++ F     G + R+ L    +     A VEF 
Sbjct: 3   SGSSGRS--KTVILAKNLPAGTLAAEIQETFSRF--GSLGRVLLPEGGI----TAIVEFL 54

Query: 264 VAESAILALNC-SGMVLGSQPIRVS 287
               A  A    +       P+ + 
Sbjct: 55  EPLEARKAFRHLAYSKFHHVPLYLE 79

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 52.1 bits (125), Expect = 2e-08
 Identities = 18/104 (17%), Positives = 39/104 (37%), Gaps = 3/104 (2%)

Query: 87  NNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC 146
           N R   +++ + R           +       ++V+ I +   E+ +   F   G++ + 
Sbjct: 43  NTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNI 102

Query: 147 RVCGDPHS--VLRFAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
            +  D  +     +A VE+     A AA   L G  +    ++V
Sbjct: 103 HLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV 146

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165

 Score = 44.1 bits (104), Expect = 1e-05
 Identities = 20/98 (20%), Positives = 41/98 (41%), Gaps = 6/98 (6%)

Query: 207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV--HSTRIAFVEFAV 264
            +R +    ++ T+I ++  + E+++ F     GE+  + L  D     S   A VE+  
Sbjct: 66  PQRSVEGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDRRTGFSKGYALVEYET 123

Query: 265 AESAILAL-NCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
            + A+ A    +G  +  Q I+V        P+  +  
Sbjct: 124 HKQALAAKEALNGAEIMGQTIQVDWCF-VKGPKRVKKS 160

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126

 Score = 50.8 bits (122), Expect = 2e-08
 Identities = 22/99 (22%), Positives = 44/99 (44%), Gaps = 6/99 (6%)

Query: 92  RNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD 151
           R +++   +   G     QR       ++V+ + +  TEE +   F+  G++ +  +  D
Sbjct: 1   REDYDSVEQD--GDEPGPQRSVE-GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLD 57

Query: 152 PHS-VLR-FAFVEFADEHGARAAL-NLGGTMLGYYPVRV 187
             +  L+ +  VE+     A+AA+  L G  L   P+ V
Sbjct: 58  RRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISV 96

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 50.8 bits (121), Expect = 3e-08
 Identities = 17/109 (15%), Positives = 30/109 (27%), Gaps = 4/109 (3%)

Query: 89  RRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSC---GQVVD 145
           R        G +++   +     E      V +  +  + + E +    S C        
Sbjct: 17  RGSHMASMTGGQQMGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAG 76

Query: 146 CRVCGDPHSVLR-FAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA 193
                         AFVE   E   + AL      +G+  + V  S   
Sbjct: 77  VHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSHRT 125

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A Length = 136

 Score = 46.9 bits (111), Expect = 6e-07
 Identities = 13/91 (14%), Positives = 22/91 (24%), Gaps = 2/91 (2%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEA-ACGGEVTRLRLLGDHVHSTR-IAFV 260
                        V    +       +V+ F            +  +          AFV
Sbjct: 34  SMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFV 93

Query: 261 EFAVAESAILALNCSGMVLGSQPIRVSPSKT 291
           E    +   +AL      +G + I V  S  
Sbjct: 94  ELGSEDDVKMALKKDRESMGHRYIEVFKSHR 124

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 50.3 bits (120), Expect = 3e-08
 Identities = 20/92 (21%), Positives = 29/92 (31%), Gaps = 3/92 (3%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAAC--GGEVTRLRLLGDHVHSTR-IAF 259
             ++   +     V    +       EV  FF   C   G    +  +          AF
Sbjct: 13  EVAQFLSKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAF 72

Query: 260 VEFAVAESAILALNCSGMVLGSQPIRVSPSKT 291
           V FA  E A  AL     +LG + I +  S  
Sbjct: 73  VLFACEEYAQNALRKHKDLLGKRYIELFRSTA 104

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 123

 Score = 43.3 bits (102), Expect = 9e-06
 Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 5/81 (6%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDC----RVCGDPHSVLR-FAFVEFADEHGARAA 172
            V +  +    T E +   F     +            P       AFV FA E  A+ A
Sbjct: 25  IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA 84

Query: 173 LNLGGTMLGYYPVRVLPSKTA 193
           L     +LG   + +  S  A
Sbjct: 85  LRKHKDLLGKRYIELFRSTAA 105

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 49.2 bits (118), Expect = 4e-08
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 8/78 (10%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAA---L 173
             +Y+ ++   +T + L  LF      +  +V         +AFV++ D++ A  A   L
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDRKLPLAGQV-LLKSG---YAFVDYPDQNWAIRAIETL 64

Query: 174 NLGGTMLGYYPVRVLPSK 191
           + G   L    + V  S 
Sbjct: 65  S-GKVELHGKIMEVDYSV 81

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 93

 Score = 39.5 bits (93), Expect = 1e-04
 Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 13/91 (14%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAIL 270
             +Y  N+   V   +++Q F           ++L      +  AFV++     A  AI 
Sbjct: 9   NKLYIGNLSPAVTADDLRQLFGDR--KLPLAGQVL----LKSGYAFVDYPDQNWAIRAIE 62

Query: 271 ALNCSGMV-LGSQPIRVSPSKTPVRPRVTRP 300
            L+  G V L  + + V  S    + R + P
Sbjct: 63  TLS--GKVELHGKIMEVDYSV-SKKLRSSGP 90

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104

 Score = 48.8 bits (117), Expect = 6e-08
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 4/83 (4%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSC-GQVVDCRVCGDPHSVLR-FAFVEFADE 166
           +        +++V D+  ++ +  L   F          +V  D   V + + FV+F DE
Sbjct: 2   SSGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDE 61

Query: 167 HGARAALNL--GGTMLGYYPVRV 187
              + AL    G   LG  PVR+
Sbjct: 62  LEQKRALTECQGAVGLGSKPVRL 84

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C Length = 229

 Score = 51.3 bits (122), Expect = 6e-08
 Identities = 20/135 (14%), Positives = 43/135 (31%), Gaps = 9/135 (6%)

Query: 58  YHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRR 117
            H   D +  VI+      N   A ++ +              + +            R 
Sbjct: 14  GHDQIDLYDDVIS---PSANNGDAPEDRDYMDTLPPTVGDDVGKGAAPNVVYTYTGK-RI 69

Query: 118 TVYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHS-VLR-FAFVEFADEHGARAAL 173
            +Y+ ++    T+E L     S G   +++ +   +  +   + FA V    E  ++  +
Sbjct: 70  ALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLM 129

Query: 174 N-LGGTMLGYYPVRV 187
           + L    L      V
Sbjct: 130 DLLPKRELHGQNPVV 144

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 49.0 bits (117), Expect = 7e-08
 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 7/78 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVV-DCRVCGDPHSVLR---FAFVEFADEHGARAA 172
             +++  I +    E +    +   + V D  V       ++   FAFVE+     A  A
Sbjct: 9   CRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMA 68

Query: 173 ---LNLGGTMLGYYPVRV 187
              L  G   L  + + V
Sbjct: 69  RRKLMPGRIQLWGHQIAV 86

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109

 Score = 45.9 bits (109), Expect = 9e-07
 Identities = 14/89 (15%), Positives = 28/89 (31%), Gaps = 7/89 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFA---VAE 266
           +  ++   I K   + E+ +         V  + +        +    AFVE+     A 
Sbjct: 8   NCRLFIGGIPKMKKREEILEEIAK-VTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAA 66

Query: 267 SAILALNCSGMVLGSQPIRVSPSKTPVRP 295
            A   L    + L    I V  ++  +  
Sbjct: 67  MARRKLMPGRIQLWGHQIAVDWAEPEIDV 95

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 48.6 bits (116), Expect = 8e-08
 Identities = 12/78 (15%), Positives = 23/78 (29%), Gaps = 7/78 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL--- 173
             V+V  + +++ E  L       G +    +        R A VEF +   A+  +   
Sbjct: 16  PVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFK----RQALVEFENIDSAKECVTFA 71

Query: 174 NLGGTMLGYYPVRVLPSK 191
                 +         S 
Sbjct: 72  ADVPVYIAGQQAFFNYST 89

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 12/92 (13%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           S  V+   + + V +A++ +  E    G +  + +    +   R A VEF   +SA   +
Sbjct: 15  SPVVHVRGLCESVVEADLVEALEKF--GTICYVMM----MPFKRQALVEFENIDSAKECV 68

Query: 273 NC---SGMVLGSQPIRVSPSKTPVRPRVTRPG 301
                  + +  Q    + S      R+TRPG
Sbjct: 69  TFAADVPVYIAGQQAFFNYST---SKRITRPG 97

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 49.1 bits (117), Expect = 9e-08
 Identities = 16/95 (16%), Positives = 25/95 (26%), Gaps = 4/95 (4%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSC---GQVVDCRVCGDPHSVLR-F 158
                    E      V +  +  + + E +    S C     V                
Sbjct: 4   GSSGMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGE 63

Query: 159 AFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA 193
           AFVE   E   + AL      +G+  + V  S   
Sbjct: 64  AFVELESEDDVKLALKKDRESMGHRYIEVFKSHRT 98

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118

 Score = 48.4 bits (115), Expect = 2e-07
 Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 2/81 (2%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFF-EAACGGEVTRLRLLGDHVHSTR-IAFVEFAVAESAIL 270
              V    +       +V+ F  +      V  +  +          AFVE    +   L
Sbjct: 17  GYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKL 76

Query: 271 ALNCSGMVLGSQPIRVSPSKT 291
           AL      +G + I V  S  
Sbjct: 77  ALKKDRESMGHRYIEVFKSHR 97

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 48.1 bits (115), Expect = 1e-07
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 1/81 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              +   N+   V   E+  FF        +      +    T  A V F   + A  A+
Sbjct: 15  PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74

Query: 273 N-CSGMVLGSQPIRVSPSKTP 292
              +   +GS+ +++     P
Sbjct: 75  IDLNDRPIGSRKVKLVLGSGP 95

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98

 Score = 45.0 bits (107), Expect = 1e-06
 Identities = 11/79 (13%), Positives = 27/79 (34%), Gaps = 3/79 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSVLR-FAFVEFADEHGARAALN- 174
            + V ++   ++ + +   F     +     +  +   +    A V F     A AA+  
Sbjct: 17  IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 175 LGGTMLGYYPVRVLPSKTA 193
           L    +G   V+++     
Sbjct: 77  LNDRPIGSRKVKLVLGSGP 95

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 16/79 (20%), Positives = 25/79 (31%), Gaps = 6/79 (7%)

Query: 96  NQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV 155
           +     +       +   S    V++  +   + E  L       G +    V       
Sbjct: 3   HHHHHHMENYDDPHKTPAS--PVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPK---- 56

Query: 156 LRFAFVEFADEHGARAALN 174
            R A VEF D  GA  A+N
Sbjct: 57  KRQALVEFEDVLGACNAVN 75

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 9/82 (10%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           S  V+   +   V +A++ +  +    G ++ + ++       R A VEF     A  A+
Sbjct: 21  SPVVHIRGLIDGVVEADLVEALQEF--GPISYVVVMPKK----RQALVEFEDVLGACNAV 74

Query: 273 NC---SGMVLGSQPIRVSPSKT 291
           N    + + +   P  V+ S +
Sbjct: 75  NYAADNQIYIAGHPAFVNYSTS 96

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 15/88 (17%), Positives = 24/88 (27%), Gaps = 4/88 (4%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSC---GQVVDCRVCGDPHSVLR-FAFVEFAD 165
           + E      +    +  + T E +   FS C             +     R  A +E   
Sbjct: 5   EEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMES 64

Query: 166 EHGARAALNLGGTMLGYYPVRVLPSKTA 193
           E   + AL      +G   V V      
Sbjct: 65  EQDVQKALEKHRMYMGQRYVEVYEINNE 92

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens} Length = 107

 Score = 47.2 bits (112), Expect = 3e-07
 Identities = 12/80 (15%), Positives = 22/80 (27%), Gaps = 2/80 (2%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAAC-GGEVTRLRLLGDHVHSTR-IAFVEFAVAESAIL 270
              +    +       +V  FF           +  L +     R  A +E    +    
Sbjct: 11  VFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQK 70

Query: 271 ALNCSGMVLGSQPIRVSPSK 290
           AL    M +G + + V    
Sbjct: 71  ALEKHRMYMGQRYVEVYEIN 90

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 49.8 bits (118), Expect = 2e-07
 Identities = 14/76 (18%), Positives = 28/76 (36%), Gaps = 1/76 (1%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALNL 175
           R+VY+     + T + +       GQV++ ++    H   +   FV F     A+  +  
Sbjct: 110 RSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169

Query: 176 GGTMLGYYPVRVLPSK 191
            G       + +L   
Sbjct: 170 PGQKYKETDLLILFKD 185

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193

 Score = 41.7 bits (97), Expect = 9e-05
 Identities = 17/96 (17%), Positives = 35/96 (36%), Gaps = 3/96 (3%)

Query: 196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHST 255
           P  P      E + ++ +R+VY           ++K++ E    G+V  +++      + 
Sbjct: 92  PSKPLPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTLHKAF 149

Query: 256 R-IAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK 290
           +   FV F   ESA   +   G       + +    
Sbjct: 150 KGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD 185

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99

 Score = 47.2 bits (113), Expect = 3e-07
 Identities = 19/81 (23%), Positives = 28/81 (34%), Gaps = 2/81 (2%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADE 166
           +    S    ++V  I  N  E  L   F   G V +  +  D        F F+ F DE
Sbjct: 3   SGSSGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDE 62

Query: 167 HGARAALNLGGTMLGYYPVRV 187
                A+N+    +    V V
Sbjct: 63  QSVDQAVNMHFHDIMGKKVEV 83

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 47.4 bits (113), Expect = 3e-07
 Identities = 18/81 (22%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 113 DSVRRTVYVSDIDQNITEER-LAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
            S+   V++ +++  + ++  +  +FS  G+V  C V         +AFV++++E  ARA
Sbjct: 24  KSINSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV------HKGYAFVQYSNERHARA 77

Query: 172 AL-NLGGTMLGYYPVRVLPSK 191
           A+    G +L    + +  + 
Sbjct: 78  AVLGENGRVLAGQTLDINMAG 98

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110

 Score = 40.4 bits (95), Expect = 8e-05
 Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 15/102 (14%)

Query: 204 RSEDEREMCSRTVYCTNID-KKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
              D + + SR V+  N++   V +++V+  F     G V    +   +      AFV++
Sbjct: 19  NKNDPKSINSR-VFIGNLNTALVKKSDVETIFSKY--GRVAGCSVHKGY------AFVQY 69

Query: 263 A---VAESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           +    A +A+L  N  G VL  Q + ++ +  P   R     
Sbjct: 70  SNERHARAAVLGEN--GRVLAGQTLDINMAGEPKPDRSGPSS 109

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens} Length = 156

 Score = 48.0 bits (114), Expect = 4e-07
 Identities = 29/158 (18%), Positives = 52/158 (32%), Gaps = 11/158 (6%)

Query: 59  HQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRT 118
           H H  H   V      ++    +++     R+  +     +       +   R       
Sbjct: 2   HHHHHHSSGVDLGT--ENLYFQSMEPPPPVRQEPSPKPNNKTPAILYTYSGLRNRRAA-- 57

Query: 119 VYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHSVLR---FAFVEFADEHGARAAL 173
           VYV       T+++L  +  S G   VV+ +   +  +  +   +A V  A E+     L
Sbjct: 58  VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRAN-GQSKGYAEVVVASENSVHKLL 116

Query: 174 N-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDERE 210
             L G +L    V V P+    L        + E  R 
Sbjct: 117 ELLPGKVLNGEKVDVRPATRQNLSQFEAQARKRECVRV 154

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 46.4 bits (110), Expect = 6e-07
 Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
           R +++  +  ++TE  +  L    G+V +  +    +     AF+E   E  A   +N
Sbjct: 17  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN----QAFIEMNTEEAANTMVN 70

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105

 Score = 42.5 bits (100), Expect = 1e-05
 Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           SR ++   +   V + EV         G+VT L +L         AF+E    E+A   +
Sbjct: 16  SRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLMLKGK----NQAFIEMNTEEAANTMV 69

Query: 273 NC---SGMVLGSQPIRVSPSK 290
           N       VL  QPI +  S 
Sbjct: 70  NYYTSVTPVLRGQPIYIQFSN 90

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101

 Score = 46.1 bits (110), Expect = 6e-07
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 6/87 (6%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFV 161
           SG +  +       +T+ +S++  + TEE L  +F     +   +V  + +   + +AF+
Sbjct: 3   SGSSGNSTWSGE-SKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFI 58

Query: 162 EFADEHGARAAL-NLGGTMLGYYPVRV 187
           EFA    A+ AL +     +    +R+
Sbjct: 59  EFASFEDAKEALNSCNKREIEGRAIRL 85

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 46.5 bits (111), Expect = 7e-07
 Identities = 18/100 (18%), Positives = 33/100 (33%), Gaps = 7/100 (7%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FA 159
                   ++D+    ++V  +  + T+  L   F   G + +  V  D  +  +   + 
Sbjct: 4   GSSGMHGSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQT-GKSRGYG 62

Query: 160 FVEFADEHGARAALNLGGTMLGYYPVRVLPSKTAILPVNP 199
           FV  AD   A  A      ++      V     A L   P
Sbjct: 63  FVTMADRAAAERACKDPNPIIDGRKANV---NLAYLGAKP 99

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87

 Score = 45.3 bits (108), Expect = 8e-07
 Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 4/69 (5%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFAD 165
           A + +     ++V  +  + +++ L   F+  G+VVDC +  DP++  R   F F+ F D
Sbjct: 4   ASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNT-GRSRGFGFILFKD 62

Query: 166 EHGARAALN 174
                  L+
Sbjct: 63  AASVEKVLD 71

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89

 Score = 45.3 bits (108), Expect = 9e-07
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEH 167
           +         V+V    +++T E L   F   G+VVD  +        R FAFV FAD+ 
Sbjct: 4   SHHHHHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPF----RAFAFVTFADDK 59

Query: 168 GARAALN 174
            A++   
Sbjct: 60  VAQSLCG 66

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97

 Score = 45.4 bits (108), Expect = 9e-07
 Identities = 14/83 (16%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 111 REDSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
           R   ++  +++ ++  +N+++E L  +FS  G ++   +         F F++F +    
Sbjct: 17  RGSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------KNAFGFIQFDNPQSV 70

Query: 170 RAALN-LGGTMLGYYPVRVLPSK 191
           R A+      M     + +  S 
Sbjct: 71  RDAIEXESQEMNFGKKLILEVSS 93

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 45.4 bits (108), Expect = 1e-06
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 1/80 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              +   N+   V   E+  FF        +      +    T  A V F   + A  A+
Sbjct: 15  PTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 74

Query: 273 N-CSGMVLGSQPIRVSPSKT 291
              +   +GS+ +++S   +
Sbjct: 75  IDLNDRPIGSRKVKLSGPSS 94

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 11/78 (14%), Positives = 27/78 (34%), Gaps = 3/78 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSVLR-FAFVEFADEHGARAALN- 174
            + V ++   ++ + +   F     +     +  +   +    A V F     A AA+  
Sbjct: 17  VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76

Query: 175 LGGTMLGYYPVRVLPSKT 192
           L    +G   V++    +
Sbjct: 77  LNDRPIGSRKVKLSGPSS 94

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 45.2 bits (107), Expect = 1e-06
 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
           R +++  +   +TE  +  L    G+V +  +    +     AF+E A E  A   +N
Sbjct: 16  RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKN----QAFLELATEEAAITMVN 69

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 101

 Score = 39.8 bits (93), Expect = 1e-04
 Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 9/81 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           SR ++   +  +V + EV         G+VT + +L         AF+E A  E+AI  +
Sbjct: 15  SRVLHIRKLPGEVTETEVIALGLPF--GKVTNILML----KGKNQAFLELATEEAAITMV 68

Query: 273 NCSGMV---LGSQPIRVSPSK 290
           N    V   L +QPI +  S 
Sbjct: 69  NYYSAVTPHLRNQPIYIQYSN 89

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens} Length = 95

 Score = 44.2 bits (105), Expect = 2e-06
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 4/62 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQ--VVDCRVCGDPHS-VLR-FAFVEFADEHGARAA 172
            T+ + +I  +   + +    S      V + R+  D  +   R FAFV+ +    A   
Sbjct: 10  DTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQL 69

Query: 173 LN 174
           L 
Sbjct: 70  LQ 71

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C Length = 90

 Score = 44.1 bits (105), Expect = 2e-06
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 15/82 (18%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHSVLR-------FAFVEFADE 166
           R  +Y+ ++    T+E L     S G   +++ +   +     R       FA V    E
Sbjct: 1   RIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFEN-----RANGQSKGFALVGVGSE 55

Query: 167 HGARAALN-LGGTMLGYYPVRV 187
             ++  ++ L    L      V
Sbjct: 56  ASSKKLMDLLPKRELHGQNPVV 77

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96

 Score = 44.1 bits (105), Expect = 3e-06
 Identities = 13/78 (16%), Positives = 33/78 (42%), Gaps = 8/78 (10%)

Query: 116 RRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL- 173
           +  +++ ++  +N+++E L  +FS  G ++   +         F F++F +    R A+ 
Sbjct: 10  KSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINI------KNAFGFIQFDNPQSVRDAIE 63

Query: 174 NLGGTMLGYYPVRVLPSK 191
                M     + +  S 
Sbjct: 64  CESQEMNFGKKLILEVSS 81

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 44.5 bits (105), Expect = 3e-06
 Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 4/58 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
           R +++  +  ++TE  +  L    G+V +  +    +     AF+E   E  A   +N
Sbjct: 32  RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKN----QAFIEMNTEEAANTMVN 85

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 119

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 21/81 (25%), Positives = 32/81 (39%), Gaps = 9/81 (11%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           SR ++   +   V + EV         G+VT L +    +     AF+E    E+A   +
Sbjct: 31  SRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLM----LKGKNQAFIEMNTEEAANTMV 84

Query: 273 NC---SGMVLGSQPIRVSPSK 290
           N       VL  QPI +  S 
Sbjct: 85  NYYTSVTPVLRGQPIYIQFSN 105

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 44.8 bits (106), Expect = 3e-06
 Identities = 23/126 (18%), Positives = 43/126 (34%), Gaps = 12/126 (9%)

Query: 79  QSAIDNFNNNRRRRNNFNQGR----KRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLA 134
            S  D   +    R    +GR    +  +   FR+         +YV ++ +++ E+ L 
Sbjct: 4   GSDSDEMPSECISRRELEKGRISREEMETLSVFRSYEPGEPNCRIYVKNLAKHVQEKDLK 63

Query: 135 GLFSSCGQVVDCRVCGDPHSVLR-------FAFVEFADEHGARAALN-LGGTMLGYYPVR 186
            +F                  L         AF+   +E  A  AL    G +L   P+ 
Sbjct: 64  YIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGKPMV 123

Query: 187 VLPSKT 192
           V  +++
Sbjct: 124 VQFARS 129

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 20/93 (21%), Positives = 38/93 (40%), Gaps = 7/93 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR-----IAFVEFAVAES 267
           +  +Y  N+ K V + ++K  F           R++ D            AF+     ++
Sbjct: 45  NCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMKEGRMKGQAFIGLPNEKA 104

Query: 268 AILALN-CSGMVLGSQPIRVSPSKTPVRPRVTR 299
           A  AL   +G VL  +P+ V  +++  RP+   
Sbjct: 105 AAKALKEANGYVLFGKPMVVQFARSA-RPKQDP 136

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111

 Score = 44.1 bits (104), Expect = 4e-06
 Identities = 10/81 (12%), Positives = 26/81 (32%), Gaps = 9/81 (11%)

Query: 116 RRTVYVSDIDQNITEE---RLAGLFSSCGQVVDCRVCGDPHSVLR-----FAFVEFADEH 167
           +  V+V  + Q + +    +    F   G++    +               A+V +    
Sbjct: 15  KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 74

Query: 168 GA-RAALNLGGTMLGYYPVRV 187
            A RA   +   ++    ++ 
Sbjct: 75  DALRAIQCVNNVVVDGRTLKA 95

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108

 Score = 43.6 bits (103), Expect = 5e-06
 Identities = 15/87 (17%), Positives = 23/87 (26%), Gaps = 6/87 (6%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
           S  +            V VS +  + + + L       G V    V  D         VE
Sbjct: 2   SSGSSGGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVE 56

Query: 163 FADEHGARAALN-LGGTMLGYYPVRVL 188
           F  +     A+  L  T    +     
Sbjct: 57  FVRKEDMTYAVRKLDNTKFRSHEGETA 83

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88

 Score = 43.0 bits (102), Expect = 6e-06
 Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 5/56 (8%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAAL 173
           V+V     ++TE+ L   FS  G V+D  +        R FAFV FAD+  A++  
Sbjct: 8   VFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPF----RAFAFVTFADDQIAQSLC 59

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 4/75 (5%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FA 159
           SG +            ++V  +D + T+E L   FS  G+VVDC +  D  +  +   F 
Sbjct: 3   SGSSGMNNSGADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTT-NQSRGFG 61

Query: 160 FVEFADEHGARAALN 174
           FV+F D +     L 
Sbjct: 62  FVKFKDPNCVGTVLA 76

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 102

 Score = 43.4 bits (103), Expect = 6e-06
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 9/89 (10%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FA 159
           SG +    R     +T++V  + ++ TEE L   F      V  R+  D  +      F 
Sbjct: 3   SGSSGPNARSQP-SKTLFVKGLSEDTTEETLKESF---DGSVRARIVTDRETG-SSKGFG 57

Query: 160 FVEFADEHGARAAL-NLGGTMLGYYPVRV 187
           FV+F  E  A+AA   +    +    V +
Sbjct: 58  FVDFNSEEDAKAAKEAMEDGEIDGNKVTL 86

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88

 Score = 42.8 bits (101), Expect = 7e-06
 Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 7/89 (7%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL 173
           S    + V ++ Q+   + +  L      +  C V        R AFV   +   A+ A+
Sbjct: 3   SGSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYV----DRNKRTAFVTLLNGEQAQNAI 57

Query: 174 -NLGGTMLGYYPVRVLPSKT-AILPVNPT 200
                       + V    T A+L   P+
Sbjct: 58  QMFHQYSFRGKDLIVQLQPTDALLCSGPS 86

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75

 Score = 42.1 bits (100), Expect = 9e-06
 Identities = 12/57 (21%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAAL 173
           ++V  +  +  EE++   F   G+V    +  D  +  R  F F+ F +E   +  +
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM 58

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111

 Score = 42.5 bits (100), Expect = 2e-05
 Identities = 11/101 (10%), Positives = 23/101 (22%), Gaps = 4/101 (3%)

Query: 88  NRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCR 147
                ++ +       G           R  + + ++ +  + + L  L           
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMSKLPAKRYR--ITMKNLPEGCSWQDLKDLARENSLETTFS 59

Query: 148 VCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV 187
                        +EF  E     AL  L         + V
Sbjct: 60  SVNT-RDFDGTGALEFPSEEILVEALERLNNIEFRGSVITV 99

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 15/69 (21%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFAD 165
            +R       + V  +    TE+ L   FS+ G+V+  +V  D  +      F FV F +
Sbjct: 8   VKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTG-HSKGFGFVRFTE 66

Query: 166 EHGARAALN 174
                  ++
Sbjct: 67  YETQVKVMS 75

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114

 Score = 41.8 bits (98), Expect = 2e-05
 Identities = 11/88 (12%), Positives = 27/88 (30%), Gaps = 5/88 (5%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG 177
           V    +   ++  +L  +   CG V    +  +      ++F  +     ++ A   L G
Sbjct: 30  VANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP----YSFARYRTTEESKRAYVTLNG 85

Query: 178 TMLGYYPVRVLPSKTAILPVNPTFLPRS 205
             +     + +      +       P S
Sbjct: 86  KEVVDDLGQKITLYLNFVEKVQWSGPSS 113

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115

 Score = 41.7 bits (98), Expect = 3e-05
 Identities = 19/88 (21%), Positives = 28/88 (31%), Gaps = 9/88 (10%)

Query: 104 GRAFRAQREDSVRRT---VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAF 160
           G A R +     RR+   V VS +  + + + L       G V    V  D         
Sbjct: 1   GGAPRGRYGPPSRRSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGV 55

Query: 161 VEFADEHGARAALN-LGGTMLGYYPVRV 187
           VEF  +     A+  L  T    +    
Sbjct: 56  VEFVRKEDMTYAVRKLDNTKFRSHEGET 83

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A Length = 130

 Score = 41.9 bits (98), Expect = 3e-05
 Identities = 21/108 (19%), Positives = 36/108 (33%), Gaps = 5/108 (4%)

Query: 93  NNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP 152
            N        +  A  A    S    + V ++   +T + L  +FS  G V+        
Sbjct: 5   GNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN 64

Query: 153 HSVLRFAFVEFADEHGARAALNLGGTM---LGYYPVRVLPSKTAILPV 197
           +     A +++AD   A+ A               +R+  SK   L V
Sbjct: 65  NQF--QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNV 110

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240

 Score = 43.2 bits (101), Expect = 3e-05
 Identities = 23/124 (18%), Positives = 39/124 (31%), Gaps = 18/124 (14%)

Query: 74  ADDNKQSAIDNFNNNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNIT---- 129
            +D  + A+     +   R  F   R+ + G            +T+YV  ID  +     
Sbjct: 96  EEDIGKLALRTEVLDCFGREKFADYREDMGG----IGSFRKKNKTLYVGGIDGALNSKHL 151

Query: 130 -----EERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA-RAALNLGGTMLGYY 183
                E R+  +FS  G +   R            FV+F  +  A  A   +    L   
Sbjct: 152 KPAQIESRIRFVFSRLGDIDRIRY----VESKNCGFVKFKYQANAEFAKEAMSNQTLLLP 207

Query: 184 PVRV 187
             + 
Sbjct: 208 SDKE 211

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75

 Score = 39.8 bits (94), Expect = 5e-05
 Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 2/61 (3%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARAALNLG 176
           ++V  +  N T E +   F   G+V D  +  D  +     F FV F  E        + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 177 G 177
            
Sbjct: 62  F 62

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116

 Score = 40.7 bits (96), Expect = 6e-05
 Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 4/70 (5%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFA 164
           R +RE    R +++  +    TEE L   +   G++ DC V  DP S  R   F FV F+
Sbjct: 19  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK-RSRGFGFVTFS 77

Query: 165 DEHGARAALN 174
                 AA+ 
Sbjct: 78  SMAEVDAAMA 87

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 43.3 bits (101), Expect = 7e-05
 Identities = 32/165 (19%), Positives = 58/165 (35%), Gaps = 39/165 (23%)

Query: 25  LETK-KSESEFTV-QKLVDMFTKL-----NPLAKEFFPSYYHQHTDHHFSVINNNFADDN 77
           LE K K E+E+ + + +VD +        + L   +   Y++ H  HH   I +      
Sbjct: 433 LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEH------ 486

Query: 78  KQSAIDNFNNNRRRRNNFN--QGRKRLSGRAFRAQREDSVRRTV--------YVSDIDQN 127
                +     R    +F   + + R    A+ A    S+  T+        Y+ D D  
Sbjct: 487 ----PERMTLFRMVFLDFRFLEQKIRHDSTAWNAS--GSILNTLQQLKFYKPYICDND-P 539

Query: 128 ITEERLAGL--FS-SCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
             E  +  +  F     + +   +C     +LR A +    E  A
Sbjct: 540 KYERLVNAILDFLPKIEENL---ICSKYTDLLRIALM---AEDEA 578

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A Length = 164

 Score = 41.6 bits (97), Expect = 7e-05
 Identities = 26/125 (20%), Positives = 45/125 (36%), Gaps = 6/125 (4%)

Query: 77  NKQSAIDNFN-NNRRRRNNFNQGRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAG 135
           +  SA       N  +  N        +  A  A    S    + V ++   +T + L  
Sbjct: 6   HHGSAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQ 65

Query: 136 LFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NLGGTML--GYYPVRVLPSKT 192
           +FS  G V+        +     A +++AD   A+ A  +L G  +      +R+  SK 
Sbjct: 66  IFSKFGTVLKIITFTKNNQF--QALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL 123

Query: 193 AILPV 197
             L V
Sbjct: 124 TSLNV 128

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109

 Score = 40.3 bits (95), Expect = 7e-05
 Identities = 20/70 (28%), Positives = 29/70 (41%), Gaps = 4/70 (5%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFA 164
           R     S    +++  +    T+E L   F   G+V +C V  DP +  R   F FV F 
Sbjct: 17  RGSHMGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT-KRSRGFGFVTFM 75

Query: 165 DEHGARAALN 174
           D+ G    L 
Sbjct: 76  DQAGVDKVLA 85

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77

 Score = 39.0 bits (92), Expect = 1e-04
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAALN 174
           +++  +    T+E L   F   G+V +C V  DP +  R   F FV F D+ G    L 
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLT-KRSRGFGFVTFMDQAGVDKVLA 60

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A* Length = 437

 Score = 41.8 bits (97), Expect = 2e-04
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAA 172
           +T++V+ ++ + TE +L   F   G +    +     S     +AF+E+  E    +A
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114

 Score = 39.2 bits (91), Expect = 2e-04
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 4/75 (5%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR----FAFVEFADEHGARAA 172
           R V+V  +  +I E+ +   F   G +V                 +AF+ F +E   +A 
Sbjct: 9   RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQAL 68

Query: 173 LNLGGTMLGYYPVRV 187
           ++      G   + V
Sbjct: 69  IDACLEEDGKLYLCV 83

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105

 Score = 38.2 bits (89), Expect = 4e-04
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 7/82 (8%)

Query: 107 FRAQREDSVRRTVYVSDI------DQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAF 160
            R Q  D +   + V ++           +  +  +FS  G++ +     +      + F
Sbjct: 6   DRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIF 65

Query: 161 VEFADEHGARAAL-NLGGTMLG 181
           +E+A    A  A+ N  G  L 
Sbjct: 66  LEYASPAHAVDAVKNADGYKLD 87

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100

 Score = 37.4 bits (87), Expect = 7e-04
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 3/65 (4%)

Query: 120 YVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL-NLG 176
            +      + ++ L  LFS  G+VV+     D  +     F FVE    + A+  + +  
Sbjct: 16  VIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFH 75

Query: 177 GTMLG 181
           G  L 
Sbjct: 76  GKRLD 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	303
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	100.0
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	100.0
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	100.0
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	100.0
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	100.0
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	100.0
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	100.0
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	100.0
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	100.0
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	100.0
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	100.0
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	100.0
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	100.0
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	100.0
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.98
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.98
2ghp_A	292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.98
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.97
4f02_A	213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.97
3smz_A	284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.97
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.97
3md3_A	166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.97
3nmr_A	175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.96
1b7f_A	168	Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP	99.96
2cjk_A	167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.96
2qfj_A	216	FBP-interacting repressor; protein-DNA complex; HE	99.96
1l3k_A	196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.96
1fxl_A	167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.96
2g4b_A	172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.94
3tyt_A	205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.94
1fje_B	175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.94
2yh0_A	198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.94
3pgw_A	282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.93
2adc_A	229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.93
1qm9_A	198	Polypyrimidine tract-binding protein; ribonucleopr	99.93
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.92
3sde_A	261	Paraspeckle component 1; RRM, anti parallel right	99.92
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.9
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.89
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
4fxv_A	99	ELAV-like protein 1; RNA recognition motif, putati	99.83
2kn4_A	158	Immunoglobulin G-binding protein G, splicing FACT	99.81
4f25_A	115	Polyadenylate-binding protein 1; RRM fold, transla	99.79
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.79
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.79
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.79
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.79
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.79
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.78
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.78
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.78
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.78
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.78
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.78
2lxi_A	91	RNA-binding protein 10; NMR {Homo sapiens}	99.78
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.78
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.78
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.77
2cqi_A	103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.77
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.77
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.77
2cq3_A	103	RNA-binding protein 9; RRM domain, structural geno	99.77
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.77
3s8s_A	110	Histone-lysine N-methyltransferase SETD1A; chromat	99.77
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.77
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.77
2dgo_A	115	Cytotoxic granule-associated RNA binding protein 1	99.76
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.76
2lkz_A	95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.76
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.76
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.76
3p5t_L	90	Cleavage and polyadenylation specificity factor S;	99.76
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.76
3bs9_A	87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.76
2dgs_A	99	DAZ-associated protein 1; RRM domain, structural g	99.76
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.76
2dnz_A	95	Probable RNA-binding protein 23; RNA recognition m	99.76
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.76
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.76
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.76
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.76
2cq0_A	103	Eukaryotic translation initiation factor 3 subunit	99.76
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.76
3md1_A	83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.76
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.76
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.76
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
2lea_A	135	Serine/arginine-rich splicing factor 2; SR protein	99.75
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.75
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.75
1whw_A	99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.75
2do4_A	100	Squamous cell carcinoma antigen recognized by T- c	99.75
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.75
2dnh_A	105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.75
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.75
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.75
2cpz_A	115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.75
1x5u_A	105	Splicing factor 3B subunit 4 (spliceosome associat	99.75
2dgv_A	92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.75
2d9p_A	103	Polyadenylate-binding protein 3; RRM domain, struc	99.75
2cpf_A	98	RNA binding motif protein 19; RNA recognition moti	99.75
2dgx_A	96	KIAA0430 protein; RRM domain, structural genomics,	99.75
2i2y_A	150	Fusion protein consists of immunoglobin G- binding	99.75
1x5t_A	96	Splicing factor 3B subunit 4; structure genomics,	99.75
3mdf_A	85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.75
2dnm_A	103	SRP46 splicing factor; RRM domain, RBD, structural	99.75
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.75
2x1f_A	96	MRNA 3'-END-processing protein RNA15; transcriptio	99.75
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.74
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.74
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.74
2cqb_A	102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.74
2fy1_A	116	RNA-binding motif protein, Y chromosome, family 1	99.74
2err_A	109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.74
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.74
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
1oo0_B	110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.74
1x5s_A	102	Cold-inducible RNA-binding protein; structure geno	99.74
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.74
2cph_A	107	RNA binding motif protein 19; RNA recognition moti	99.74
2cqc_A	95	Arginine/serine-rich splicing factor 10; RNA recog	99.74
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.74
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.74
1p27_B	106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.74
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.74
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.74
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.74
2div_A	99	TRNA selenocysteine associated protein; structural	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.74
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.74
2jrs_A	108	RNA-binding protein 39; RNA binding motif of RBM39	99.74
1x4h_A	111	RNA-binding protein 28; structural genomics, RRM d	99.74
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.74
3ucg_A	89	Polyadenylate-binding protein 2; ferredoxin-like,	99.74
2e5h_A	94	Zinc finger CCHC-type and RNA-binding motif- conta	99.73
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.73
1x4a_A	109	Splicing factor, arginine/serine-rich 1 (splicing	99.73
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.73
2ywk_A	95	Putative RNA-binding protein 11; RRM-domain, struc	99.73
2div_A	99	TRNA selenocysteine associated protein; structural	99.73
4a8x_A	88	RNA-binding protein with serine-rich domain 1; tra	99.73
1s79_A	103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.73
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.73
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.73
2do0_A	114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.73
2cqd_A	116	RNA-binding region containing protein 1; RNA recog	99.73
2dhg_A	104	TRNA selenocysteine associated protein (SECP43); R	99.73
2dgp_A	106	Bruno-like 4, RNA binding protein; RRM domain, str	99.73
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.73
2dng_A	103	Eukaryotic translation initiation factor 4H; RRM d	99.73
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.73
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.73
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.72
3pgw_S	437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.72
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.72
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.72
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.72
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.72
2la6_A	99	RNA-binding protein FUS; structural genomics, nort	99.72
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.72
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.72
2wbr_A	89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.72
1sjq_A	105	Polypyrimidine tract-binding protein 1; babbab mot	99.72
3s7r_A	87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.72
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.72
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.72
3ns6_A	100	Eukaryotic translation initiation factor 3 subuni;	99.72
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.72
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.72
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.72
2cpi_A	111	CCR4-NOT transcription complex subunit 4; RNA reco	99.72
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.72
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.72
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.71
2dh8_A	105	DAZ-associated protein 1; RRM domain, structural g	99.71
3r27_A	100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.71
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.71
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.71
2cpe_A	113	RNA-binding protein EWS; RNA recognition motif, RR	99.71
2cqg_A	103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.71
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.71
2khc_A	118	Testis-specific RNP-type RNA binding protein; RRM,	99.71
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.71
1x4d_A	102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.71
1u6f_A	139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.71
1wez_A	102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.71
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.71
2jvr_A	111	Nucleolar protein 3; RNA recognition motif, nucleu	99.71
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.71
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.71
2cq1_A	101	PTB-like protein L; RRM domain, structural genomic	99.71
3ulh_A	107	THO complex subunit 4; nuclear protein, RNA bindin	99.71
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.71
2kxn_B	129	Transformer-2 protein homolog beta; SR protein, RR	99.71
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.71
2nlw_A	105	Eukaryotic translation initiation factor 3 subunit	99.7
2hvz_A	101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.7
2dnq_A	90	RNA-binding protein 4B; RRM domain,RBD, structural	99.7
1p1t_A	104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.7
1wi8_A	104	EIF-4B, eukaryotic translation initiation factor 4	99.7
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.7
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.7
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.7
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.7
2rs2_A	109	Musashi-1, RNA-binding protein musashi homolog 1;	99.7
2mss_A	75	Protein (musashi1); RNA-binding domain, RNA bindin	99.7
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.7
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.7
2dis_A	109	Unnamed protein product; structural genomics, RRM	99.7
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.7
3n9u_C	156	Cleavage and polyadenylation specificity factor S;	99.7
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.7
2cqp_A	98	RNA-binding protein 12; RNA recognition motif, RRM	99.7
1x4b_A	116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.7
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.7
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.7
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.7
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.7
1x4g_A	109	Nucleolysin TIAR; structural genomics, RRM domain,	99.7
2jwn_A	124	Embryonic polyadenylate-binding protein 2-B; epabp	99.7
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.7
1h2v_Z	156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.7
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.7
2ad9_A	119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.7
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.69
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.69
2cpy_A	114	RNA-binding protein 12; RRM domain, structural gen	99.69
2kt5_A	124	RNA and export factor-binding protein 2; chaperone	99.69
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.69
3ex7_B	126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.69
1x4c_A	108	Splicing factor, arginine/serine-rich 1; structura	99.69
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.69
2krb_A	81	Eukaryotic translation initiation factor 3 subunit	99.69
2jvo_A	108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.69
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.69
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.69
2ki2_A	90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.69
2j76_E	100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.69
2cq4_A	114	RNA binding motif protein 23; RRM domain, structur	99.69
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.69
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.69
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.69
2ek1_A	95	RNA-binding protein 12; RNA recognition motif, dim	99.68
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.68
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.68
2a3j_A	127	U1 small nuclear ribonucleoprotein A; computationa	99.68
1x4e_A	85	RNA binding motif, single-stranded interacting pro	99.68
1rk8_A	165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.68
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.68
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.68
1x5o_A	114	RNA binding motif, single-stranded interacting pro	99.68
1why_A	97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.68
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.68
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.68
2fc9_A	101	NCL protein; structure genomics, RRM_1 domain, str	99.68
2m2b_A	131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.68
2dnp_A	90	RNA-binding protein 14; RRM domain, RBD, structura	99.68
2cpj_A	99	Non-POU domain-containing octamer-binding protein;	99.67
2dgt_A	92	RNA-binding protein 30; RRM domain, structural gen	99.67
2xnq_A	97	Nuclear polyadenylated RNA-binding protein 3; tran	99.67
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.67
1wg5_A	104	Heterogeneous nuclear ribonucleoprotein H; structu	99.67
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.67
1wex_A	104	Hypothetical protein (riken cDNA 2810036L13); stru	99.67
2dgw_A	91	Probable RNA-binding protein 19; RRM domain, struc	99.67
1iqt_A	75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.67
2db1_A	118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.67
2e5j_A	97	Methenyltetrahydrofolate synthetase domain contain	99.67
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.67
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.67
2dnn_A	109	RNA-binding protein 12; RRM domain, RBD, structura	99.67
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.67
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.67
2ytc_A	85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.66
1uaw_A	77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.66
2ku7_A	140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.66
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.66
3lqv_A	115	PRE-mRNA branch site protein P14; cysless mutant,	99.66
2dgu_A	103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.66
2cpd_A	99	Apobec-1 stimulating protein; RNA recognition moti	99.66
1nu4_A	97	U1A RNA binding domain; RNA recognition motif, U1	99.66
2kvi_A	96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.66
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.66
2hgl_A	136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.65
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.65
1fj7_A	101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.65
1wf1_A	110	RNA-binding protein RALY; structural genomics, RRM	99.65
2lmi_A	107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.65
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.65
2hgn_A	139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.65
1whx_A	111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.64
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.64
2cpx_A	115	Hypothetical protein FLJ11016; RRM domain, structu	99.64
1fjc_A	96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.64
2cqh_A	93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.64
2fc8_A	102	NCL protein; structure genomics, RRM_1 domain, str	99.64
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.64
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.64
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.64
2la4_A	101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.64
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.63
2xs2_A	102	Deleted in azoospermia-like; RNA binding protein-R	99.63
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.63
3q2s_C	229	Cleavage and polyadenylation specificity factor S;	99.63
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.63
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.43
1x5p_A	97	Negative elongation factor E; structure genomics,	99.62
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.62
1wel_A	124	RNA-binding protein 12; structural genomics, NPPSF	99.62
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.62
2cq2_A	114	Hypothetical protein LOC91801; RRM domain, structu	99.62
1x4f_A	112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.62
3egn_A	143	RNA-binding protein 40; RNA recognition motif (RRM	99.62
2lcw_A	116	RNA-binding protein FUS; RRM, nucleic acid binding	99.41
2e5g_A	94	U6 snRNA-specific terminal uridylyltransferase 1;	99.61
2e44_A	96	Insulin-like growth factor 2 mRNA binding protein	99.61
2dha_A	123	FLJ20171 protein; RRM domain, structural genomics,	99.61
3beg_B	115	Splicing factor, arginine/serine-rich 1; kinase, S	99.61
3zzy_A	130	Polypyrimidine tract-binding protein 1; protein bi	99.6
1x5p_A	97	Negative elongation factor E; structure genomics,	99.6
1sjr_A	164	Polypyrimidine tract-binding protein 1; extended b	99.6
2f3j_A	177	RNA and export factor binding protein 2; RRM domai	99.6
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.6
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.6
2hgm_A	126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.6
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.59
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.59
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.59
1wg1_A	88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.59
1wf0_A	88	TDP-43, TAR DNA-binding protein-43; structural gen	99.59
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.59
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.59
3d2w_A	89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.58
2diu_A	96	KIAA0430 protein; structural genomics, RRM domain,	99.58
2voo_A	193	Lupus LA protein; RNA-binding protein, RNA recogni	99.58
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.57
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.57
2e5i_A	124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.56
2pe8_A	105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.56
2bz2_A	121	Negative elongation factor E; NELF E, RNA recognit	99.56
2dnl_A	114	Cytoplasmic polyadenylation element binding protei	99.56
2hzc_A	87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.53
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.52
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.52
2dit_A	112	HIV TAT specific factor 1 variant; structural geno	99.5
2j8a_A	136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.5
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.49
3u1l_A	240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.49
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.47
3v4m_A	105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.45
1jmt_A	104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.44
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.42
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.41
3ue2_A	118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.39
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.32
2d9o_A	100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.32
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.31
3s6e_A	114	RNA-binding protein 39; ferredoxin-like, structura	99.31
3tht_A	345	Alkylated DNA repair protein ALKB homolog 8; struc	99.2
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.17
2dnr_A	91	Synaptojanin-1; RRM domain, RBD, structural genomi	99.03
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	99.01
1owx_A	121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.96
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.94
1ufw_A	95	Synaptojanin 2; RNP domain, structural genomics, r	98.82
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.79
3dxb_A	222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.77
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.56
2l9w_A	117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	98.53
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	98.1
2dhx_A	104	Poly (ADP-ribose) polymerase family, member 10 var	97.99
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.79
1wey_A	104	Calcipressin 1; structural genomics, RRM domain, r	97.4
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.34
1wwh_A	119	Nucleoporin 35, nucleoporin; structural genomics,	97.27
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.2
1uw4_A	91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	97.16
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	97.08
1whv_A	100	Poly(A)-specific ribonuclease; RNA recognition mot	96.88
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.71
3ctr_A	101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	96.64
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	96.52
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.81
3p3d_A	132	Nucleoporin 53; structural genomics, PSI-2, protei	95.77
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	95.55
2l08_A	97	Regulator of nonsense transcripts 3A; NESG, nonsen	95.32
3pq1_A	464	Poly(A) RNA polymerase; nucleotidyl transferase, R	94.86
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	85.14
3d45_A	507	Poly(A)-specific ribonuclease PARN; CAP analogue,	83.9

>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=100.00  E-value=4.1e-44  Score=320.91  Aligned_cols=245  Identities=15%  Similarity=0.223  Sum_probs=199.7

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc-eeeeecchhhhhhchhhhccccchHHhhhhcccC
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH-HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQG   98 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~-~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g   98 (303)
                      ..+.+|||+|||+++|+++|+++|++||+|.+|+|+.+..+..+. ||+|     .+     .+    +|.+|+. +++ 
T Consensus        39 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f-----~~-----~~----~A~~A~~-~~~-  102 (292)
T 2ghp_A           39 RELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEF-----AR-----YD----GALAAIT-KTH-  102 (292)
T ss_dssp             ---CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEE-----SS-----HH----HHHHHHT-TTT-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEE-----CC-----HH----HHHHHHH-hCC-
Confidence            456689999999999999999999999999999999988765444 9999     88     88    8999994 665 


Q ss_pred             CCCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCC-ceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-h
Q 022058           99 RKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCG-QVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-L  175 (303)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l  175 (303)
                      .. +..+....  .....++|||+|||+++++++|+++|+.|| .|.+|.++.+..+ ++|||||+|.+.++|.+|+. |
T Consensus       103 ~~-~~g~~i~v--~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l  179 (292)
T 2ghp_A          103 KV-VGQNEIIV--SHLTECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKL  179 (292)
T ss_dssp             CE-ETTEECEE--EECCSCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHH
T ss_pred             cE-eCCcEEEE--EECCCCEEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeCCCCCcceEEEEEECCHHHHHHHHHHh
Confidence            11 11111111  122578999999999999999999999999 9999999988765 89999999999999999999 9


Q ss_pred             CCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCC---
Q 022058          176 GGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDH---  251 (303)
Q Consensus       176 ~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~---  251 (303)
                      ||..+.|++|.|.++.+......       ........++|||+|||.. +++++|+++|++|  |.|..|.|+++.   
T Consensus       180 ~g~~~~g~~l~v~~a~~~~~~~~-------~~~~~~~~~~l~v~nlp~~~~t~~~l~~~F~~~--G~v~~v~i~~~~~~t  250 (292)
T 2ghp_A          180 NGLKIEGYTLVTKVSNPLEKSKR-------TDSATLEGREIMIRNLSTELLDENLLRESFEGF--GSIEKINIPAGQKEH  250 (292)
T ss_dssp             TTCEETTEECEEEECCCC----------------CCTTTEEEEEEECTTTCCHHHHHHHHGGG--SCEEEEECCSCCC--
T ss_pred             CCCEeCCcEEEEEECCCCccccc-------ccccCCCCceEEEECCCcccCCHHHHHHHHhcc--CCeeEEEEEecCCcC
Confidence            99999999999999865432110       0122345689999999999 9999999999999  999999999984   


Q ss_pred             CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCCC
Q 022058          252 VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       252 ~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~~  292 (303)
                      |.++|||||+|.+.++|.+|+.|||..|+|+.|.|.|+++.
T Consensus       251 g~~~g~afV~F~~~~~A~~A~~l~g~~~~g~~i~V~~a~~k  291 (292)
T 2ghp_A          251 SFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLADKK  291 (292)
T ss_dssp             -CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEECCCC
T ss_pred             CCCceEEEEEeCCHHHHHHHHHhcCCEECCcEEEEEEecCC
Confidence            78899999999999999999999999999999999999864

>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=100.00  E-value=1.9e-43  Score=315.40  Aligned_cols=241  Identities=19%  Similarity=0.238  Sum_probs=203.1

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhcccCC
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGR   99 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~   99 (303)
                      ..+.+|||+|||+++|+++|+++|++|| |.+|++...+   ...||+|     .+     .+    +|.+|+..+++-.
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~~~~~---g~afV~f-----~~-----~~----~A~~A~~~l~~~~   81 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFVDKYK---GTAFVTL-----LN-----GE----QAEAAINAFHQSR   81 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEEETTT---TEEEEEE-----SS-----HH----HHHHHHHHHTTCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEEecCC---CEEEEEe-----CC-----HH----HHHHHHHHcCCCe
Confidence            4556899999999999999999999999 9999983221   1229999     88     88    9999999888711


Q ss_pred             CCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hC
Q 022058          100 KRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LG  176 (303)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~  176 (303)
                        +..+..... .....++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|+. +|
T Consensus        82 --~~g~~i~v~-~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~  158 (284)
T 3smz_A           82 --LRERELSVQ-LQPTDALLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLL  158 (284)
T ss_dssp             --ETTEECEEE-ECCCSCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHT
T ss_pred             --eCCeEEEEE-ecCCCCEEEEcCCCCcCCHHHHHHHHHhcCCeeEEEEEeeCCCCccceEEEEEECCHHHHHHHHHHhC
Confidence              111111111 1235689999999999999999999999999999999988654  79999999999999999997 99


Q ss_pred             CcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCC-CHHHHHHHhhhhcCcceeEEEEecCC-CCc
Q 022058          177 GTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKV-PQAEVKQFFEAACGGEVTRLRLLGDH-VHS  254 (303)
Q Consensus       177 g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~-t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~  254 (303)
                      |..+.|++|.|.++......           .......+|||+|||..+ ++++|+++|++|  |.|.++.|+++. |.+
T Consensus       159 ~~~~~g~~i~v~~a~~~~~~-----------~~~~~~~~l~v~nlp~~~~~~~~l~~~f~~~--G~i~~v~i~~~~~g~~  225 (284)
T 3smz_A          159 GKPLGPRTLYVHWTDAGQLT-----------PALLHSRCLCVDRLPPGFNDVDALCRALSAV--HSPTFCQLACGQDGQL  225 (284)
T ss_dssp             TCEETTEECEEEECCGGGCC-----------TTTTSCSEEEEECCCTTCCCHHHHHHHTCSS--SCCSEEEEEECSSCCE
T ss_pred             CCEeCCcEEEEEECCCCCCC-----------cccCCccEEEEecCCcccCCHHHHHHHhhCC--CCeEEEEEEECCCCCc
Confidence            99999999999998654321           112345899999999995 999999999999  999999999985 789


Q ss_pred             ccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          255 TRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       255 ~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      +|+|||+|.+.++|.+|+. |||..++|+.|.|.|+++...
T Consensus       226 ~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~~~~~  266 (284)
T 3smz_A          226 KGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGPP  266 (284)
T ss_dssp             EEEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCSSSC
T ss_pred             ccEEEEEeCCHHHHHHHHHHhCCCccCCeEEEEEEecCCCc
Confidence            9999999999999999999 999999999999999987654

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=100.00  E-value=8.5e-36  Score=255.38  Aligned_cols=164  Identities=27%  Similarity=0.424  Sum_probs=148.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++|+++|+++|+.||+|.+|+|++|..+  ++|||||+|.+.++|.+|+. +|+..+.|+.|++.++.
T Consensus        14 p~~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~~~~~~~~g~~i~~~~~~   93 (213)
T 4f02_A           14 PMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   93 (213)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCccccccceeCCHHHHHHHHHHhhhhhcCCccccccccc
Confidence            5689999999999999999999999999999999998765  78999999999999999998 99999999999999874


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA  271 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~A  271 (303)
                      ...            ........+|||+|||..+++++|+++|++|  |.|.+|.|++|.+.++|||||+|.+.++|.+|
T Consensus        94 ~~~------------~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~--G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~A  159 (213)
T 4f02_A           94 RDP------------SLRKSGVGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERA  159 (213)
T ss_dssp             CCT------------HHHHHCTTEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEEETTEEEEEEEEEESSHHHHHHH
T ss_pred             ccc------------cccccccccceECCcccccHHHHHHHHHhhc--CCeEEEEeeccCCCCceEEEEEeCCHHHHHHH
Confidence            221            1122245789999999999999999999999  99999999999888899999999999999999


Q ss_pred             HH-hCCceeCCeeeEEeecCCC
Q 022058          272 LN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       272 i~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      +. |||..|+|+.|+|.++++.
T Consensus       160 i~~lng~~~~g~~i~V~~a~~~  181 (213)
T 4f02_A          160 IEKMNGMLLNDRKVFVGRFKSR  181 (213)
T ss_dssp             HHHHTTCEETTEECEEEECCCH
T ss_pred             HHHhCCCEECCEEEEEEEcCCC
Confidence            98 9999999999999999763

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A

Probab=100.00  E-value=6.9e-35  Score=245.44  Aligned_cols=180  Identities=17%  Similarity=0.267  Sum_probs=148.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      ++...++|||+|||+++|+++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+.+++..+.|+.|.|.+
T Consensus         9 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~l~v~~   88 (196)
T 1l3k_A            9 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   88 (196)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEeCCHHHHHHHHhcCCCEECCEEeeeec
Confidence            4446889999999999999999999999999999999998764  79999999999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHH
Q 022058          190 SKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAES  267 (303)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~  267 (303)
                      +.......        ........++|||+|||..+++++|+++|++|  |.|..|.|+++.  |.++|||||+|.+.++
T Consensus        89 ~~~~~~~~--------~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~F~~~~~  158 (196)
T 1l3k_A           89 AVSREDSQ--------RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDHDS  158 (196)
T ss_dssp             CCC-------------------CCSEEEEECCTTTCCHHHHHHHHTTT--SCEEEEEEEECTTTCCEEEEEEEEESSHHH
T ss_pred             ccCccccc--------ccccCCCcceEEEeCCCCCCCHHHHHHHHhcC--CCeEEEEEeecCCCCCccceEEEEECCHHH
Confidence            75432111        11122345899999999999999999999999  999999999984  7899999999999999


Q ss_pred             HHHHHHhCCceeCCeeeEEeecCCCCCCCCCCCC
Q 022058          268 AILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG  301 (303)
Q Consensus       268 A~~Ai~l~g~~~~g~~l~v~~a~~~~~~r~~r~~  301 (303)
                      |.+|+.++|..++|+.|.|.++.+....+..+.+
T Consensus       159 A~~A~~~~~~~~~G~~i~v~~a~~k~~~~~~~~~  192 (196)
T 1l3k_A          159 VDKIVIQKYHTVNGHNCEVRKALSKQEMASASSS  192 (196)
T ss_dssp             HHHHHHCSCCEETTEECEEEECC-----------
T ss_pred             HHHHHHhCCcEECCEEEEEEecCChhHhcccccc
Confidence            9999997899999999999999877665544443

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.4e-35  Score=238.39  Aligned_cols=161  Identities=22%  Similarity=0.348  Sum_probs=146.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~  194 (303)
                      ++|||+|||+++++++|+++|+.||.|.++.++.++.+ ++|||||+|.+.++|.+|+. +||..+.|++|.|.++....
T Consensus         1 R~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~g~~i~v~~~~~~~   80 (166)
T 3md3_A            1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIVKINWAFQSQ   80 (166)
T ss_dssp             CEEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCCCC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEeCCHHHHHHHHHHcCCCccCCCeeEEEEcCCCC
Confidence            68999999999999999999999999999999998865 89999999999999999997 99999999999999975432


Q ss_pred             CCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHH
Q 022058          195 LPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILAL  272 (303)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai  272 (303)
                      .            ....+..+|||+|||..+++++|+++|++|  |.|.++.++++.  |.++|+|||+|.+.++|.+|+
T Consensus        81 ~------------~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~  146 (166)
T 3md3_A           81 Q------------SSSDDTFNLFVGDLNVNVDDETLRNAFKDF--PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM  146 (166)
T ss_dssp             C------------CCCTTCEEEEEESCCTTCCHHHHHHHHTTS--TTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHH
T ss_pred             C------------CCCCCCceEEECCCCCCCCHHHHHHHHhcc--CCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHH
Confidence            1            112345799999999999999999999999  999999999884  788999999999999999999


Q ss_pred             H-hCCceeCCeeeEEeecCC
Q 022058          273 N-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       273 ~-l~g~~~~g~~l~v~~a~~  291 (303)
                      . |||..++|+.|+|.||++
T Consensus       147 ~~l~g~~~~g~~i~v~~a~~  166 (166)
T 3md3_A          147 DSMQGQDLNGRPLRINWAAK  166 (166)
T ss_dssp             HHHTTCEETTEECEEEESCC
T ss_pred             HHhCCCccCCcEEEEEecCC
Confidence            8 999999999999999974

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=100.00  E-value=1.1e-34  Score=247.94  Aligned_cols=177  Identities=24%  Similarity=0.355  Sum_probs=150.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++++..+  ++|||||+|.+.++|.+|++ +|+..+.|+.|.|.++.
T Consensus        27 ~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~l~v~~~~  106 (216)
T 2qfj_A           27 IMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPS  106 (216)
T ss_dssp             HHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEESSHHHHHHHHHHHSSCCCC-CCCEEECCS
T ss_pred             cCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEeCCHHHHHHHHHHccCCeeCCeeEEEecCC
Confidence            5789999999999999999999999999999999998744  79999999999999999999 99999999999998864


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~  269 (303)
                      ...... +  ............++|||+|||..+++++|+++|++|  |.|.++.|+++.  |.++|||||+|.+.++|.
T Consensus       107 ~~~~~~-~--~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~g~~~g~afV~F~~~~~A~  181 (216)
T 2qfj_A          107 NIGQAQ-P--IIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAF--GKIKSATLARDPTTGKHKGYGFIEYEKAQSSQ  181 (216)
T ss_dssp             CCGGGH-H--HHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTS--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             Cccccc-h--hhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhcc--CCeeEEEEEecCCCCCcCceEEEEecCHHHHH
Confidence            321000 0  000001123456899999999999999999999999  999999999984  788999999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeecCCCCCCC
Q 022058          270 LALN-CSGMVLGSQPIRVSPSKTPVRPR  296 (303)
Q Consensus       270 ~Ai~-l~g~~~~g~~l~v~~a~~~~~~r  296 (303)
                      +|+. |||..|+|+.|+|.|++++..+.
T Consensus       182 ~A~~~l~g~~~~g~~i~V~~a~~~~~~~  209 (216)
T 2qfj_A          182 DAVSSMNLFDLGGQYLRVGKAVTPPMPL  209 (216)
T ss_dssp             HHHHHHTTCBCSSSBCEEEECSSCSSTT
T ss_pred             HHHHHccCCEeCCcEEEEEEecCCCCCC
Confidence            9999 99999999999999998875544

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A

Probab=100.00  E-value=1.4e-33  Score=231.64  Aligned_cols=159  Identities=22%  Similarity=0.413  Sum_probs=145.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      .+++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|+. +||..+.|++|.|.++.
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~   81 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYAR   81 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEECCHHHHHHHHHhcCCCEeCCcEEEEEecC
Confidence            4689999999999999999999999999999999998654  78999999999999999998 99999999999999985


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~  269 (303)
                      +...              .....+|||+|||..+++++|+++|++|  |.|..+.++++.  +.++|+|||+|.+.++|.
T Consensus        82 ~~~~--------------~~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~  145 (168)
T 1b7f_A           82 PGGE--------------SIKDTNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQ  145 (168)
T ss_dssp             CCSS--------------TTTTCEEEEESCCTTCCHHHHHHHHTSS--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHH
T ss_pred             CCcc--------------cCCCCCEEEeCCCCCCCHHHHHHhhhcC--CcEEEEEEEEcCCCCCcceEEEEEECCHHHHH
Confidence            4321              1244789999999999999999999999  999999999885  788999999999999999


Q ss_pred             HHHH-hCCceeCC--eeeEEeec
Q 022058          270 LALN-CSGMVLGS--QPIRVSPS  289 (303)
Q Consensus       270 ~Ai~-l~g~~~~g--~~l~v~~a  289 (303)
                      +|+. |||..+.|  +.|+|.||
T Consensus       146 ~A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          146 EAISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHHhcCCEecCCCeEEEEEeC
Confidence            9999 99999987  99999986

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A

Probab=100.00  E-value=2.9e-33  Score=229.13  Aligned_cols=158  Identities=25%  Similarity=0.425  Sum_probs=143.9

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      +++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|+. +||..+.|++|.|.++.+
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f~~~~~A~~a~~~l~~~~~~g~~l~v~~~~~   81 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEECCHHHHHHHHHHcCCCccCCceEEEEecCC
Confidence            689999999999999999999999999999999998743  78999999999999999998 999999999999999753


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                      ..              ......+|||+|||..+++++|+++|++|  |.|..+.++++.  |.++|+|||+|.+.++|.+
T Consensus        82 ~~--------------~~~~~~~l~v~nl~~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~  145 (167)
T 1fxl_A           82 SS--------------ASIRDANLYVSGLPKTMTQKELEQLFSQY--GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEE  145 (167)
T ss_dssp             CC--------------GGGTTCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             Cc--------------ccCCCCcEEECCCCCcCCHHHHHHHHHhc--CCEeEEEEEecCCCCCccceEEEEeCCHHHHHH
Confidence            21              12244789999999999999999999999  999999999885  6789999999999999999


Q ss_pred             HHH-hCCceeCCee--eEEeec
Q 022058          271 ALN-CSGMVLGSQP--IRVSPS  289 (303)
Q Consensus       271 Ai~-l~g~~~~g~~--l~v~~a  289 (303)
                      |+. |||..+.|+.  |+|.||
T Consensus       146 A~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          146 AIKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCccCCCccceEEEeC
Confidence            999 9999999965  888886

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C

Probab=100.00  E-value=1.2e-33  Score=231.87  Aligned_cols=161  Identities=16%  Similarity=0.286  Sum_probs=145.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.+++++.+  ++|||||+|.+.++|.+|+. ++..+.|+.|.|.++.+
T Consensus         2 ~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~i~v~~~~~   80 (167)
T 2cjk_A            2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK-TQHILDGKVIDPKRAIP   80 (167)
T ss_dssp             GGGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEESSTHHHHHHHH-SCCEETTEECCCEECCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEEccHHHHHHHHh-cccccCCeEcccccccc
Confidence            3689999999999999999999999999999999998653  89999999999999999999 35689999999988642


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                      .              .......+|||+|||..+++++|+++|++|  |.|.++.++.+.  |.++|||||+|.+.++|.+
T Consensus        81 ~--------------~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  144 (167)
T 2cjk_A           81 R--------------DEQDKTGKIFVGGIGPDVRPKEFEEFFSQW--GTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDR  144 (167)
T ss_dssp             H--------------HHHHHCEEEEEEEECTTCCHHHHHHHHHTT--SCCSEEECCCSSSSSTTSEEEEEEESSHHHHHH
T ss_pred             h--------------hhccCCCeEEECCCCCCCCHHHHHHHHHhC--ccEEEEEEEEcCCCCccceEEEEEECCHHHHHH
Confidence            1              112245789999999999999999999999  999999999984  7899999999999999999


Q ss_pred             HHHhCCceeCCeeeEEeecCCC
Q 022058          271 ALNCSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       271 Ai~l~g~~~~g~~l~v~~a~~~  292 (303)
                      |+++||..++|+.|+|.|++|.
T Consensus       145 A~~~~~~~~~g~~i~V~~a~pk  166 (167)
T 2cjk_A          145 VCQNKFIDFKDRKIEIKRAEPR  166 (167)
T ss_dssp             HHHCSEECSSSSCEEEEECCCC
T ss_pred             HHhCCCEEeCCeEEEEeecCCC
Confidence            9999999999999999999864

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A

Probab=100.00  E-value=1e-32  Score=227.73  Aligned_cols=161  Identities=22%  Similarity=0.303  Sum_probs=143.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcccC---CeeEE
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTMLG---YYPVR  186 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~---g~~i~  186 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++++..+    ++|||||+|.+.++|.+|++ +|+..+.   ++++.
T Consensus         2 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~~~~~~~~~~~~~~   81 (175)
T 3nmr_A            2 DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNALHNMKVLPGMHHPIQ   81 (175)
T ss_dssp             CCEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCCE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEECCHHHHHHHHHHhcCcEEccCCccceE
Confidence            4689999999999999999999999999999999998764    68999999999999999998 9998876   68888


Q ss_pred             EeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCH
Q 022058          187 VLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVA  265 (303)
Q Consensus       187 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~  265 (303)
                      +.++.....             .....++|||+|||..+++++|+++|++|  |.|.++.++++. |.++|||||+|.+.
T Consensus        82 ~~~~~~~~~-------------~~~~~~~l~v~nl~~~~t~~~l~~~F~~~--G~i~~v~~~~~~~g~~~g~afV~f~~~  146 (175)
T 3nmr_A           82 MKPADSEKN-------------NAVEDRKLFIGMISKKCTENDIRVMFSSF--GQIEECRILRGPDGLSRGCAFVTFTTR  146 (175)
T ss_dssp             EEECGGGCC-------------SCGGGSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTSCEEEEEEEEESSH
T ss_pred             Ecccccccc-------------ccCCCCeEEEcCCCCcCCHHHHHHHHHhC--CCEEEEEEEECCCCCEEEEEEEEECCH
Confidence            887643221             12245789999999999999999999999  999999999985 78899999999999


Q ss_pred             HHHHHHHH-hCCceeC---CeeeEEeecC
Q 022058          266 ESAILALN-CSGMVLG---SQPIRVSPSK  290 (303)
Q Consensus       266 e~A~~Ai~-l~g~~~~---g~~l~v~~a~  290 (303)
                      ++|.+|+. |||..+.   ++.|+|.||.
T Consensus       147 ~~A~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          147 AMAQTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHHHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99999998 9998776   4999999984

>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=100.00  E-value=1.3e-32  Score=234.24  Aligned_cols=170  Identities=17%  Similarity=0.205  Sum_probs=141.3

Q ss_pred             CCCEEEEcCCC-CCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp-~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .+++|||+||| +.+++++|+++|+.||.|.+|+++++   ++|||||+|.+.++|++||+ |||..+.|++|.|.+++.
T Consensus         3 ~~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~---~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~~s~~   79 (205)
T 3tyt_A            3 DSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKS---KPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQ   79 (205)
T ss_dssp             CCSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTT---STTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CCCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecC---CCCEEEEEECCHHHHHHHHHHhCCCEECCceEEEEEccC
Confidence            46899999999 89999999999999999999999875   36999999999999999998 999999999999999864


Q ss_pred             CCC-CCCCCCC---------------CC-cc------cccccccceEEEcCCCCCCCHHHHHHHhhhhcCcce--eEEEE
Q 022058          193 AIL-PVNPTFL---------------PR-SE------DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEV--TRLRL  247 (303)
Q Consensus       193 ~~~-~~~~~~~---------------~~-~~------~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i--~~v~i  247 (303)
                      ... +..+...               .+ ..      .....+.++|||+|||+.+++++|+++|++|  |.|  ..+.+
T Consensus        80 ~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~--G~v~~~~v~~  157 (205)
T 3tyt_A           80 PAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDEL--GVKRPTSVKV  157 (205)
T ss_dssp             SCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHH--TCCCCSEEEE
T ss_pred             CccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhc--CCcceEEEEE
Confidence            321 1100000               00 00      0002346789999999999999999999999  999  89999


Q ss_pred             ecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCe----eeEEeec
Q 022058          248 LGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQ----PIRVSPS  289 (303)
Q Consensus       248 ~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~----~l~v~~a  289 (303)
                      .++.+.++|+|||+|.+.++|.+|+. |||..|.|+    .+.|+++
T Consensus       158 ~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          158 FSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             CSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             EcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            99887777999999999999999998 999999877    4666654

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=100.00  E-value=1.1e-31  Score=226.13  Aligned_cols=174  Identities=20%  Similarity=0.301  Sum_probs=145.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC----C-------ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSC----G-------QVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYY  183 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G-------~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~  183 (303)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+..    ++|||||+|.+.++|.+|+.|||..+.|+
T Consensus         3 ~~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~----~~g~afV~F~~~~~A~~Al~l~g~~~~g~   78 (198)
T 2yh0_A            3 MARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ----DKNFAFLEFRSVDETTQAMAFDGIIFQGQ   78 (198)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEET----TTTEEEEEESCSHHHHHHGGGTTEEETTE
T ss_pred             ceeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecC----CCCEEEEEeCCHHHHHHHHHhcCCEEcCc
Confidence            46899999999999999999999999    5       566666632    57999999999999999999999999999


Q ss_pred             eEEEeecCCCCCCCCCCCCCC------cccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcc
Q 022058          184 PVRVLPSKTAILPVNPTFLPR------SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHST  255 (303)
Q Consensus       184 ~i~v~~~~~~~~~~~~~~~~~------~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~  255 (303)
                      +|.|.++............+.      .........++|||+|||..+++++|+++|++|  |.|..+.+.++.  |.++
T Consensus        79 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~v~~~~~~~~~~~~~~~  156 (198)
T 2yh0_A           79 SLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSF--GPLKAFNLVKDSATGLSK  156 (198)
T ss_dssp             EEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTB--SCEEEEEEEECTTTCSEE
T ss_pred             eEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHc--CCccEEEEeecCCCCCcc
Confidence            999999865432111000000      011112456899999999999999999999999  999999999984  7889


Q ss_pred             cEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          256 RIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       256 g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      |||||+|.+.++|.+|+. |||..++|+.|+|.++++..+
T Consensus       157 g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  196 (198)
T 2yh0_A          157 GYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAK  196 (198)
T ss_dssp             EEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCCCC
T ss_pred             eEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCC
Confidence            999999999999999998 999999999999999987643

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A

Probab=100.00  E-value=8.9e-33  Score=228.67  Aligned_cols=164  Identities=19%  Similarity=0.250  Sum_probs=140.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCC-CCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP-HSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      .+...++|||+|||+++++++|+++|+.||.+..+.+.... ..++|||||+|.+.++|.+|++|||..+.|++|.|.++
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~v~~~   88 (175)
T 1fje_B            9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (175)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEECCHHHHHHHHhcCCCEeCCeEEEEecC
Confidence            44568999999999999999999999999987663222222 23789999999999999999999999999999999998


Q ss_pred             CCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHH
Q 022058          191 KTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~  270 (303)
                      .....            ......++|||+|||..+++++|+++|++|  |.|..+   ...+.++|||||+|.+.++|.+
T Consensus        89 ~~~~~------------~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~--g~v~~~---~~~~~~~g~afV~f~~~~~A~~  151 (175)
T 1fje_B           89 KGRDS------------KKVRAARTLLAKNLSFNITEDELKEVFEDA--LEIRLV---SQDGKSKGIAYIEFKSEADAEK  151 (175)
T ss_dssp             CCSSC------------STTGGGGEEEEESCCSSCCHHHHHHHCTTC--SEEEEE---CSSSSCCSEEEEECSSHHHHHH
T ss_pred             CCccc------------cccccCCEEEEeCCCCCCCHHHHHHHHHhc--CeEEEe---cCCCCCceEEEEEECCHHHHHH
Confidence            54321            112345899999999999999999999999  988877   4457899999999999999999


Q ss_pred             HHH-hCCceeCCeeeEEeecCCC
Q 022058          271 ALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       271 Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      |+. |||..++|+.|+|.|++|.
T Consensus       152 A~~~l~g~~~~g~~i~v~~a~~k  174 (175)
T 1fje_B          152 NLEEKQGAEIDGRSVSLYYTGEK  174 (175)
T ss_dssp             HHHHHTEEEETTEEEEEEECSSC
T ss_pred             HHHHhCCCEECCeEEEEEecCCC
Confidence            999 9999999999999999864

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A

Probab=100.00  E-value=1e-31  Score=221.45  Aligned_cols=155  Identities=21%  Similarity=0.340  Sum_probs=139.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC----C-------ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSC----G-------QVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYY  183 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G-------~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~  183 (303)
                      ..++|||+|||+++|+++|+++|+.|    |       .|.++.+..    ++|||||+|.+.++|.+|+.+|+..+.|+
T Consensus         3 ~~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~----~~g~afV~f~~~~~A~~A~~~~~~~~~g~   78 (172)
T 2g4b_A            3 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQ----DKNFAFLEFRSVDETTQAMAFDGIIFQGQ   78 (172)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEET----TTTEEEEEESSHHHHHHHGGGTTCEETTE
T ss_pred             cccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecC----CCCEEEEEeCCHHHHHHHHHhCCcEecCc
Confidence            36899999999999999999999999    6       777777754    36899999999999999999999999999


Q ss_pred             eEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEE
Q 022058          184 PVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVE  261 (303)
Q Consensus       184 ~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~  261 (303)
                      +|.|.++.....              .....+|||+|||..+++++|+++|++|  |.|..+.+++++  |.++|+|||+
T Consensus        79 ~i~v~~~~~~~~--------------~~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~g~~~g~afV~  142 (172)
T 2g4b_A           79 SLKIRRPHDYQP--------------LPGAHKLFIGGLPNYLNDDQVKELLTSF--GPLKAFNLVKDSATGLSKGYAFCE  142 (172)
T ss_dssp             ECEEECCSSCCC--------------CTTTTCEEEECCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTTCSEEEEEEEE
T ss_pred             eeeecCCcccCC--------------CCCCCEEEEEcCCCcCCHHHHHHHHHhc--CCceEEEEEecCCCCCcceEEEEE
Confidence            999998653221              1135889999999999999999999999  999999999984  7889999999


Q ss_pred             EcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          262 FAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       262 f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      |.+.++|.+|+. |||..++|+.|.|.||
T Consensus       143 f~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          143 YVDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             ESSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             eCCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            999999999998 9999999999999997

>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=99.98  E-value=3.8e-31  Score=228.88  Aligned_cols=173  Identities=25%  Similarity=0.333  Sum_probs=145.9

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+ ++++++|+++|+.||.|.+|+++.+.   +|||||+|.+.++|.+|++ +||..+.|++|.|.++
T Consensus        31 ~~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~---~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~v~~a  107 (229)
T 2adc_A           31 GAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLS  107 (229)
T ss_dssp             CCCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT---SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECC
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECC---CCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEe
Confidence            34689999999999 99999999999999999999999876   6899999999999999998 9999999999999998


Q ss_pred             CCCCCCCCC------------------CCCCCc---ccccccccceEEEcCCCCCCCHHHHHHHhhhhcCc-ceeEEEEe
Q 022058          191 KTAILPVNP------------------TFLPRS---EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGG-EVTRLRLL  248 (303)
Q Consensus       191 ~~~~~~~~~------------------~~~~~~---~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G-~i~~v~i~  248 (303)
                      .........                  .+....   ......+.++|||+|||..+++++|+++|++|  | .|..+.+.
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~~i~~v~i~  185 (229)
T 2adc_A          108 KHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSN--GGVVKGFKFF  185 (229)
T ss_dssp             SCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTT--SCCEEEEEEC
T ss_pred             cCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHc--CCCeeEEEEE
Confidence            654211000                  000000   00112346899999999999999999999999  9 99999997


Q ss_pred             cCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC-CeeeEEeecCCCC
Q 022058          249 GDHVHSTRIAFVEFAVAESAILALN-CSGMVLG-SQPIRVSPSKTPV  293 (303)
Q Consensus       249 ~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~-g~~l~v~~a~~~~  293 (303)
                      ++   ++|+|||+|.+.++|.+|+. |||..++ |+.|+|.|+++++
T Consensus       186 ~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~~i  229 (229)
T 2adc_A          186 QK---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI  229 (229)
T ss_dssp             SS---STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSSCC
T ss_pred             EC---CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecCCC
Confidence            64   24699999999999999999 9999999 9999999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.98  E-value=1.6e-31  Score=225.61  Aligned_cols=171  Identities=25%  Similarity=0.334  Sum_probs=144.7

Q ss_pred             CCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .+++|||+|||+ ++++++|+++|+.||.|.+|.++.+.   +|||||+|.+.++|.+|+. |||..+.|++|.|.++..
T Consensus         2 ~~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~---~g~afV~f~~~~~a~~A~~~l~~~~~~g~~l~v~~a~~   78 (198)
T 1qm9_A            2 GNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH   78 (198)
T ss_dssp             CCCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTC---SSCCEEECTTTHHHHHHHHHHTTCCCSSCCCEEEECCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCC---CCEEEEEECCHHHHHHHHHHhCCCeecCeEEEEEEecC
Confidence            468999999999 99999999999999999999998876   6899999999999999998 999999999999999865


Q ss_pred             CCCCCCC------------------CCCCCc---ccccccccceEEEcCCCCCCCHHHHHHHhhhhcCc-ceeEEEEecC
Q 022058          193 AILPVNP------------------TFLPRS---EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGG-EVTRLRLLGD  250 (303)
Q Consensus       193 ~~~~~~~------------------~~~~~~---~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G-~i~~v~i~~d  250 (303)
                      .......                  .+.+..   ......+.++|||+|||..+++++|+++|++|  | .|..+.+.++
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~--G~~v~~v~i~~~  156 (198)
T 1qm9_A           79 QNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSN--GGVVKGFKFFQK  156 (198)
T ss_dssp             CSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHT--TSCCCEEEESST
T ss_pred             CCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHc--CCCceEEEEEeC
Confidence            4211100                  000000   00112347899999999999999999999999  9 9999999775


Q ss_pred             CCCcccEEEEEEcCHHHHHHHHH-hCCceeC-CeeeEEeecCCCC
Q 022058          251 HVHSTRIAFVEFAVAESAILALN-CSGMVLG-SQPIRVSPSKTPV  293 (303)
Q Consensus       251 ~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~-g~~l~v~~a~~~~  293 (303)
                      .   +|+|||+|.+.++|.+|+. |||..++ |+.|+|.|+++++
T Consensus       157 ~---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~~i  198 (198)
T 1qm9_A          157 D---RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI  198 (198)
T ss_dssp             T---SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECCCC
T ss_pred             C---CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecccC
Confidence            3   5799999999999999999 9999999 9999999999864

>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=99.98  E-value=1.8e-31  Score=238.79  Aligned_cols=160  Identities=20%  Similarity=0.320  Sum_probs=141.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      .+...++|||+|||+++|+++|+++|+.||.|.+|.++.+..+++|||||+|.+.++|.+|+++|+..+.|++|.|.++ 
T Consensus        37 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~A~~A~~~~~~~~~g~~i~v~~~-  115 (292)
T 2ghp_A           37 RNRELTTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL-  115 (292)
T ss_dssp             -----CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC-
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcEEEEEEECCHHHHHHHHHhCCcEeCCcEEEEEEC-
Confidence            3446899999999999999999999999999999999998888899999999999999999999999999999999985 


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCc-ceeEEEEecCC-CCcccEEEEEEcCHHHHH
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGG-EVTRLRLLGDH-VHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G-~i~~v~i~~d~-~~~~g~afV~f~~~e~A~  269 (303)
                                          ..++|||+|||..+++++|+++|++|  | .|..|.++++. |.++|||||+|.+.++|.
T Consensus       116 --------------------~~~~l~v~nlp~~~t~~~l~~~f~~~--G~~i~~v~i~~~~~~~~~g~afV~f~~~~~a~  173 (292)
T 2ghp_A          116 --------------------TECTLWMTNFPPSYTQRNIRDLLQDI--NVVALSIRLPSLRFNTSRRFAYIDVTSKEDAR  173 (292)
T ss_dssp             --------------------CSCEEEEECCCTTCCHHHHHHHHHHT--TCCCCEEECC-------CCEEEEECSSHHHHH
T ss_pred             --------------------CCCEEEEECCCCCCCHHHHHHHHHHh--CCCeEEEEEEeCCCCCcceEEEEEECCHHHHH
Confidence                                23789999999999999999999999  9 99999999986 788999999999999999


Q ss_pred             HHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          270 LALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       270 ~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      +|+. |||..+.|+.|.|.++.|...
T Consensus       174 ~A~~~l~g~~~~g~~l~v~~a~~~~~  199 (292)
T 2ghp_A          174 YCVEKLNGLKIEGYTLVTKVSNPLEK  199 (292)
T ss_dssp             HHHHHHTTCEETTEECEEEECCCC--
T ss_pred             HHHHHhCCCEeCCcEEEEEECCCCcc
Confidence            9999 999999999999999987654

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A

Probab=99.97  E-value=1.1e-30  Score=232.45  Aligned_cols=173  Identities=24%  Similarity=0.359  Sum_probs=144.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHH----HHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 022058          112 EDSVRRTVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVR  186 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~  186 (303)
                      +....++|||+|||+++++++|+    ++|+.||.|.+|++++ ...++|||||+|.+.++|.+|++ |||..+.|+.|.
T Consensus         5 ~~~~~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~-~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   83 (282)
T 3pgw_A            5 ETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMR   83 (282)
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcC-CCCcceEEEEEECCHHHHHHHHHHhcCCeeCCcEEE
Confidence            34568999999999999999977    8999999999999986 23379999999999999999997 999999999999


Q ss_pred             EeecCCCCCCC---CCCCC-------------------------------------------------------------
Q 022058          187 VLPSKTAILPV---NPTFL-------------------------------------------------------------  202 (303)
Q Consensus       187 v~~~~~~~~~~---~~~~~-------------------------------------------------------------  202 (303)
                      |.++.......   ...+.                                                             
T Consensus        84 v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  163 (282)
T 3pgw_A           84 IQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPY  163 (282)
T ss_pred             EEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCcccccccccccCCCCCCC
Confidence            99985432100   00000                                                             


Q ss_pred             -------------CC--------------------cccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEec
Q 022058          203 -------------PR--------------------SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLG  249 (303)
Q Consensus       203 -------------~~--------------------~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~  249 (303)
                                   +.                    .........++|||+|||..+++++|+++|++|  |.|.+|.|.+
T Consensus       164 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~--G~i~~v~~~~  241 (282)
T 3pgw_A          164 MPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQF--PGFKEVRLVP  241 (282)
T ss_pred             CCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhc--CCeEEEEEec
Confidence                         00                    000122346889999999999999999999999  9999999997


Q ss_pred             CCCCcccEEEEEEcCHHHHHHHHH-hCCceeC-CeeeEEeecC
Q 022058          250 DHVHSTRIAFVEFAVAESAILALN-CSGMVLG-SQPIRVSPSK  290 (303)
Q Consensus       250 d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~-g~~l~v~~a~  290 (303)
                      +.   +|||||+|.+.++|.+|+. |||..+. |+.|+|.|++
T Consensus       242 ~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          242 GR---HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             CC---CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            75   4699999999999999999 9999999 9999999986

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*

Probab=99.97  E-value=4.6e-32  Score=232.12  Aligned_cols=156  Identities=19%  Similarity=0.286  Sum_probs=132.5

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc--
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ--   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~--   97 (303)
                      .+|||+|||+++|+++|+++|++||+|.+|+|++++.++.++   ||+|     .+     .+    +|.+|+..+++  
T Consensus        16 ~tlfVgnLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F-----~~-----~~----~A~~Ai~~~~~~~   81 (213)
T 4f02_A           16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNF-----QQ-----PA----DAERALDTMNFDV   81 (213)
T ss_dssp             CEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEE-----SS-----HH----HHHHHHHHHTTCE
T ss_pred             cEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEecccCCCCcccccccee-----CC-----HH----HHHHHHHHhhhhh
Confidence            379999999999999999999999999999999998766554   9999     88     78    89999998887  


Q ss_pred             --CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH
Q 022058           98 --GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN  174 (303)
Q Consensus        98 --g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~  174 (303)
                        |+. .+..............++|||+|||+++++++|+++|+.||.|.+|+|+++..+++|||||+|.+.++|.+|++
T Consensus        82 ~~g~~i~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~~~i~~d~~~~~g~~fV~f~~~~~a~~Ai~  161 (213)
T 4f02_A           82 IKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIE  161 (213)
T ss_dssp             ETTEECEEEECCCCTHHHHHCTTEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESSHHHHHHHHH
T ss_pred             cCCcccccccccccccccccccccceECCcccccHHHHHHHHHhhcCCeEEEEeeccCCCCceEEEEEeCCHHHHHHHHH
Confidence              332 11111111111122467899999999999999999999999999999999987799999999999999999998


Q ss_pred             -hCCcccCCeeEEEeecCC
Q 022058          175 -LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       175 -l~g~~~~g~~i~v~~~~~  192 (303)
                       |||..|.|++|.|.++.+
T Consensus       162 ~lng~~~~g~~i~V~~a~~  180 (213)
T 4f02_A          162 KMNGMLLNDRKVFVGRFKS  180 (213)
T ss_dssp             HHTTCEETTEECEEEECCC
T ss_pred             HhCCCEECCEEEEEEEcCC
Confidence             999999999999999854

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E

Probab=99.97  E-value=8.4e-30  Score=226.96  Aligned_cols=154  Identities=20%  Similarity=0.253  Sum_probs=141.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..+++|||+|||+++|+++|+++|+.|| |.+|.+    ..++|||||+|.+.++|.+|+. +||..+.|++|.|.++. 
T Consensus        20 ~~~~~l~V~nLp~~~te~~l~~~F~~~G-i~~~~~----~~~~g~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~~~-   93 (284)
T 3smz_A           20 RNRRKILIRGLPGDVTNQEVHDLLSDYE-LKYCFV----DKYKGTAFVTLLNGEQAEAAINAFHQSRLRERELSVQLQP-   93 (284)
T ss_dssp             HCCCEEEEECCCTTCCHHHHHHHTTTSC-EEEEEE----ETTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC-
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcC-CEEEEE----ecCCCEEEEEeCCHHHHHHHHHHcCCCeeCCeEEEEEecC-
Confidence            3678999999999999999999999999 999988    3367999999999999999998 99999999999999852 


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                                         ...+|||+|||..+++++|+++|++|  |.|..+.++.+.  |.++|||||+|.+.++|.+
T Consensus        94 -------------------~~~~l~v~nlp~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~  152 (284)
T 3smz_A           94 -------------------TDALLCVANLPPSLTQQQFEELVRPF--GSLERCFLVYSERTGQSKGYGFAEYMKKDSAAR  152 (284)
T ss_dssp             -------------------CSCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             -------------------CCCEEEEcCCCCcCCHHHHHHHHHhc--CCeeEEEEEeeCCCCccceEEEEEECCHHHHHH
Confidence                               23789999999999999999999999  999999999874  7899999999999999999


Q ss_pred             HHH-hCCceeCCeeeEEeecCCCCC
Q 022058          271 ALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       271 Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      |+. |||..++|+.|.|.++.+...
T Consensus       153 A~~~l~~~~~~g~~i~v~~a~~~~~  177 (284)
T 3smz_A          153 AKSDLLGKPLGPRTLYVHWTDAGQL  177 (284)
T ss_dssp             HHHHHTTCEETTEECEEEECCGGGC
T ss_pred             HHHHhCCCEeCCcEEEEEECCCCCC
Confidence            997 999999999999999976653

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B

Probab=99.97  E-value=7.5e-30  Score=225.05  Aligned_cols=156  Identities=27%  Similarity=0.388  Sum_probs=141.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++|+++|+++|+.||.|.+|.+.++    +|||||+|.+.++|.+|+. +||..+.|++|.|.++
T Consensus        18 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~----kg~afV~f~~~~~A~~A~~~l~g~~i~g~~l~v~~a   93 (261)
T 3sde_A           18 TYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD----RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFA   93 (261)
T ss_dssp             SSCGGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETT----TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCC----CcEEEEEECCHHHHHHHHHHcCCcEECCceeEeeec
Confidence            3446789999999999999999999999999999999653    6899999999999999998 9999999999999997


Q ss_pred             CCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHH
Q 022058          191 KTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAI  269 (303)
Q Consensus       191 ~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~  269 (303)
                      .+                    ..+|||+|||..+++++|+++|++|  |.|.+|.|+++. |.++|||||+|.+.++|.
T Consensus        94 ~~--------------------~~~l~v~nl~~~~t~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~  151 (261)
T 3sde_A           94 TH--------------------GAALTVKNLSPVVSNELLEQAFSQF--GPVEKAVVVVDDRGRATGKGFVEFAAKPPAR  151 (261)
T ss_dssp             CC--------------------SSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEEETTSCEEEEEEEEESSHHHHH
T ss_pred             cc--------------------CCcccccCCCCCCCHHHHHHHHHhc--CCeEEEEeeeCCCCCcCcEEEEEeCCHHHHH
Confidence            42                    3689999999999999999999999  999999999885 789999999999999999


Q ss_pred             HHHH-h-CCceeC---CeeeEEeecCCCC
Q 022058          270 LALN-C-SGMVLG---SQPIRVSPSKTPV  293 (303)
Q Consensus       270 ~Ai~-l-~g~~~~---g~~l~v~~a~~~~  293 (303)
                      +|+. | +|..+.   ++.|.|.++.+..
T Consensus       152 ~A~~~l~~~~~~~~~~~r~i~v~~~~~~~  180 (261)
T 3sde_A          152 KALERCGDGAFLLTTTPRPVIVEPMEQFD  180 (261)
T ss_dssp             HHHHHHHHSCEESSSSCCBCEEEECCCEE
T ss_pred             HHHHHhcCCeEEecCCCceEEEeeccccC
Confidence            9998 8 555554   9999999997653

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae}

Probab=99.97  E-value=1.9e-30  Score=212.13  Aligned_cols=154  Identities=16%  Similarity=0.196  Sum_probs=131.5

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhccc----
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ----   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~----   97 (303)
                      +|||+|||+++|+++|+++|++||+|.+|+++.++.++.++  ||+|     .+     .+    +|.+|+..+++    
T Consensus         2 ~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~g~afV~f-----~~-----~~----~a~~A~~~l~~~~~~   67 (166)
T 3md3_A            2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEY-----HQ-----SH----DANIALQTLNGKQIE   67 (166)
T ss_dssp             EEEEEEEETTCCHHHHHHHHGGGSCEEEEEEECCCC-CCEEEEEEEE-----SS-----HH----HHHHHHHHHTTCEET
T ss_pred             EEEECCCCCcCCHHHHHHHHHhcCCeEEEEEEECCCCCCCCEEEEEe-----CC-----HH----HHHHHHHHcCCCccC
Confidence            68999999999999999999999999999999998766554  9999     88     78    89999988887    


Q ss_pred             CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH
Q 022058           98 GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN  174 (303)
Q Consensus        98 g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~  174 (303)
                      |+. .+..............++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|+.
T Consensus        68 g~~i~v~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~A~~  147 (166)
T 3md3_A           68 NNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMD  147 (166)
T ss_dssp             TEECEEEECCCCCCCCCTTCEEEEEESCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHH
T ss_pred             CCeeEEEEcCCCCCCCCCCCceEEECCCCCCCCHHHHHHHHhccCCeeEEEEEecCCCCCcceEEEEEeCCHHHHHHHHH
Confidence            332 222211222233446788999999999999999999999999999999998654  78999999999999999998


Q ss_pred             -hCCcccCCeeEEEeecC
Q 022058          175 -LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       175 -l~g~~~~g~~i~v~~~~  191 (303)
                       |||..+.|++|.|.|++
T Consensus       148 ~l~g~~~~g~~i~v~~a~  165 (166)
T 3md3_A          148 SMQGQDLNGRPLRINWAA  165 (166)
T ss_dssp             HHTTCEETTEECEEEESC
T ss_pred             HhCCCccCCcEEEEEecC
Confidence             99999999999999975

>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=99.96  E-value=8.7e-30  Score=210.09  Aligned_cols=155  Identities=16%  Similarity=0.228  Sum_probs=129.0

Q ss_pred             CCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCC---CCc--eeeeecchhhhhhchhhhccccchHHhhhhccc
Q 022058           23 NNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQH---TDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ   97 (303)
Q Consensus        23 ~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~---~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~   97 (303)
                      .+|||+|||+++|+++|+++|++||+|.+|++++++.++   .++  ||+|     .+     .+    +|++|+..+++
T Consensus         4 ~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~~~g~afV~f-----~~-----~~----~A~~A~~~l~~   69 (175)
T 3nmr_A            4 IKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTF-----YT-----RK----AALEAQNALHN   69 (175)
T ss_dssp             EEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEECSSSSCEEEEEEEEEE-----SS-----HH----HHHHHHHHHTT
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCCCcceEEEEEE-----CC-----HH----HHHHHHHHhcC
Confidence            479999999999999999999999999999999998874   233  9999     88     78    89999988876


Q ss_pred             CC-----C-CCCch-hhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHH
Q 022058           98 GR-----K-RLSGR-AFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGA  169 (303)
Q Consensus        98 g~-----~-~~~~~-~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A  169 (303)
                      ..     . .+... ...........++|||+|||+++++++|+++|+.||.|.++.++.+..+ ++|||||+|.+.++|
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~~~~~~~g~~~g~afV~f~~~~~A  149 (175)
T 3nmr_A           70 MKVLPGMHHPIQMKPADSEKNNAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMA  149 (175)
T ss_dssp             TCCCTTCSSCCEEEECGGGCCSCGGGSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSHHHH
T ss_pred             cEEccCCccceEEccccccccccCCCCeEEEcCCCCcCCHHHHHHHHHhCCCEEEEEEEECCCCCEEEEEEEEECCHHHH
Confidence            21     1 11111 1111222336788999999999999999999999999999999998765 799999999999999


Q ss_pred             HHHHH-hCCcccC---CeeEEEeecC
Q 022058          170 RAALN-LGGTMLG---YYPVRVLPSK  191 (303)
Q Consensus       170 ~~Ai~-l~g~~~~---g~~i~v~~~~  191 (303)
                      .+|+. |||..+.   +++|.|.|++
T Consensus       150 ~~A~~~l~g~~~~~g~~~~l~V~~ad  175 (175)
T 3nmr_A          150 QTAIKAMHQAQTMEGCSSPMVVKFAD  175 (175)
T ss_dssp             HHHHHHHTTSCCCTTCSSCCEEEECC
T ss_pred             HHHHHHhcCCcccCCCCCCeEEEecC
Confidence            99998 9998776   4999999873

>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=99.96  E-value=1.6e-29  Score=207.32  Aligned_cols=155  Identities=19%  Similarity=0.310  Sum_probs=130.5

Q ss_pred             CCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc
Q 022058           21 KNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ   97 (303)
Q Consensus        21 ~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~   97 (303)
                      .+.+|||+|||+++|+++|+++|++||+|.+|++++++.++.++   ||+|     .+     .+    +|++|+..+++
T Consensus         2 ~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f-----~~-----~~----~A~~a~~~l~~   67 (168)
T 1b7f_A            2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDF-----TS-----EM----DSQRAIKVLNG   67 (168)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEE-----SS-----HH----HHHHHHHHHTT
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEeCCCCccceEEEEEE-----CC-----HH----HHHHHHHhcCC
Confidence            45689999999999999999999999999999999987654433   9999     88     78    89999988877


Q ss_pred             ----CCCCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHH
Q 022058           98 ----GRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARA  171 (303)
Q Consensus        98 ----g~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~  171 (303)
                          |+. +..............++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+
T Consensus        68 ~~~~g~~-l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~A~~  146 (168)
T 1b7f_A           68 ITVRNKR-LKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQE  146 (168)
T ss_dssp             CEETTEE-CEEEECCCCSSTTTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHH
T ss_pred             CEeCCcE-EEEEecCCCcccCCCCCEEEeCCCCCCCHHHHHHhhhcCCcEEEEEEEEcCCCCCcceEEEEEECCHHHHHH
Confidence                322 11111112223446789999999999999999999999999999999998743  78999999999999999


Q ss_pred             HHH-hCCcccCC--eeEEEeec
Q 022058          172 ALN-LGGTMLGY--YPVRVLPS  190 (303)
Q Consensus       172 Ai~-l~g~~~~g--~~i~v~~~  190 (303)
                      |+. |||..+.|  ++|.|.++
T Consensus       147 A~~~l~g~~~~g~~~~l~V~~A  168 (168)
T 1b7f_A          147 AISALNNVIPEGGSQPLSVRLA  168 (168)
T ss_dssp             HHHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHHhcCCEecCCCeEEEEEeC
Confidence            999 99999987  99999875

>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=99.96  E-value=3.5e-30  Score=211.12  Aligned_cols=155  Identities=11%  Similarity=0.127  Sum_probs=128.2

Q ss_pred             CCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc-
Q 022058           22 NNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-   97 (303)
Q Consensus        22 ~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-   97 (303)
                      +.+|||+|||+++|+++|+++|++||+|.+|++++++.++.++   ||+|     .+     .+    +|++|+...+. 
T Consensus         3 ~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f-----~~-----~~----~a~~A~~~~~~~   68 (167)
T 2cjk_A            3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF-----EK-----PS----SVDEVVKTQHIL   68 (167)
T ss_dssp             GGEEEECSCCTTCCHHHHHHHHTTTCCEEEEECCCCTTTSSCCSCEEEEE-----SS-----TH----HHHHHHHSCCEE
T ss_pred             CcEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEECCCCCCccceEEEEE-----cc-----HH----HHHHHHhccccc
Confidence            4489999999999999999999999999999999997654443   9999     77     77    88888876221 


Q ss_pred             -CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHH
Q 022058           98 -GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL  173 (303)
Q Consensus        98 -g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai  173 (303)
                       |+. .+.....  .......++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|+
T Consensus        69 ~g~~i~v~~~~~--~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~  146 (167)
T 2cjk_A           69 DGKVIDPKRAIP--RDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVC  146 (167)
T ss_dssp             TTEECCCEECCC--HHHHHHCEEEEEEEECTTCCHHHHHHHHHTTSCCSEEECCCSSSSSTTSEEEEEEESSHHHHHHHH
T ss_pred             CCeEcccccccc--hhhccCCCeEEECCCCCCCCHHHHHHHHHhCccEEEEEEEEcCCCCccceEEEEEECCHHHHHHHH
Confidence             333 1111111  111224678999999999999999999999999999999998643  8999999999999999999


Q ss_pred             HhCCcccCCeeEEEeecCC
Q 022058          174 NLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       174 ~l~g~~~~g~~i~v~~~~~  192 (303)
                      ++++..+.|++|.|.++.+
T Consensus       147 ~~~~~~~~g~~i~V~~a~p  165 (167)
T 2cjk_A          147 QNKFIDFKDRKIEIKRAEP  165 (167)
T ss_dssp             HCSEECSSSSCEEEEECCC
T ss_pred             hCCCEEeCCeEEEEeecCC
Confidence            9999999999999999864

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A

Probab=99.96  E-value=1.9e-29  Score=215.29  Aligned_cols=162  Identities=14%  Similarity=0.220  Sum_probs=132.3

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhcc
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFN   96 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~   96 (303)
                      ..+.+|||+|||+++|+++|+++|++||+|.+|+++.+..++..+   ||+|     .+     .+    +|.+|+..++
T Consensus        26 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~g~~~g~afV~f-----~~-----~~----~A~~A~~~l~   91 (216)
T 2qfj_A           26 AIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEY-----EV-----PE----AAQLALEQMN   91 (216)
T ss_dssp             HHHTEEEEECCCTTCCHHHHHHHHGGGSCEEEEEECCC-CC-CCCSEEEEEE-----SS-----HH----HHHHHHHHHS
T ss_pred             CcCCEEEEECCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccCceEEEEe-----CC-----HH----HHHHHHHHcc
Confidence            344589999999999999999999999999999999988544333   9999     88     88    8999999887


Q ss_pred             c----CCC-CCCchhhh---------hccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEE
Q 022058           97 Q----GRK-RLSGRAFR---------AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAF  160 (303)
Q Consensus        97 ~----g~~-~~~~~~~~---------~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~f  160 (303)
                      +    |+. .+......         ........++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++||||
T Consensus        92 ~~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~af  171 (216)
T 2qfj_A           92 SVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGF  171 (216)
T ss_dssp             SCCCC-CCCEEECCSCCGGGHHHHHHHHHHHTTSCEEEEECCCTTCCHHHHHHHHTTSSCEEEEEEEECTTTCCEEEEEE
T ss_pred             CCeeCCeeEEEecCCCccccchhhhhhhcccCCCcEEEEeCCCCcCCHHHHHHHHhccCCeeEEEEEecCCCCCcCceEE
Confidence            6    333 11111000         0112245689999999999999999999999999999999998654  789999


Q ss_pred             EEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCC
Q 022058          161 VEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAIL  195 (303)
Q Consensus       161 V~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~  195 (303)
                      |+|.+.++|.+|+. |||..+.|+.|.|.++.+...
T Consensus       172 V~F~~~~~A~~A~~~l~g~~~~g~~i~V~~a~~~~~  207 (216)
T 2qfj_A          172 IEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPM  207 (216)
T ss_dssp             EEESSHHHHHHHHHHHTTCBCSSSBCEEEECSSCSS
T ss_pred             EEecCHHHHHHHHHHccCCEeCCcEEEEEEecCCCC
Confidence            99999999999999 999999999999999876543

>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=99.96  E-value=6.2e-29  Score=208.96  Aligned_cols=158  Identities=16%  Similarity=0.132  Sum_probs=127.1

Q ss_pred             CCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc
Q 022058           21 KNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ   97 (303)
Q Consensus        21 ~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~   97 (303)
                      .+.+|||+|||+++|+++|+++|++||+|.+|+|+.++.++.++   ||+|     .+     .+    +|.+|+.. ++
T Consensus        12 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f-----~~-----~~----~A~~A~~~-~~   76 (196)
T 1l3k_A           12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-----AT-----VE----EVDAAMNA-RP   76 (196)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEE-----SS-----HH----HHHHHHHT-CS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEEcCCCCCccceEEEEe-----CC-----HH----HHHHHHhc-CC
Confidence            34489999999999999999999999999999999998765544   9999     77     77    88888876 32


Q ss_pred             ----CCC-CCCch--h--hhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCH
Q 022058           98 ----GRK-RLSGR--A--FRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADE  166 (303)
Q Consensus        98 ----g~~-~~~~~--~--~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~  166 (303)
                          |+. .+...  .  ..........++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.
T Consensus        77 ~~~~g~~l~v~~~~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~  156 (196)
T 1l3k_A           77 HKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH  156 (196)
T ss_dssp             CEETTEECEEEECCC-----------CCSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSH
T ss_pred             CEECCEEeeeecccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHhcCCCeEEEEEeecCCCCCccceEEEEECCH
Confidence                332 11110  0  111112235689999999999999999999999999999999998644  799999999999


Q ss_pred             HHHHHHHHhCCcccCCeeEEEeecCCC
Q 022058          167 HGARAALNLGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       167 ~~A~~Ai~l~g~~~~g~~i~v~~~~~~  193 (303)
                      ++|.+|+..++..+.|+.|.|.++.+.
T Consensus       157 ~~A~~A~~~~~~~~~G~~i~v~~a~~k  183 (196)
T 1l3k_A          157 DSVDKIVIQKYHTVNGHNCEVRKALSK  183 (196)
T ss_dssp             HHHHHHHHCSCCEETTEECEEEECC--
T ss_pred             HHHHHHHHhCCcEECCEEEEEEecCCh
Confidence            999999997899999999999998654

>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=99.96  E-value=6.7e-29  Score=203.04  Aligned_cols=154  Identities=17%  Similarity=0.234  Sum_probs=128.2

Q ss_pred             CCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc-
Q 022058           22 NNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-   97 (303)
Q Consensus        22 ~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-   97 (303)
                      +.+|||+|||+++|+++|+++|++||+|.+|++++++.++.++   ||+|     .+     .+    +|.+|+..+++ 
T Consensus         2 ~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~~~~~~~~~~~~g~afV~f-----~~-----~~----~A~~a~~~l~~~   67 (167)
T 1fxl_A            2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNY-----ID-----PK----DAEKAINTLNGL   67 (167)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEE-----SS-----HH----HHHHHHHHHTTC
T ss_pred             cceEEEcCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCcceeEEEEEE-----CC-----HH----HHHHHHHHcCCC
Confidence            3489999999999999999999999999999999998555443   9999     88     88    89999998887 


Q ss_pred             ---CCCCCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHH
Q 022058           98 ---GRKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAA  172 (303)
Q Consensus        98 ---g~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~A  172 (303)
                         |+. +..............++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|
T Consensus        68 ~~~g~~-l~v~~~~~~~~~~~~~~l~v~nl~~~~t~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A  146 (167)
T 1fxl_A           68 RLQTKT-IKVSYARPSSASIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEA  146 (167)
T ss_dssp             EETTEE-CEEEECCCCCGGGTTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHH
T ss_pred             ccCCce-EEEEecCCCcccCCCCcEEECCCCCcCCHHHHHHHHHhcCCEeEEEEEecCCCCCccceEEEEeCCHHHHHHH
Confidence               322 11111111122335788999999999999999999999999999999998744  689999999999999999


Q ss_pred             HH-hCCcccCCee--EEEeec
Q 022058          173 LN-LGGTMLGYYP--VRVLPS  190 (303)
Q Consensus       173 i~-l~g~~~~g~~--i~v~~~  190 (303)
                      +. |||..+.|+.  |.|.|+
T Consensus       147 ~~~l~g~~~~g~~~~i~v~~A  167 (167)
T 1fxl_A          147 IKGLNGQKPSGATEPITVKFA  167 (167)
T ss_dssp             HHHHTTCCCTTCSSCCEEEEC
T ss_pred             HHHhcCCccCCCccceEEEeC
Confidence            99 9999999965  888874

>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=99.94  E-value=3e-27  Score=194.56  Aligned_cols=149  Identities=14%  Similarity=0.228  Sum_probs=123.3

Q ss_pred             CCCCcccccchhhhHHHHHHHHhcc----C-------CcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHH
Q 022058           22 NNNLETKKSESEFTVQKLVDMFTKL----N-------PLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRR   90 (303)
Q Consensus        22 ~~~~~~~nl~~~~t~~~L~~~F~~~----G-------~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~   90 (303)
                      +.+|||+|||+++|+++|+++|++|    |       +|.++++.+++   ...||+|     .+     .+    +|++
T Consensus         4 ~~~l~V~nLp~~~t~~~l~~~F~~~g~~~g~~~~~~~~v~~~~~~~~~---g~afV~f-----~~-----~~----~A~~   66 (172)
T 2g4b_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK---NFAFLEF-----RS-----VD----ETTQ   66 (172)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEEETTT---TEEEEEE-----SS-----HH----HHHH
T ss_pred             ccEEEEcCCCcccCHHHHHHHHHHHhhhcccccCCCCceeeeEecCCC---CEEEEEe-----CC-----HH----HHHH
Confidence            3489999999999999999999999    6       77777776542   1129999     88     88    8999


Q ss_pred             hhhhccc----CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEe
Q 022058           91 RRNNFNQ----GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEF  163 (303)
Q Consensus        91 a~~~~~~----g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f  163 (303)
                      |+ .+++    |+. .+..  ..........++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|
T Consensus        67 A~-~~~~~~~~g~~i~v~~--~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~g~~~g~afV~f  143 (172)
T 2g4b_A           67 AM-AFDGIIFQGQSLKIRR--PHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEY  143 (172)
T ss_dssp             HG-GGTTCEETTEECEEEC--CSSCCCCTTTTCEEEECCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCSEEEEEEEEE
T ss_pred             HH-HhCCcEecCceeeecC--CcccCCCCCCCEEEEEcCCCcCCHHHHHHHHHhcCCceEEEEEecCCCCCcceEEEEEe
Confidence            99 7776    332 1111  111223345788999999999999999999999999999999998643  799999999


Q ss_pred             cCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          164 ADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       164 ~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .+.++|.+|+. |||..+.|++|.|.++
T Consensus       144 ~~~~~A~~A~~~l~g~~~~g~~l~V~~A  171 (172)
T 2g4b_A          144 VDINVTDQAIAGLNGMQLGDKKLLVQRA  171 (172)
T ss_dssp             SSTTHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCHHHHHHHHHHcCCCEECCeEEEEEeC
Confidence            99999999998 9999999999999986

>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=99.94  E-value=3.4e-27  Score=200.72  Aligned_cols=153  Identities=14%  Similarity=0.159  Sum_probs=122.1

Q ss_pred             CCCCcccccc-hhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           22 NNNLETKKSE-SEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        22 ~~~~~~~nl~-~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      +.+|||+||| +++|+++|+++|++||+|.+|++++++.  ...||+|     .+     .+    +|++|+..||+   
T Consensus         4 ~~~l~V~nL~~~~~~~~~L~~~F~~~G~v~~v~i~~~~~--g~afV~f-----~~-----~~----~A~~Ai~~lng~~~   67 (205)
T 3tyt_A            4 SPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKP--GAAMVEM-----AD-----GY----AVDRAITHLNNNFM   67 (205)
T ss_dssp             CSEEEEECCCTTTCCHHHHHHHHTTTSCEEEEEECTTST--TCEEEEE-----SS-----HH----HHHHHHHHHTTCEE
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHHhcCCeEEEEEecCCC--CEEEEEE-----CC-----HH----HHHHHHHHhCCCEE
Confidence            3489999999 8999999999999999999999997631  1229999     88     88    99999999987   


Q ss_pred             -CCC-CCC--c-----hhh-----------h-----------------hccCCCCCCEEEEcCCCCCCCHHHHHHHhhcC
Q 022058           98 -GRK-RLS--G-----RAF-----------R-----------------AQREDSVRRTVYVSDIDQNITEERLAGLFSSC  140 (303)
Q Consensus        98 -g~~-~~~--~-----~~~-----------~-----------------~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~  140 (303)
                       |+. .+.  .     +..           .                 ..+.....++|||+|||+++|+++|+++|+.|
T Consensus        68 ~g~~l~v~~s~~~~~~p~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~p~~~l~v~NLp~~~t~~~L~~~F~~~  147 (205)
T 3tyt_A           68 FGQKMNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFFEICDEL  147 (205)
T ss_dssp             TTEECEEEECSCSCCCCCSCCBCTTSCBSEEECTTCTTCSCSSHHHHTTSCCCCCCSEEEEEEECTTCCHHHHHHHHHHH
T ss_pred             CCceEEEEEccCCccCCCcccccccCCccccccCCCccccccCcccccccccCCCcceEEEeCCCCCCCHHHHHHHHHhc
Confidence             332 000  0     000           0                 00011235689999999999999999999999


Q ss_pred             Cce--eEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCe----eEEEeec
Q 022058          141 GQV--VDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYY----PVRVLPS  190 (303)
Q Consensus       141 G~i--~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~----~i~v~~~  190 (303)
                      |.|  .+++++.+...++|||||+|.+.++|.+||. |||..+.|+    ++.|+++
T Consensus       148 G~v~~~~v~~~~~~~~~~g~gfV~f~~~~~A~~Ai~~lng~~~~g~~~~~p~~vk~~  204 (205)
T 3tyt_A          148 GVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQMKNPNGPYPYTLKLC  204 (205)
T ss_dssp             TCCCCSEEEECSCCSSSSEEEEEECSSHHHHHHHHHHHTTCEECCSSSSSCEECEEE
T ss_pred             CCcceEEEEEEcCCCCCceEEEEEeCCHHHHHHHHHHhCCCCccCCCCCcceEEEec
Confidence            999  8999988875567999999999999999998 999999874    6666653

>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=99.94  E-value=1.5e-27  Score=197.15  Aligned_cols=155  Identities=16%  Similarity=0.158  Sum_probs=122.7

Q ss_pred             cCCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc--eeeeecchhhhhhchhhhccccchHHhhhhccc
Q 022058           20 NKNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH--HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ   97 (303)
Q Consensus        20 ~~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~--~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~   97 (303)
                      ..+.+|||+|||+++|+++|+++|++||+|..+.+.....+..++  ||+|     .+     .+    +|.+|+ .+++
T Consensus        11 ~~~~~l~V~nLp~~~t~~~l~~~f~~~g~~~~~~~~~~~~~~~~g~afV~f-----~~-----~~----~a~~A~-~l~g   75 (175)
T 1fje_B           11 TTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF-----ES-----AE----DLEKAL-ELTG   75 (175)
T ss_dssp             SSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEE-----SS-----HH----HHHHHH-HGGG
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEECCCCccccEEEEEE-----CC-----HH----HHHHHH-hcCC
Confidence            344589999999999999999999999999884444333343334  9999     88     88    899999 5776


Q ss_pred             ----CCC-CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHH
Q 022058           98 ----GRK-RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAA  172 (303)
Q Consensus        98 ----g~~-~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~A  172 (303)
                          |+. .+..............++|||+|||+++++++|+++|+.||.|..+   ...+.++|||||+|.+.++|.+|
T Consensus        76 ~~~~g~~l~v~~~~~~~~~~~~~~~~l~v~nlp~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~A~~A  152 (175)
T 1fje_B           76 LKVFGNEIKLEKPKGRDSKKVRAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKN  152 (175)
T ss_dssp             EEETTEEEEEECCCCSSCSTTGGGGEEEEESCCSSCCHHHHHHHCTTCSEEEEE---CSSSSCCSEEEEECSSHHHHHHH
T ss_pred             CEeCCeEEEEecCCCccccccccCCEEEEeCCCCCCCHHHHHHHHHhcCeEEEe---cCCCCCceEEEEEECCHHHHHHH
Confidence                443 2222222222233457899999999999999999999999998766   33334899999999999999999


Q ss_pred             HH-hCCcccCCeeEEEeecCC
Q 022058          173 LN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       173 i~-l~g~~~~g~~i~v~~~~~  192 (303)
                      +. |||..+.|++|.|.++.+
T Consensus       153 ~~~l~g~~~~g~~i~v~~a~~  173 (175)
T 1fje_B          153 LEEKQGAEIDGRSVSLYYTGE  173 (175)
T ss_dssp             HHHHTEEEETTEEEEEEECSS
T ss_pred             HHHhCCCEECCeEEEEEecCC
Confidence            99 999999999999999854

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A

Probab=99.94  E-value=4.2e-27  Score=198.05  Aligned_cols=154  Identities=14%  Similarity=0.214  Sum_probs=122.2

Q ss_pred             CCCCcccccchhhhHHHHHHHHhccC-----------CcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHH
Q 022058           22 NNNLETKKSESEFTVQKLVDMFTKLN-----------PLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRR   90 (303)
Q Consensus        22 ~~~~~~~nl~~~~t~~~L~~~F~~~G-----------~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~   90 (303)
                      +.+|||+|||+++|+++|+++|++||           +|.++.+.+++   ...||+|     .+     .+    +|++
T Consensus         4 ~~~l~V~nLp~~~te~~l~~~F~~~g~i~g~~~~~~~~v~~~~~~~~~---g~afV~F-----~~-----~~----~A~~   66 (198)
T 2yh0_A            4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDK---NFAFLEF-----RS-----VD----ETTQ   66 (198)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHHHHHHHTCCSSSSCSEEEEEEETTT---TEEEEEE-----SC-----SH----HHHH
T ss_pred             eeEEEEcCCCCCCCHHHHHHHHHHHHhhcccccCCCCceEEeEecCCC---CEEEEEe-----CC-----HH----HHHH
Confidence            34899999999999999999999995           55555554331   1129999     88     77    8999


Q ss_pred             hhhhccc----CCC-CCCchhh------------------hhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEE
Q 022058           91 RRNNFNQ----GRK-RLSGRAF------------------RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCR  147 (303)
Q Consensus        91 a~~~~~~----g~~-~~~~~~~------------------~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~  147 (303)
                      |+ .+++    |+. .+.....                  .........++|||+|||+++++++|+++|+.||.|.++.
T Consensus        67 Al-~l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~v~~~~  145 (198)
T 2yh0_A           67 AM-AFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFN  145 (198)
T ss_dssp             HG-GGTTEEETTEEEEEECCCCCCCCCCSSSCSSCCCTTSSCCCSSCCCCEEEEECCCTTCCHHHHHHHHHTBSCEEEEE
T ss_pred             HH-HhcCCEEcCceEEEeCCCCCCCCCCCcCCCcCCCCCCccCCCCCCCCEEEEeCCCCCCCHHHHHHHHHHcCCccEEE
Confidence            99 7776    332 1111000                  0111124578999999999999999999999999999999


Q ss_pred             EeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          148 VCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       148 i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ++.+..+  ++|||||+|.+.++|.+|+. |||..+.|+.|.|.++.+.
T Consensus       146 ~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~  194 (198)
T 2yh0_A          146 LVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVG  194 (198)
T ss_dssp             EEECTTTCSEEEEEEEEESSSSHHHHHHHHHTTCEETTEECEEEESCCC
T ss_pred             EeecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCC
Confidence            9998643  79999999999999999999 9999999999999998653

>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=99.93  E-value=6.7e-26  Score=201.51  Aligned_cols=153  Identities=14%  Similarity=0.227  Sum_probs=122.8

Q ss_pred             CCCCcccccchhhhHHHHH----HHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc
Q 022058           22 NNNLETKKSESEFTVQKLV----DMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ   97 (303)
Q Consensus        22 ~~~~~~~nl~~~~t~~~L~----~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~   97 (303)
                      +.+|||+|||+++|+++|+    ++|++||+|.+|+++++...+...||+|     .+     .+    +|.+|+..+++
T Consensus         9 ~~~l~V~nlp~~~~~~~l~~~L~~~F~~~G~i~~v~~~~~~~~~g~afV~f-----~~-----~~----~a~~A~~~l~g   74 (282)
T 3pgw_A            9 NHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIF-----KE-----VS----SATNALRSMQG   74 (282)
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcCCCCcceEEEEEE-----CC-----HH----HHHHHHHHhcC
Confidence            4589999999999999977    8999999999999987332221229999     88     78    89999988877


Q ss_pred             ----CCC-CCCchhhhh---------------------------------------------------------------
Q 022058           98 ----GRK-RLSGRAFRA---------------------------------------------------------------  109 (303)
Q Consensus        98 ----g~~-~~~~~~~~~---------------------------------------------------------------  109 (303)
                          |+. .+.......                                                               
T Consensus        75 ~~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (282)
T 3pgw_A           75 FPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPATKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIM  154 (282)
T ss_pred             CeeCCcEEEEEEeccCcchhhhhcCCcccchhhhhhhhccccchhhhhhhccCcCCcccCCCCCCCCCCCCccccccccc
Confidence                322 100000000                                                               


Q ss_pred             ----------------------------------------------ccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCce
Q 022058          110 ----------------------------------------------QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQV  143 (303)
Q Consensus       110 ----------------------------------------------~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i  143 (303)
                                                                    .......++|||+|||+++++++|+++|+.||.|
T Consensus       155 ~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~F~~~G~i  234 (282)
T 3pgw_A          155 HHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGF  234 (282)
T ss_pred             ccCCCCCCCCCCCCCCCCCCCCccccCcccCcccccCccccCccCCccCCCCCCEEEEeCCCCcCCHHHHHHHHHhcCCe
Confidence                                                          0111245789999999999999999999999999


Q ss_pred             eEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEeecC
Q 022058          144 VDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG-YYPVRVLPSK  191 (303)
Q Consensus       144 ~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~i~v~~~~  191 (303)
                      .+|+++.+.   +|||||+|.+.++|.+|+. |||..+. |+.|+|.|++
T Consensus       235 ~~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~ak  281 (282)
T 3pgw_A          235 KEVRLVPGR---HDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAK  281 (282)
T ss_pred             EEEEEecCC---CcEEEEEeCCHHHHHHHHHHcCCcEeCCCCEEEEEEec
Confidence            999998655   5899999999999999999 9999999 9999999975

>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=99.93  E-value=9.1e-26  Score=195.05  Aligned_cols=154  Identities=24%  Similarity=0.225  Sum_probs=125.1

Q ss_pred             cCCCCCcccccch-hhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc-
Q 022058           20 NKNNNLETKKSES-EFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ-   97 (303)
Q Consensus        20 ~~~~~~~~~nl~~-~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~-   97 (303)
                      ..+.+|||+|||+ ++|+++|+++|++||+|.+|++++++.  ...||+|     .+     .+    +|++|+..+++ 
T Consensus        32 ~~~~~l~V~nLp~~~~te~~L~~~F~~~G~i~~v~i~~~~~--g~afV~F-----~~-----~~----~A~~Ai~~l~g~   95 (229)
T 2adc_A           32 AGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK--ENALVQM-----AD-----GN----QAQLAMSHLNGH   95 (229)
T ss_dssp             CCCSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTTS--CCEEEEE-----SC-----HH----HHHHHHHHHTTC
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEEEECCC--CEEEEEE-----CC-----HH----HHHHHHHHhCCC
Confidence            3455899999999 999999999999999999999998861  1239999     88     88    89999988876 


Q ss_pred             ---CCC-CC--Cchh----hh-h--------------------------ccCCCCCCEEEEcCCCCCCCHHHHHHHhhcC
Q 022058           98 ---GRK-RL--SGRA----FR-A--------------------------QREDSVRRTVYVSDIDQNITEERLAGLFSSC  140 (303)
Q Consensus        98 ---g~~-~~--~~~~----~~-~--------------------------~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~  140 (303)
                         |+. .+  ....    .. .                          .......++|||+|||+.+++++|+++|+.|
T Consensus        96 ~~~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~f~~~  175 (229)
T 2adc_A           96 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSN  175 (229)
T ss_dssp             BCSSSBCEEECCSCCCCCCCCSSSSTTTTEEECTTCSSCCCCSTTSGGGTTCCCSCSEEEEECCCTTCCHHHHHHHHHTT
T ss_pred             eECCeEEEEEEecCccccCccccccccccccccccCcccccCCccccccccCCCCCCEEEEeCCCccCCHHHHHHHHHHc
Confidence               333 11  0000    00 0                          0001236889999999999999999999999


Q ss_pred             C-ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEeecCC
Q 022058          141 G-QVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG-YYPVRVLPSKT  192 (303)
Q Consensus       141 G-~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~i~v~~~~~  192 (303)
                      | .|.++.++.+   ++|||||+|.+.++|.+|+. |||..+. |++|.|.|+++
T Consensus       176 G~~i~~v~i~~~---~~g~afV~f~~~~~A~~Ai~~l~g~~~~~g~~l~v~~a~~  227 (229)
T 2adc_A          176 GGVVKGFKFFQK---DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  227 (229)
T ss_dssp             SCCEEEEEECSS---STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCeeEEEEEEC---CCcEEEEEECCHHHHHHHHHHHCCCccCCCCeEEEEEecC
Confidence            9 9999999653   36899999999999999999 9999999 99999999864

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1

Probab=99.93  E-value=7.5e-26  Score=190.79  Aligned_cols=152  Identities=24%  Similarity=0.234  Sum_probs=124.2

Q ss_pred             CCCCcccccch-hhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           22 NNNLETKKSES-EFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        22 ~~~~~~~nl~~-~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      +.+|||+|||+ ++|+++|+++|++||+|.+|+++.++.  ...||+|     .+     .+    +|.+|+..+++   
T Consensus         3 ~~~l~v~nlp~~~~~~~~l~~~F~~~G~i~~v~i~~~~~--g~afV~f-----~~-----~~----~a~~A~~~l~~~~~   66 (198)
T 1qm9_A            3 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKK--ENALVQM-----AD-----GN----QAQLAMSHLNGHKL   66 (198)
T ss_dssp             CCEEEEECCCSSSCCHHHHHHHHHTTCCCSEEECSTTCS--SCCEEEC-----TT-----TH----HHHHHHHHHTTCCC
T ss_pred             CcEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEEeCCC--CEEEEEE-----CC-----HH----HHHHHHHHhCCCee
Confidence            35899999999 999999999999999999999998862  1239999     88     77    89999988877   


Q ss_pred             -CCC-CCC--chh----hh-h--------------------------ccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCC-
Q 022058           98 -GRK-RLS--GRA----FR-A--------------------------QREDSVRRTVYVSDIDQNITEERLAGLFSSCG-  141 (303)
Q Consensus        98 -g~~-~~~--~~~----~~-~--------------------------~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-  141 (303)
                       |+. .+.  .+.    .. .                          .......++|||+|||+.+++++|+++|+.|| 
T Consensus        67 ~g~~l~v~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~v~nl~~~~~~~~l~~~f~~~G~  146 (198)
T 1qm9_A           67 HGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGG  146 (198)
T ss_dssp             SSCCCEEEECCCCSCCCSSSSSSSSSCEEESSCCCTTSSSSCCCCCCSCCCCCCCEEEECCCCTTCCHHHHHHHHHHTTS
T ss_pred             cCeEEEEEEecCCCcCCCCcCCccccccccccCCchhhccCccccccccCCCCccEEEEeCCCCCCCHHHHHHHHHHcCC
Confidence             332 110  000    00 0                          00012377899999999999999999999999 


Q ss_pred             ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEeecCC
Q 022058          142 QVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG-YYPVRVLPSKT  192 (303)
Q Consensus       142 ~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~i~v~~~~~  192 (303)
                      .|.++.++.+.   +|||||+|.+.++|.+|+. |||..+. |++|.|.|+++
T Consensus       147 ~v~~v~i~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~a~~  196 (198)
T 1qm9_A          147 VVKGFKFFQKD---RKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS  196 (198)
T ss_dssp             CCCEEEESSTT---SSCEEEECSSHHHHHHHHHHHTSSCCSSCCSCCEEEECC
T ss_pred             CceEEEEEeCC---CcEEEEEeCCHHHHHHHHHHhcCCccCCCCeEEEEeecc
Confidence            99999997643   6899999999999999999 9999999 99999999864

>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=99.92  E-value=3.6e-24  Score=174.41  Aligned_cols=147  Identities=14%  Similarity=0.097  Sum_probs=112.3

Q ss_pred             EEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCC
Q 022058          145 DCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDK  223 (303)
Q Consensus       145 ~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~  223 (303)
                      ++.++.+...++|||||+|.+.++|++|+. +++....+..+.+............ ..............+|||+|||.
T Consensus         2 ~~kl~ln~~~~~G~~fV~f~~~~~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~l~v~nl~~   80 (158)
T 2kn4_A            2 QYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEG-SHHHHHHMDVEGMTSLKVDNLTY   80 (158)
T ss_dssp             EEEEEEECSSCEEEEEEECSSHHHHHHHHHHHHHHHTCCCEEEEETTTTEEEEECC-CCCSSCCCCCCBCCEEEEESCCT
T ss_pred             cEEEEecCccccchhHHHHHHHHhHHHHHHhhcccCCCCCcccccCcccccccccc-ccccccccCCCCCCEEEEeCCCC
Confidence            467777777899999999999999999997 7764443333333322111000000 00011111223568999999999


Q ss_pred             CCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCC
Q 022058          224 KVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       224 ~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~  294 (303)
                      .+++++|+++|++|  |.|..|.|++|.  |.++|||||+|.+.++|.+|+. |||..++|+.|.|.++++...
T Consensus        81 ~~~~~~l~~~F~~~--G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~~  152 (158)
T 2kn4_A           81 RTSPDTLRRVFEKY--GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRP  152 (158)
T ss_dssp             TCCHHHHHHHHHHH--SCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEECCSSC
T ss_pred             CCCHHHHHHHHHhc--CCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEECCCCCC
Confidence            99999999999999  999999999984  7899999999999999999998 999999999999999987643

>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=99.92  E-value=7.6e-25  Score=192.94  Aligned_cols=153  Identities=20%  Similarity=0.220  Sum_probs=124.2

Q ss_pred             CCCCCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCceeeeecchhhhhhchhhhccccchHHhhhhcccCCC
Q 022058           21 KNNNLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDHHFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQGRK  100 (303)
Q Consensus        21 ~~~~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g~~  100 (303)
                      .+.+|||+|||+++|+++|+++|++||+|.+|++.+++   ...||+|     .+     .+    +|.+|+..+++-.-
T Consensus        21 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~k---g~afV~f-----~~-----~~----~A~~A~~~l~g~~i   83 (261)
T 3sde_A           21 QRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRDR---GFGFIRL-----ES-----RT----LAEIAKAELDGTIL   83 (261)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHTGGGCCCSEEEEETTT---TEEEEEC-----SS-----HH----HHHHHHHHHTTCEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEeCCC---cEEEEEE-----CC-----HH----HHHHHHHHcCCcEE
Confidence            34479999999999999999999999999999997652   1229999     88     77    89999998887111


Q ss_pred             CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-h-CC
Q 022058          101 RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-L-GG  177 (303)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l-~g  177 (303)
                        ..+... -......++|||+|||+.+|+++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. | ++
T Consensus        84 --~g~~l~-v~~a~~~~~l~v~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~~  160 (261)
T 3sde_A           84 --KSRPLR-IRFATHGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALERCGDG  160 (261)
T ss_dssp             --TTEECE-EEECCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTSCEEEEEEEEESSHHHHHHHHHHHHHS
T ss_pred             --CCceeE-eeecccCCcccccCCCCCCCHHHHHHHHHhcCCeEEEEeeeCCCCCcCcEEEEEeCCHHHHHHHHHHhcCC
Confidence              010000 011224678999999999999999999999999999999998655 79999999999999999998 8 45


Q ss_pred             cccC---CeeEEEeecCCC
Q 022058          178 TMLG---YYPVRVLPSKTA  193 (303)
Q Consensus       178 ~~~~---g~~i~v~~~~~~  193 (303)
                      ..+.   +++|.|.++...
T Consensus       161 ~~~~~~~~r~i~v~~~~~~  179 (261)
T 3sde_A          161 AFLLTTTPRPVIVEPMEQF  179 (261)
T ss_dssp             CEESSSSCCBCEEEECCCE
T ss_pred             eEEecCCCceEEEeecccc
Confidence            5554   899999998653

>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=99.90  E-value=5.3e-24  Score=164.42  Aligned_cols=108  Identities=22%  Similarity=0.356  Sum_probs=74.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ...+|||+|||+++++++|+++|+.||.|.+|+|+.+.++++|||||+|.+.++|++||+ |||..+.|++|.|.++...
T Consensus         4 ~~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~~   83 (115)
T 4f25_A            4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSR   83 (115)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSCC
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHhccCCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCc
Confidence            467899999999999999999999999999999999987799999999999999999998 9999999999999998653


Q ss_pred             CCCCCCCCCCCcccccccccceEEEcCCCCCCCHH
Q 022058          194 ILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQA  228 (303)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~  228 (303)
                      ...      ............+|||+|||+.+|++
T Consensus        84 ~~~------~~~~~~~~~~~~~lyv~Nl~~~~T~~  112 (115)
T 4f25_A           84 KER------EAELGARAKEFTNVYIKNFGPGSTRA  112 (115)
T ss_dssp             CC---------------------------------
T ss_pred             ccc------ccccccccCCCCceEeCCCCCCcccc
Confidence            211      11111122344679999999999886

>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=99.89  E-value=1.7e-22  Score=163.18  Aligned_cols=141  Identities=15%  Similarity=0.120  Sum_probs=114.1

Q ss_pred             EEeeCCCCCceEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEeecCCCCCCCC--CCCCCCcccccccccceEEEcCCC
Q 022058          147 RVCGDPHSVLRFAFVEFADEHGARAALN-L-GGTMLGYYPVRVLPSKTAILPVN--PTFLPRSEDEREMCSRTVYCTNID  222 (303)
Q Consensus       147 ~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l-~g~~~~g~~i~v~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~V~nL~  222 (303)
                      .+..+....+|+++|+|.+.++|++|++ + ||..+.| +|.+.++........  ...............++|||+|||
T Consensus         4 al~l~g~~l~G~~~ve~~~~~~A~~a~~~~~ng~~~~G-~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nl~   82 (150)
T 2i2y_A            4 KLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDG-EWTYDDATKTFTVTEGSHHHHHHMHRDSCPLDCKVYVGNLG   82 (150)
T ss_dssp             EEEECCSSSCEEEEEECSSHHHHTTTHHHHHHHHTCCC-EEEEETTTTEEEEECSSSSCCCCSCSSSSTTSCEEEEESCC
T ss_pred             EeeeccccccccceeeecCHHHHHHHHHHHhcCCCCCC-ceecccccCccccccccccccccccccCCCCCCEEEEeCCC
Confidence            3444444578999999999999999998 8 9999999 999998754311000  000111112223456899999999


Q ss_pred             CCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCC
Q 022058          223 KKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       223 ~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~  293 (303)
                      +.+++++|+++|++|  |.|.+|.|+++   ++|||||+|.+.++|.+|+. |||..+.|+.|+|.|++++.
T Consensus        83 ~~~t~~~l~~~F~~~--G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~~~  149 (150)
T 2i2y_A           83 NNGNKTELERAFGYY--GPLRSVWVARN---PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEK  149 (150)
T ss_dssp             SCCSCHHHHHHHHHH--SCEEEEEECSS---SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECCCCC
T ss_pred             CCCCHHHHHHHHHhh--CCEEEEEEeeC---CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcCCCC
Confidence            999999999999999  99999999988   46799999999999999998 99999999999999998763

>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=99.83  E-value=2.4e-20  Score=139.94  Aligned_cols=78  Identities=28%  Similarity=0.447  Sum_probs=73.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++|+++|+++|+.||.|.+|++++|+.+  ++|||||+|.+.++|.+|++ |||..+.|++|.|.|++
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~Ak   97 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSYAR   97 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            4678999999999999999999999999999999998764  79999999999999999998 99999999999999986


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      +
T Consensus        98 P   98 (99)
T 4fxv_A           98 P   98 (99)
T ss_dssp             B
T ss_pred             C
Confidence            4

>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=99.83  E-value=3e-20  Score=139.41  Aligned_cols=78  Identities=28%  Similarity=0.458  Sum_probs=74.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+++|||+|||..+|+++|+++|++|  |.|.+|.|++|+  |.++|||||+|.+.++|.+|+. |||..++|+.|+|.|
T Consensus        18 ~gt~lfV~nLp~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~   95 (99)
T 4fxv_A           18 QGTNLIVNYLPQNMTQDELRSLFSSI--GEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTIKVSY   95 (99)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECSSSCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEeEeeecCCCCcccccEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            35789999999999999999999999  999999999985  7899999999999999999998 999999999999999


Q ss_pred             cCC
Q 022058          289 SKT  291 (303)
Q Consensus       289 a~~  291 (303)
                      |+|
T Consensus        96 AkP   98 (99)
T 4fxv_A           96 ARP   98 (99)
T ss_dssp             CCB
T ss_pred             eeC
Confidence            986

>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=8.4e-20  Score=148.44  Aligned_cols=129  Identities=16%  Similarity=0.208  Sum_probs=99.1

Q ss_pred             eeeeccCCCCCCCc-eeeeecchhhhhhchhhhccccchHHhhhhcccC-----CCCC-----------CchhhhhccCC
Q 022058           51 KEFFPSYYHQHTDH-HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQG-----RKRL-----------SGRAFRAQRED  113 (303)
Q Consensus        51 ~v~i~~~~~~~~~~-~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~g-----~~~~-----------~~~~~~~~~~~  113 (303)
                      ++.|+.+.....+. ||+|     .+     .+    +|++|+..+++.     ....           ...........
T Consensus         2 ~~kl~ln~~~~~G~~fV~f-----~~-----~~----~A~~al~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   67 (158)
T 2kn4_A            2 QYKLILNGKTLKGETTTEA-----VD-----AA----TAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDV   67 (158)
T ss_dssp             EEEEEEECSSCEEEEEEEC-----SS-----HH----HHHHHHHHHHHHHTCCCEEEEETTTTEEEEECCCCCSSCCCCC
T ss_pred             cEEEEecCccccchhHHHH-----HH-----HH----hHHHHHHhhcccCCCCCcccccCccccccccccccccccccCC
Confidence            45666665533333 9999     88     77    888888777641     1100           00000111122


Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. |||..+.|++|.|.++
T Consensus        68 ~~~~~l~v~nl~~~~~~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a  147 (158)
T 2kn4_A           68 EGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA  147 (158)
T ss_dssp             CBCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEECCCCSSCTTSCCEEEEEESBHHHHHHHHHHSTTEESSSSEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            34788999999999999999999999999999999998643  89999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ++.
T Consensus       148 ~~~  150 (158)
T 2kn4_A          148 RYG  150 (158)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            754

>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=99.79  E-value=3.8e-19  Score=137.05  Aligned_cols=79  Identities=25%  Similarity=0.393  Sum_probs=74.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      ..+|||+|||+.+++++|+++|++|  |.|.+|+|++|.++++|||||+|.+.++|.+|+. |||..++|+.|+|.++++
T Consensus         5 ~~~lfV~nLp~~~te~~L~~~F~~~--G~v~~v~i~~d~~~~kg~afV~f~~~~~A~~Ai~~l~~~~~~g~~i~V~~a~~   82 (115)
T 4f25_A            5 SGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   82 (115)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEEETTEEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEESSC
T ss_pred             CCEEEECCCCCCCCHHHHHHHHhcc--CCEEEEEEeecCCCCCceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            4689999999999999999999999  9999999999988899999999999999999998 999999999999999986


Q ss_pred             CC
Q 022058          292 PV  293 (303)
Q Consensus       292 ~~  293 (303)
                      ..
T Consensus        83 ~~   84 (115)
T 4f25_A           83 RK   84 (115)
T ss_dssp             CC
T ss_pred             cc
Confidence            53

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.79  E-value=1.6e-19  Score=143.20  Aligned_cols=125  Identities=17%  Similarity=0.178  Sum_probs=79.8

Q ss_pred             eEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhh
Q 022058          157 RFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFE  235 (303)
Q Consensus       157 G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~  235 (303)
                      -+.|.+|++...+..|+. ++|....|+. ...+..           +   .......++|||+|||..+++++|+++|+
T Consensus         5 ~~~~~~~~~~~~~~~a~~~~~g~~~~g~~-~~~~~~-----------~---~~~~~~~~~l~V~nLp~~~te~~L~~~F~   69 (135)
T 2lea_A            5 HHHHHHSSGLVPRGSHMASMTGGQQMGRG-SMSYGR-----------P---PPDVEGMTSLKVDNLTYRTSPDTLRRVFE   69 (135)
T ss_dssp             -------------------------------CCSCC-----------S---CSSGGGCCCEEEECCCSSCHHHHHHHHHG
T ss_pred             ccccccccCCCchhhhhhhccCCCCCCCC-CCCcCC-----------C---CCCCCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            368888999999999998 8876665543 111111           1   11123458999999999999999999999


Q ss_pred             hhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCCCCC
Q 022058          236 AACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRPRVT  298 (303)
Q Consensus       236 ~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~r~~  298 (303)
                      +|  |.|..|.|+.+.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.++++...+...
T Consensus        70 ~~--G~i~~v~i~~~~~~g~~~G~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~~~~~~  133 (135)
T 2lea_A           70 KY--GRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGRPPDSH  133 (135)
T ss_dssp             GG--SCCSEEECCCCSSSSSCCSCCEEECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCCCCTTC
T ss_pred             hc--CCEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCCCCccc
Confidence            99  999999999884  7899999999999999999998 9999999999999999876555433

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.79  E-value=5.1e-19  Score=135.23  Aligned_cols=79  Identities=19%  Similarity=0.220  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|++||.|.+|.|++|+.+  ++|||||+|.+.++|.+|++ |||..+.|+.|.|.++
T Consensus         4 ~p~~~lfV~nL~~~~te~~L~~~F~~~G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~a   83 (110)
T 3s8s_A            4 IPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQLD   83 (110)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCcEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45789999999999999999999999999999999999875  79999999999999999998 9999999999999997


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ..
T Consensus        84 ~~   85 (110)
T 3s8s_A           84 IK   85 (110)
T ss_dssp             ST
T ss_pred             CC
Confidence            53

>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=99.79  E-value=4.2e-19  Score=145.54  Aligned_cols=136  Identities=18%  Similarity=0.162  Sum_probs=76.4

Q ss_pred             EEecCHHHHHHHHH-hCCcccC--CeeEEEeecCCCCC-CCCCCC--C---CCcccccccccceEEEcCCCCCCCHHHHH
Q 022058          161 VEFADEHGARAALN-LGGTMLG--YYPVRVLPSKTAIL-PVNPTF--L---PRSEDEREMCSRTVYCTNIDKKVPQAEVK  231 (303)
Q Consensus       161 V~f~~~~~A~~Ai~-l~g~~~~--g~~i~v~~~~~~~~-~~~~~~--~---~~~~~~~~~~~~~l~V~nL~~~~t~~~L~  231 (303)
                      .+|++.++|..|+. +++....  |+.+.+.+...... ...+..  .   ....+......++|||+|||..+++++|+
T Consensus        11 ee~e~~~d~e~~~~~~~~~~~~~kgr~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~   90 (165)
T 1rk8_A           11 EEFEVDEDGDQGIVRLKEKAKHRKGRGFGSDSNTREAIHSYERVRNEDDDELEPGPQRSVEGWILFVTSIHEEAQEDEIQ   90 (165)
T ss_dssp             -------------------------------------------------------CCCCC-CEEEEEESCCTTCCHHHHH
T ss_pred             hhhhccccccccchhhccccccccCCCCCCCccccccccCccccccCCCCCCCCCCCCCCCCCEEEEeCCCCCCCHHHHH
Confidence            68999999999998 8887665  67766665322110 000000  0   00111223456789999999999999999


Q ss_pred             HHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCCCCC
Q 022058          232 QFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRPRVT  298 (303)
Q Consensus       232 ~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~r~~  298 (303)
                      .+|++|  |.|..|.|+.+.  |.++|||||+|.+.++|.+|+. |||..|.|+.|.|.|+.+...++..
T Consensus        91 ~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~~~~~~~  158 (165)
T 1rk8_A           91 EKFCDY--GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFVKGPKRVK  158 (165)
T ss_dssp             HHHGGG--SCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESEECC-----
T ss_pred             HHhhcC--CCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEecCCCCCCCC
Confidence            999999  999999999884  7889999999999999999998 9999999999999999876654433

>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=99.79  E-value=2.3e-18  Score=129.79  Aligned_cols=86  Identities=23%  Similarity=0.377  Sum_probs=79.2

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+++.+.++|||||+|.+.++|.+|+. |||..+.|+.|+|.|+
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           13 GQPRTLYVGNLSRDVTEVLILQLFSQI--GPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHHHH--SCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCccCCHHHHHHHHHhc--CCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            356899999999999999999999999  9999999999987789999999999999999998 9999999999999999


Q ss_pred             CCCCCCCCC
Q 022058          290 KTPVRPRVT  298 (303)
Q Consensus       290 ~~~~~~r~~  298 (303)
                      +++...+..
T Consensus        91 ~~~~~~~~~   99 (103)
T 2cqi_A           91 TTPSSQKSG   99 (103)
T ss_dssp             CCTTCCCCC
T ss_pred             CCCcccccC
Confidence            987655443

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.79  E-value=2.1e-19  Score=132.64  Aligned_cols=79  Identities=16%  Similarity=0.270  Sum_probs=72.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCc-ceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-h-CCceeCCeeeEEee
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGG-EVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-C-SGMVLGSQPIRVSP  288 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G-~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l-~g~~~~g~~l~v~~  288 (303)
                      ++|||+|||+.+|+++|+++|++|  | .|.+|+|++|+  |.++|||||+|.+.++|.+|++ | |+..++|+.|+|.|
T Consensus         2 ~~i~v~nLp~~~te~~l~~~F~~~--G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~   79 (91)
T 2lxi_A            2 NIVMLRMLPQAATEDDIRGQLQSH--GVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHY   79 (91)
T ss_dssp             CEEEEETCCSSCCHHHHHHHHHHH--TCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHHh--CCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEE
Confidence            689999999999999999999999  9 89999999985  7899999999999999999998 6 56789999999999


Q ss_pred             cCCCCC
Q 022058          289 SKTPVR  294 (303)
Q Consensus       289 a~~~~~  294 (303)
                      ++|..+
T Consensus        80 a~~~~~   85 (91)
T 2lxi_A           80 SDPKPK   85 (91)
T ss_dssp             CCSCCC
T ss_pred             cCCCCC
Confidence            987643

>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=99.78  E-value=2e-18  Score=129.17  Aligned_cols=88  Identities=23%  Similarity=0.371  Sum_probs=80.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|+++.  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            7 GSGRLFVRNLSYTSSEEDLEKLFSAY--GPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            45899999999999999999999999  999999999985  7889999999999999999997 999999999999999


Q ss_pred             cCCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRPG  301 (303)
Q Consensus       289 a~~~~~~r~~r~~  301 (303)
                      +++........++
T Consensus        85 a~~~~~~~~~~~~   97 (99)
T 1whw_A           85 STIKKEASQSGPS   97 (99)
T ss_dssp             CCCCSTTCCCCCC
T ss_pred             cCCCcccccCCCC
Confidence            9987665554444

>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=99.78  E-value=3.6e-19  Score=136.97  Aligned_cols=103  Identities=24%  Similarity=0.354  Sum_probs=90.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|||+++++++|+++|+.||.|.+|.++.+.. ++|||||+|.+.++|.+|+. |||..+.|+.|.|.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~-~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            5 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE-TRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECSTT-TTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCC-CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            34678999999999999999999999999999999997644 58999999999999999999 99999999999999975


Q ss_pred             CCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCc
Q 022058          192 TAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGG  240 (303)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G  240 (303)
                      +...                  .    .+++...++++|.++|++|  |
T Consensus        84 ~~~~------------------~----~~~~~~~~~~~l~~~~~~~--g  108 (115)
T 3lqv_A           84 ANRA------------------F----QKMDTKKKEEQLKLLKEKY--G  108 (115)
T ss_dssp             HHHH------------------T----TTSCHHHHHHHHHHHHHHH--C
T ss_pred             CChh------------------h----hhhhHhHhHHHHHHHHHHh--C
Confidence            3210                  0    5677778899999999998  7

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.78  E-value=4.6e-19  Score=133.20  Aligned_cols=99  Identities=23%  Similarity=0.283  Sum_probs=81.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAIL  195 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~  195 (303)
                      ++|||+|||+++++++|+++|+.||.|.+|.++.+   ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.++.....
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~~~   77 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR   77 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHHCCCSEEEEESS---SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSCCC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeC---CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCCCC
Confidence            47999999999999999999999999999999987   68999999999999999999 999999999999999876532


Q ss_pred             CCCCCCCCCcccccccccceEEEcCCC
Q 022058          196 PVNPTFLPRSEDEREMCSRTVYCTNID  222 (303)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~l~V~nL~  222 (303)
                      ....    ...........+|||+||+
T Consensus        78 ~~~~----~~~~~~~~~~~~ifvg~L~  100 (101)
T 2hvz_A           78 RSRF----DRPPARRKLLEVLFNGPLE  100 (101)
T ss_dssp             SSCC----CSCCCSCCCCSCCCSCCCC
T ss_pred             cccC----CCCCccccCCCceecCCCC
Confidence            1110    0111112235789999997

>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=99.78  E-value=3.9e-18  Score=128.52  Aligned_cols=84  Identities=19%  Similarity=0.292  Sum_probs=77.9

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+++.+.++|||||+|.+.++|.+|+. |||..|.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           13 STPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHGGGT--SCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            356899999999999999999999999  9999999999986799999999999999999998 9999999999999999


Q ss_pred             CCCCCCC
Q 022058          290 KTPVRPR  296 (303)
Q Consensus       290 ~~~~~~r  296 (303)
                      ++.....
T Consensus        91 ~~~~~~~   97 (103)
T 2cq3_A           91 TARVMTN   97 (103)
T ss_dssp             CSSCCCC
T ss_pred             ccCCCCC
Confidence            8775443

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.78  E-value=1.8e-18  Score=130.38  Aligned_cols=84  Identities=19%  Similarity=0.366  Sum_probs=77.9

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+.+.++|||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           13 YQVVNLYVKNLDDGIDDERLRKAFSPF--GTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             SSCCCEEEECCCTTCCHHHHHHTTTTT--SCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            356899999999999999999999999  9999999999877889999999999999999998 9999999999999999


Q ss_pred             CCCCCCC
Q 022058          290 KTPVRPR  296 (303)
Q Consensus       290 ~~~~~~r  296 (303)
                      ++...++
T Consensus        91 ~~~~~~~   97 (103)
T 2d9p_A           91 QRKEERQ   97 (103)
T ss_dssp             SSCCCCC
T ss_pred             cccccCC
Confidence            8765443

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.78  E-value=2.8e-18  Score=127.24  Aligned_cols=86  Identities=22%  Similarity=0.366  Sum_probs=78.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.+++++  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   81 (95)
T 2dnz_A            4 GSSGLYVGSLHFNITEDMLRGIFEPF--GKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGH   81 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEE
Confidence            45899999999999999999999999  999999999985  7889999999999999999999 999999999999999


Q ss_pred             cCCCCCCCCCC
Q 022058          289 SKTPVRPRVTR  299 (303)
Q Consensus       289 a~~~~~~r~~r  299 (303)
                      +++...++...
T Consensus        82 a~~~~~~~~~~   92 (95)
T 2dnz_A           82 VTERLDGGSGP   92 (95)
T ss_dssp             SSCCCCCCCCC
T ss_pred             cccccCCCCCC
Confidence            98776555433

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}

Probab=99.78  E-value=2.2e-19  Score=132.53  Aligned_cols=78  Identities=24%  Similarity=0.244  Sum_probs=71.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCC-ceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEeec
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCG-QVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-L-GGTMLGYYPVRVLPS  190 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l-~g~~~~g~~i~v~~~  190 (303)
                      +.+|||+|||+++|+++|+++|+.|| .|.+|+|++|+.+  ++|||||+|.+.++|.+|++ + |+..+.|++|.|.++
T Consensus         1 S~~i~v~nLp~~~te~~l~~~F~~~G~~v~~v~i~~d~~t~~~rg~aFV~F~~~~~A~~Ai~~~~~~~~~~gr~i~V~~a   80 (91)
T 2lxi_A            1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQKVSMHYS   80 (91)
T ss_dssp             CCEEEEETCCSSCCHHHHHHHHHHHTCCCSBCCSSSCSSSCCCSSEEEEECSSHHHHHHHHHTTTTEEEETTEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCEeEEEEEEecCCCCCcCceEEEEecCHHHHHHHHHhcCCCeEECCEEEEEEEc
Confidence            46899999999999999999999999 8999999998764  89999999999999999998 6 567899999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        81 ~~~   83 (91)
T 2lxi_A           81 DPK   83 (91)
T ss_dssp             CSC
T ss_pred             CCC
Confidence            654

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.78  E-value=1.5e-18  Score=130.47  Aligned_cols=88  Identities=17%  Similarity=0.283  Sum_probs=80.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.+
T Consensus        11 ~~~~l~v~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A           11 DEGKLFVGGLSFDTNEQSLEQVFSKY--GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHH--SCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45899999999999999999999999  999999999984  6789999999999999999997 999999999999999


Q ss_pred             cCCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRPG  301 (303)
Q Consensus       289 a~~~~~~r~~r~~  301 (303)
                      +++....+..+.+
T Consensus        89 a~~~~~~~~~~~~  101 (102)
T 1x5s_A           89 AGKSSDNRSGPSS  101 (102)
T ss_dssp             EECCCCCCCCCCC
T ss_pred             CCCCCCCCCCCCC
Confidence            9988776655443

>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=99.78  E-value=2.6e-18  Score=129.94  Aligned_cols=88  Identities=19%  Similarity=0.245  Sum_probs=78.9

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCC---eeeE
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGS---QPIR  285 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g---~~l~  285 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+++. +.++|||||+|.+.++|.+|+. |||..+.|   +.|+
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~   90 (105)
T 2dnh_A           13 GRDRKLFVGMLNKQQSEEDVLRLFQPF--GVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLV   90 (105)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEE
Confidence            456899999999999999999999999  999999999985 7889999999999999999998 99999988   9999


Q ss_pred             EeecCCCCCCCCCCCC
Q 022058          286 VSPSKTPVRPRVTRPG  301 (303)
Q Consensus       286 v~~a~~~~~~r~~r~~  301 (303)
                      |.++++.. .+.+++|
T Consensus        91 V~~a~~~~-~~~~~~G  105 (105)
T 2dnh_A           91 VKFADTDK-ESGPSSG  105 (105)
T ss_dssp             EEESCSSC-CCSCSCC
T ss_pred             EEECccCc-ccCCCCC
Confidence            99998765 4444443

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.9e-18  Score=128.42  Aligned_cols=87  Identities=23%  Similarity=0.342  Sum_probs=78.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEE-EEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRL-RLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v-~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+ .|++++  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   81 (96)
T 1x5t_A            4 GSSGIFIGNLDPEIDEKLLYDTFSAF--GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS   81 (96)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTT--SCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            45899999999999999999999999  999999 999984  7889999999999999999999 99999999999999


Q ss_pred             ecCCCCCCCCCCCC
Q 022058          288 PSKTPVRPRVTRPG  301 (303)
Q Consensus       288 ~a~~~~~~r~~r~~  301 (303)
                      ++++....+ .|.|
T Consensus        82 ~a~~~~~~~-~~~g   94 (96)
T 1x5t_A           82 YAFKKDSKG-SGPS   94 (96)
T ss_dssp             ESCCCCCCC-CCCC
T ss_pred             EecccCCCC-CCCC
Confidence            998776443 3443

>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=99.77  E-value=2.7e-18  Score=129.40  Aligned_cols=82  Identities=30%  Similarity=0.458  Sum_probs=76.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+..+++|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2cqi_A           11 DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CCCCCCEEEEeCCCccCCHHHHHHHHHhcCCEeEEEEEecCCCCCCEEEEEECCHHHHHHHHHHhCCCCcCCCeEEEEEC
Confidence            445689999999999999999999999999999999999987789999999999999999999 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ...
T Consensus        91 ~~~   93 (103)
T 2cqi_A           91 TTP   93 (103)
T ss_dssp             CCT
T ss_pred             CCC
Confidence            654

>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=99.77  E-value=3.1e-18  Score=131.72  Aligned_cols=85  Identities=16%  Similarity=0.286  Sum_probs=77.8

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|+++.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|
T Consensus        22 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   99 (115)
T 2cpz_A           22 GPEGANLFIYHLPQEFGDQDLLQMFMPF--GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKV   99 (115)
T ss_dssp             CSTTCCEEEESCCSSCCHHHHHHHHGGG--SCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            3456899999999999999999999999  999999999985  7899999999999999999998 9999999999999


Q ss_pred             eecCCCCCCC
Q 022058          287 SPSKTPVRPR  296 (303)
Q Consensus       287 ~~a~~~~~~r  296 (303)
                      .|+++....+
T Consensus       100 ~~a~~~~~~~  109 (115)
T 2cpz_A          100 QLKRSKNDSK  109 (115)
T ss_dssp             ECCCCSCCCC
T ss_pred             EEcCCCCcCC
Confidence            9998775443

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.77  E-value=3.3e-18  Score=127.99  Aligned_cols=83  Identities=17%  Similarity=0.257  Sum_probs=77.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+.|||..+.|+.|+|.++
T Consensus         9 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~a   86 (99)
T 2dgs_A            9 KSNKIFVGGIPHNCGETELREYFKKF--GVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKRA   86 (99)
T ss_dssp             SCCEEEEESCCSSCCHHHHHHHHSSS--SCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEEC
Confidence            45899999999999999999999999  999999999985  77899999999999999999999999999999999999


Q ss_pred             CCCCCCC
Q 022058          290 KTPVRPR  296 (303)
Q Consensus       290 ~~~~~~r  296 (303)
                      +++...+
T Consensus        87 ~~~~~~~   93 (99)
T 2dgs_A           87 EPRDSKS   93 (99)
T ss_dssp             CCCCCCC
T ss_pred             CCCcccC
Confidence            8775444

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=4e-18  Score=128.44  Aligned_cols=83  Identities=22%  Similarity=0.344  Sum_probs=77.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|+.+..+++|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   90 (103)
T 2cq3_A           11 SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA   90 (103)
T ss_dssp             CSCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcEEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            344678999999999999999999999999999999999887789999999999999999998 9999999999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      .+..
T Consensus        91 ~~~~   94 (103)
T 2cq3_A           91 TARV   94 (103)
T ss_dssp             CSSC
T ss_pred             ccCC
Confidence            7543

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.77  E-value=4.5e-19  Score=131.81  Aligned_cols=78  Identities=19%  Similarity=0.226  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCc--eeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCc----ccCCeeE
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQ--VVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGT----MLGYYPV  185 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~--i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~----~~~g~~i  185 (303)
                      .-.+|||+|||+++|+++|+++|++||.  |.+|++++|+.+  ++|||||+|.+.++|.+|++ |||.    .++||+|
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr~i   87 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTI   87 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTTCCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTEEE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhhCCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCEEE
Confidence            4678999999999999999999999995  679999998865  89999999999999999998 9987    4889999


Q ss_pred             EEeecCC
Q 022058          186 RVLPSKT  192 (303)
Q Consensus       186 ~v~~~~~  192 (303)
                      .|.|++.
T Consensus        88 ~V~~Aks   94 (95)
T 2lkz_A           88 GVDFAKS   94 (95)
T ss_dssp             EEEECCC
T ss_pred             EEEEccC
Confidence            9999863

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.77  E-value=5.5e-18  Score=130.32  Aligned_cols=87  Identities=20%  Similarity=0.262  Sum_probs=79.1

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+++.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   90 (115)
T 2dgo_A           13 SNHFHVFVGDLSPEITTEDIKAAFAPF--GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTN   90 (115)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            356899999999999999999999999  999999999984  7889999999999999999998 99999999999999


Q ss_pred             ecCCCCCCCCCC
Q 022058          288 PSKTPVRPRVTR  299 (303)
Q Consensus       288 ~a~~~~~~r~~r  299 (303)
                      |+++....+...
T Consensus        91 ~a~~~~~~~~~~  102 (115)
T 2dgo_A           91 WATRKPPAPKST  102 (115)
T ss_dssp             ESSCCCCCSCCC
T ss_pred             EccCCCCCCccc
Confidence            998776555443

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens}

Probab=99.77  E-value=2.2e-18  Score=131.69  Aligned_cols=78  Identities=15%  Similarity=0.114  Sum_probs=74.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||+.+++++|+++|++|  |.|.+|.|++|+  ++++|||||+|.+.++|.+|++ |||..+.|+.|+|.+
T Consensus         5 p~~~lfV~nL~~~~te~~L~~~F~~~--G~i~~v~i~~d~~tg~~rG~aFV~f~~~~~A~~Ai~~lng~~~~gr~i~V~~   82 (110)
T 3s8s_A            5 PLKEVTFARLNDNVRETFLKDMCRKY--GEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVKNLHLTSVMGNIIHAQL   82 (110)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCcEEEEECCCCCCCHHHHHHHHHhc--CCeeEEEEEECCCCCceeeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            45899999999999999999999999  999999999985  7899999999999999999998 999999999999999


Q ss_pred             cCC
Q 022058          289 SKT  291 (303)
Q Consensus       289 a~~  291 (303)
                      +..
T Consensus        83 a~~   85 (110)
T 3s8s_A           83 DIK   85 (110)
T ss_dssp             CST
T ss_pred             CCC
Confidence            864

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.77  E-value=2.5e-18  Score=128.37  Aligned_cols=85  Identities=20%  Similarity=0.304  Sum_probs=77.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---C--CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---V--HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~--~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|+++.   |  .++|||||+|.+.++|.+|+. |||..+.|+.|+
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~   81 (98)
T 2cpf_A            4 GSSGLFIKNLNFSTTEETLKGVFSKV--GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLE   81 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEE
Confidence            45899999999999999999999999  999999999874   3  789999999999999999999 999999999999


Q ss_pred             EeecCCCCCCCCC
Q 022058          286 VSPSKTPVRPRVT  298 (303)
Q Consensus       286 v~~a~~~~~~r~~  298 (303)
                      |.++++...++..
T Consensus        82 V~~a~~~~~~~~~   94 (98)
T 2cpf_A           82 VRISERATKPASG   94 (98)
T ss_dssp             EECSSCSSCCCCC
T ss_pred             EEEccCCCCCCCC
Confidence            9999887655543

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.77  E-value=1.1e-18  Score=131.83  Aligned_cols=80  Identities=19%  Similarity=0.250  Sum_probs=74.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++|+++|+++|+.||+|.+|.|++++.+ ++|||||+|.+.++|.+|+.+|+..+.|+.|.|.++
T Consensus         7 ~~~~~~~lfV~~Lp~~~te~~L~~~F~~~G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~   86 (103)
T 1s79_A            7 NDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFK   86 (103)
T ss_dssp             SCSGGGCEEEECCCTTCCHHHHHHHHHTSSCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEH
T ss_pred             ccCCCCEEEEECCCCCCCHHHHHHHHhhcCCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            3445789999999999999999999999999999999998765 899999999999999999999999999999999986


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      .
T Consensus        87 ~   87 (103)
T 1s79_A           87 D   87 (103)
T ss_dssp             H
T ss_pred             h
Confidence            4

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A

Probab=99.76  E-value=6e-18  Score=130.09  Aligned_cols=84  Identities=27%  Similarity=0.451  Sum_probs=76.9

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       111 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      .+....++|||+|||+++++++|+++|+.||.|.+|.|+.+..+  ++|||||+|.+.++|.+|+. ||+..+.|+.|.|
T Consensus        10 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   89 (115)
T 2dgo_A           10 KDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRT   89 (115)
T ss_dssp             CCSTTCEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEE
T ss_pred             CCCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            34557889999999999999999999999999999999998644  78999999999999999998 9999999999999


Q ss_pred             eecCCCC
Q 022058          188 LPSKTAI  194 (303)
Q Consensus       188 ~~~~~~~  194 (303)
                      .++....
T Consensus        90 ~~a~~~~   96 (115)
T 2dgo_A           90 NWATRKP   96 (115)
T ss_dssp             EESSCCC
T ss_pred             EEccCCC
Confidence            9987654

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.3e-18  Score=129.49  Aligned_cols=84  Identities=25%  Similarity=0.322  Sum_probs=77.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|+++.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.+
T Consensus        11 ~~~~l~V~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A           11 TKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTT--SCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcc--CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            55899999999999999999999999  999999999884  6789999999999999999998 999999999999999


Q ss_pred             cCCCCCCCC
Q 022058          289 SKTPVRPRV  297 (303)
Q Consensus       289 a~~~~~~r~  297 (303)
                      ++++...+.
T Consensus        89 a~~~~~~~~   97 (102)
T 2cqb_A           89 AKPMRIKES   97 (102)
T ss_dssp             CCCCCCCCC
T ss_pred             CCCCCCCCC
Confidence            987754443

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.76  E-value=5.2e-19  Score=130.13  Aligned_cols=77  Identities=19%  Similarity=0.270  Sum_probs=68.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCC--ceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      .+|||+|||+++++++|+++|+.||  .|.+++++.++.+  ++|||||+|.+.++|.+|++ |||..+.|+.|.|.++.
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~~~   81 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTPSN   81 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTTTCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECCC-
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHhCCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEECC
Confidence            5799999999999999999999999  9999999998754  79999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        82 ~~   83 (90)
T 3p5t_L           82 KL   83 (90)
T ss_dssp             --
T ss_pred             CC
Confidence            54

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=9e-18  Score=129.35  Aligned_cols=89  Identities=17%  Similarity=0.301  Sum_probs=81.2

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+. ||+ .|.|+.|+|
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V   90 (116)
T 2cqd_A           14 DTTFTKIFVGGLPYHTTDASLRKYFEGF--GDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANV   90 (116)
T ss_dssp             SCSSSEEEEECCCSSCCHHHHHHHHHTT--SCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEE
Confidence            3456899999999999999999999999  999999999985  7899999999999999999999 898 899999999


Q ss_pred             eecCCCCCCCCCCCC
Q 022058          287 SPSKTPVRPRVTRPG  301 (303)
Q Consensus       287 ~~a~~~~~~r~~r~~  301 (303)
                      .++++...++..+++
T Consensus        91 ~~a~~~~~~~~~~~~  105 (116)
T 2cqd_A           91 NLAYLGAKPRSLQTG  105 (116)
T ss_dssp             EESTTTCCCCCCCCC
T ss_pred             EEcccCCCccccCCC
Confidence            999888777776654

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}

Probab=99.76  E-value=7.3e-19  Score=130.68  Aligned_cols=78  Identities=21%  Similarity=0.266  Sum_probs=71.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcc--eeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCc----eeCCe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGE--VTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGM----VLGSQ  282 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~--i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~----~~~g~  282 (303)
                      .-.+|||+|||+.+|+++|+++|++|  |.  |.+|+|++|+  |+++|||||+|.+.++|.+|++ |||.    .++||
T Consensus         8 ~m~tlfV~nL~~~~tee~L~~~F~~~--G~i~v~~v~i~~d~~tg~srG~aFV~f~~~~~A~~Ai~~lng~~~~~~i~Gr   85 (95)
T 2lkz_A            8 HMDTIILRNIAPHTVVDSIMTALSPY--ASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGK   85 (95)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHSTTT--CCCCGGGEECCCCSSSSSCSSEEEEECSSSHHHHHHHHHHHSSSSCEEETTE
T ss_pred             ccCEEEEeCCCCcCCHHHHHHHHHhh--CCccEEEEEEEecCCCCCCceEeEEEECCHHHHHHHHHHhcCCCCCceECCE
Confidence            34789999999999999999999999  95  6789999985  7899999999999999999998 9986    58999


Q ss_pred             eeEEeecCC
Q 022058          283 PIRVSPSKT  291 (303)
Q Consensus       283 ~l~v~~a~~  291 (303)
                      .|.|+||+.
T Consensus        86 ~i~V~~Aks   94 (95)
T 2lkz_A           86 TIGVDFAKS   94 (95)
T ss_dssp             EEEEEECCC
T ss_pred             EEEEEEccC
Confidence            999999985

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.76  E-value=5.9e-18  Score=128.30  Aligned_cols=85  Identities=20%  Similarity=0.285  Sum_probs=77.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC---CCCcccEEEEEEcCHHHHHHHHH-h-CCceeCCeee
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD---HVHSTRIAFVEFAVAESAILALN-C-SGMVLGSQPI  284 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d---~~~~~g~afV~f~~~e~A~~Ai~-l-~g~~~~g~~l  284 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|+++   .+.++|||||+|.+.++|.+|+. | ||..|.|+.|
T Consensus        12 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l   89 (107)
T 2cph_A           12 KQTTSKILVRNIPFQANQREIRELFSTF--GELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRL   89 (107)
T ss_dssp             SSCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHHcc--CCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEE
Confidence            3456899999999999999999999999  99999999988   47889999999999999999998 9 9999999999


Q ss_pred             EEeecCCCCCCC
Q 022058          285 RVSPSKTPVRPR  296 (303)
Q Consensus       285 ~v~~a~~~~~~r  296 (303)
                      +|.|+++.....
T Consensus        90 ~v~~a~~~~~~~  101 (107)
T 2cph_A           90 VLEWADSEVTVQ  101 (107)
T ss_dssp             EEEECCCCCCCC
T ss_pred             EEEeCCCCCCCC
Confidence            999998765443

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.76  E-value=3.3e-18  Score=126.13  Aligned_cols=82  Identities=21%  Similarity=0.246  Sum_probs=77.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.|.++.+.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~f~~~--G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            7 GACQIFVRNLPFDFTWKMLKDKFNEC--GHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SCCEEEECSCCTTCCHHHHHHHHHTT--SCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45899999999999999999999999  9999999999888899999999999999999998 99999999999999998


Q ss_pred             CCCCC
Q 022058          291 TPVRP  295 (303)
Q Consensus       291 ~~~~~  295 (303)
                      ++..+
T Consensus        85 ~~~~~   89 (92)
T 2dgv_A           85 NASGP   89 (92)
T ss_dssp             CCSSC
T ss_pred             CCCCC
Confidence            76544

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C

Probab=99.76  E-value=5.2e-19  Score=130.14  Aligned_cols=81  Identities=15%  Similarity=0.204  Sum_probs=68.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCc--ceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGG--EVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G--~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+|||+|||..+++++|+++|++|  |  .|.++.|+.++  |+++|||||+|.+.++|.+|++ |||..++|+.|+|.+
T Consensus         2 ~~l~V~nL~~~~t~~~l~~~F~~~--G~~~v~~v~i~~~~~~g~~kG~afV~f~~~~~a~~Ai~~l~g~~~~gr~i~V~~   79 (90)
T 3p5t_L            2 IALYIGNLTWWTTDEDLTEAVHSL--GVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP   79 (90)
T ss_dssp             --CEEESCCTTCCHHHHHHHHHTT--TCCCCCCEEEEECTTTCCEEEEEEECC-CHHHHHHHHHHGGGSCSSSCCCEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHHh--CCCceEEEEEEecCCCCccCcEEEEEECCHHHHHHHHHHcCCCeeCCEEEEEEE
Confidence            579999999999999999999999  9  99999999984  7899999999999999999998 999999999999999


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      +.|+..+.
T Consensus        80 ~~~~~~~~   87 (90)
T 3p5t_L           80 SNKLEHHH   87 (90)
T ss_dssp             C-------
T ss_pred             CCCCcccc
Confidence            98876443

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*

Probab=99.76  E-value=2.4e-18  Score=124.85  Aligned_cols=78  Identities=27%  Similarity=0.399  Sum_probs=73.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|++ |||..+.|++|.|.++
T Consensus         5 ~~~~~l~V~nl~~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   84 (85)
T 3mdf_A            5 TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   84 (85)
T ss_dssp             CCSSEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhccCCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            46789999999999999999999999999999999998654  79999999999999999997 9999999999999987


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      +
T Consensus        85 k   85 (85)
T 3mdf_A           85 K   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.76  E-value=3.9e-18  Score=123.20  Aligned_cols=76  Identities=22%  Similarity=0.386  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .+|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|+. |||..+.|++|.|.++++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~~   80 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAAK   80 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTSTTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecCc
Confidence            57999999999999999999999999999999998654  79999999999999999999 999999999999999864

>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=99.76  E-value=2.8e-18  Score=125.14  Aligned_cols=78  Identities=28%  Similarity=0.466  Sum_probs=72.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|+. |||..+.|+.|.|.+++
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   84 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWAT   84 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEecC
Confidence            5788999999999999999999999999999999998644  78999999999999999999 99999999999999986


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      +
T Consensus        85 ~   85 (87)
T 3bs9_A           85 R   85 (87)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.76  E-value=4.4e-18  Score=124.05  Aligned_cols=79  Identities=22%  Similarity=0.301  Sum_probs=72.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|.++.++++.  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus         5 ~~~~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (87)
T 3bs9_A            5 SHFHVFVGDLSPEITTAAIAAAFAPF--GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNW   82 (87)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEe
Confidence            45899999999999999999999999  999999999984  7889999999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      +++.
T Consensus        83 a~~k   86 (87)
T 3bs9_A           83 ATRK   86 (87)
T ss_dssp             EC--
T ss_pred             cCCC
Confidence            9864

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=7e-18  Score=126.18  Aligned_cols=82  Identities=23%  Similarity=0.293  Sum_probs=75.8

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+.+|+..+.|++|.|.+
T Consensus         6 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~l~V~~   85 (99)
T 2dgs_A            6 SGSKSNKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDIMGKKVEVKR   85 (99)
T ss_dssp             CCSSCCEEEEESCCSSCCHHHHHHHHSSSSCEEEEEECCCTTTCSCCSEEEEEESSHHHHHHHHHHCCCBSSSCBCEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCCCceEEEEECCHHHHHHHHHhCCCEECCeEEEEEE
Confidence            3446789999999999999999999999999999999998754  79999999999999999999999999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      +.+.
T Consensus        86 a~~~   89 (99)
T 2dgs_A           86 AEPR   89 (99)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8654

>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=99.76  E-value=4.9e-18  Score=130.98  Aligned_cols=86  Identities=21%  Similarity=0.342  Sum_probs=78.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|+.+. +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            6 HPGKLFIGGLNRETNEKMLKAVFGKH--GPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             SCCEEEEECCTTTCCHHHHHHHHHTS--SCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            45899999999999999999999999  999999999986 7889999999999999999998 9999999999999999


Q ss_pred             CCCCCCCCCC
Q 022058          290 KTPVRPRVTR  299 (303)
Q Consensus       290 ~~~~~~r~~r  299 (303)
                      +++......|
T Consensus        84 ~~~~~~~~~~   93 (116)
T 2fy1_A           84 KKPSFQSGGR   93 (116)
T ss_dssp             CCSSCSSSSS
T ss_pred             CCCCCCCCCC
Confidence            8877554433

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.76  E-value=7.6e-18  Score=124.91  Aligned_cols=81  Identities=31%  Similarity=0.477  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   82 (95)
T 2dnz_A            3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPMRVGHV   82 (95)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEECCSSSCCCCSEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEEES
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            46789999999999999999999999999999999998754  79999999999999999999 9999999999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      ....
T Consensus        83 ~~~~   86 (95)
T 2dnz_A           83 TERL   86 (95)
T ss_dssp             SCCC
T ss_pred             cccc
Confidence            6543

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.76  E-value=3.2e-18  Score=128.99  Aligned_cols=81  Identities=21%  Similarity=0.247  Sum_probs=75.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|+.+.  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   89 (103)
T 2dnm_A           12 GMITLKVDNLTYRTSPDSLRRVFEKY--GRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQV   89 (103)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEEE
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            45899999999999999999999999  999999999885  6889999999999999999999 999999999999999


Q ss_pred             cCCCCC
Q 022058          289 SKTPVR  294 (303)
Q Consensus       289 a~~~~~  294 (303)
                      +++..+
T Consensus        90 a~~~~~   95 (103)
T 2dnm_A           90 ARYGRR   95 (103)
T ss_dssp             CSSCCS
T ss_pred             CCcCCC
Confidence            987643

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=4e-18  Score=128.48  Aligned_cols=82  Identities=21%  Similarity=0.301  Sum_probs=75.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      +....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           11 RADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             CCSSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            4456889999999999999999999999999999999998654  79999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      ++.+.
T Consensus        91 ~a~~~   95 (103)
T 2cq0_A           91 WAKPS   95 (103)
T ss_dssp             ESSCC
T ss_pred             ECCCC
Confidence            98654

>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=99.76  E-value=7.4e-18  Score=128.62  Aligned_cols=87  Identities=21%  Similarity=0.305  Sum_probs=78.6

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hC------CceeCC
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CS------GMVLGS  281 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~------g~~~~g  281 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..|.|+++.  +.++|||||+|.+.++|.+|+. ||      |..+.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           13 TEGKTVFIRNLSFDSEEEALGEVLQQF--GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            356899999999999999999999999  999999999985  6789999999999999999998 99      999999


Q ss_pred             eeeEEeecCCCCCCCCCC
Q 022058          282 QPIRVSPSKTPVRPRVTR  299 (303)
Q Consensus       282 ~~l~v~~a~~~~~~r~~r  299 (303)
                      +.|+|.++++.......+
T Consensus        91 ~~l~v~~a~~~~~~~~~~  108 (111)
T 1x4h_A           91 RQLKVDLAVTRDEAASGP  108 (111)
T ss_dssp             CEEEEECCCCCCCCCCCC
T ss_pred             EEEEEEECCCCccCCCCC
Confidence            999999998775544433

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=2.9e-18  Score=129.17  Aligned_cols=79  Identities=19%  Similarity=0.225  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG--GTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~--g~~~~g~~i~v~  188 (303)
                      .+...++|||+|||+++++++|+++|++||.|.+|.|+++    +|||||+|.+.++|.+|++ ++  +..+.|++|.|.
T Consensus        12 ~~~~~~~LfV~nLp~~vte~dL~~lF~~fG~V~~v~i~~~----kGfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   87 (105)
T 1sjq_A           12 SGVPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQ   87 (105)
T ss_dssp             CCCCCCEEEECSCCTTSCHHHHHHHHHHHCCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            4557899999999999999999999999999999999875    6899999999999999998 76  478999999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      +++...
T Consensus        88 ~A~~~~   93 (105)
T 1sjq_A           88 FSNHKE   93 (105)
T ss_dssp             CCSSSS
T ss_pred             EcCCCC
Confidence            987553

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.76  E-value=5.7e-18  Score=127.62  Aligned_cols=82  Identities=23%  Similarity=0.344  Sum_probs=76.4

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (103)
T 2cq0_A           13 DDNATIRVTNLSEDTRETDLQELFRPF--GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVE   90 (103)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTT--CCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEeecCCCCceeeEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            356899999999999999999999999  999999999884  7899999999999999999999 99999999999999


Q ss_pred             ecCCCCC
Q 022058          288 PSKTPVR  294 (303)
Q Consensus       288 ~a~~~~~  294 (303)
                      ++++...
T Consensus        91 ~a~~~~~   97 (103)
T 2cq0_A           91 WAKPSTN   97 (103)
T ss_dssp             ESSCCCC
T ss_pred             ECCCCCC
Confidence            9987653

>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=99.76  E-value=4.7e-18  Score=124.02  Aligned_cols=79  Identities=20%  Similarity=0.375  Sum_probs=73.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+++++..+.|+.|.|.+
T Consensus         7 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            7 NEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             CCSCTTEEEEECCCTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            4457889999999999999999999999999999999998764  79999999999999999999888899999999987


Q ss_pred             c
Q 022058          190 S  190 (303)
Q Consensus       190 ~  190 (303)
                      +
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.76  E-value=6.8e-18  Score=121.92  Aligned_cols=77  Identities=17%  Similarity=0.265  Sum_probs=73.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      .+|||+|||..+++++|+++|++|  |.|.++.++++.  +.++|||||+|.+.++|.+|+. |||..++|+.|+|.+++
T Consensus         2 ~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   79 (83)
T 3md1_A            2 FNLFVGDLNVNVDDETLRNAFKDF--PSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRINWAA   79 (83)
T ss_dssp             EEEEEECCCTTCCHHHHHHHHTTS--TTEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             eEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEEcCCCCCccceEEEEECCHHHHHHHHHHhcCCeeCCcEEEEEecC
Confidence            689999999999999999999999  999999999884  7889999999999999999999 99999999999999998


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        80 ~~   81 (83)
T 3md1_A           80 KL   81 (83)
T ss_dssp             CC
T ss_pred             cC
Confidence            65

>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=99.76  E-value=4.2e-18  Score=126.83  Aligned_cols=79  Identities=23%  Similarity=0.233  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          114 SVRRTVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ...++|||+|||+++++++|+    ++|+.||.|.+|.++.+..+ +|||||+|.+.++|.+|+. |||..+.|++|+|.
T Consensus         7 ~~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~G~v~~v~i~~~~~~-rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~   85 (96)
T 2dgx_A            7 GNGADVQVSNIDYRLSRKELQQLLQEAFARHGKVKSVELSPHTDY-QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVS   85 (96)
T ss_dssp             SSCEEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECSCCST-TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhccccCcEEEEEEEeCCCC-CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            356889999999999999999    99999999999999998887 9999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      ++++.
T Consensus        86 ~a~~~   90 (96)
T 2dgx_A           86 LATGA   90 (96)
T ss_dssp             ECCCS
T ss_pred             EcCCC
Confidence            98654

>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=99.76  E-value=8.4e-18  Score=127.07  Aligned_cols=84  Identities=27%  Similarity=0.344  Sum_probs=77.6

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           13 NQDATVYVGGLDEKVSEPLLWELFLQA--GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CTTTEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            355899999999999999999999999  999999999985  7899999999999999999999 99999999999999


Q ss_pred             ecCCCCCCC
Q 022058          288 PSKTPVRPR  296 (303)
Q Consensus       288 ~a~~~~~~r  296 (303)
                      ++++....+
T Consensus        91 ~a~~~~~~~   99 (105)
T 1x5u_A           91 KASAHNKNL   99 (105)
T ss_dssp             ETTTTSCCC
T ss_pred             ECCCCCcCC
Confidence            998775444

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=5.7e-18  Score=126.92  Aligned_cols=82  Identities=21%  Similarity=0.331  Sum_probs=75.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. ||+..+.|++|.|.+
T Consensus        13 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           13 TSLEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             SCCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            3446789999999999999999999999999999999998844 78999999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      +++.
T Consensus        93 a~~~   96 (100)
T 2do4_A           93 SNSG   96 (100)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A

Probab=99.75  E-value=9.9e-19  Score=138.59  Aligned_cols=106  Identities=21%  Similarity=0.293  Sum_probs=77.2

Q ss_pred             chHHhhhhcccCCC----CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEE
Q 022058           87 NNRRRRNNFNQGRK----RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAF  160 (303)
Q Consensus        87 ~A~~a~~~~~~g~~----~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~f  160 (303)
                      .+..|+..+++|..    ....  ..........++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++||||
T Consensus        16 ~~~~a~~~~~g~~~~g~~~~~~--~~~~~~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~~g~~~G~af   93 (135)
T 2lea_A           16 PRGSHMASMTGGQQMGRGSMSY--GRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAF   93 (135)
T ss_dssp             -------------------CCS--CCSCSSGGGCCCEEEECCCSSCHHHHHHHHHGGGSCCSEEECCCCSSSSSCCSCCE
T ss_pred             chhhhhhhccCCCCCCCCCCCc--CCCCCCCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCccceEEE
Confidence            67778888877333    1111  112223345789999999999999999999999999999999988654  899999


Q ss_pred             EEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCC
Q 022058          161 VEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAI  194 (303)
Q Consensus       161 V~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~  194 (303)
                      |+|.+.++|.+|+. ||+..+.|++|.|.+++...
T Consensus        94 V~F~~~~~A~~Ai~~l~g~~i~g~~l~V~~a~~~~  128 (135)
T 2lea_A           94 VRFHDKRDAEDAMDAMDGAVLDGRELRVQMARYGR  128 (135)
T ss_dssp             EECSCHHHHHHHHTTTTTCCSSSSCCEEEECCCCC
T ss_pred             EEECCHHHHHHHHHHcCCCEECCEEEEEEECCCCC
Confidence            99999999999998 99999999999999987543

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=3.3e-18  Score=130.51  Aligned_cols=82  Identities=22%  Similarity=0.333  Sum_probs=76.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+..+++|||||+|.+.++|.+|+. |||..+.|++|.|.++
T Consensus        25 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  104 (109)
T 2err_A           25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA  104 (109)
T ss_dssp             CTTCCCEEEEESCCTTCCHHHHHHHGGGTCCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCCEEEEECCCCcCCHHHHHHHHHhcCCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            344688999999999999999999999999999999999877789999999999999999999 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus       105 ~~~  107 (109)
T 2err_A          105 TAR  107 (109)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            643

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=4.3e-18  Score=126.19  Aligned_cols=80  Identities=26%  Similarity=0.297  Sum_probs=74.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. ||+..+.|++|.|.
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             SCCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3446788999999999999999999999999999999998764  78999999999999999999 99999999999999


Q ss_pred             ecC
Q 022058          189 PSK  191 (303)
Q Consensus       189 ~~~  191 (303)
                      +++
T Consensus        91 ~a~   93 (95)
T 2cqc_A           91 GPS   93 (95)
T ss_dssp             CCS
T ss_pred             ecC
Confidence            975

>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=99.75  E-value=7.2e-18  Score=126.06  Aligned_cols=82  Identities=27%  Similarity=0.316  Sum_probs=75.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+. ||+..+.|++|.|.+
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   84 (99)
T 1whw_A            5 SSGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             CCSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEEecCCCCCcCeEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            346789999999999999999999999999999999998744  79999999999999999997 999999999999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      +.+..
T Consensus        85 a~~~~   89 (99)
T 1whw_A           85 STIKK   89 (99)
T ss_dssp             CCCCS
T ss_pred             cCCCc
Confidence            87653

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=1e-17  Score=125.56  Aligned_cols=81  Identities=21%  Similarity=0.350  Sum_probs=75.9

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+. +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus        15 ~~~~~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   92 (100)
T 2do4_A           15 LEKHKLFISGLPFSCTKEELEEICKAH--GTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENIIKVAI   92 (100)
T ss_dssp             CCCSCEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEEECCCCCEEeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            355899999999999999999999999  999999999986 7889999999999999999998 999999999999999


Q ss_pred             cCCCC
Q 022058          289 SKTPV  293 (303)
Q Consensus       289 a~~~~  293 (303)
                      ++++.
T Consensus        93 a~~~~   97 (100)
T 2do4_A           93 SNSGP   97 (100)
T ss_dssp             CCCCS
T ss_pred             CCCCC
Confidence            98764

>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=99.75  E-value=3.9e-18  Score=126.51  Aligned_cols=80  Identities=28%  Similarity=0.465  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+ ++|||||+|.+.++|.+|+. ||+..+.|++|.|.+
T Consensus        12 ~~~~~~~l~v~nlp~~~~~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~   91 (95)
T 2ywk_A           12 QEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSG   91 (95)
T ss_dssp             CTTGGGEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEE
Confidence            3446789999999999999999999999999999999998765 79999999999999999999 999999999999998


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      ++
T Consensus        92 a~   93 (95)
T 2ywk_A           92 PS   93 (95)
T ss_dssp             CC
T ss_pred             cC
Confidence            75

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A

Probab=99.75  E-value=8.8e-18  Score=126.97  Aligned_cols=82  Identities=26%  Similarity=0.377  Sum_probs=75.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCC---eeEEE
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGY---YPVRV  187 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g---~~i~v  187 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+.++.+ ++|||||+|.+.++|.+|+. ||+..+.|   ++|.|
T Consensus        12 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gg~~~~l~V   91 (105)
T 2dnh_A           12 GGRDRKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGSQTMPGASSSLVV   91 (105)
T ss_dssp             CCCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECSSSCEEEEEEEEESSHHHHHHHHHHHSSCCCCTTCSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcCcEEEEEeCCHHHHHHHHHHHcCCccCCCCCccEEE
Confidence            346789999999999999999999999999999999998754 79999999999999999998 99999988   99999


Q ss_pred             eecCCCC
Q 022058          188 LPSKTAI  194 (303)
Q Consensus       188 ~~~~~~~  194 (303)
                      .+++...
T Consensus        92 ~~a~~~~   98 (105)
T 2dnh_A           92 KFADTDK   98 (105)
T ss_dssp             EESCSSC
T ss_pred             EECccCc
Confidence            9987543

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.75  E-value=2.8e-18  Score=123.91  Aligned_cols=72  Identities=14%  Similarity=0.124  Sum_probs=68.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .+..|||+||++.+|+++|+++|.+||+|.++++..    ++|||||+|.+.++|.+|++ ||+..+.|++|+|.++
T Consensus         6 ~~~wL~VgNL~~~~te~~L~~lF~q~G~V~~~~l~~----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A   78 (89)
T 2wbr_A            6 GSSWLLLKNLTAQIDGPTLRTLCMQHGPLVSFHPYL----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESP   78 (89)
T ss_dssp             CCCEEEEECCCTTCCCHHHHHHHHHHSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECC
T ss_pred             ccceEEEeCCCccCCHHHHHHHHHhhCCEEEEEEcC----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEEC
Confidence            467899999999999999999999999999999965    58999999999999999999 9999999999999986

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.75  E-value=4.4e-18  Score=125.94  Aligned_cols=80  Identities=24%  Similarity=0.325  Sum_probs=74.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|++ ||+..+.|++|.|.
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   91 (94)
T 2e5h_A           12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKAS   91 (94)
T ss_dssp             CCCCTTSEEEESCCTTSCHHHHHHHTTTTSCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEE
T ss_pred             CCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEE
Confidence            3446789999999999999999999999999999999998764  79999999999999999998 99999999999999


Q ss_pred             ecC
Q 022058          189 PSK  191 (303)
Q Consensus       189 ~~~  191 (303)
                      +++
T Consensus        92 ~ak   94 (94)
T 2e5h_A           92 IAI   94 (94)
T ss_dssp             ECC
T ss_pred             ecC
Confidence            873

>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=99.75  E-value=7.9e-18  Score=129.45  Aligned_cols=83  Identities=22%  Similarity=0.401  Sum_probs=75.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|+.++.+  ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.
T Consensus        21 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~  100 (115)
T 2cpz_A           21 EGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ  100 (115)
T ss_dssp             CCSTTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCCcCccEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3446789999999999999999999999999999999998754  78999999999999999998 99999999999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      ++++..
T Consensus       101 ~a~~~~  106 (115)
T 2cpz_A          101 LKRSKN  106 (115)
T ss_dssp             CCCCSC
T ss_pred             EcCCCC
Confidence            986543

>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=99.75  E-value=6.3e-18  Score=127.76  Aligned_cols=83  Identities=30%  Similarity=0.388  Sum_probs=76.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+. ||+..+.|++|.|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   90 (105)
T 1x5u_A           11 ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVN   90 (105)
T ss_dssp             CCCTTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCcCCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            4456889999999999999999999999999999999998754  79999999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      ++.+..
T Consensus        91 ~a~~~~   96 (105)
T 1x5u_A           91 KASAHN   96 (105)
T ss_dssp             ETTTTS
T ss_pred             ECCCCC
Confidence            986543

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A

Probab=99.75  E-value=8.2e-18  Score=123.97  Aligned_cols=81  Identities=20%  Similarity=0.251  Sum_probs=74.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ....++|||+|||+++++++|+++|+.||.|.++.++.+...++|||||+|.+.++|.+|+. ||+..+.|+.|.|.+++
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~f~~~G~v~~~~i~~~~g~~~g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a~   84 (92)
T 2dgv_A            5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNGMKLSGREIDVRIDR   84 (92)
T ss_dssp             SSSCCEEEECSCCTTCCHHHHHHHHHTTSCEEEEEEEESSSCEEEEEEEEESSHHHHHHHHHHHTTCCBTTBCCCCEECS
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEccCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            34678999999999999999999999999999999998655589999999999999999999 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        85 ~~   86 (92)
T 2dgv_A           85 NA   86 (92)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=8.4e-18  Score=126.67  Aligned_cols=83  Identities=24%  Similarity=0.386  Sum_probs=75.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+...++|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   90 (103)
T 2d9p_A           11 TRYQVVNLYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA   90 (103)
T ss_dssp             CCSSCCCEEEECCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEEC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEcCCCCcCEEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEEe
Confidence            344688999999999999999999999999999999999833479999999999999999999 9999999999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      .+..
T Consensus        91 ~~~~   94 (103)
T 2d9p_A           91 QRKE   94 (103)
T ss_dssp             SSCC
T ss_pred             cccc
Confidence            7543

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.75  E-value=6.3e-18  Score=126.16  Aligned_cols=81  Identities=27%  Similarity=0.456  Sum_probs=74.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC-----CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH-----SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~-----~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.+..     .++|||||+|.+.++|.+|+. ||+..+.|++|.|
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~gt~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V   82 (98)
T 2cpf_A            3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEV   82 (98)
T ss_dssp             CCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCcCcccEEEEEECCHHHHHHHHHHhCCCeeCCeEEEE
Confidence            3578999999999999999999999999999999998765     378999999999999999999 9999999999999


Q ss_pred             eecCCCC
Q 022058          188 LPSKTAI  194 (303)
Q Consensus       188 ~~~~~~~  194 (303)
                      .+++...
T Consensus        83 ~~a~~~~   89 (98)
T 2cpf_A           83 RISERAT   89 (98)
T ss_dssp             ECSSCSS
T ss_pred             EEccCCC
Confidence            9987653

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=1.1e-17  Score=124.49  Aligned_cols=80  Identities=25%  Similarity=0.265  Sum_probs=74.3

Q ss_pred             ccceEEEcCCCCCCCHHHHH----HHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVK----QFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~----~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ..++|||+|||..+++++|+    ++|++|  |.|.+|.|+++... +|||||+|.+.++|.+|+. |||..+.|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~~~~~l~~~l~~~F~~~--G~v~~v~i~~~~~~-rg~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V   84 (96)
T 2dgx_A            8 NGADVQVSNIDYRLSRKELQQLLQEAFARH--GKVKSVELSPHTDY-QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILV   84 (96)
T ss_dssp             SCEEEEEESCCTTSCHHHHHHHHHHHHHHH--SCEEEEEECSCCST-TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhcccc--CcEEEEEEEeCCCC-CeEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            44789999999999999999    999999  99999999999755 8999999999999999999 9999999999999


Q ss_pred             eecCCCCC
Q 022058          287 SPSKTPVR  294 (303)
Q Consensus       287 ~~a~~~~~  294 (303)
                      .++++...
T Consensus        85 ~~a~~~~~   92 (96)
T 2dgx_A           85 SLATGASG   92 (96)
T ss_dssp             EECCCSSC
T ss_pred             EEcCCCCC
Confidence            99986643

>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=99.75  E-value=2.9e-18  Score=138.23  Aligned_cols=77  Identities=31%  Similarity=0.377  Sum_probs=71.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|+++.+   ++|||||+|.+.++|.+|+. |||..+.|++|.|.++.
T Consensus        70 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~  146 (150)
T 2i2y_A           70 CPLDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN---PPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSN  146 (150)
T ss_dssp             STTSCEEEEESCCSCCSCHHHHHHHHHHSCEEEEEECSS---SCSEEEEEESSHHHHHHHHHHHSSSCSSSSCCEEEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhhCCEEEEEEeeC---CCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEcC
Confidence            346789999999999999999999999999999999877   57999999999999999998 99999999999999986


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      +
T Consensus       147 ~  147 (150)
T 2i2y_A          147 G  147 (150)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.75  E-value=7e-18  Score=125.37  Aligned_cols=80  Identities=25%  Similarity=0.459  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEE-EEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~-~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ...++|||+|||+++++++|+++|+.||.|.++ .++.++.+  ++|||||+|.+.++|.+|+. ||+..+.|++|.|.+
T Consensus         3 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   82 (96)
T 1x5t_A            3 SGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSY   82 (96)
T ss_dssp             SCCCEEEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEEEcCCCCCcCeEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            357899999999999999999999999999999 99998554  79999999999999999999 999999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      +.+.
T Consensus        83 a~~~   86 (96)
T 1x5t_A           83 AFKK   86 (96)
T ss_dssp             SCCC
T ss_pred             eccc
Confidence            8654

>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=99.75  E-value=6.2e-18  Score=122.70  Aligned_cols=77  Identities=27%  Similarity=0.385  Sum_probs=72.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|.++.++++.  +.++|||||+|.+.++|.+|+. |||..++|+.|+|.|
T Consensus         6 ~~~~l~V~nl~~~~~~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   83 (85)
T 3mdf_A            6 TKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   83 (85)
T ss_dssp             CSSEEEEECCCTTCCHHHHHHHHGGG--SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcc--CCEEEEEEEECCCCCccccEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEE
Confidence            55899999999999999999999999  999999998874  6789999999999999999997 999999999999999


Q ss_pred             cC
Q 022058          289 SK  290 (303)
Q Consensus       289 a~  290 (303)
                      ++
T Consensus        84 ak   85 (85)
T 3mdf_A           84 AK   85 (85)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.75  E-value=6.8e-18  Score=125.56  Aligned_cols=78  Identities=31%  Similarity=0.474  Sum_probs=73.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      +++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|++ |||..+.|+.|.|.++.+
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~   81 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYSSN   81 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECSC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEcCC
Confidence            579999999999999999999999999999999998654  79999999999999999998 999999999999999865


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus        82 ~   82 (96)
T 2x1f_A           82 S   82 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A

Probab=99.75  E-value=1.2e-17  Score=126.37  Aligned_cols=84  Identities=23%  Similarity=0.351  Sum_probs=76.9

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCcee---CCeee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVL---GSQPI  284 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~---~g~~l  284 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+. |||..+   .|+.|
T Consensus        11 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A           11 HDAIKLFIGQIPRNLDEKDLKPLFEEF--GKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             TTCEEEEEESCCTTCCHHHHHHHHHHH--SCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            355899999999999999999999999  999999999985  7899999999999999999998 999998   89999


Q ss_pred             EEeecCCCCCCC
Q 022058          285 RVSPSKTPVRPR  296 (303)
Q Consensus       285 ~v~~a~~~~~~r  296 (303)
                      +|.++++....+
T Consensus        89 ~v~~a~~~~~~~  100 (106)
T 2dgp_A           89 QVKPADSESRGG  100 (106)
T ss_dssp             EEEECCCCSCCC
T ss_pred             EEEECCcccccC
Confidence            999998775443

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.75  E-value=5.2e-18  Score=127.81  Aligned_cols=82  Identities=26%  Similarity=0.364  Sum_probs=75.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   88 (103)
T 2dnm_A            9 DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDGAELDGRELRVQ   88 (103)
T ss_dssp             CCSCCCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCBCSSSCSBCSCEEEEESSSSHHHHHHHHHSSCCBTTBCCEEE
T ss_pred             CCCCCeEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCCCeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEE
Confidence            3446799999999999999999999999999999999998764  78999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      +++..
T Consensus        89 ~a~~~   93 (103)
T 2dnm_A           89 VARYG   93 (103)
T ss_dssp             ECSSC
T ss_pred             ECCcC
Confidence            98754

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.75  E-value=1.9e-18  Score=129.68  Aligned_cols=78  Identities=22%  Similarity=0.301  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCC------CCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCC-e
Q 022058          114 SVRRTVYVSDIDQ------NITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGY-Y  183 (303)
Q Consensus       114 ~~~~~l~V~nlp~------~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g-~  183 (303)
                      ..+++|||+|||+      ++++++|+++|+.||.|.+|.|+.++.+  ++|||||+|.+.++|.+|++ |||..+.| +
T Consensus         4 ~~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~r   83 (100)
T 3ns6_A            4 GSDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKH   83 (100)
T ss_dssp             CGGGEEEEESCCCCBGGGHHHHHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSSC
T ss_pred             CcCcEEEEeCCCcCChHHHHHHHHHHHHHHHhcCCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCCe
Confidence            3468999999999      9999999999999999999999999874  89999999999999999998 99999999 9


Q ss_pred             eEEEeecC
Q 022058          184 PVRVLPSK  191 (303)
Q Consensus       184 ~i~v~~~~  191 (303)
                      +|.|.++.
T Consensus        84 ~l~V~~a~   91 (100)
T 3ns6_A           84 RLFLYTMK   91 (100)
T ss_dssp             BCEEEESH
T ss_pred             EEEEEECc
Confidence            99999975

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B

Probab=99.75  E-value=1e-17  Score=124.66  Aligned_cols=80  Identities=28%  Similarity=0.349  Sum_probs=75.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .++|||+|||..+++++|+++|++|  |.|.++.|+.+.  |.++|||||+|.+.++|.+|+. |||..++|+.|+|.++
T Consensus         2 ~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   79 (96)
T 2x1f_A            2 SRVVYLGSIPYDQTEEQILDLCSNV--GPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFLKCGYS   79 (96)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCTTTCCBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEc
Confidence            4799999999999999999999999  999999999885  7889999999999999999998 9999999999999999


Q ss_pred             CCCCC
Q 022058          290 KTPVR  294 (303)
Q Consensus       290 ~~~~~  294 (303)
                      +++..
T Consensus        80 ~~~~~   84 (96)
T 2x1f_A           80 SNSDI   84 (96)
T ss_dssp             SCSSG
T ss_pred             CCCCC
Confidence            87643

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.74  E-value=7.9e-18  Score=125.94  Aligned_cols=79  Identities=25%  Similarity=0.384  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeE--------EEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCccc
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD--------CRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTML  180 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~--------~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~  180 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+        ++++.++.+  ++|||||+|.+.++|.+|++ |||..+
T Consensus         9 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~   88 (99)
T 2la6_A            9 SHSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEF   88 (99)
T ss_dssp             SCCCCSEEEEECCCSSCCHHHHHHHHTTTSCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBS
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEe
Confidence            4456889999999999999999999999999999        999998654  79999999999999999998 999999


Q ss_pred             CCeeEEEeec
Q 022058          181 GYYPVRVLPS  190 (303)
Q Consensus       181 ~g~~i~v~~~  190 (303)
                      .|+.|+|.++
T Consensus        89 ~g~~l~V~~A   98 (99)
T 2la6_A           89 SGNPIKVSFA   98 (99)
T ss_dssp             SSSBCEEEEC
T ss_pred             CCcEEEEEec
Confidence            9999999986

>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=99.74  E-value=2.6e-17  Score=125.35  Aligned_cols=84  Identities=18%  Similarity=0.230  Sum_probs=75.8

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|..+ +.++|||||+|.+.++|.+|++ ||+..|.|+.|+|.|+
T Consensus        20 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           20 NNDCRIYVGNLPPDIRTKDIEDVFYKY--GAIRDIDLKNR-RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEECCS-SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEC-CCCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            356899999999999999999999999  99999999765 4578999999999999999997 9999999999999999


Q ss_pred             CCCCCCCC
Q 022058          290 KTPVRPRV  297 (303)
Q Consensus       290 ~~~~~~r~  297 (303)
                      ++..++++
T Consensus        97 ~~~~~~~~  104 (109)
T 1x4a_A           97 RSGRGTGS  104 (109)
T ss_dssp             CCCCCCCC
T ss_pred             ccCCCCCC
Confidence            87754443

>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=99.74  E-value=1.3e-17  Score=125.84  Aligned_cols=83  Identities=22%  Similarity=0.333  Sum_probs=76.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  | |..|.|+++.   +.++|||||+|.+.++|.+|+.|||..|.|+.|+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   90 (104)
T 1wi8_A           14 PPYTAFLGNLPYDVTEESIKEFFRGL--N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTS--C-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHC--C-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEE
Confidence            45899999999999999999999999  9 9999999885   6789999999999999999999999999999999999


Q ss_pred             cCCCCCCCC
Q 022058          289 SKTPVRPRV  297 (303)
Q Consensus       289 a~~~~~~r~  297 (303)
                      +++....++
T Consensus        91 a~~~~~~~~   99 (104)
T 1wi8_A           91 ADQAQDKDS   99 (104)
T ss_dssp             CCCCCCCCC
T ss_pred             ccCCCCCCC
Confidence            987755443

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=6.5e-18  Score=127.00  Aligned_cols=82  Identities=26%  Similarity=0.366  Sum_probs=75.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|++ ||+..+.|++|.|.+
T Consensus         9 ~~~~~~l~V~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   88 (102)
T 2cqb_A            9 ATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   88 (102)
T ss_dssp             CCCCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHhhccCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEe
Confidence            346789999999999999999999999999999999998654  79999999999999999998 999999999999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      +.+..
T Consensus        89 a~~~~   93 (102)
T 2cqb_A           89 AKPMR   93 (102)
T ss_dssp             CCCCC
T ss_pred             CCCCC
Confidence            87553

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens}

Probab=99.74  E-value=1.3e-17  Score=128.60  Aligned_cols=82  Identities=20%  Similarity=0.360  Sum_probs=75.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|++|++ |||..+.|+.|.|.++
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   83 (116)
T 2fy1_A            4 ADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA   83 (116)
T ss_dssp             TCSCCEEEEECCTTTCCHHHHHHHHHTSSCCSEEEEECSTTTTCCCEEEEECSSHHHHHHHHHHCSSCBCSSSBCEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            346789999999999999999999999999999999998744 89999999999999999998 9999999999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      +...
T Consensus        84 ~~~~   87 (116)
T 2fy1_A           84 KKPS   87 (116)
T ss_dssp             CCSS
T ss_pred             CCCC
Confidence            7654

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=5.9e-18  Score=129.05  Aligned_cols=81  Identities=19%  Similarity=0.291  Sum_probs=76.4

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.++++.+.++|||||+|.+.++|.+|+. |||..++|+.|+|.+
T Consensus        26 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  103 (109)
T 2err_A           26 KSQPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNN  103 (109)
T ss_dssp             TTCCCEEEEESCCTTCCHHHHHHHGGGT--CCCSCEEECCBTTBCTTEEEEECCCSHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCEEEEECCCCcCCHHHHHHHHHhc--CCEEEEEEEECCCCCceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4456899999999999999999999999  9999999999987799999999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      +++.
T Consensus       104 a~~~  107 (109)
T 2err_A          104 ATAR  107 (109)
T ss_dssp             CCCS
T ss_pred             CCCC
Confidence            9864

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.74  E-value=1.9e-17  Score=124.75  Aligned_cols=83  Identities=23%  Similarity=0.366  Sum_probs=76.1

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      .+.++|||+|||..+++++|+++|++|  | |..|.|+++.  ++++|||||+|.+.++|.+|+.|||..|.|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~   89 (103)
T 2dng_A           13 EPPYTAYVGNLPFNTVQGDIDAIFKDL--S-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDI   89 (103)
T ss_dssp             SSCEEEEEESCCTTCCHHHHHHHTTTS--C-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEE
T ss_pred             CCCeEEEEeCCCCCCCHHHHHHHHHhC--C-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEE
Confidence            345899999999999999999999999  8 9999999985  7889999999999999999999999999999999999


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      +++....+
T Consensus        90 a~~~~~~~   97 (103)
T 2dng_A           90 AEGRKQDK   97 (103)
T ss_dssp             CCCCCCCC
T ss_pred             ecCCCCCC
Confidence            98765433

>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=99.74  E-value=8.5e-18  Score=127.98  Aligned_cols=81  Identities=27%  Similarity=0.443  Sum_probs=75.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+.+++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|++ +||..+.|++|.|.
T Consensus        22 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V~  101 (108)
T 2jrs_A           22 GSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVG  101 (108)
T ss_dssp             SCSSCEEEEEECCCSSCCHHHHHHHHTTTSCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            4456789999999999999999999999999999999998664  78999999999999999998 99999999999999


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      ++.+
T Consensus       102 ~a~~  105 (108)
T 2jrs_A          102 HVTE  105 (108)
T ss_dssp             CSCS
T ss_pred             Eccc
Confidence            9854

>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=99.74  E-value=9.9e-18  Score=127.82  Aligned_cols=83  Identities=22%  Similarity=0.260  Sum_probs=76.6

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|+.+.  |.++|||||+|.+.++|.+|+. |||..+.|+.|+|
T Consensus        23 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V  100 (110)
T 1oo0_B           23 SVEGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQV  100 (110)
T ss_dssp             BTTBEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEE
Confidence            3456899999999999999999999999  999999999885  7889999999999999999998 9999999999999


Q ss_pred             eecCCCCC
Q 022058          287 SPSKTPVR  294 (303)
Q Consensus       287 ~~a~~~~~  294 (303)
                      .|+++...
T Consensus       101 ~~a~~~~~  108 (110)
T 1oo0_B          101 DWCFVKGP  108 (110)
T ss_dssp             EESEESSC
T ss_pred             EEcccCCC
Confidence            99986543

>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=99.74  E-value=6.1e-18  Score=129.01  Aligned_cols=80  Identities=19%  Similarity=0.247  Sum_probs=74.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+. |||..+.|++|.|.++
T Consensus        24 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a  103 (110)
T 1oo0_B           24 VEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWC  103 (110)
T ss_dssp             TTBEEEEEESCCTTCCHHHHHHHHGGGSCEEEEECCBCTTTSSBCSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEc
Confidence            35788999999999999999999999999999999988654  78999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus       104 ~~~  106 (110)
T 1oo0_B          104 FVK  106 (110)
T ss_dssp             EES
T ss_pred             ccC
Confidence            643

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=8e-18  Score=126.51  Aligned_cols=82  Identities=23%  Similarity=0.368  Sum_probs=75.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|++ ||+..+.|++|.|.+
T Consensus         9 ~~~~~~l~v~nLp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   88 (102)
T 1x5s_A            9 ASDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   88 (102)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEE
Confidence            346789999999999999999999999999999999998654  79999999999999999997 999999999999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      +.+..
T Consensus        89 a~~~~   93 (102)
T 1x5s_A           89 AGKSS   93 (102)
T ss_dssp             EECCC
T ss_pred             CCCCC
Confidence            86543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=8.4e-18  Score=127.30  Aligned_cols=80  Identities=21%  Similarity=0.306  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+. |||..+.|+.|.|.++
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a  100 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC  100 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhccCCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEee
Confidence            35688999999999999999999999999999999998764  78999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus       101 ~~~  103 (106)
T 1p27_B          101 FVR  103 (106)
T ss_dssp             EES
T ss_pred             cCC
Confidence            643

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.74  E-value=1.3e-17  Score=126.41  Aligned_cols=82  Identities=21%  Similarity=0.292  Sum_probs=74.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeC-CC--CCceEEEEEecCHHHHHHHHH-h-CCcccCCeeEE
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD-PH--SVLRFAFVEFADEHGARAALN-L-GGTMLGYYPVR  186 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~-~~--~~~G~~fV~f~~~~~A~~Ai~-l-~g~~~~g~~i~  186 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+ ..  .++|||||+|.+.++|.+|+. | |+..+.|++|.
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~~~~~~~g~~l~   90 (107)
T 2cph_A           11 KKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLV   90 (107)
T ss_dssp             CSSCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCE
T ss_pred             cCCCCCEEEEeCCCCcCCHHHHHHHHHccCCeEEEEEecCCCCCCCcCceEEEEECCHHHHHHHHHHhccCCeECCCEEE
Confidence            3446789999999999999999999999999999999988 33  379999999999999999998 9 99999999999


Q ss_pred             EeecCCC
Q 022058          187 VLPSKTA  193 (303)
Q Consensus       187 v~~~~~~  193 (303)
                      |.++.+.
T Consensus        91 v~~a~~~   97 (107)
T 2cph_A           91 LEWADSE   97 (107)
T ss_dssp             EEECCCC
T ss_pred             EEeCCCC
Confidence            9998654

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2e-17  Score=122.60  Aligned_cols=79  Identities=22%  Similarity=0.286  Sum_probs=74.3

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..|.+++++  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~   90 (95)
T 2cqc_A           13 DPNCCLGVFGLSLYTTERDLREVFSKY--GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVS   90 (95)
T ss_dssp             CGGGCEEEESCCSSCCHHHHHHHHHTT--SCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhc--CCeeEEEEEEcCCCCCcccEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            356899999999999999999999999  999999999885  6789999999999999999999 99999999999999


Q ss_pred             ecCC
Q 022058          288 PSKT  291 (303)
Q Consensus       288 ~a~~  291 (303)
                      ++++
T Consensus        91 ~a~~   94 (95)
T 2cqc_A           91 GPSS   94 (95)
T ss_dssp             CCSC
T ss_pred             ecCC
Confidence            9974

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=2.3e-17  Score=127.01  Aligned_cols=88  Identities=11%  Similarity=0.190  Sum_probs=79.6

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+.+||..|+|+.|+|.+
T Consensus        25 ~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~  102 (116)
T 1x4b_A           25 EQFRKLFIGGLSFETTEESLRNYYEQW--GKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKR  102 (116)
T ss_dssp             HHHTEEEEECCTTCCCHHHHHHHHTSS--CCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEE
Confidence            346899999999999999999999999  999999999985  7889999999999999999998899999999999999


Q ss_pred             cCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRP  300 (303)
Q Consensus       289 a~~~~~~r~~r~  300 (303)
                      +++.......+.
T Consensus       103 a~~~~~~~~~~~  114 (116)
T 1x4b_A          103 AVAREESGSGPS  114 (116)
T ss_dssp             CSSCCCCCCSCC
T ss_pred             CCCCccCCCCCC
Confidence            988765554443

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=2.6e-17  Score=126.24  Aligned_cols=80  Identities=30%  Similarity=0.429  Sum_probs=74.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|.|+.+. +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.++
T Consensus        14 ~~~~l~V~nlp~~~~~~~l~~~f~~~--G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           14 LGSTVFVANLDYKVGWKKLKEVFSMA--GVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCSCEEEESCCTTCCHHHHHHHHTTT--SCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            45899999999999999999999999  999999999885 7889999999999999999999 9999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      ++..
T Consensus        92 ~~~~   95 (114)
T 2do0_A           92 ERAL   95 (114)
T ss_dssp             SCCC
T ss_pred             ccCC
Confidence            7543

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.2e-17  Score=126.52  Aligned_cols=81  Identities=20%  Similarity=0.252  Sum_probs=75.5

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+.  |.++|||||+|.+.++|.+|+. |||..+.|+.|+|.
T Consensus        21 ~~~~~l~V~nlp~~~t~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~   98 (106)
T 1p27_B           21 VEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   98 (106)
T ss_dssp             TTBEEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTSSEEEEEEEEESCHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhcc--CCeEEEEEEecCCCCceeeEEEEEECCHHHHHHHHHHhcCCEECCcEEEEE
Confidence            356899999999999999999999999  999999999885  6889999999999999999998 99999999999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      ++++..
T Consensus        99 ~a~~~~  104 (106)
T 1p27_B           99 WCFVRG  104 (106)
T ss_dssp             ESEESS
T ss_pred             eecCCC
Confidence            998654

>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=99.74  E-value=7.8e-18  Score=131.56  Aligned_cols=88  Identities=20%  Similarity=0.270  Sum_probs=78.0

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   97 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEY--GEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVD   97 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEE
Confidence            356899999999999999999999999  999999999884  7889999999999999999998 99999999999999


Q ss_pred             ecCCCCCCCCCCC
Q 022058          288 PSKTPVRPRVTRP  300 (303)
Q Consensus       288 ~a~~~~~~r~~r~  300 (303)
                      |+++...++..|.
T Consensus        98 ~a~~~~~~~~~~~  110 (126)
T 3ex7_B           98 WCFVRGPPKGKRR  110 (126)
T ss_dssp             ESEESSSCCC---
T ss_pred             EecCCCCCCCCCC
Confidence            9987665554443

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.74  E-value=1.6e-17  Score=127.35  Aligned_cols=84  Identities=17%  Similarity=0.256  Sum_probs=76.8

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCccee--------EEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCcee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVT--------RLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVL  279 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~--------~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~  279 (303)
                      ...++|||+|||..+++++|+++|++|  |.|.        .|.|+.+.  +.++|||||+|.+.++|.+|+. |||..|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           13 SDNSAIYVQGLNDSVTLDDLADFFKQC--GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTT--SCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhc--CCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            356899999999999999999999999  9999        69999884  7889999999999999999998 999999


Q ss_pred             CCeeeEEeecCCCCCCC
Q 022058          280 GSQPIRVSPSKTPVRPR  296 (303)
Q Consensus       280 ~g~~l~v~~a~~~~~~r  296 (303)
                      .|+.|+|.++++.....
T Consensus        91 ~g~~l~V~~a~~~~~~~  107 (113)
T 2cpe_A           91 QGSKLKVSLARKKPPMN  107 (113)
T ss_dssp             TTEECEEECSSCCCCST
T ss_pred             CCCEEEEEECCCCCCCC
Confidence            99999999998775443

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=126.11  Aligned_cols=84  Identities=23%  Similarity=0.318  Sum_probs=77.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhh-hcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCce-eCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEA-ACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMV-LGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~-~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~-~~g~~l~v~  287 (303)
                      +.++|||+|||..+++++|+++|++ |  |.|.+|.|+++. +.++|||||+|.+.++|.+|+. |||.. +.|+.|+|.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~~--G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v~   85 (104)
T 2dhg_A            8 PEYSLFVGDLTPDVDDGMLYEFFVKVY--PSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLS   85 (104)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHHC--TTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHhC--CCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEEE
Confidence            4589999999999999999999999 9  999999999985 7789999999999999999999 99999 999999999


Q ss_pred             ecCCCCCCCC
Q 022058          288 PSKTPVRPRV  297 (303)
Q Consensus       288 ~a~~~~~~r~  297 (303)
                      ++++....+.
T Consensus        86 ~a~~~~~~~~   95 (104)
T 2dhg_A           86 VAIPKASRVK   95 (104)
T ss_dssp             BCCCCCSCCC
T ss_pred             EccCCCcCCC
Confidence            9987655443

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.74  E-value=1.1e-17  Score=125.16  Aligned_cols=81  Identities=19%  Similarity=0.356  Sum_probs=74.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCcee-EEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCee----
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVV-DCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYP----  184 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~-~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~----  184 (303)
                      ....++|||+|||+++++++|+++|+.||.|. +|.++.++.+  ++|||||+|.+.++|++|+. |||..+.|+.    
T Consensus         6 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            6 SGMAASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             CSSSSEEEECSCCTTCCHHHHHHHHHHTTCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CCCccEEEEeCCCCCCCHHHHHHHHHHhCCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            34678999999999999999999999999999 9999998754  78999999999999999999 9999999999    


Q ss_pred             EEEeecCCC
Q 022058          185 VRVLPSKTA  193 (303)
Q Consensus       185 i~v~~~~~~  193 (303)
                      |+|.|++..
T Consensus        86 l~v~~a~~~   94 (99)
T 2div_A           86 FKLNYATYS   94 (99)
T ss_dssp             CCEEETTCC
T ss_pred             EEEeecCCC
Confidence            999998654

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.74  E-value=1.2e-17  Score=122.22  Aligned_cols=77  Identities=31%  Similarity=0.598  Sum_probs=72.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      .++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|+.+|+..+.|+.|.|.++++
T Consensus         6 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a~~   84 (89)
T 3ucg_A            6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRT   84 (89)
T ss_dssp             HTEEEEESCCTTCCHHHHHHHHGGGCCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEETTT
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEccC
Confidence            578999999999999999999999999999999998644  79999999999999999999999999999999999865

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens}

Probab=99.74  E-value=1e-17  Score=122.25  Aligned_cols=80  Identities=20%  Similarity=0.292  Sum_probs=74.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--C-CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--V-HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.++.|+.+.  + +++|||||+|.+.++|.+|+. |||..++|+.|+|.
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~   80 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTY--GKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITAT   80 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEE
Confidence            34789999999999999999999999  999999999886  3 389999999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      ++.++.
T Consensus        81 ~a~~~~   86 (88)
T 4a8x_A           81 AVLAPW   86 (88)
T ss_dssp             EECCCC
T ss_pred             ECCCCC
Confidence            997664

>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=99.74  E-value=1.2e-17  Score=127.11  Aligned_cols=81  Identities=21%  Similarity=0.385  Sum_probs=75.5

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ..+.++|||+|||..+++++|+++|++|  |.|..|.|++++  |.++|||||+|.+.++|.+|+. |||..+.|+.|+|
T Consensus        23 ~~~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~F~~~~~A~~Ai~~l~g~~i~g~~l~V  100 (108)
T 2jrs_A           23 SAGPMRLYVGSLHFNITEDMLRGIFEPF--GRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKV  100 (108)
T ss_dssp             CSSCEEEEEECCCSSCCHHHHHHHHTTT--SCEEEEEEEEETTTTEEEEEEEEEESCHHHHHHHHHHHTTCCSSSSCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4456899999999999999999999999  999999999884  6789999999999999999998 9999999999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      .++++.
T Consensus       101 ~~a~~k  106 (108)
T 2jrs_A          101 GHVTER  106 (108)
T ss_dssp             ECSCSS
T ss_pred             EEcccC
Confidence            999865

>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=99.74  E-value=1.6e-17  Score=126.83  Aligned_cols=82  Identities=22%  Similarity=0.316  Sum_probs=75.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hC------CcccCC
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LG------GTMLGY  182 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~------g~~~~g  182 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. +|      +..+.|
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~~~~~~~~~~~~~~g   90 (111)
T 1x4h_A           11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDG   90 (111)
T ss_dssp             CCCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSS
T ss_pred             cCCCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCCccEEEEEECCHHHHHHHHHHhccccccCCcEEcC
Confidence            3446789999999999999999999999999999999998764  79999999999999999998 99      999999


Q ss_pred             eeEEEeecCCC
Q 022058          183 YPVRVLPSKTA  193 (303)
Q Consensus       183 ~~i~v~~~~~~  193 (303)
                      ++|.|.++.+.
T Consensus        91 ~~l~v~~a~~~  101 (111)
T 1x4h_A           91 RQLKVDLAVTR  101 (111)
T ss_dssp             CEEEEECCCCC
T ss_pred             EEEEEEECCCC
Confidence            99999998654

>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=99.74  E-value=2.9e-17  Score=125.04  Aligned_cols=86  Identities=21%  Similarity=0.331  Sum_probs=77.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|+++    +|||||+|.+.++|.+|+. |||..+.|+.|+|.|
T Consensus        22 ~~~~~~l~V~nl~~~~t~~~l~~~F~~~--G~i~~v~i~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   95 (109)
T 1x4g_A           22 SPKNCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPE----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYW   95 (109)
T ss_dssp             CSSCCEEEEECCSSCCCHHHHHHHHHHH--SCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEe
Confidence            3456899999999999999999999999  99999999988    4699999999999999998 999999999999999


Q ss_pred             cCCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRPG  301 (303)
Q Consensus       289 a~~~~~~r~~r~~  301 (303)
                      +++....+..+++
T Consensus        96 a~~~~~~~~~~~s  108 (109)
T 1x4g_A           96 GKESPDMTSGPSS  108 (109)
T ss_dssp             CCCCCSSCCCCCC
T ss_pred             cCCCCCCCCCCCC
Confidence            9988766655544

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A

Probab=99.74  E-value=1.8e-17  Score=121.35  Aligned_cols=79  Identities=28%  Similarity=0.486  Sum_probs=74.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.++.++.+.  +.++|||||+|.+.++|.+|+.|||..+.|+.|+|.++
T Consensus         5 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~g~~~~g~~l~V~~a   82 (89)
T 3ucg_A            5 DARSIYVGNVDYGATAEELEAHFHGC--GSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPK   82 (89)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHGGG--CCEEEEEEEESCSSSSCCEEEEEEESSTHHHHHHGGGTTCEETTEECEEEET
T ss_pred             cCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEEecCCCCCcceEEEEEECCHHHHHHHHhcCCCEECCcEEEEEEc
Confidence            35899999999999999999999999  999999999884  78899999999999999999999999999999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      +++
T Consensus        83 ~~~   85 (89)
T 3ucg_A           83 RTN   85 (89)
T ss_dssp             TTT
T ss_pred             cCC
Confidence            865

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.3e-17  Score=122.08  Aligned_cols=77  Identities=22%  Similarity=0.320  Sum_probs=73.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.|++++  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.|
T Consensus        15 ~~~~l~V~nlp~~~t~~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   92 (94)
T 2e5h_A           15 SKSTVYVSNLPFSLTNNDLYRIFSKY--GKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAINNKQLFGRVIKASI   92 (94)
T ss_dssp             CTTSEEEESCCTTSCHHHHHHHTTTT--SCEEEEEECCCSSSCCCTTCEEEEESCHHHHHHHHHHTTTEEETTEEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEEEEEeCCCCCCcccEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEe
Confidence            45899999999999999999999999  999999999985  6789999999999999999998 999999999999999


Q ss_pred             cC
Q 022058          289 SK  290 (303)
Q Consensus       289 a~  290 (303)
                      ++
T Consensus        93 ak   94 (94)
T 2e5h_A           93 AI   94 (94)
T ss_dssp             CC
T ss_pred             cC
Confidence            85

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.73  E-value=4.4e-18  Score=120.61  Aligned_cols=73  Identities=21%  Similarity=0.245  Sum_probs=68.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      +|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|++|+++|+..+.|++|.|.++
T Consensus         1 ~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~v~~A   75 (75)
T 2mss_A            1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            4899999999999999999999999999999998753  899999999999999999999999999999999874

>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=99.73  E-value=2.8e-17  Score=125.17  Aligned_cols=81  Identities=23%  Similarity=0.354  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+. .++|||||+|.+.++|.+|++ ||+..+.|+.|.|.++
T Consensus        18 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   96 (109)
T 1x4a_A           18 AGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR-GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFP   96 (109)
T ss_dssp             CCCCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS-SSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECC-CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEc
Confidence            34467899999999999999999999999999999997653 378999999999999999997 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      +..
T Consensus        97 ~~~   99 (109)
T 1x4a_A           97 RSG   99 (109)
T ss_dssp             CCC
T ss_pred             ccC
Confidence            654

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=2e-17  Score=124.17  Aligned_cols=86  Identities=24%  Similarity=0.318  Sum_probs=75.9

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC-CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d-~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|   .++.+ .++++|||||+|.+.++|.+|+. |||..|.|+.|+|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           13 GESKTLVLSNLSYSATEETLQEVFEKA--TFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHCSSC--SEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC--CEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            356899999999999999999999999  987   55665 47889999999999999999999 999999999999999


Q ss_pred             cCCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRPG  301 (303)
Q Consensus       289 a~~~~~~r~~r~~  301 (303)
                      ++++.+++...++
T Consensus        88 a~~~~~~~~~~~~  100 (101)
T 2fc9_A           88 QGPRGSPNSGPSS  100 (101)
T ss_dssp             CSSCCCCCCCSSC
T ss_pred             cCCCCCCCCCCCC
Confidence            9988766655444

>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=99.73  E-value=1.9e-17  Score=122.70  Aligned_cols=78  Identities=28%  Similarity=0.451  Sum_probs=73.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|.|+++. +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus        15 ~~~~l~v~nlp~~~~~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   92 (95)
T 2ywk_A           15 ADRTVFVGNLEARVREEILYELFLQA--GPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLNGIRLYGRPINVSGP   92 (95)
T ss_dssp             GGGEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTSCEEEEEEEEESSTHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEEECCCCCCceEEEEEECCHHHHHHHHHHhCCCEECCCEEEEEEc
Confidence            45899999999999999999999999  999999999885 7889999999999999999999 9999999999999998


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      +.
T Consensus        93 ~~   94 (95)
T 2ywk_A           93 SS   94 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.73  E-value=1.5e-17  Score=124.38  Aligned_cols=81  Identities=15%  Similarity=0.260  Sum_probs=75.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCccee-EEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCee----
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVT-RLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQP----  283 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~-~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~----  283 (303)
                      ..++|||+|||..+++++|+++|++|  |.|. .|.|++++  +.++|||||+|.+.++|.+|+. |||..+.|+.    
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~   85 (99)
T 2div_A            8 MAASLWMGDLEPYMDENFISRAFATM--GETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKR   85 (99)
T ss_dssp             SSSEEEECSCCTTCCHHHHHHHHHHT--TCCCCEEEEEECSSSCCEEEEEEEECSCHHHHHHHHHTTTTSEESSCSSCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHh--CCcceEEEEeecCCCCCcCCEEEEEeCCHHHHHHHHHHHcCCccCCCCccee
Confidence            45899999999999999999999999  9999 99999885  7889999999999999999999 9999999999    


Q ss_pred             eEEeecCCCCC
Q 022058          284 IRVSPSKTPVR  294 (303)
Q Consensus       284 l~v~~a~~~~~  294 (303)
                      |+|.|+++...
T Consensus        86 l~v~~a~~~~~   96 (99)
T 2div_A           86 FKLNYATYSGP   96 (99)
T ss_dssp             CCEEETTCCSS
T ss_pred             EEEeecCCCCC
Confidence            99999987643

>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=99.73  E-value=1.3e-17  Score=121.71  Aligned_cols=78  Identities=18%  Similarity=0.308  Sum_probs=73.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC---CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS---VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~---~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.+..+   ++|||||+|.+.++|.+|+. |||..+.|+.|.|.++
T Consensus         3 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   82 (88)
T 4a8x_A            3 KPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAV   82 (88)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTEEEEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEEeCCCCCCCCCcEEEEEEecHHHHHHHHHHcCCCeECCeEEEEEEC
Confidence            4688999999999999999999999999999999998753   78999999999999999999 9999999999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      .+
T Consensus        83 ~~   84 (88)
T 4a8x_A           83 LA   84 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=1.2e-17  Score=125.94  Aligned_cols=78  Identities=18%  Similarity=0.239  Sum_probs=73.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||+.+|+++|+++|++|  |.|.+|.|++++ |.++|||||+|.+.++|.+|+.+||..+.|+.|.|.++.
T Consensus        10 ~~~~lfV~~Lp~~~te~~L~~~F~~~--G~v~~v~i~~d~~g~~rG~aFV~F~~~e~a~~Ai~~~~~~~~gr~l~V~~~~   87 (103)
T 1s79_A           10 KNRSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   87 (103)
T ss_dssp             GGGCEEEECCCTTCCHHHHHHHHHTS--SCEEEEEEECCCTTSCCCEEEEEESSHHHHHHHHTSSCCCCTTTTCEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc--CCEEEEEEEECCCCCCccEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEch
Confidence            45899999999999999999999999  999999999986 789999999999999999999999999999999999875


Q ss_pred             C
Q 022058          291 T  291 (303)
Q Consensus       291 ~  291 (303)
                      .
T Consensus        88 ~   88 (103)
T 1s79_A           88 D   88 (103)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.73  E-value=8.5e-18  Score=157.98  Aligned_cols=80  Identities=20%  Similarity=0.298  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+.+|+++|+++|+.||.|..|.|+.+..+  ++|||||+|.+.++|.+||. |||..|.|+.|.|.++
T Consensus       100 ~~~~~lfV~nL~~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~lng~~i~gr~i~V~~a  179 (437)
T 3pgw_S          100 DAFKTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVE  179 (437)
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            35689999999999999999999999999999999998654  79999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ...
T Consensus       180 ~~~  182 (437)
T 3pgw_S          180 RGR  182 (437)
T ss_pred             CCC
Confidence            754

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.73  E-value=1.6e-17  Score=123.92  Aligned_cols=76  Identities=24%  Similarity=0.230  Sum_probs=69.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcc--cCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTM--LGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~--~~g~~i~v~~~  190 (303)
                      ..+++|||+|||+++|+++|+++|++||.|.++.+++    +||||||+|++.++|.+|+. +++..  +.|++|.|.++
T Consensus        19 ~ps~~l~V~NLp~~~te~~L~~lF~~fG~V~~v~i~~----~kg~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V~~S   94 (100)
T 3r27_A           19 PASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMP----KKRQALVEFEDVLGACNAVNYAADNQIYIAGHPAFVNYS   94 (100)
T ss_dssp             CCCSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEEc----CCCEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEEEec
Confidence            4688999999999999999999999999999999985    36899999999999999998 98875  78999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      +.+
T Consensus        95 ~~k   97 (100)
T 3r27_A           95 TSQ   97 (100)
T ss_dssp             SCS
T ss_pred             ccc
Confidence            654

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=5e-17  Score=124.63  Aligned_cols=81  Identities=25%  Similarity=0.352  Sum_probs=75.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.|+.+..+ ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   91 (114)
T 2do0_A           12 GRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDRPMHVKMD   91 (114)
T ss_dssp             CCCCSCEEEESCCTTCCHHHHHHHHTTTSCEEEEEEEECTTCSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeCCCEEEEEEc
Confidence            345789999999999999999999999999999999998765 79999999999999999999 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      +..
T Consensus        92 ~~~   94 (114)
T 2do0_A           92 ERA   94 (114)
T ss_dssp             SCC
T ss_pred             ccC
Confidence            654

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.73  E-value=2.9e-17  Score=126.45  Aligned_cols=81  Identities=19%  Similarity=0.271  Sum_probs=74.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|+.++.+  ++|||||+|.+.++|++|+. +|+ .+.|++|.|.
T Consensus        13 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~-~~~g~~l~V~   91 (116)
T 2cqd_A           13 KDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVN   91 (116)
T ss_dssp             CSCSSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCeeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHhCCC-cCCCEEEEEE
Confidence            4456899999999999999999999999999999999998754  89999999999999999999 888 8999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      ++...
T Consensus        92 ~a~~~   96 (116)
T 2cqd_A           92 LAYLG   96 (116)
T ss_dssp             ESTTT
T ss_pred             EcccC
Confidence            98654

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.73  E-value=2.2e-17  Score=124.50  Aligned_cols=82  Identities=23%  Similarity=0.378  Sum_probs=75.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhc-CCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcc-cCCeeEEE
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSS-CGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTM-LGYYPVRV  187 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~-~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~-~~g~~i~v  187 (303)
                      +....++|||+|||+++++++|+++|+. ||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. ||+.. +.|++|.|
T Consensus         5 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~g~~l~v   84 (104)
T 2dhg_A            5 SSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRL   84 (104)
T ss_dssp             CSSCCCCEEEECCCTTCCHHHHHHHHHHHCTTEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHHHTTTCCSSSSSCCCC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHHHccCCcccCCEeEEE
Confidence            3446789999999999999999999999 999999999998744 79999999999999999999 99999 99999999


Q ss_pred             eecCCC
Q 022058          188 LPSKTA  193 (303)
Q Consensus       188 ~~~~~~  193 (303)
                      .++.+.
T Consensus        85 ~~a~~~   90 (104)
T 2dhg_A           85 SVAIPK   90 (104)
T ss_dssp             CBCCCC
T ss_pred             EEccCC
Confidence            998654

>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=99.73  E-value=1.8e-17  Score=125.48  Aligned_cols=83  Identities=22%  Similarity=0.354  Sum_probs=75.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCccc---CCeeE
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTML---GYYPV  185 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~---~g~~i  185 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. ||+..+   .|++|
T Consensus         9 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~~~~g~~l   88 (106)
T 2dgp_A            9 KDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSALHEQKTLPGMNRPI   88 (106)
T ss_dssp             CCTTCEEEEEESCCTTCCHHHHHHHHHHHSCCCEEECCCCSSSCSCCSEEEEEESSHHHHHHHHHHHTTTCCCTTCSSCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEecCCCCCcceEEEEEECCHHHHHHHHHHhcCCcccCCCCceE
Confidence            4456789999999999999999999999999999999998764  79999999999999999998 999887   89999


Q ss_pred             EEeecCCCC
Q 022058          186 RVLPSKTAI  194 (303)
Q Consensus       186 ~v~~~~~~~  194 (303)
                      .|.++....
T Consensus        89 ~v~~a~~~~   97 (106)
T 2dgp_A           89 QVKPADSES   97 (106)
T ss_dssp             EEEECCCCS
T ss_pred             EEEECCccc
Confidence            999986543

>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=99.73  E-value=3.7e-17  Score=122.79  Aligned_cols=77  Identities=21%  Similarity=0.225  Sum_probs=70.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-h--CCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L--GGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l--~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|++||.|.+|.++++    +|||||+|.+.++|.+|++ +  ++..+.|++|.|.++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~v~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~a   88 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQYS   88 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEEEc
Confidence            46789999999999999999999999999999999865    6899999999999999998 6  577899999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      +...
T Consensus        89 ~~~~   92 (101)
T 2cq1_A           89 NHKE   92 (101)
T ss_dssp             SCSS
T ss_pred             Cccc
Confidence            7554

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.73  E-value=2.7e-17  Score=123.93  Aligned_cols=80  Identities=23%  Similarity=0.395  Sum_probs=74.0

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++++++|+++|+.|| |.+|.++.+..+  ++|||||+|.+.++|.+|+.||+..+.|++|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g-i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   90 (103)
T 2dng_A           12 TEPPYTAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGDRSLRVDIA   90 (103)
T ss_dssp             SSSCEEEEEESCCTTCCHHHHHHHTTTSC-EEEEEEEECSSSCSEEEEEEEEESSHHHHHHHGGGTTCEETTEECEEEEC
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCC-ceEEEEeecCCCCccceEEEEEECCHHHHHHHHhhCCCeECCeEEEEEEe
Confidence            34578999999999999999999999997 999999998764  799999999999999999999999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        91 ~~~   93 (103)
T 2dng_A           91 EGR   93 (103)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.73  E-value=7.1e-17  Score=121.53  Aligned_cols=87  Identities=15%  Similarity=0.227  Sum_probs=77.8

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.++  +.++|||||+|.+.++|.+|+. +++.++|+.|.|.+
T Consensus        13 ~~~~~l~v~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           13 QKTSDLIVLGLPWKTTEQDLKEYFSTF--GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCEEEESCCSSCCHHHHHHHHGGG--SCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEEC
T ss_pred             CCCCEEEEEcCCCcCCHHHHHHHHHhc--CCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEEe
Confidence            355899999999999999999999999  999999999985  7899999999999999999998 57899999999999


Q ss_pred             cCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRP  300 (303)
Q Consensus       289 a~~~~~~r~~r~  300 (303)
                      +++......++.
T Consensus        90 a~~~~~~~~~~~  101 (103)
T 2cqg_A           90 PNSKQSQDSGPS  101 (103)
T ss_dssp             CCTTCCCCCSSC
T ss_pred             cCCCCcCCCCCC
Confidence            988766554443

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.73  E-value=2e-17  Score=128.83  Aligned_cols=84  Identities=27%  Similarity=0.464  Sum_probs=77.1

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+.|||..|.|+.|+|.
T Consensus        33 ~~~~~~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           33 EIDKRSVYVGNVDYGSTAQDLEAHFSSC--GSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVL  110 (124)
T ss_dssp             HHHHTEEEEEEECTTCCHHHHHHHHHTT--SCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEE
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            3456899999999999999999999999  999999999874  789999999999999999999999999999999999


Q ss_pred             ecCCCCCC
Q 022058          288 PSKTPVRP  295 (303)
Q Consensus       288 ~a~~~~~~  295 (303)
                      ++++....
T Consensus       111 ~a~~~~~~  118 (124)
T 2jwn_A          111 PKRTNMPG  118 (124)
T ss_dssp             ESSCCCSS
T ss_pred             ECCCCCCC
Confidence            99866443

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.72  E-value=1.2e-17  Score=129.07  Aligned_cols=80  Identities=25%  Similarity=0.423  Sum_probs=73.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|++ |||..+.|+.|+|.
T Consensus        36 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~  115 (118)
T 2khc_A           36 EGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKVQ  115 (118)
T ss_dssp             CCCCSEEEEEECSCTTCCHHHHHHHTTTSCEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            3446789999999999999999999999999999999988654  79999999999999999998 99999999999999


Q ss_pred             ecC
Q 022058          189 PSK  191 (303)
Q Consensus       189 ~~~  191 (303)
                      +++
T Consensus       116 ~ak  118 (118)
T 2khc_A          116 LKK  118 (118)
T ss_dssp             EC-
T ss_pred             ecC
Confidence            863

>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=99.72  E-value=4.2e-18  Score=160.09  Aligned_cols=160  Identities=14%  Similarity=0.174  Sum_probs=106.8

Q ss_pred             HHHHHhhcCCceeEEEE----eeCCCCC---ceEE--EEEecCHHHHHHHHH-hCCcccCCeeEEEeec--CCCCCCCCC
Q 022058          132 RLAGLFSSCGQVVDCRV----CGDPHSV---LRFA--FVEFADEHGARAALN-LGGTMLGYYPVRVLPS--KTAILPVNP  199 (303)
Q Consensus       132 ~l~~~F~~~G~i~~~~i----~~~~~~~---~G~~--fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~--~~~~~~~~~  199 (303)
                      .|..+|.++|+|..|..    +.+....   .|++  |+.|....++..++. ++......+.......  .........
T Consensus         8 ~L~~lF~p~pPl~~~~P~~~~p~~~~~~~~~~gia~~~~~f~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~~~~~   87 (437)
T 3pgw_S            8 NLLALFAPRDPIPYLPPLEKLPHEKHHNQPYCGIAPYIREFEDPRDAPPPTRAETREERMERKRREKIERRQQEVETELK   87 (437)
T ss_pred             cHHHhcCCCCCCcCCCCcccccccccCCCCcccHHHHHHhhcCcccccccccccCHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            37889999999988733    2222222   3444  888887666655554 3322221110000000  000000000


Q ss_pred             CCCCCc-ccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hC
Q 022058          200 TFLPRS-EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CS  275 (303)
Q Consensus       200 ~~~~~~-~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~  275 (303)
                      .+.+.. ......+.++|||+|||..+|+++|..+|++|  |.|..|.|+.+.  +.++|||||+|.+.++|.+||. ||
T Consensus        88 ~~~p~~~~~~~~~~~~~lfV~nL~~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~~kG~aFV~F~~~e~A~~Ai~~ln  165 (437)
T 3pgw_S           88 MWDPHNDPNAQGDAFKTLFVARVNYDTTESKLRREFEVY--GPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD  165 (437)
T ss_pred             hcCCcccccccCCCCCEEEEeCCCCCCCHHHHHHHHHHc--CCeeEEEeeccCCCCCccceEEEeeccHHHHHHHHHHcC
Confidence            011111 11122345899999999999999999999999  999999999884  7889999999999999999998 99


Q ss_pred             CceeCCeeeEEeecCCCC
Q 022058          276 GMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       276 g~~~~g~~l~v~~a~~~~  293 (303)
                      |..|.|+.|.|.|+++..
T Consensus       166 g~~i~gr~i~V~~a~~~~  183 (437)
T 3pgw_S          166 GKKIDGRRVLVDVERGRT  183 (437)
T ss_pred             CCEECCEEEEEEEeCCCC
Confidence            999999999999998654

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.72  E-value=4.8e-17  Score=129.22  Aligned_cols=85  Identities=20%  Similarity=0.330  Sum_probs=77.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ....++|||+|||..+++++|+++|+.|  |.|.+|.|+++.  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|
T Consensus        39 ~~~~~~l~V~nLp~~~~~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  116 (139)
T 1u6f_A           39 PDVLRNLMVNYIPTTVDEVQLRQLFERY--GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKV  116 (139)
T ss_dssp             TTTTSEEEEESCSTTCCHHHHHHHHHHH--SCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEE
Confidence            3456899999999999999999999999  999999999885  6789999999999999999998 9999999999999


Q ss_pred             eecCCCCCCC
Q 022058          287 SPSKTPVRPR  296 (303)
Q Consensus       287 ~~a~~~~~~r  296 (303)
                      .++++....+
T Consensus       117 ~~a~~~~~~~  126 (139)
T 1u6f_A          117 ALAASGHQRP  126 (139)
T ss_dssp             EESSCCCCCC
T ss_pred             EECCCCCCCC
Confidence            9998765443

>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=99.72  E-value=2.5e-17  Score=124.92  Aligned_cols=80  Identities=21%  Similarity=0.269  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+.+++++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.+
T Consensus        25 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           25 GVETGGKLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCCCSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            3346789999999999999999999999999999999998854 79999999999999999999 999999999999998


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            74

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=1.7e-17  Score=125.44  Aligned_cols=83  Identities=25%  Similarity=0.355  Sum_probs=76.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+..|+..+.|+.|.|.+
T Consensus        12 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           12 GADEIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             CSSSSSEECCBSCCTTCCHHHHHHHHHTTSCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            4456899999999999999999999999999999999998654  78999999999999999998899999999999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      +.+..
T Consensus        92 a~~~~   96 (105)
T 2dh8_A           92 CTPRG   96 (105)
T ss_dssp             SCCSS
T ss_pred             ccCCC
Confidence            86543

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=1.3e-17  Score=127.55  Aligned_cols=80  Identities=13%  Similarity=0.237  Sum_probs=74.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHH---HHhhcCCceeEEEEeeCCC-----CCceEEEEEecCHHHHHHHHH-hCCcccCCeeE
Q 022058          115 VRRTVYVSDIDQNITEERLA---GLFSSCGQVVDCRVCGDPH-----SVLRFAFVEFADEHGARAALN-LGGTMLGYYPV  185 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~---~~F~~~G~i~~~~i~~~~~-----~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i  185 (303)
                      ..++|||+|||+++++++|+   ++|+.||.|.+|.++.+..     .++|||||+|.+.++|++|++ |||..+.|++|
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr~l   93 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   93 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhccCCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCEEE
Confidence            57889999999999999999   9999999999999998875     257999999999999999999 99999999999


Q ss_pred             EEeecCCCC
Q 022058          186 RVLPSKTAI  194 (303)
Q Consensus       186 ~v~~~~~~~  194 (303)
                      .|.++.+..
T Consensus        94 ~V~~a~~k~  102 (111)
T 2cpi_A           94 KASLGTTKY  102 (111)
T ss_dssp             EEESCCCCS
T ss_pred             EEEeccccc
Confidence            999987654

>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=99.72  E-value=1.6e-17  Score=130.59  Aligned_cols=82  Identities=28%  Similarity=0.280  Sum_probs=75.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. |||..|.|++|.|.
T Consensus        42 ~~~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           42 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCCCSSCBCEETCTTSCCHHHHHHHHTTTSCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            4456789999999999999999999999999999999998764  79999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      ++.+.
T Consensus       122 ~a~~~  126 (129)
T 2kxn_B          122 FSITK  126 (129)
T ss_dssp             CCSSS
T ss_pred             EecCC
Confidence            98653

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}

Probab=99.72  E-value=2.9e-17  Score=122.82  Aligned_cols=77  Identities=23%  Similarity=0.355  Sum_probs=72.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE--------EEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR--------LRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~--------v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..        +.|+.++  |+++|||||+|.+.++|.+|++ |||..+.
T Consensus        12 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~v~i~~~~~~g~~~G~afV~f~~~~~a~~Ai~~l~g~~~~   89 (99)
T 2la6_A           12 DNNTIFVQGLGENVTIESVADYFKQI--GIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   89 (99)
T ss_dssp             CCSEEEEECCCSSCCHHHHHHHHTTT--SCBCEETTTTEESEEEEECTTTCSEEEEEEEEBSSHHHHHHHHHHHTTCBSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCEeeccccccccEEEEecCCCCCeeeEEEEEECCHHHHHHHHHHhCCCEeC
Confidence            45899999999999999999999999  99999        9999884  7899999999999999999998 9999999


Q ss_pred             CeeeEEeecC
Q 022058          281 SQPIRVSPSK  290 (303)
Q Consensus       281 g~~l~v~~a~  290 (303)
                      |+.|+|.+|+
T Consensus        90 g~~l~V~~A~   99 (99)
T 2la6_A           90 GNPIKVSFAT   99 (99)
T ss_dssp             SSBCEEEECC
T ss_pred             CcEEEEEecC
Confidence            9999999985

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.72  E-value=5.4e-17  Score=119.19  Aligned_cols=78  Identities=19%  Similarity=0.282  Sum_probs=71.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.++      +|||||+|.+.++|.+|+. |||..+.|+.|+|.+++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            7 GMVKLFIGNLPREATEQEIRSLFEQY--GKVLECDII------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHHHTS--SCEEEEEEE------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCeEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEE------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            45899999999999999999999999  999999998      4699999999999999998 99999999999999998


Q ss_pred             CCCCCCC
Q 022058          291 TPVRPRV  297 (303)
Q Consensus       291 ~~~~~r~  297 (303)
                      +....+.
T Consensus        79 ~~~~~~~   85 (90)
T 2dnq_A           79 NKSKASS   85 (90)
T ss_dssp             CCCCCCS
T ss_pred             CCCCCCC
Confidence            8765443

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=7e-17  Score=122.82  Aligned_cols=78  Identities=19%  Similarity=0.209  Sum_probs=72.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCC-----eeeE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGS-----QPIR  285 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g-----~~l~  285 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|+.+     |||||+|.+.++|.+||+ |||..|.|     +.|+
T Consensus        14 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~   86 (108)
T 1x4c_A           14 SENRVVVSGLPPSGSWQDLKDHMREA--GDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   86 (108)
T ss_dssp             CCCEEEEESCCSSCCHHHHHHHHGGG--SCEEEEEEETT-----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEeEEEEecC-----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEE
Confidence            45899999999999999999999999  99999999988     699999999999999999 99999999     9999


Q ss_pred             EeecCCCCCCC
Q 022058          286 VSPSKTPVRPR  296 (303)
Q Consensus       286 v~~a~~~~~~r  296 (303)
                      |.++++..+.+
T Consensus        87 V~~a~~~~~~~   97 (108)
T 1x4c_A           87 VKVDGPRSPSY   97 (108)
T ss_dssp             EEESSCCSCCC
T ss_pred             EEeCCCCCCCC
Confidence            99998765443

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}

Probab=99.72  E-value=3.2e-17  Score=118.36  Aligned_cols=72  Identities=15%  Similarity=0.182  Sum_probs=67.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +..|||+||++.+|+++|+++|.+|  |+|.++++..    ++|||||+|.+.++|.+|++ |||..+.|+.|+|.+|.
T Consensus         7 ~~wL~VgNL~~~~te~~L~~lF~q~--G~V~~~~l~~----~kGfaFVey~~~~eA~~Ai~~Ln~~~l~gr~I~V~~A~   79 (89)
T 2wbr_A            7 SSWLLLKNLTAQIDGPTLRTLCMQH--GPLVSFHPYL----NQGIALCKYTTREEANKAQMALNNCVLANTTIFAESPS   79 (89)
T ss_dssp             CCEEEEECCCTTCCCHHHHHHHHHH--SCEEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTEEETTEEEEEECCC
T ss_pred             cceEEEeCCCccCCHHHHHHHHHhh--CCEEEEEEcC----CCcEEEEEECCHHHHHHHHHHhcCCEECCcEEEEEECC
Confidence            4679999999999999999999999  9999999977    45799999999999999999 99999999999999983

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=3.8e-17  Score=123.06  Aligned_cols=78  Identities=28%  Similarity=0.288  Sum_probs=70.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC--CceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS--GMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~--g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||+.+++++|+++|++|  |.|.+|.|++++    |||||+|.+.++|.+|+. |+  +..+.|+.|.|.|
T Consensus        15 ~~~~LfV~nLp~~vte~dL~~lF~~f--G~V~~v~i~~~k----GfaFVeF~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~~   88 (105)
T 1sjq_A           15 PSRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLMLKGK----NQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQF   88 (105)
T ss_dssp             CCCEEEECSCCTTSCHHHHHHHHHHH--CCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHTTSCCEETTEECCBCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEcCC----CEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEE
Confidence            55899999999999999999999999  999999999874    699999999999999998 75  4789999999999


Q ss_pred             cCCCCCC
Q 022058          289 SKTPVRP  295 (303)
Q Consensus       289 a~~~~~~  295 (303)
                      +++....
T Consensus        89 A~~~~~~   95 (105)
T 1sjq_A           89 SNHKELK   95 (105)
T ss_dssp             CSSSSCC
T ss_pred             cCCCCCC
Confidence            9865433

>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=99.72  E-value=3.5e-17  Score=119.32  Aligned_cols=77  Identities=18%  Similarity=0.220  Sum_probs=72.1

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      .+.++|||+|||+.+++++|+++|++|  |.|..+.+++++  |+++|||||+|.+.++|.+|+.+++..+.|+.|.|.+
T Consensus         9 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~~~~~~~g~~i~v~~   86 (87)
T 3s7r_A            9 EDAGKMFVGGLSWDTSKKDLKDYFTKF--GEVVDCTIKMDPNTGRSRGFGFILFKDAASVEKVLDQKEHRLDGRVIDPKK   86 (87)
T ss_dssp             SCTTEEEEECCCTTCCHHHHHHHHTTT--SCEEEEEEEECTTTCCEEEEEEEEESSTHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEeecCCCCccccEEEEEECCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            355899999999999999999999999  999999999885  7899999999999999999999888999999999988


Q ss_pred             c
Q 022058          289 S  289 (303)
Q Consensus       289 a  289 (303)
                      |
T Consensus        87 A   87 (87)
T 3s7r_A           87 A   87 (87)
T ss_dssp             C
T ss_pred             C
Confidence            6

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.72  E-value=6.2e-18  Score=122.79  Aligned_cols=78  Identities=18%  Similarity=0.293  Sum_probs=72.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|+. |||..+.|+.|++.++
T Consensus         3 ~~~~~l~v~nlp~~~t~~~l~~~f~~~G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~~   82 (85)
T 1x4e_A            3 SGSSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSGP   82 (85)
T ss_dssp             CCCCEEEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSCC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecCC
Confidence            45789999999999999999999999999999999998654  79999999999999999999 9999999999998875


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      .
T Consensus        83 ~   83 (85)
T 1x4e_A           83 S   83 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.72  E-value=2.9e-17  Score=126.63  Aligned_cols=77  Identities=19%  Similarity=0.230  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG--GTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~--g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|++||.|.+|.|+.+    +|||||+|++.++|.+|++ ++  +..+.|++|.|.++
T Consensus        29 ~ps~~LfVgNLp~~vte~dL~~lF~~fG~V~~v~i~~~----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V~~a  104 (119)
T 2ad9_A           29 VPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKG----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFS  104 (119)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTTSCCCEEEEEGG----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEEEEc
Confidence            35789999999999999999999999999999999876    6899999999999999998 87  46899999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      +...
T Consensus       105 ~~k~  108 (119)
T 2ad9_A          105 NHKE  108 (119)
T ss_dssp             SSSS
T ss_pred             cCCC
Confidence            7654

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A

Probab=99.72  E-value=4.9e-18  Score=127.46  Aligned_cols=78  Identities=17%  Similarity=0.206  Sum_probs=73.7

Q ss_pred             ccceEEEcCCCC------CCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCC-
Q 022058          212 CSRTVYCTNIDK------KVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGS-  281 (303)
Q Consensus       212 ~~~~l~V~nL~~------~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g-  281 (303)
                      ..++|||+|||.      .+++++|+++|++|  |.|.+|.|++++  |+++|||||+|.+.++|.+|+. |||..+.| 
T Consensus         5 ~~~~vfV~nLp~v~~~~~~~~~~~L~~~F~~~--G~i~~v~i~~d~~tg~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~   82 (100)
T 3ns6_A            5 SDQYIVVNGAPVIPSAKVPVLKKALTSLFSKA--GKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLDLK   82 (100)
T ss_dssp             GGGEEEEESCCCCBGGGHHHHHHHHHHHHHTT--SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCBSSSS
T ss_pred             cCcEEEEeCCCcCChHHHHHHHHHHHHHHHhc--CCEeEEEEEEcCCCCccceEEEEEECCHHHHHHHHHHhCCcccCCC
Confidence            358999999999      99999999999999  999999999986  7899999999999999999998 99999999 


Q ss_pred             eeeEEeecCC
Q 022058          282 QPIRVSPSKT  291 (303)
Q Consensus       282 ~~l~v~~a~~  291 (303)
                      +.|+|.++.|
T Consensus        83 r~l~V~~a~~   92 (100)
T 3ns6_A           83 HRLFLYTMKD   92 (100)
T ss_dssp             CBCEEEESHH
T ss_pred             eEEEEEECch
Confidence            9999999975

>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=99.72  E-value=1.7e-17  Score=124.62  Aligned_cols=82  Identities=23%  Similarity=0.293  Sum_probs=72.3

Q ss_pred             ccceEEEcCCCC-CCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCC--ceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDK-KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSG--MVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~-~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g--~~~~g~~l~v~  287 (303)
                      +.++|||+|||+ .+++++|+++|++|  |.|.+|.|++++    |||||+|.+.++|..|+. ||+  ..|.|+.|.|.
T Consensus        14 p~~~l~V~nLp~~~~te~dL~~lF~~f--G~V~~v~i~~~k----g~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   87 (102)
T 1x4d_A           14 TRRVVHIMDFQRGKNLRYQLLQLVEPF--GVISNHLILNKI----NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVH   87 (102)
T ss_dssp             CCCEEEEESCCCSSSHHHHHHTTTGGG--SCEEEEEECSSS----SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCEEEEeCCCCCcCCHHHHHHHHHhc--CCEEEEEEEcCC----CEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEE
Confidence            568999999999 99999999999999  999999999876    599999999999999998 875  45999999999


Q ss_pred             ecCCCCCCCCCC
Q 022058          288 PSKTPVRPRVTR  299 (303)
Q Consensus       288 ~a~~~~~~r~~r  299 (303)
                      ++++.......+
T Consensus        88 ~a~~~~~~~~~~   99 (102)
T 1x4d_A           88 LSQKYKRIKSGP   99 (102)
T ss_dssp             EECCCTTSSCCS
T ss_pred             ECCCCCCCCCCC
Confidence            998765444333

>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=99.72  E-value=3.3e-17  Score=124.98  Aligned_cols=78  Identities=23%  Similarity=0.366  Sum_probs=71.1

Q ss_pred             ccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||.. +++++|+++|++|  |.|..|.|      ++|||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~--G~v~~v~i------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   97 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKY--GRVAGCSV------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA   97 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGG--SCCSEEEE------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEES
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhC--CCeEEEEE------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            4589999999999 9999999999999  99999999      45799999999999999997 9999999999999999


Q ss_pred             CCCCCCCC
Q 022058          290 KTPVRPRV  297 (303)
Q Consensus       290 ~~~~~~r~  297 (303)
                      +++...+.
T Consensus        98 ~~~~~~~~  105 (110)
T 1wf1_A           98 GEPKPDRS  105 (110)
T ss_dssp             CCCCSCCC
T ss_pred             CCCCCCCC
Confidence            87655443

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.72  E-value=1.3e-17  Score=131.34  Aligned_cols=82  Identities=16%  Similarity=0.255  Sum_probs=75.4

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE--EEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCc----eeC
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR--LRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGM----VLG  280 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~--v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~----~~~  280 (303)
                      ....++|||+|||+.+++++|+++|++|  |.|..  |+|++|+  |+++|||||+|.+. +|.+|+. |||.    .+.
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~--G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~   96 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPY--AVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTID   96 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGG--CCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGG
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHh--CCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCC
Confidence            4456899999999999999999999999  99976  9999986  78999999999999 9999998 9999    999


Q ss_pred             CeeeEEeecCCCCC
Q 022058          281 SQPIRVSPSKTPVR  294 (303)
Q Consensus       281 g~~l~v~~a~~~~~  294 (303)
                      |+.|.|.++++..+
T Consensus        97 gr~l~V~~a~~~~~  110 (131)
T 2m2b_A           97 GKTINVEFAKGSKR  110 (131)
T ss_dssp             GCCCCCEECCCSCC
T ss_pred             CEEEEEEECCCCCC
Confidence            99999999987643

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.72  E-value=2.5e-17  Score=126.00  Aligned_cols=81  Identities=16%  Similarity=0.348  Sum_probs=74.9

Q ss_pred             ccceEEEcCCCCCCCHHHHH---HHhhhhcCcceeEEEEecCCC-----CcccEEEEEEcCHHHHHHHHH-hCCceeCCe
Q 022058          212 CSRTVYCTNIDKKVPQAEVK---QFFEAACGGEVTRLRLLGDHV-----HSTRIAFVEFAVAESAILALN-CSGMVLGSQ  282 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~---~~F~~~~~G~i~~v~i~~d~~-----~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~  282 (303)
                      ..++|||+|||+.+++++|+   ++|++|  |.|..|.|+++.+     +++|||||+|.+.++|.+|+. |||..|.|+
T Consensus        14 ~~~~l~V~nLp~~~~~~~l~~~~~~F~~~--G~i~~v~i~~~~~~~~~~~~~G~afV~f~~~~~A~~Ai~~lng~~~~gr   91 (111)
T 2cpi_A           14 QKNLVFVVGLSQRLADPEVLKRPEYFGKF--GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGR   91 (111)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTT--SCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhhcc--CCEEEEEEecCCCcCccCCCCeEEEEEECcHHHHHHHHHHhCCCEECCE
Confidence            45789999999999999999   999999  9999999998863     567999999999999999999 999999999


Q ss_pred             eeEEeecCCCCC
Q 022058          283 PIRVSPSKTPVR  294 (303)
Q Consensus       283 ~l~v~~a~~~~~  294 (303)
                      .|+|.++++...
T Consensus        92 ~l~V~~a~~k~~  103 (111)
T 2cpi_A           92 TLKASLGTTKYC  103 (111)
T ss_dssp             EEEEESCCCCSC
T ss_pred             EEEEEecccccc
Confidence            999999987753

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.72  E-value=8.5e-18  Score=121.07  Aligned_cols=72  Identities=19%  Similarity=0.254  Sum_probs=65.9

Q ss_pred             CCEEEEcCCCCCC------CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCe-eEEE
Q 022058          116 RRTVYVSDIDQNI------TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYY-PVRV  187 (303)
Q Consensus       116 ~~~l~V~nlp~~~------t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~-~i~v  187 (303)
                      +++|||+|||+.+      ++++|+++|+.||.|.++.++.+.+.++|||||+|.+.++|.+|+. |||..+.|+ +|+|
T Consensus         1 ~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~V   80 (81)
T 2krb_A            1 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRV   80 (81)
T ss_dssp             CCEEEEESCCCCCTTTHHHHHHHHHHHHHTTCCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCCC
T ss_pred             CCEEEEeCCCCCcHHHHHHHHHHHHHHHhhcCCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEEe
Confidence            4789999999999      7899999999999999999985444589999999999999999999 999999999 8876

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.72  E-value=2.6e-17  Score=125.71  Aligned_cols=80  Identities=15%  Similarity=0.128  Sum_probs=70.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCc-ceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGG-EVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G-~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+.+++++|+++|++|  | .|..+.|..+  .++|||||+|.+.++|.+|+. |||..+.|+.|.|.++
T Consensus        27 ~~~~l~VgnLp~~~te~dL~~~F~~~--G~~v~~v~i~~~--~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           27 KRYRITMKNLPEGCSWQDLKDLAREN--SLETTFSSVNTR--DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCEEEEEECSSCCCCHHHHHHHHHHH--TCCCSEEECSSC--SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHh--CCeeEEEEEEcC--CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            34789999999999999999999999  9 8999998643  477899999999999999998 9999999999999999


Q ss_pred             CCCCCC
Q 022058          290 KTPVRP  295 (303)
Q Consensus       290 ~~~~~~  295 (303)
                      +.+...
T Consensus       103 ~~~p~~  108 (111)
T 2jvr_A          103 DNPPPI  108 (111)
T ss_dssp             CC----
T ss_pred             CCCCCC
Confidence            766433

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=7.8e-17  Score=118.32  Aligned_cols=79  Identities=20%  Similarity=0.291  Sum_probs=72.0

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..+.++++      ||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus         7 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~~~~~~~------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            7 GNTWKIFVGNVSAACTSQELRSLFERR--GRVIECDVVKD------YAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             CCSCCEEEESCCTTCCHHHHHHHHHHH--SCEEEEEECSS------CEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHcC--CCEEEEEEECC------EEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            355899999999999999999999999  99999999855      99999999999999998 9999999999999999


Q ss_pred             CCCCCCCC
Q 022058          290 KTPVRPRV  297 (303)
Q Consensus       290 ~~~~~~r~  297 (303)
                      ++....+.
T Consensus        79 ~~~~~~~~   86 (90)
T 2dnp_A           79 TKGQKKSG   86 (90)
T ss_dssp             CCCCCCCS
T ss_pred             CCCCCCCC
Confidence            88754433

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=2.5e-17  Score=124.49  Aligned_cols=83  Identities=18%  Similarity=0.245  Sum_probs=76.5

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+.+|+..|.|+.|.|.+
T Consensus        14 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~~~~g~~~g~afV~f~~~~~a~~a~~~~~~~~~g~~l~V~~   91 (105)
T 2dh8_A           14 DEIGKLFVGGLDWSTTQETLRSYFSQY--GEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASRPHTLDGRNIDPKP   91 (105)
T ss_dssp             SSSSEECCBSCCTTCCHHHHHHHHHTT--SCEEEEEEEECSSSCCEEEEEEEEESSTTHHHHHHHHCSEEETTEEEBCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeeCCCCCCcceEEEEEECCHHHHHHHHHhCCCeECCEEEEEEE
Confidence            355899999999999999999999999  999999999984  7889999999999999999998899999999999999


Q ss_pred             cCCCCCC
Q 022058          289 SKTPVRP  295 (303)
Q Consensus       289 a~~~~~~  295 (303)
                      +++....
T Consensus        92 a~~~~~~   98 (105)
T 2dh8_A           92 CTPRGMQ   98 (105)
T ss_dssp             SCCSSCC
T ss_pred             ccCCCCC
Confidence            9876543

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens}

Probab=99.71  E-value=4.5e-17  Score=121.47  Aligned_cols=77  Identities=21%  Similarity=0.234  Sum_probs=70.1

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCce--eCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMV--LGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~--~~g~~l~v  286 (303)
                      ..+.++|||+|||+.+++++|+++|++|  |.|.++.+++++    |+|||+|.+.++|.+|+. |||..  +.|+.|.|
T Consensus        18 ~~ps~~l~V~NLp~~~te~~L~~lF~~f--G~V~~v~i~~~k----g~AFVef~~~~~A~~Av~~ln~~~~~i~Gr~i~V   91 (100)
T 3r27_A           18 TPASPVVHIRGLIDGVVEADLVEALQEF--GPISYVVVMPKK----RQALVEFEDVLGACNAVNYAADNQIYIAGHPAFV   91 (100)
T ss_dssp             CCCCSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHHHSCEEETTEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHhcc--CCEEEEEEEcCC----CEEEEEECCHHHHHHHHHHhcCCCceeCCcEEEE
Confidence            4467899999999999999999999999  999999998754    699999999999999998 98875  78999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      .|+++.
T Consensus        92 ~~S~~k   97 (100)
T 3r27_A           92 NYSTSQ   97 (100)
T ss_dssp             EECSCS
T ss_pred             Eecccc
Confidence            999854

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.71  E-value=2.6e-17  Score=133.49  Aligned_cols=78  Identities=27%  Similarity=0.345  Sum_probs=72.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC--ceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ..++|||+|||+++++++|+++|+.||  .|.+|.++.|+.+  ++|||||+|.+.++|.+||. |||..|.|+.|.|.+
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V~~  133 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDVRP  133 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHTTCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHCCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEEEE
Confidence            468999999999999999999999999  9999999998754  79999999999999999999 999999999999999


Q ss_pred             cCC
Q 022058          190 SKT  192 (303)
Q Consensus       190 ~~~  192 (303)
                      +.+
T Consensus       134 a~~  136 (156)
T 3n9u_C          134 ATR  136 (156)
T ss_dssp             CCH
T ss_pred             cCC
Confidence            753

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.71  E-value=6.6e-17  Score=125.97  Aligned_cols=81  Identities=22%  Similarity=0.283  Sum_probs=75.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ...++|||+|||+.+++++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. |||..+.|+.|.|.++.
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  112 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  112 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTTSCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEEeC
Confidence            45788999999999999999999999999999999998744 79999999999999999999 99999999999999987


Q ss_pred             CCC
Q 022058          192 TAI  194 (303)
Q Consensus       192 ~~~  194 (303)
                      ...
T Consensus       113 ~~~  115 (124)
T 2kt5_A          113 SQI  115 (124)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            654

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=3.5e-17  Score=125.33  Aligned_cols=82  Identities=26%  Similarity=0.372  Sum_probs=75.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCcee--------EEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCccc
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVV--------DCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTML  180 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~  180 (303)
                      .....++|||+|||+++++++|+++|+.||.|.        .|.++.++.+  ++|||||+|.+.++|.+|+. ||+..+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~   90 (113)
T 2cpe_A           11 EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDF   90 (113)
T ss_dssp             CCCCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEE
T ss_pred             cCCCCCEEEEcCCCCCCCHHHHHHHHHhcCCEeEccccCccCEEEEEeCCCCCeeeEEEEEECCHHHHHHHHHHcCCCcc
Confidence            445688999999999999999999999999999        6999988654  79999999999999999998 999999


Q ss_pred             CCeeEEEeecCCC
Q 022058          181 GYYPVRVLPSKTA  193 (303)
Q Consensus       181 ~g~~i~v~~~~~~  193 (303)
                      .|+.|.|.+++..
T Consensus        91 ~g~~l~V~~a~~~  103 (113)
T 2cpe_A           91 QGSKLKVSLARKK  103 (113)
T ss_dssp             TTEECEEECSSCC
T ss_pred             CCCEEEEEECCCC
Confidence            9999999998654

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=6.9e-17  Score=121.62  Aligned_cols=82  Identities=18%  Similarity=0.187  Sum_probs=74.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. ++..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~v~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~-~~~~~~g~~l~v~~   89 (103)
T 2cqg_A           11 AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKL   89 (103)
T ss_dssp             CCCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEEC
T ss_pred             ccCCCCEEEEEcCCCcCCHHHHHHHHHhcCCeEEEEEEecCCCCCccceEEEEECCHHHHHHHHH-cCCeeCCeEEEEEe
Confidence            4446788999999999999999999999999999999998754  79999999999999999999 56789999999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      +....
T Consensus        90 a~~~~   94 (103)
T 2cqg_A           90 PNSKQ   94 (103)
T ss_dssp             CCTTC
T ss_pred             cCCCC
Confidence            86543

>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=99.71  E-value=2.3e-17  Score=124.39  Aligned_cols=79  Identities=30%  Similarity=0.461  Sum_probs=73.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|++ |||..+.|+.|.|.++.
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   86 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAA   86 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETT
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhcCCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEeCC
Confidence            4688999999999999999999999999999999998654  79999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus        87 ~~   88 (104)
T 1p1t_A           87 SE   88 (104)
T ss_dssp             CT
T ss_pred             Cc
Confidence            43

>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=99.71  E-value=1.7e-17  Score=124.99  Aligned_cols=80  Identities=23%  Similarity=0.206  Sum_probs=72.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|||+++|+++|+++|+.||.+ +|.|+.++.+ ++|||||+|.+.++|++||++|+..|.||.|.|.++.
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~-~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           12 STTGHCVHMRGLPYRATENDIYNFFSPLNPM-RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCCS-EEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHcCce-EEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            3467899999999999999999999999954 9999998754 7999999999999999999999999999999999876


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus        91 ~~   92 (102)
T 1wez_A           91 TA   92 (102)
T ss_dssp             CC
T ss_pred             CC
Confidence            44

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster}

Probab=99.71  E-value=4.5e-17  Score=125.75  Aligned_cols=79  Identities=19%  Similarity=0.336  Sum_probs=73.5

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ....++|||+|||..+++++|+++|++|  |.|.+|.|++++  ++++|||||+|.+.++|.+|+. |||..++|+.|+|
T Consensus        37 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V  114 (118)
T 2khc_A           37 GPEGCNLFIYHLPQEFTDTDLASTFLPF--GNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNGFQVGTKRLKV  114 (118)
T ss_dssp             CCCSEEEEEECSCTTCCHHHHHHHTTTS--CEEEEEEECCCSSSSCCCCEEEEEEESSHHHHHHHHHCCCCEETTEECCE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEeCCCCCCcCcEEEEEECCHHHHHHHHHHcCCCEECCEEEEE
Confidence            4456899999999999999999999999  999999999884  6889999999999999999998 9999999999999


Q ss_pred             eecC
Q 022058          287 SPSK  290 (303)
Q Consensus       287 ~~a~  290 (303)
                      .|++
T Consensus       115 ~~ak  118 (118)
T 2khc_A          115 QLKK  118 (118)
T ss_dssp             EEC-
T ss_pred             EecC
Confidence            9985

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=4.9e-17  Score=119.61  Aligned_cols=80  Identities=21%  Similarity=0.359  Sum_probs=73.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|||+++++++|+++|+.| .|.+|.++.+..+ ++|||||+|.+.++|.+|+.+|+..+.|+.|.|.++.
T Consensus         7 ~~~~~~l~v~nLp~~~t~~~l~~~F~~~-~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            7 GTTCHTVKLRGAPFNVTEKNVMEFLAPL-KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCCCEEEEECCCSSCCHHHHHHHHTTS-CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CCCccEEEEECCCCCCCHHHHHHHHhhC-CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            4467899999999999999999999999 9999999998544 7999999999999999999999999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus        86 ~~   87 (91)
T 2dgw_A           86 SG   87 (91)
T ss_dssp             SC
T ss_pred             cC
Confidence            43

>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=99.71  E-value=1.7e-17  Score=124.65  Aligned_cols=76  Identities=25%  Similarity=0.314  Sum_probs=69.0

Q ss_pred             CCCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCC--cccCCeeEEEee
Q 022058          114 SVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG--TMLGYYPVRVLP  189 (303)
Q Consensus       114 ~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g--~~~~g~~i~v~~  189 (303)
                      ...++|||+|||+ ++++++|+++|++||.|.+|.|+++    +|||||+|++.++|.+|++ ||+  ..+.|++|.|.+
T Consensus        13 ~p~~~l~V~nLp~~~~te~dL~~lF~~fG~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~~   88 (102)
T 1x4d_A           13 ETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNK----INEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRVHL   88 (102)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSS----SSCEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCcCCHHHHHHHHHhcCCEEEEEEEcC----CCEEEEEECCHHHHHHHHHHHcCCCceECCcEEEEEE
Confidence            3678999999999 9999999999999999999999875    4799999999999999998 885  459999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      ++..
T Consensus        89 a~~~   92 (102)
T 1x4d_A           89 SQKY   92 (102)
T ss_dssp             ECCC
T ss_pred             CCCC
Confidence            8753

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1

Probab=99.71  E-value=4.8e-17  Score=129.24  Aligned_cols=83  Identities=23%  Similarity=0.352  Sum_probs=76.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.
T Consensus        38 ~~~~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  117 (139)
T 1u6f_A           38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEEcCCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            4456789999999999999999999999999999999998765  79999999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      +++...
T Consensus       118 ~a~~~~  123 (139)
T 1u6f_A          118 LAASGH  123 (139)
T ss_dssp             ESSCCC
T ss_pred             ECCCCC
Confidence            987553

>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=99.71  E-value=2.2e-17  Score=124.32  Aligned_cols=83  Identities=17%  Similarity=0.149  Sum_probs=75.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||+.+++++|+++|++|  | +..|.|+.|+ ++++|||||+|.+.++|.+|+.+|+..|+|+.|+|.++.
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~--G-~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~~~   90 (102)
T 1wez_A           14 TGHCVHMRGLPYRATENDIYNFFSPL--N-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             SSCEEEEESCCTTCCHHHHHHSSCSC--C-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc--C-ceEEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            45899999999999999999999999  9 5599999885 789999999999999999999999999999999999998


Q ss_pred             CCCCCCC
Q 022058          291 TPVRPRV  297 (303)
Q Consensus       291 ~~~~~r~  297 (303)
                      ++...+-
T Consensus        91 ~~~~~~~   97 (102)
T 1wez_A           91 TAGTSGS   97 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            7765543

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.71  E-value=1.2e-16  Score=117.72  Aligned_cols=78  Identities=24%  Similarity=0.327  Sum_probs=71.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.++++      ||||+|.+.++|.+|+. |||..+.|+.|+|.+++
T Consensus         9 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~v~~~~~------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   80 (92)
T 2dgt_A            9 ASTKLHVGNISPTCTNQELRAKFEEY--GPVIECDIVKD------YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLST   80 (92)
T ss_dssp             SSEEEEEESCCSSCCHHHHHHHHHTT--SCCCEEEECSS------EEEEEESCHHHHHHHHHHHTTEEETTEEEEEEESS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEECC------EEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEcc
Confidence            45899999999999999999999999  99999999855      99999999999999998 99999999999999998


Q ss_pred             CCCCCCC
Q 022058          291 TPVRPRV  297 (303)
Q Consensus       291 ~~~~~r~  297 (303)
                      +....+.
T Consensus        81 ~~~~~~~   87 (92)
T 2dgt_A           81 SRLRTAS   87 (92)
T ss_dssp             CCCSCCC
T ss_pred             CCCCCCC
Confidence            7755443

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A

Probab=99.71  E-value=1.9e-17  Score=126.47  Aligned_cols=78  Identities=14%  Similarity=0.077  Sum_probs=70.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCC-ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCG-QVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G-~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      +...++|||+|||+++++++|+++|+.|| .|..+.++.+  .++|||||+|.+.++|++||+ |||..+.|+.|.|.++
T Consensus        25 p~~~~~l~VgnLp~~~te~dL~~~F~~~G~~v~~v~i~~~--~~rGfaFV~F~~~e~A~~Ai~~lng~~l~Gr~i~V~~a  102 (111)
T 2jvr_A           25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTR--DFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERD  102 (111)
T ss_dssp             CCCCEEEEEECSSCCCCHHHHHHHHHHHTCCCSEEECSSC--SSSCCEEEEESSHHHHHHHHHHTTTEEETTEEEEEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHhCCeeEEEEEEcC--CCCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            44578899999999999999999999999 8999988643  368999999999999999998 9999999999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ..
T Consensus       103 ~~  104 (111)
T 2jvr_A          103 DN  104 (111)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.71  E-value=4.5e-17  Score=124.16  Aligned_cols=82  Identities=23%  Similarity=0.344  Sum_probs=71.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+..++..+.|+.|.|.+
T Consensus        21 ~~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~~  100 (109)
T 2rs2_A           21 MGSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKV  100 (109)
T ss_dssp             -----CCEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHccCCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEEE
Confidence            4456889999999999999999999999999999999998754  89999999999999999999446999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      +.+.
T Consensus       101 a~~~  104 (109)
T 2rs2_A          101 AFPR  104 (109)
T ss_dssp             CCCC
T ss_pred             ccCC
Confidence            8643

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.71  E-value=1.3e-17  Score=118.62  Aligned_cols=73  Identities=25%  Similarity=0.407  Sum_probs=68.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ++|||+|||+++++++|+++|+.||+|.++.++.++.+  ++|||||+|.+.++|.+|+. ++ ..+.|++|.|.++
T Consensus         1 ~~l~v~nlp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~g~afV~f~~~~~a~~a~~~~~-~~~~g~~l~v~~a   76 (77)
T 1uaw_A            1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            47999999999999999999999999999999998754  79999999999999999999 88 9999999999985

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.71  E-value=1.9e-17  Score=125.31  Aligned_cols=79  Identities=18%  Similarity=0.213  Sum_probs=71.7

Q ss_pred             CCCCEEEEcCCCCCC------CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCe-eE
Q 022058          114 SVRRTVYVSDIDQNI------TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYY-PV  185 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~------t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~-~i  185 (303)
                      ...++|||+|||+.+      ++++|+++|+.||.|.+|.++...+.++|||||+|.+.++|.+|+. |||..+.|+ +|
T Consensus        13 ~~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~l   92 (105)
T 2nlw_A           13 GIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTF   92 (105)
T ss_dssp             SCCSEEEEESCCCCCTTTTTHHHHHHHHHHGGGSCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCEE
T ss_pred             CCCCEEEEeCCCcchhhhhHHHHHHHHHHHhcCCCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCceE
Confidence            357899999999999      7899999999999999999985444489999999999999999999 999999998 99


Q ss_pred             EEeecCC
Q 022058          186 RVLPSKT  192 (303)
Q Consensus       186 ~v~~~~~  192 (303)
                      .|.++..
T Consensus        93 ~V~~a~~   99 (105)
T 2nlw_A           93 RVNLFTD   99 (105)
T ss_dssp             EEECSCC
T ss_pred             EEEEcch
Confidence            9999853

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.71  E-value=1.7e-16  Score=119.12  Aligned_cols=80  Identities=28%  Similarity=0.279  Sum_probs=72.2

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h--CCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C--SGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l--~g~~~~g~~l~v~  287 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|.+|.++++    +|||||+|.+.++|.+|+. |  ++..+.|+.|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~f--G~v~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~~~Gr~l~V~   86 (101)
T 2cq1_A           13 APSRVLHIRKLPGEVTETEVIALGLPF--GKVTNILMLKG----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQ   86 (101)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCcEEEEE
Confidence            456899999999999999999999999  99999999987    4699999999999999997 6  5788999999999


Q ss_pred             ecCCCCCCC
Q 022058          288 PSKTPVRPR  296 (303)
Q Consensus       288 ~a~~~~~~r  296 (303)
                      |+++..-.+
T Consensus        87 ~a~~~~~~~   95 (101)
T 2cq1_A           87 YSNHKELKT   95 (101)
T ss_dssp             ECSCSSCCC
T ss_pred             EcCcccCcC
Confidence            998765554

>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=99.71  E-value=6.4e-17  Score=122.60  Aligned_cols=78  Identities=21%  Similarity=0.328  Sum_probs=73.7

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..|.|+.+. +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus        27 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~  104 (107)
T 3ulh_A           27 ETGGKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL  104 (107)
T ss_dssp             CCSEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEEE
Confidence            356899999999999999999999999  999999999885 7889999999999999999999 999999999999999


Q ss_pred             cC
Q 022058          289 SK  290 (303)
Q Consensus       289 a~  290 (303)
                      +.
T Consensus       105 a~  106 (107)
T 3ulh_A          105 VT  106 (107)
T ss_dssp             EC
T ss_pred             eC
Confidence            85

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.71  E-value=2.6e-17  Score=127.34  Aligned_cols=80  Identities=19%  Similarity=0.204  Sum_probs=74.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCc---eeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEe
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQ---VVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVL  188 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~---i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~  188 (303)
                      ....++|||+|||+++|+++|+++|+.||.   |.+|+|+.+..+ ++|||||+|.+.++|++||++|+..|.|+.|.|.
T Consensus        14 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             BCCCCEEEEESCCTTCCHHHHHHHTTTSCBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            446789999999999999999999999999   899999998766 7999999999999999999999999999999999


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      ++..
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8743

>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=99.71  E-value=4.3e-17  Score=128.07  Aligned_cols=80  Identities=23%  Similarity=0.266  Sum_probs=75.2

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..|.|++++  +.++|||||+|.+.++|.+|+. |||..|.|+.|.|.
T Consensus        44 ~~~~~l~V~nLp~~~te~~L~~~F~~~--G~I~~v~i~~d~~tg~~~G~afV~F~~~~~A~~Ai~~lng~~i~g~~l~V~  121 (129)
T 2kxn_B           44 DPNCCLGVFGLSLYTTERDLREVFSKY--GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVD  121 (129)
T ss_dssp             CCSSCBCEETCTTSCCHHHHHHHHTTT--SCEEEEEEECCSSSSCCCCEEEEEESCHHHHHHHHHHHTTCCSSSSCCEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            456899999999999999999999999  999999999985  6889999999999999999998 99999999999999


Q ss_pred             ecCCC
Q 022058          288 PSKTP  292 (303)
Q Consensus       288 ~a~~~  292 (303)
                      |+++.
T Consensus       122 ~a~~~  126 (129)
T 2kxn_B          122 FSITK  126 (129)
T ss_dssp             CCSSS
T ss_pred             EecCC
Confidence            99864

>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=99.71  E-value=2e-17  Score=123.38  Aligned_cols=79  Identities=14%  Similarity=0.143  Sum_probs=72.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|..+.++.++.+  ++|||||+|.+.++|++|+. ||+..+.|+.|.|.++
T Consensus        13 ~~~~~l~v~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   92 (98)
T 2cqp_A           13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   92 (98)
T ss_dssp             CSSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHcCCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEc
Confidence            35688999999999999999999999999998888877654  78999999999999999997 9999999999999997


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ..
T Consensus        93 ~~   94 (98)
T 2cqp_A           93 SG   94 (98)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens}

Probab=99.70  E-value=4.3e-17  Score=123.38  Aligned_cols=79  Identities=18%  Similarity=0.229  Sum_probs=73.4

Q ss_pred             ccceEEEcCCCCCC------CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCe-e
Q 022058          212 CSRTVYCTNIDKKV------PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQ-P  283 (303)
Q Consensus       212 ~~~~l~V~nL~~~~------t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~-~  283 (303)
                      ..++|||+|||..+      ++++|+++|++|  |.|..|.|++..|+++|||||+|.+.++|.+|+. |||..+.|+ .
T Consensus        14 ~~~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~--G~v~~v~i~~~~g~~~G~afV~f~~~~~A~~Ai~~l~g~~~~g~~~   91 (105)
T 2nlw_A           14 IDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKF--GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT   91 (105)
T ss_dssp             CCSEEEEESCCCCCTTTTTHHHHHHHHHHGGG--SCEEEEECCCBTTBSCCEEEEEECSSSHHHHHHHHCSSEECSTTCE
T ss_pred             CCCEEEEeCCCcchhhhhHHHHHHHHHHHhcC--CCEEEEEeeCCCCCeeeEEEEEECCHHHHHHHHHHhCCcccCCCce
Confidence            45899999999999      789999999999  9999999997678999999999999999999999 999999998 9


Q ss_pred             eEEeecCCC
Q 022058          284 IRVSPSKTP  292 (303)
Q Consensus       284 l~v~~a~~~  292 (303)
                      |+|.++...
T Consensus        92 l~V~~a~~~  100 (105)
T 2nlw_A           92 FRVNLFTDF  100 (105)
T ss_dssp             EEEECSCCC
T ss_pred             EEEEEcchH
Confidence            999999744

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens}

Probab=99.70  E-value=4.6e-17  Score=122.13  Aligned_cols=77  Identities=25%  Similarity=0.323  Sum_probs=72.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      ++|||+|||..+++++|+++|++|  |.|..|.++++   ++|||||+|.+.++|.+|+. |||..+.|+.|+|.++++.
T Consensus         1 ~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~---~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~~~   75 (101)
T 2hvz_A            1 MKVYVGNLGTGAGKGELERAFSYY--GPLRTVWIARN---PPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELSTGM   75 (101)
T ss_dssp             CEEEEECCCSSCSHHHHHHHHHHH--CCCSEEEEESS---SSSEEEEECSSHHHHHHHHHHHHHSCSSSCCCEEEESSSC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeeC---CCCEEEEEECCHHHHHHHHHHHCCCeECCcEEEEEEccCC
Confidence            479999999999999999999999  99999999988   67899999999999999998 9999999999999999877


Q ss_pred             CCC
Q 022058          293 VRP  295 (303)
Q Consensus       293 ~~~  295 (303)
                      .+.
T Consensus        76 ~~~   78 (101)
T 2hvz_A           76 PRR   78 (101)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            643

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.70  E-value=9.8e-17  Score=117.79  Aligned_cols=75  Identities=24%  Similarity=0.432  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|||+++++++|+++|+.||.|.+|.++      +|||||+|.+.++|.+|+. ||+..+.|++|.|.++.
T Consensus         5 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   78 (90)
T 2dnq_A            5 SSGMVKLFIGNLPREATEQEIRSLFEQYGKVLECDII------KNYGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASK   78 (90)
T ss_dssp             SSCCEEEEEESCCSSCCHHHHHHHHHTSSCEEEEEEE------TTEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEECSS
T ss_pred             CCCCeEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEE------CCEEEEEECCHHHHHHHHHHhcCCccCCcEEEEEECC
Confidence            4467899999999999999999999999999999997      5899999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        79 ~~   80 (90)
T 2dnq_A           79 NK   80 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.70  E-value=2e-17  Score=124.67  Aligned_cols=81  Identities=23%  Similarity=0.409  Sum_probs=75.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..+.++++.  |.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus         7 ~~~~l~V~nlp~~~~~~~l~~~f~~~--G~i~~~~i~~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~   84 (104)
T 1p1t_A            7 SLRSVFVGNIPYEATEEQLKDIFSEV--GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDN   84 (104)
T ss_dssp             HHSCEEEESCCTTSCHHHHHHHHHTT--SCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEE
T ss_pred             CccEEEEeCCCCcCCHHHHHHHHHhc--CCeeEEEEEeCCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEe
Confidence            45899999999999999999999999  999999999884  7889999999999999999998 999999999999999


Q ss_pred             cCCCCC
Q 022058          289 SKTPVR  294 (303)
Q Consensus       289 a~~~~~  294 (303)
                      +++...
T Consensus        85 a~~~~~   90 (104)
T 1p1t_A           85 AASEKN   90 (104)
T ss_dssp             TTCTTH
T ss_pred             CCCccc
Confidence            987643

>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=99.70  E-value=5.7e-17  Score=122.33  Aligned_cols=79  Identities=25%  Similarity=0.407  Sum_probs=73.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC---CCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH---SVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~---~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.|| |.+|.|+.++.   .++|||||+|.+.++|.+||.||+..+.|+.|.|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   91 (104)
T 1wi8_A           13 SPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVA   91 (104)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEEC
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHHHCC-ceEEEEecCCCCCCCcCeEEEEEECCHHHHHHHHhcCCCEeCCcEEEEEEc
Confidence            3578999999999999999999999999 99999999875   2799999999999999999999999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        92 ~~~   94 (104)
T 1wi8_A           92 DQA   94 (104)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            654

>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=99.70  E-value=2.3e-17  Score=126.71  Aligned_cols=81  Identities=20%  Similarity=0.139  Sum_probs=74.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCce-eEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQV-VDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i-~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      +...++|||+|||+++++++|+++|+.||.| .+|.|+.+..+ ++|||||+|.+.++|.+||.+|+..|.|+.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~a   91 (114)
T 2cpy_A           12 NSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVV   91 (114)
T ss_dssp             CSCCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEE
T ss_pred             CCCccEEEEeCcCCcCCHHHHHHHHHhCCCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEEC
Confidence            3467899999999999999999999999999 89999998854 899999999999999999999999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ...
T Consensus        92 ~~~   94 (114)
T 2cpy_A           92 TLE   94 (114)
T ss_dssp             CHH
T ss_pred             CHH
Confidence            543

>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=99.70  E-value=9.4e-17  Score=122.10  Aligned_cols=82  Identities=17%  Similarity=0.191  Sum_probs=74.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcc-eeEEEEe-cCC--CCcccEEEEEEcCHHHHHHHHH-hC--CceeCCeee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGE-VTRLRLL-GDH--VHSTRIAFVEFAVAESAILALN-CS--GMVLGSQPI  284 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~-i~~v~i~-~d~--~~~~g~afV~f~~~e~A~~Ai~-l~--g~~~~g~~l  284 (303)
                      +.++|||+|||..+++++|+++|++|  |. |.++.++ .+.  +.++|||||+|.+.++|.+|+. ||  +..+.|+.|
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~f~~~--G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l   84 (109)
T 2dis_A            7 GNCRLFIGGIPKMKKREEILEEIAKV--TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQI   84 (109)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHH--STTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHh--cCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeE
Confidence            45899999999999999999999999  98 9999998 564  5789999999999999999999 96  589999999


Q ss_pred             EEeecCCCCCC
Q 022058          285 RVSPSKTPVRP  295 (303)
Q Consensus       285 ~v~~a~~~~~~  295 (303)
                      +|.|+++...+
T Consensus        85 ~V~~a~~~~~~   95 (109)
T 2dis_A           85 AVDWAEPEIDV   95 (109)
T ss_dssp             EEEESCSSCST
T ss_pred             EEEEcCCCCCc
Confidence            99999876553

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=8.3e-17  Score=121.55  Aligned_cols=77  Identities=18%  Similarity=0.158  Sum_probs=69.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCC--cccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG--TMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g--~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|++||.|.+|.++++    +|||||+|.+.++|.+|++ |++  ..+.|++|.|.++
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~fG~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~~a   88 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNYS   88 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhCCCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEEEc
Confidence            35789999999999999999999999999999999864    6899999999999999998 765  4589999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      ....
T Consensus        89 ~~~~   92 (104)
T 1wex_A           89 TSKR   92 (104)
T ss_dssp             SSSS
T ss_pred             cCcc
Confidence            7543

>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=99.70  E-value=4.3e-17  Score=123.14  Aligned_cols=81  Identities=21%  Similarity=0.195  Sum_probs=73.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeE-EEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD-CRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+ |.|+.+..+ ++|||||+|.+.++|.+||..|+..++||.|.|.++
T Consensus        12 ~~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           12 TANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CSCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            346789999999999999999999999999987 888888544 799999999999999999988999999999999987


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ...
T Consensus        92 ~~~   94 (104)
T 1wg5_A           92 SRA   94 (104)
T ss_dssp             CTT
T ss_pred             CHH
Confidence            543

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}

Probab=99.70  E-value=1e-16  Score=122.14  Aligned_cols=82  Identities=18%  Similarity=0.201  Sum_probs=72.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.|+++.  |.++|||||+|.+.++|.+|+...|..++|+.|.|.
T Consensus        22 ~~~~~~lfV~nLp~~~te~~L~~~F~~~--G~i~~v~i~~~~~tg~~kg~afV~f~~~~~A~~Ai~~~~~~l~g~~l~V~   99 (109)
T 2rs2_A           22 GSSGCKMFIGGLSWQTTQEGLREYFGQF--GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPK   99 (109)
T ss_dssp             ----CCEEEESCCTTCCHHHHHHHHTTT--SCEEEEEECCCTTTCCCTTCEEEEESSHHHHHHHHHSSCEEETTEEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHcc--CCeEEEEEEECCCCCCcCcEEEEEECCHHHHHHHHHHCCCcCCCEEEEEE
Confidence            3456899999999999999999999999  999999999985  789999999999999999999944699999999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      ++.+..
T Consensus       100 ~a~~~~  105 (109)
T 2rs2_A          100 VAFPRR  105 (109)
T ss_dssp             ECCCCC
T ss_pred             EccCCC
Confidence            998543

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A

Probab=99.70  E-value=2.3e-17  Score=116.80  Aligned_cols=73  Identities=15%  Similarity=0.254  Sum_probs=69.4

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      +|||+|||..+++++|+++|++|  |.|..+.+++++  +.++|||||+|.+.++|.+|+.|||..++|+.|.|.+|
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 KIFVGGLSVNTTVEDVKHYFEQF--GKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT--SCCSEECCCBCSSSTTSCBEEEEECSCHHHHHHHHSSSCCCSSSCCCEEECC
T ss_pred             CEEEecCCCCCCHHHHHHHHHhc--CCEEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHCCCCEECCEEEEEEeC
Confidence            48999999999999999999999  999999999885  78999999999999999999999999999999999986

>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=99.70  E-value=2e-17  Score=122.61  Aligned_cols=77  Identities=14%  Similarity=0.139  Sum_probs=71.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.++.+  ++|||||+|.+.++|.+|++ ||+..+.|++|.|.++.
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~a~   93 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSGPS   93 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTSCBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEecc
Confidence            4689999999999999999999999999998888887654  78999999999999999998 99999999999999864

>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=99.70  E-value=1.7e-16  Score=119.46  Aligned_cols=81  Identities=23%  Similarity=0.420  Sum_probs=73.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|+++      ||||+|.+.++|.+|+. |||..|.|+.|+|.+++
T Consensus        10 ~~~~l~V~nl~~~~t~~~l~~~F~~~--G~i~~v~~~~~------~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~   81 (103)
T 2dgu_A           10 KVKVLFVRNLANTVTEEILEKAFSQF--GKLERVKKLKD------YAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAK   81 (103)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHH--SCEEEEEECSS------CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEECC------EEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcC
Confidence            45899999999999999999999999  99999999843      99999999999999999 99999999999999998


Q ss_pred             CCCCCCCCCC
Q 022058          291 TPVRPRVTRP  300 (303)
Q Consensus       291 ~~~~~r~~r~  300 (303)
                      ++...+..|.
T Consensus        82 ~~~~~~~~~~   91 (103)
T 2dgu_A           82 PPDQKRKERK   91 (103)
T ss_dssp             CCCCCCCCCC
T ss_pred             CCcccchhhh
Confidence            8776654443

>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=99.70  E-value=1.1e-16  Score=129.64  Aligned_cols=84  Identities=20%  Similarity=0.260  Sum_probs=77.5

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.
T Consensus        37 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           37 KKSCTLYVGNLSFYTTEEQIYELFSKS--GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            356899999999999999999999999  999999999985  6789999999999999999999 99999999999999


Q ss_pred             ecCCCCCCC
Q 022058          288 PSKTPVRPR  296 (303)
Q Consensus       288 ~a~~~~~~r  296 (303)
                      |+++....+
T Consensus       115 ~a~~~~~~~  123 (156)
T 1h2v_Z          115 WDAGFKEGR  123 (156)
T ss_dssp             EESCCCTTC
T ss_pred             ECCCCCCcC
Confidence            998765444

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.70  E-value=7.2e-17  Score=122.81  Aligned_cols=77  Identities=30%  Similarity=0.523  Sum_probs=71.2

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..|.+.      +|||||+|.+.++|.+|+. |||..+.|+.|.|.+
T Consensus        28 ~~~~~~l~V~nLp~~~t~~~L~~~F~~~--G~i~~v~i~------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           28 ELSNTRLFVRPFPLDVQESELNEIFGPF--GPMKEVKIL------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             CCSCSEEEECSSCTTCCHHHHHHHHTTT--SCCCEEEEE------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhc--CCEEEEEEE------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            4567899999999999999999999999  999999998      5799999999999999998 999999999999999


Q ss_pred             cCCCCC
Q 022058          289 SKTPVR  294 (303)
Q Consensus       289 a~~~~~  294 (303)
                      ++++..
T Consensus       100 a~~~~~  105 (108)
T 2jvo_A          100 SKLPAK  105 (108)
T ss_dssp             CSCCC-
T ss_pred             ecCCCC
Confidence            987643

>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=99.70  E-value=9.2e-17  Score=122.14  Aligned_cols=81  Identities=21%  Similarity=0.191  Sum_probs=73.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCc-eeEEEEe-eCCCC--CceEEEEEecCHHHHHHHHH-hC--CcccCCeeEE
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQ-VVDCRVC-GDPHS--VLRFAFVEFADEHGARAALN-LG--GTMLGYYPVR  186 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~~~i~-~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~--g~~~~g~~i~  186 (303)
                      ...++|||+|||+++++++|+++|+.||. |.++.++ .+..+  ++|||||+|.+.++|.+|+. ||  +..+.|+.|.
T Consensus         6 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~~v~~v~i~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~~g~~~~~g~~l~   85 (109)
T 2dis_A            6 SGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIA   85 (109)
T ss_dssp             CCSEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCE
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHhcCCceEEEEEccCCCCCCcCcEEEEEecCHHHHHHHHHHhhCCCceecCCeEE
Confidence            35789999999999999999999999998 9999998 66653  79999999999999999999 96  5899999999


Q ss_pred             EeecCCCC
Q 022058          187 VLPSKTAI  194 (303)
Q Consensus       187 v~~~~~~~  194 (303)
                      |.|+.+..
T Consensus        86 V~~a~~~~   93 (109)
T 2dis_A           86 VDWAEPEI   93 (109)
T ss_dssp             EEESCSSC
T ss_pred             EEEcCCCC
Confidence            99987654

>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=99.70  E-value=2.7e-17  Score=130.19  Aligned_cols=80  Identities=19%  Similarity=0.207  Sum_probs=74.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCc---eeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEE
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQ---VVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRV  187 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~---i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v  187 (303)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|.|++++.+ ++|||||+|.+.++|++||++|+..+.||.|.|
T Consensus        40 ~~~~~~~lfVgnLp~~~te~dL~~~F~~~G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V  119 (136)
T 2hgl_A           40 EGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEV  119 (136)
T ss_dssp             SCCTTCEEEEESCCTTCCHHHHHHHTTTCCCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEE
Confidence            3446789999999999999999999999999   899999998766 899999999999999999999999999999999


Q ss_pred             eecC
Q 022058          188 LPSK  191 (303)
Q Consensus       188 ~~~~  191 (303)
                      .++.
T Consensus       120 ~~a~  123 (136)
T 2hgl_A          120 FKSH  123 (136)
T ss_dssp             EECC
T ss_pred             EECC
Confidence            9874

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}

Probab=99.70  E-value=5.8e-17  Score=131.49  Aligned_cols=78  Identities=22%  Similarity=0.271  Sum_probs=72.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCc--ceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGG--EVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G--~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ..++|||+|||..+++++|+++|++|  |  .|..|.|+.|.  |+++|||||+|.+.++|.+|+. |||..|+|+.|.|
T Consensus        54 ~~~~lfVgnLp~~~te~~L~~~F~~~--G~i~v~~v~i~~d~~tg~skGfaFV~f~~~~~A~~Ai~~lng~~~~Gr~l~V  131 (156)
T 3n9u_C           54 RRAAVYVGSFSWWTTDQQLIQVIRSI--GVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLELLPGKVLNGEKVDV  131 (156)
T ss_dssp             --CEEEEECCCTTCCHHHHHHHHHHT--TCCCEEEEEEEECTTTCCEEEEEEEEESCHHHHHHHHHHSTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHH--CCccEEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCEECCeEeEE
Confidence            45799999999999999999999999  9  99999999884  7899999999999999999999 9999999999999


Q ss_pred             eecCC
Q 022058          287 SPSKT  291 (303)
Q Consensus       287 ~~a~~  291 (303)
                      .++.+
T Consensus       132 ~~a~~  136 (156)
T 3n9u_C          132 RPATR  136 (156)
T ss_dssp             EECCH
T ss_pred             EEcCC
Confidence            99975

>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=99.70  E-value=8.5e-17  Score=123.40  Aligned_cols=81  Identities=17%  Similarity=0.350  Sum_probs=73.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCccc--------C
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTML--------G  181 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~--------~  181 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. |||..+        .
T Consensus        21 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           21 QEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            3446789999999999999999999999999999999998744 79999999999999999999 999999        5


Q ss_pred             CeeEEEeecCC
Q 022058          182 YYPVRVLPSKT  192 (303)
Q Consensus       182 g~~i~v~~~~~  192 (303)
                      +++|.|.++++
T Consensus       101 ~~~l~v~~a~p  111 (114)
T 1x5o_A          101 TEPLLCKFSGP  111 (114)
T ss_dssp             SSCBEEEECCC
T ss_pred             CCceeEEccCC
Confidence            78899998763

>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=99.70  E-value=3.6e-17  Score=121.96  Aligned_cols=80  Identities=19%  Similarity=0.184  Sum_probs=73.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..+.++.+.  ++++|||||+|.+.++|.+|+. |||..|.|+.|+|.+
T Consensus        14 ~~~~l~v~nLp~~~t~~~l~~~F~~~--G~v~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~   91 (98)
T 2cqp_A           14 GPTIIKVQNMPFTVSIDEILDFFYGY--QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   91 (98)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTS--CCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc--CCccceEEEEECCCCCeeeEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEE
Confidence            45889999999999999999999999  999887777663  6789999999999999999997 999999999999999


Q ss_pred             cCCCC
Q 022058          289 SKTPV  293 (303)
Q Consensus       289 a~~~~  293 (303)
                      +..+.
T Consensus        92 a~~~~   96 (98)
T 2cqp_A           92 GSGPS   96 (98)
T ss_dssp             SSCSS
T ss_pred             cCCCC
Confidence            97653

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.1e-17  Score=123.65  Aligned_cols=79  Identities=24%  Similarity=0.350  Sum_probs=73.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+||..++..+.|+.|.|.++.+
T Consensus        26 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~V~~a~~  105 (116)
T 1x4b_A           26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA  105 (116)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEECCCCCCcCceEEEEeCCHHHHHHHHHhCCcEECCEEEEEEECCC
Confidence            4688999999999999999999999999999999998764  79999999999999999998899999999999999865


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus       106 ~  106 (116)
T 1x4b_A          106 R  106 (116)
T ss_dssp             C
T ss_pred             C
Confidence            4

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=6.7e-17  Score=120.40  Aligned_cols=78  Identities=24%  Similarity=0.355  Sum_probs=70.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|. +.++.+  .++|||||+|.+.++|.+|+. |||..+.|+.|.|.++
T Consensus        15 ~~~~~~~l~V~nL~~~~t~~~l~~~F~~~G~v~-~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   91 (97)
T 2e5j_A           15 GAPLAADVYVGNLPRDARVSDLKRALRELGSVP-LRLTWQ--GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALA   91 (97)
T ss_dssp             SSCCCCEEEEECCCTTCCHHHHHHHHHHTTCCC-SEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEEC
T ss_pred             CCCCCCEEEEeCCCCcCcHHHHHHHHHhcCCEE-EEEEcC--CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            344578999999999999999999999999997 777764  468999999999999999998 9999999999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ++
T Consensus        92 ~~   93 (97)
T 2e5j_A           92 RQ   93 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.70  E-value=5.2e-17  Score=124.63  Aligned_cols=78  Identities=31%  Similarity=0.444  Sum_probs=73.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.+..+  ++|||||+|.+.++|.+|+.||+..|.|+.|.|.++..
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  103 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQA  103 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHHH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEecCC
Confidence            4678999999999999999999999999999999998864  79999999999999999999999999999999999753

>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=99.70  E-value=1.9e-17  Score=124.16  Aligned_cols=80  Identities=24%  Similarity=0.401  Sum_probs=70.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCC-C-C-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP-H-S-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~-~-~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.|| |.+|.++.+. . + ++|||||+|.+.++|.+|+.|||..+.|+.|.|.
T Consensus        15 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           15 PKSPPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVD   93 (100)
T ss_dssp             -----CEEEESCCSSCCSSSHHHHHSCSSC-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCE
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEE
Confidence            344688999999999999999999999999 9999999986 2 2 8999999999999999999999999999999999


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      +++.
T Consensus        94 ~a~~   97 (100)
T 2j76_E           94 VADQ   97 (100)
T ss_dssp             ECCC
T ss_pred             eccC
Confidence            9854

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}

Probab=99.70  E-value=8.9e-18  Score=123.33  Aligned_cols=76  Identities=28%  Similarity=0.426  Sum_probs=69.7

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.+ |.+|+. |||..+.|++|.|.++.+.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~~~   80 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEANPK   80 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHHTCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC---
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhcCCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcCCC
Confidence            57999999999999999999999999999999998754  7999999999999 999999 9999999999999998654

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.70  E-value=9.7e-17  Score=122.14  Aligned_cols=79  Identities=25%  Similarity=0.386  Sum_probs=73.0

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+.+++++|+++|+.||.|.+|.++.+    +|||||+|.+.++|.+|+. |||..+.|++|.|.|+
T Consensus        21 ~~~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~i~~~----~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   96 (109)
T 1x4g_A           21 SSPKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG   96 (109)
T ss_dssp             SCSSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEec
Confidence            4456889999999999999999999999999999999876    6899999999999999998 9999999999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      +...
T Consensus        97 ~~~~  100 (109)
T 1x4g_A           97 KESP  100 (109)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7543

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}

Probab=99.70  E-value=8e-17  Score=125.41  Aligned_cols=79  Identities=32%  Similarity=0.554  Sum_probs=73.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+.|||..+.|+.|.|.+++.
T Consensus        35 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~~  114 (124)
T 2jwn_A           35 DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKVLPKRT  114 (124)
T ss_dssp             HHTEEEEEEECTTCCHHHHHHHHHTTSCEEEEEEEEECTTSSCEEEEEEEESSHHHHHHHHTTTTCEETTEECEEEESSC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEEecCCCCCcccEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCC
Confidence            4689999999999999999999999999999999998643  79999999999999999999999999999999999865


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus       115 ~  115 (124)
T 2jwn_A          115 N  115 (124)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.70  E-value=8.2e-17  Score=119.88  Aligned_cols=77  Identities=22%  Similarity=0.294  Sum_probs=70.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC--CeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG--YYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~--g~~i~v~~  189 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++.+    +|||||+|.+.++|.+|++ ||+..+.  |++|.|.+
T Consensus        14 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~v~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~~   89 (97)
T 1why_A           14 ANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDF   89 (97)
T ss_dssp             CCCCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeeEEEEeCC----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEEE
Confidence            345789999999999999999999999999999999764    6899999999999999999 9999999  99999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      +++.
T Consensus        90 a~~~   93 (97)
T 1why_A           90 AKSG   93 (97)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>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=99.70  E-value=8.5e-17  Score=130.42  Aligned_cols=82  Identities=26%  Similarity=0.276  Sum_probs=75.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.|+.+..+  ++|||||+|.+.++|.+||. ||+..|.|+.|.|.
T Consensus        35 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~  114 (156)
T 1h2v_Z           35 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTD  114 (156)
T ss_dssp             TTTTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEE
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEE
Confidence            3346789999999999999999999999999999999998765  78999999999999999999 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      |+.+.
T Consensus       115 ~a~~~  119 (156)
T 1h2v_Z          115 WDAGF  119 (156)
T ss_dssp             EESCC
T ss_pred             ECCCC
Confidence            98654

>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=99.70  E-value=8.2e-17  Score=116.77  Aligned_cols=75  Identities=24%  Similarity=0.330  Sum_probs=69.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L-GGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l-~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+|.++++    +|||||+|.+.++|.+|+. | |+..+.|++|.|.|+
T Consensus         9 ~~~~~~l~V~~l~~~~t~~~l~~~f~~~G~i~~~~~~~~----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A            9 DKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQR----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             CSSCCCEEEECCTTTSCHHHHHHHHHTTSCEEEEEEEGG----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CCCccEEEEcCCCCCCCHHHHHHHHHhCCCEeEEEEECC----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            346789999999999999999999999999999999874    6899999999999999999 8 999999999999986


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      +
T Consensus        85 k   85 (85)
T 2ytc_A           85 R   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.70  E-value=9.5e-17  Score=123.76  Aligned_cols=85  Identities=27%  Similarity=0.289  Sum_probs=74.5

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC--CceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS--GMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~--g~~~~g~~l~v  286 (303)
                      ..+.++|||+|||+.+++++|+++|++|  |.|.+|.|+++    +|||||+|.+.++|.+|+. |+  +..+.|+.|.|
T Consensus        28 ~~ps~~LfVgNLp~~vte~dL~~lF~~f--G~V~~v~i~~~----kG~AFVeF~~~e~A~~Ai~~l~~~~~~l~Gr~l~V  101 (119)
T 2ad9_A           28 GVPSRVIHIRKLPIDVTEGEVISLGLPF--GKVTNLLMLKG----KNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYI  101 (119)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHHHTTT--SCCCEEEEEGG----GTEEEEECSCHHHHHHHHHHHHHHCCCBTTBCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEeCC----CCEEEEEECCHHHHHHHHHHhccCCceECCeEEEE
Confidence            3456899999999999999999999999  99999999987    4699999999999999998 86  46899999999


Q ss_pred             eecCCCCCCCCCCC
Q 022058          287 SPSKTPVRPRVTRP  300 (303)
Q Consensus       287 ~~a~~~~~~r~~r~  300 (303)
                      .|+++..-.+...+
T Consensus       102 ~~a~~k~~~~~~~~  115 (119)
T 2ad9_A          102 QFSNHKELKTDSSP  115 (119)
T ss_dssp             EECSSSSCCCCCCT
T ss_pred             EEccCCCCCccccc
Confidence            99987665554433

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=6.7e-17  Score=120.83  Aligned_cols=78  Identities=23%  Similarity=0.285  Sum_probs=71.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.++++    +|||||+|.+.++|.+|++ ||+..+.|++|.|.++
T Consensus        11 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~~~~~----kg~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           11 TFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCCCTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             cCCCCCEEEEeCCCCCCCHHHHHHHHhhcCCeEEEEEecC----CCEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            3446789999999999999999999999999999999864    6899999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        87 ~~~   89 (99)
T 2cpj_A           87 CHS   89 (99)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            654

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=6.2e-17  Score=123.28  Aligned_cols=75  Identities=17%  Similarity=0.137  Sum_probs=70.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ..+|||+|||+++++++|+++|+.| .|.+|.|+.++.+ ++|||||+|.+.++|++||.+|+..|+||.|.|..+.
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~-~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~   91 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPAT   91 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS-CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC-CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECC
Confidence            5689999999999999999999999 8999999998766 8999999999999999999999999999999998864

>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=99.69  E-value=3.2e-17  Score=125.94  Aligned_cols=81  Identities=19%  Similarity=0.112  Sum_probs=75.0

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcce-eEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEV-TRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i-~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      ...++|||+|||..+++++|+++|++|  |.| ..|.|+.|. |+++|||||+|.+.++|.+|+.+||..|+|+.|.|.+
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--g~v~~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~v~~   90 (114)
T 2cpy_A           13 SAKVCAHITNIPFSITKMDVLQFLEGI--PVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHV   90 (114)
T ss_dssp             SCCCEEEEESCCTTSCHHHHHHHTTTS--CCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEE
T ss_pred             CCccEEEEeCcCCcCCHHHHHHHHHhC--CCcCCeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCCCccCCeEEEEEE
Confidence            345899999999999999999999999  999 889999986 7899999999999999999998999999999999999


Q ss_pred             cCCCC
Q 022058          289 SKTPV  293 (303)
Q Consensus       289 a~~~~  293 (303)
                      +.+..
T Consensus        91 a~~~~   95 (114)
T 2cpy_A           91 VTLED   95 (114)
T ss_dssp             ECHHH
T ss_pred             CCHHH
Confidence            87554

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus}

Probab=99.69  E-value=1.3e-16  Score=124.23  Aligned_cols=84  Identities=19%  Similarity=0.298  Sum_probs=77.5

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..|.|+.+. |.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus        33 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~  110 (124)
T 2kt5_A           33 ETGAKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL  110 (124)
T ss_dssp             SSCEEEEEESCCSSCCHHHHHHHHHTT--SCCSEEEEECCSSSSCCSEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEEECCCCCEeeEEEEEECCHHHHHHHHHHcCCCEECCcEEEEEE
Confidence            356899999999999999999999999  999999999986 7789999999999999999999 999999999999999


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      +.+...+.
T Consensus       111 a~~~~~~~  118 (124)
T 2kt5_A          111 VASQIDLE  118 (124)
T ss_dssp             ECCTTCCC
T ss_pred             eCCCCCCC
Confidence            98765544

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.69  E-value=2e-16  Score=121.48  Aligned_cols=82  Identities=20%  Similarity=0.282  Sum_probs=72.4

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcce----eEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEV----TRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i----~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|    ..+.+.  .+.++|||||+|.+.++|.+|+. |||..+.|+.|+
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~--G~v~~~~~~~~~~--~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~   98 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARF--QEKKGPPIQFRMM--TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILV   98 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHH--HHSSSSCCEEEEE--CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHh--CCccceEEEEEcC--CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEE
Confidence            356899999999999999999999999  999    455554  56788999999999999999998 999999999999


Q ss_pred             EeecCCCCCCC
Q 022058          286 VSPSKTPVRPR  296 (303)
Q Consensus       286 v~~a~~~~~~r  296 (303)
                      |.|+++....+
T Consensus        99 v~~a~~~~~~~  109 (115)
T 2cpx_A           99 IEFGKNKKQRS  109 (115)
T ss_dssp             EEECCCCSCCC
T ss_pred             EEEccCCCCCC
Confidence            99998765433

>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=99.69  E-value=6.2e-17  Score=126.39  Aligned_cols=81  Identities=21%  Similarity=0.284  Sum_probs=74.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.|+.+..+  ++|||||+|.+.++|.+|++ ||+..|.|+.|.|.++
T Consensus        20 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   99 (126)
T 3ex7_B           20 VEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWC   99 (126)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCTTTSSBCSCEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHhCCCeeCCeEEEEEEe
Confidence            35788999999999999999999999999999999998654  79999999999999999998 9999999999999998


Q ss_pred             CCCC
Q 022058          191 KTAI  194 (303)
Q Consensus       191 ~~~~  194 (303)
                      ....
T Consensus       100 ~~~~  103 (126)
T 3ex7_B          100 FVRG  103 (126)
T ss_dssp             EESS
T ss_pred             cCCC
Confidence            6543

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.69  E-value=1.7e-16  Score=120.68  Aligned_cols=76  Identities=21%  Similarity=0.182  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCC-----eeEEE
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGY-----YPVRV  187 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g-----~~i~v  187 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.|+.+     |||||+|.+.++|++||+ ||+..+.|     +.|.|
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~~~~~~i~V   87 (108)
T 1x4c_A           13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   87 (108)
T ss_dssp             SCCCEEEEESCCSSCCHHHHHHHHGGGSCEEEEEEETT-----TEEEEEESSHHHHHHHHHHSSSEEEECTTSCEEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEeEEEEecC-----CEEEEEECCHHHHHHHHHHHCcCCccCCcCcceEEEE
Confidence            35789999999999999999999999999999999887     799999999999999999 99999999     99999


Q ss_pred             eecCCCC
Q 022058          188 LPSKTAI  194 (303)
Q Consensus       188 ~~~~~~~  194 (303)
                      .++.+..
T Consensus        88 ~~a~~~~   94 (108)
T 1x4c_A           88 KVDGPRS   94 (108)
T ss_dssp             EESSCCS
T ss_pred             EeCCCCC
Confidence            9987643

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.69  E-value=6.1e-17  Score=121.46  Aligned_cols=76  Identities=20%  Similarity=0.235  Sum_probs=70.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|||+++++++|+++|+.||.|.++.+.    .++|||||+|.+.++|.+|+. |||..+.|+.|.|.|++
T Consensus        24 ~~~~~~l~V~nlp~~~~~~~l~~~f~~~G~i~~~~~~----~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           24 PPRVTTAYIGNIPHFATEADLIPLFQNFGFILDFKHY----PEKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             CSSCCEEEEESCCTTCCHHHHHHHHHTTSCCSEEEEE----TTTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCCCEEEEcCCCcccCHHHHHHHHHhCCCEEEEEEe----cCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            3457899999999999999999999999999999997    357899999999999999998 99999999999999985


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            3

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens}

Probab=99.69  E-value=2.8e-17  Score=118.30  Aligned_cols=72  Identities=19%  Similarity=0.295  Sum_probs=67.3

Q ss_pred             ceEEEcCCCCCC------CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCe-eeE
Q 022058          214 RTVYCTNIDKKV------PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQ-PIR  285 (303)
Q Consensus       214 ~~l~V~nL~~~~------t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~-~l~  285 (303)
                      ++|||+|||..+      ++++|+++|++|  |.|.++.++++.|+++|||||+|.+.++|.+|+. |||..+.|+ .|+
T Consensus         2 ~~l~V~nLp~~~~~~~~~t~~~l~~~F~~~--G~i~~v~i~~~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~~~l~   79 (81)
T 2krb_A            2 SVIVVDNVPQVGPDRLEKLKNVIHKIFSKF--GKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFR   79 (81)
T ss_dssp             CEEEEESCCCCCTTTHHHHHHHHHHHHHTT--CCEEEEECCCBTTBCCCEEEEEESSHHHHHHHHTTSSSCCCSSSSCCC
T ss_pred             CEEEEeCCCCCcHHHHHHHHHHHHHHHhhc--CCeEEEEecCCCCcEeEEEEEEECCHHHHHHHHHHhcCcccCCceeEE
Confidence            689999999999      679999999999  9999999987678999999999999999999998 999999999 887


Q ss_pred             Ee
Q 022058          286 VS  287 (303)
Q Consensus       286 v~  287 (303)
                      |+
T Consensus        80 V~   81 (81)
T 2krb_A           80 VN   81 (81)
T ss_dssp             CC
T ss_pred             eC
Confidence            63

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A

Probab=99.69  E-value=9e-17  Score=122.27  Aligned_cols=77  Identities=23%  Similarity=0.440  Sum_probs=70.5

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       111 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ......++|||+|||+++++++|+++|+.||.|.+|.++      +|||||+|.+.++|.+|+. |||..+.|+.|.|.+
T Consensus        26 ~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~------kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   99 (108)
T 2jvo_A           26 EGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL------NGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVY   99 (108)
T ss_dssp             --CCSCSEEEECSSCTTCCHHHHHHHHTTTSCCCEEEEE------TTEEEEECSSHHHHHHHHHHHTTCEETTEECEEES
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHhcCCEEEEEEE------CCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEE
Confidence            344578999999999999999999999999999999998      6899999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      ++..
T Consensus       100 a~~~  103 (108)
T 2jvo_A          100 SKLP  103 (108)
T ss_dssp             CSCC
T ss_pred             ecCC
Confidence            8653

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.69  E-value=8.6e-17  Score=119.45  Aligned_cols=79  Identities=22%  Similarity=0.305  Sum_probs=71.6

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..+   ...+.++|||||+|.+.++|.+|+. |||..+.|+.|.|.++
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~--g~v~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   88 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDA--LEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYT   88 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSE--EEECCE---EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhC--CcEEEe---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEc
Confidence            356899999999999999999999999  988777   4457889999999999999999999 9999999999999999


Q ss_pred             CCCCC
Q 022058          290 KTPVR  294 (303)
Q Consensus       290 ~~~~~  294 (303)
                      ++..+
T Consensus        89 ~~~~~   93 (96)
T 1fjc_A           89 GEKGG   93 (96)
T ss_dssp             SSSCC
T ss_pred             CCCCC
Confidence            86643

>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=99.69  E-value=1.6e-17  Score=117.67  Aligned_cols=73  Identities=16%  Similarity=0.331  Sum_probs=68.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      +|||+|||+++++++|+++|+.||+|.++.++.++.+  ++|||||+|.+.++|.+|+.+++..+.|+.|.|.++
T Consensus         1 ~l~v~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~Ai~~~~~~~~g~~l~v~~a   75 (75)
T 1iqt_A            1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHHSCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            5899999999999999999999999999999988764  799999999999999999998999999999999874

>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=99.69  E-value=1.8e-17  Score=121.66  Aligned_cols=80  Identities=21%  Similarity=0.321  Sum_probs=70.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ++|||+|||..+++++|+++|++|  |.|.++.++++.  |.++|||||+|.+.+ |.+|+. |||..++|+.|+|.+|.
T Consensus         2 ~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~-a~~a~~~l~g~~~~g~~l~V~~a~   78 (90)
T 2ki2_A            2 RNIYVGNLVYSATSEQVKELFSQF--GKVFNVKLIYDRETKKPKGFGFVEMQEES-VSEAIAKLDNTDFMGRTIRVTEAN   78 (90)
T ss_dssp             EEEEEEEECTTSSHHHHTTTHHHH--TCCSEEEECCCSSSCCCCEEEEEEECTTH-HHHHHHTSCSSCCSSSSCSEEEC-
T ss_pred             cEEEECCCCCCCCHHHHHHHHHhc--CCEEEEEEEEcCCCCCcceEEEEEECCHH-HHHHHHHhCCCEECCeEEEEEEcC
Confidence            589999999999999999999999  999999999985  788999999999999 999998 99999999999999998


Q ss_pred             CCCCCC
Q 022058          291 TPVRPR  296 (303)
Q Consensus       291 ~~~~~r  296 (303)
                      +...+.
T Consensus        79 ~~~~~~   84 (90)
T 2ki2_A           79 PKKSLE   84 (90)
T ss_dssp             ------
T ss_pred             CCCCCC
Confidence            765443

>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=99.69  E-value=3.6e-17  Score=122.62  Aligned_cols=79  Identities=23%  Similarity=0.359  Sum_probs=72.4

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ...++|||+|||..+++++|+++|++|  | |.+|.|+++.   |+++|||||+|.+.++|.+|+.|||..++|+.|+|.
T Consensus        17 ~~~~~l~V~nLp~~~t~~~l~~~F~~~--G-i~~v~i~~~~~~~g~~~g~afV~f~~~~~a~~Ai~l~g~~~~g~~l~V~   93 (100)
T 2j76_E           17 SPPYTAFLGNLPYDVTEESIKEFFRGL--N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNRRIRVD   93 (100)
T ss_dssp             ---CEEEESCCSSCCSSSHHHHHSCSS--C-EEEEECSCCTTTTCCCCSCEEEEECCHHHHHHHHHTTTCCBTTBCCCCE
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhc--C-CeEEEEEecCCcCCccCeEEEEEECCHHHHHHHHhcCCCEECCeEEEEE
Confidence            356899999999999999999999999  9 9999999874   678999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022058          288 PSKTP  292 (303)
Q Consensus       288 ~a~~~  292 (303)
                      ++++.
T Consensus        94 ~a~~~   98 (100)
T 2j76_E           94 VADQA   98 (100)
T ss_dssp             ECCCS
T ss_pred             eccCC
Confidence            99865

>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=99.69  E-value=3.2e-17  Score=125.80  Aligned_cols=80  Identities=33%  Similarity=0.562  Sum_probs=75.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|+.+.  +.++|||||+|.+.++|.+|+.|||..|.|+.|+|.++
T Consensus        24 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a  101 (114)
T 2cq4_A           24 DARTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS  101 (114)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhC--CCEeEEEEEecCCCCccCcEEEEEeCcHHHHHHHHHcCCCEeCCeEEEEEec
Confidence            45899999999999999999999999  999999999886  68899999999999999999999999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      ++..
T Consensus       102 ~~~~  105 (114)
T 2cq4_A          102 QAEK  105 (114)
T ss_dssp             HHHH
T ss_pred             CCCc
Confidence            7543

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A

Probab=99.69  E-value=1.6e-16  Score=118.43  Aligned_cols=75  Identities=17%  Similarity=0.346  Sum_probs=69.2

Q ss_pred             CCCCCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+ ++++++|+++|+.||.|.++.+.      +|||||+|.+.++|.+|+. +||..+.|+.|.|.+
T Consensus        18 ~~~~~~~l~V~nLp~~~~t~~~L~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   91 (97)
T 2xnq_A           18 GSHMKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILEV   91 (97)
T ss_dssp             -CCTTCEEEEESCCSSCCCHHHHHHHHGGGSCEEEEEEC------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEEE
T ss_pred             CCCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEEe
Confidence            445689999999998 99999999999999999999983      6899999999999999999 999999999999999


Q ss_pred             cCC
Q 022058          190 SKT  192 (303)
Q Consensus       190 ~~~  192 (303)
                      ++.
T Consensus        92 a~~   94 (97)
T 2xnq_A           92 SSS   94 (97)
T ss_dssp             CCC
T ss_pred             cCC
Confidence            854

>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=99.69  E-value=9e-17  Score=118.67  Aligned_cols=78  Identities=23%  Similarity=0.289  Sum_probs=68.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcc-eeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCC-ceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGE-VTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSG-MVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~-i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g-~~~~g~~l~v~~  288 (303)
                      ..++|||+|||..+++++|+++|++|  |. |..+.+.     ++|||||+|.+.++|.+|+. ||| ..+.|+.|+|.+
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~vv~~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            7 GMNKLYIGNLSPAVTADDLRQLFGDR--KLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHHHHT--TCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHc--CCceEEEEEc-----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            45899999999999999999999999  99 6666663     45799999999999999998 999 999999999999


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      +++.....
T Consensus        80 a~~~~~~~   87 (93)
T 2cqh_A           80 SVSKKLRS   87 (93)
T ss_dssp             CCCCCCCC
T ss_pred             ccCccccC
Confidence            98765443

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.69  E-value=6.4e-17  Score=126.54  Aligned_cols=79  Identities=24%  Similarity=0.364  Sum_probs=71.7

Q ss_pred             ccceEEEcCCCCCCCHHHHH----HHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVK----QFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~----~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      +.++|||+|||+.+++++|+    ++|++|  |.|.+|.+.. .++++|||||+|.+.++|..|+. |||..|.|+.|+|
T Consensus        28 p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~--G~I~~v~i~~-~~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V  104 (127)
T 2a3j_A           28 PSQVVLITNINPEVPKEKLQALLYALASSQ--GDILDIVVDL-SDDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVI  104 (127)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHHHH--SCEEEEEECC-CCSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccC--CCeEEEEecc-CCCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEE
Confidence            46899999999999999876    799999  9999998865 36789999999999999999998 9999999999999


Q ss_pred             eecCCCC
Q 022058          287 SPSKTPV  293 (303)
Q Consensus       287 ~~a~~~~  293 (303)
                      .|+++..
T Consensus       105 ~~a~~~~  111 (127)
T 2a3j_A          105 TFSETPQ  111 (127)
T ss_dssp             EECCCCC
T ss_pred             EEccCcc
Confidence            9998654

>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=99.68  E-value=4.4e-17  Score=120.77  Aligned_cols=78  Identities=19%  Similarity=0.191  Sum_probs=71.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.++.++  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~gr~l~v~~   91 (95)
T 2ek1_A           14 GPTVIKVQNMPFTVSIDEILDFFYGY--QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLSG   91 (95)
T ss_dssp             -CEEEEEECCCTTCCHHHHHHHTTTS--CBCTTCCEEEECTTSCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCccceEEEEeCCCCCEeeEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEe
Confidence            45899999999999999999999999  999988877764  6789999999999999999998 999999999999999


Q ss_pred             cCC
Q 022058          289 SKT  291 (303)
Q Consensus       289 a~~  291 (303)
                      +.+
T Consensus        92 a~s   94 (95)
T 2ek1_A           92 PSS   94 (95)
T ss_dssp             CC-
T ss_pred             ccC
Confidence            863

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.2e-16  Score=118.57  Aligned_cols=84  Identities=18%  Similarity=0.251  Sum_probs=72.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ..+.++|||+|||..+++++|+++|+.|  +   .+.++.+.  +.++|||||+|.+.++|.+|+. |||..|.|+.|+|
T Consensus        12 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~--~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V   86 (102)
T 2fc8_A           12 SQPSKTLFVKGLSEDTTEETLKESFDGS--V---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTL   86 (102)
T ss_dssp             SCCCSSEEEECCCTTCCHHHHHHTSTTC--S---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCccCHHHHHHHhcCC--e---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEE
Confidence            3456899999999999999999999987  5   45566653  7889999999999999999998 9999999999999


Q ss_pred             eecCCCCCCCCC
Q 022058          287 SPSKTPVRPRVT  298 (303)
Q Consensus       287 ~~a~~~~~~r~~  298 (303)
                      .++++.......
T Consensus        87 ~~a~~~~~~~~~   98 (102)
T 2fc8_A           87 DWAKPKGEGGSG   98 (102)
T ss_dssp             EECCCCCSSSCS
T ss_pred             EEecCCCCCCCC
Confidence            999987654443

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.68  E-value=7.7e-17  Score=119.87  Aligned_cols=82  Identities=15%  Similarity=0.252  Sum_probs=70.6

Q ss_pred             cccceEEEcCCCC-CCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          211 MCSRTVYCTNIDK-KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~-~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+.++|||+|||. .+++++|+++|++|  |.|..+.|.      +|||||+|.+.++|.+|+. |||..+.|+.|+|.+
T Consensus         8 ~~~~~l~V~nlp~~~~t~~~l~~~F~~~--G~v~~v~i~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~   79 (96)
T 2kvi_A            8 PPKSRLFIGNLPLKNVSKEDLFRIFSPY--GHIMQINIK------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEV   79 (96)
T ss_dssp             -CCEEEEEESSTTSCCCHHHHHHHHTTT--CCCCEEEEE------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEE
T ss_pred             CCCCEEEEeCCCcccCCHHHHHHHHHhc--CCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEE
Confidence            3568999999998 99999999999999  999999995      5699999999999999998 999999999999999


Q ss_pred             cCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRP  300 (303)
Q Consensus       289 a~~~~~~r~~r~  300 (303)
                      +++..+++..+.
T Consensus        80 a~~~~~~~~~~~   91 (96)
T 2kvi_A           80 SSSNARPQFDHG   91 (96)
T ss_dssp             EECCCC------
T ss_pred             cCcCCCCCCCCC
Confidence            988776665543

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens}

Probab=99.68  E-value=9.1e-17  Score=125.70  Aligned_cols=78  Identities=24%  Similarity=0.324  Sum_probs=70.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHH----HHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          114 SVRRTVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ...++|||+|||+.+++++|+    ++|+.||.|.+|.+..+ ..++|||||+|.+.++|.+|+. |||..+.|++|.|.
T Consensus        27 ~p~~~LfV~nL~~~~~e~~L~~~L~~~F~~~G~I~~v~i~~~-~~~rG~aFV~F~~~~~A~~Ai~~lng~~l~gr~l~V~  105 (127)
T 2a3j_A           27 EPSQVVLITNINPEVPKEKLQALLYALASSQGDILDIVVDLS-DDNSGKAYIVFATQESAQAFVEAFQGYPFQGNPLVIT  105 (127)
T ss_dssp             SCCSEEEEESCCTTSCHHHHHHHHHHHHHHHSCEEEEEECCC-CSSCCCEEEEESSHHHHHHHHHHSTTCCCTTSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHhccCCCeEEEEeccC-CCcCCEEEEEECCHHHHHHHHHHHCCCEeCCCEEEEE
Confidence            357899999999999999876    69999999999988642 3479999999999999999998 99999999999999


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      |++.
T Consensus       106 ~a~~  109 (127)
T 2a3j_A          106 FSET  109 (127)
T ss_dssp             ECCC
T ss_pred             EccC
Confidence            9864

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.68  E-value=2.4e-17  Score=119.68  Aligned_cols=77  Identities=14%  Similarity=0.215  Sum_probs=71.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.|+.++  +.++|||||+|.+.++|.+|+. |||..+.|+.|++++
T Consensus         4 ~~~~l~v~nlp~~~t~~~l~~~f~~~--G~i~~~~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~~~~~~   81 (85)
T 1x4e_A            4 GSSGLYIRGLQPGTTDQDLVKLCQPY--GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAKQSG   81 (85)
T ss_dssp             CCCEEEEESCCTTCCHHHHHTTSTTT--SCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCCSSC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhcCCeEeeEEEeecC
Confidence            45899999999999999999999999  999999999984  7889999999999999999999 999999999998877


Q ss_pred             cC
Q 022058          289 SK  290 (303)
Q Consensus       289 a~  290 (303)
                      +.
T Consensus        82 ~~   83 (85)
T 1x4e_A           82 PS   83 (85)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.68  E-value=1.1e-16  Score=131.17  Aligned_cols=79  Identities=19%  Similarity=0.254  Sum_probs=73.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+.+++++|+++|+.||.|..|.|+.+..+  ++|||||+|.+.++|.+||. |||..|.|++|.|.|+.
T Consensus        71 ~~~~l~V~nLp~~~t~~~L~~~F~~~G~i~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~  150 (165)
T 1rk8_A           71 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF  150 (165)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHhhcCCCEEEEEEEecCCCCcEeeEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            4667999999999999999999999999999999998654  78999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus       151 ~~  152 (165)
T 1rk8_A          151 VK  152 (165)
T ss_dssp             EC
T ss_pred             CC
Confidence            54

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.68  E-value=1e-16  Score=127.24  Aligned_cols=79  Identities=25%  Similarity=0.380  Sum_probs=72.5

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.||.|.++.++.++.+  ++|||||+|.+.++|.+|++ |||..+.|++|.|.
T Consensus        59 ~~~~~~~l~v~nlp~~~~~~~l~~~f~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~  138 (140)
T 2ku7_A           59 SATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVN  138 (140)
T ss_dssp             SCSSCCEEEEECCCTTCCHHHHHHHHGGGSCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCCHHHHHHHHHhcCCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3346889999999999999999999999999999999998654  79999999999999999998 99999999999998


Q ss_pred             ec
Q 022058          189 PS  190 (303)
Q Consensus       189 ~~  190 (303)
                      ++
T Consensus       139 ~A  140 (140)
T 2ku7_A          139 LA  140 (140)
T ss_dssp             C-
T ss_pred             eC
Confidence            74

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}

Probab=99.68  E-value=2.9e-17  Score=124.76  Aligned_cols=81  Identities=17%  Similarity=0.126  Sum_probs=74.3

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCc---eeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEE
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQ---VVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRV  187 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~---i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v  187 (303)
                      .....++|||+|||+++|+++|+++|+.||.   |.+|.|+.+..+ ++|||||+|.+.++|.+||.+|+..++|+.|.|
T Consensus         7 ~~~~~~~l~V~nLp~~~te~~l~~~F~~~g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V   86 (107)
T 2lmi_A            7 EVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEV   86 (107)
T ss_dssp             CCSSCCEEEEECCCSSCCSHHHHHHTTTSCBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCC
T ss_pred             CCCCccEEEEeCCCCCCCHHHHHHHHHhcCCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEE
Confidence            3446789999999999999999999999998   899999988765 899999999999999999999999999999999


Q ss_pred             eecCC
Q 022058          188 LPSKT  192 (303)
Q Consensus       188 ~~~~~  192 (303)
                      .++..
T Consensus        87 ~~a~~   91 (107)
T 2lmi_A           87 YEINN   91 (107)
T ss_dssp             EECCH
T ss_pred             EECCH
Confidence            98753

>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=99.68  E-value=2.3e-16  Score=120.95  Aligned_cols=81  Identities=17%  Similarity=0.313  Sum_probs=74.7

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCcee--------C
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVL--------G  280 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~--------~  280 (303)
                      ...++|||+|||..+++++|+++|++|  |.|..+.|+++. +.++|||||+|.+.++|.+|+. |||..+        .
T Consensus        23 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~g~~~g~afV~f~~~~~a~~A~~~l~g~~~~~~~~~~~~  100 (114)
T 1x5o_A           23 QDPTNLYISNLPLSMDEQELENMLKPF--GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAP  100 (114)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEEECCCCCcceEEEEEECCHHHHHHHHHHhCCCEEcCCccccCC
Confidence            356899999999999999999999999  999999999985 7789999999999999999998 999999        6


Q ss_pred             CeeeEEeecCCCC
Q 022058          281 SQPIRVSPSKTPV  293 (303)
Q Consensus       281 g~~l~v~~a~~~~  293 (303)
                      ++.|.|.|++|+.
T Consensus       101 ~~~l~v~~a~p~~  113 (114)
T 1x5o_A          101 TEPLLCKFSGPSS  113 (114)
T ss_dssp             SSCBEEEECCCSC
T ss_pred             CCceeEEccCCCC
Confidence            7889999998653

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.68  E-value=4e-16  Score=116.13  Aligned_cols=77  Identities=16%  Similarity=0.299  Sum_probs=71.4

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC--CeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG--SQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~--g~~l~v~  287 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|.+|.+.++    +|||||+|.+.++|.+|+. |||..+.  |+.|+|.
T Consensus        15 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~~~~~----~g~afV~f~~~~~A~~A~~~l~g~~~~~~g~~l~V~   88 (97)
T 1why_A           15 NPTTRLWVGGLGPNTSLAALAREFDRF--GSIRTIDHVKG----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTT--SCEEEEEECSS----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhc--CCeeEEEEeCC----CCEEEEEECCHHHHHHHHHHHCCCEeCCCCcEEEEE
Confidence            345899999999999999999999999  99999999876    4699999999999999998 9999999  9999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      |+++..
T Consensus        89 ~a~~~~   94 (97)
T 1why_A           89 FAKSGP   94 (97)
T ss_dssp             ECCCCC
T ss_pred             ECCCCC
Confidence            998753

>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=99.68  E-value=8.4e-17  Score=123.06  Aligned_cols=76  Identities=16%  Similarity=0.155  Sum_probs=70.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.    ++|||||+|.+.++|.+|+. |||..+.|++|.|.|+...
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~v~i~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~~~   84 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEeC----CCCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECCCC
Confidence            467899999999999999999999999999999874    56899999999999999998 9999999999999998654


Q ss_pred             C
Q 022058          194 I  194 (303)
Q Consensus       194 ~  194 (303)
                      .
T Consensus        85 ~   85 (111)
T 1whx_A           85 V   85 (111)
T ss_dssp             T
T ss_pred             c
Confidence            3

>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=99.68  E-value=1.9e-17  Score=131.51  Aligned_cols=125  Identities=14%  Similarity=0.068  Sum_probs=74.6

Q ss_pred             eEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhh
Q 022058          157 RFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFE  235 (303)
Q Consensus       157 G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~  235 (303)
                      |+||.+|..++.+-.++. +... .+|...--...            ...........++|||+|||+++|+++|+++|+
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~-~gg~~~g~~~g------------~~~~~~~~~~~~~lfV~nLp~~~te~dL~~~F~   68 (139)
T 2hgn_A            2 GSSHHHHHHSSGLVPRGSHMASM-TGGQQMGRGSG------------DSEFTVQSTTGHCVHMRGLPYKATENDIYNFFS   68 (139)
T ss_dssp             --------------------------------------------------------CCCCEECCSCCTTCCHHHHHHHHC
T ss_pred             CcccccccCccccchhcccchhc-cCCCCCCCCCC------------CcccCCCCCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            678888887777766665 3321 22222210100            001111223458999999999999999999999


Q ss_pred             hhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCCCCCCCC
Q 022058          236 AACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRV  297 (303)
Q Consensus       236 ~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~~~~~r~  297 (303)
                      +|  | |..|.|+.|+ ++++|||||+|.+.++|.+|+.+|+..|+|+.|.|.++.++...+.
T Consensus        69 ~~--G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~~~~~~~~  128 (139)
T 2hgn_A           69 PL--N-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGASNG  128 (139)
T ss_dssp             SC--C-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECCCSCC---
T ss_pred             hc--C-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECCCCCCCCC
Confidence            99  9 7799999885 7899999999999999999999999999999999999987765443

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=1.9e-16  Score=118.72  Aligned_cols=80  Identities=23%  Similarity=0.272  Sum_probs=70.4

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .....++|||+|||+++++++|+++|+.||.|   .++.+..+ ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.+
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~g~v---~~~~~~~g~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~   87 (101)
T 2fc9_A           11 WSGESKTLVLSNLSYSATEETLQEVFEKATFI---KVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL   87 (101)
T ss_dssp             CSCCCSEEEEESCCTTCCHHHHHHHCSSCSEE---ECCBCSSSCBCSEEEEECSSHHHHHHHHHHTSSEEETTEEEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhCCEE---EEEECCCCCEeeEEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEE
Confidence            34468999999999999999999999999987   45555333 79999999999999999999 999999999999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      +++..
T Consensus        88 a~~~~   92 (101)
T 2fc9_A           88 QGPRG   92 (101)
T ss_dssp             CSSCC
T ss_pred             cCCCC
Confidence            87653

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}

Probab=99.68  E-value=3.8e-17  Score=128.69  Aligned_cols=80  Identities=18%  Similarity=0.277  Sum_probs=73.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeE--EEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCc----ccCCe
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD--CRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGT----MLGYY  183 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~--~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~----~~~g~  183 (303)
                      ....++|||+|||+++++++|+++|+.||.|..  |+|++|+.+  ++|||||+|.+. +|.+|+. |||.    .+.|+
T Consensus        20 ~~~~~~lfV~nL~~~~te~~L~~~F~~~G~v~~~~v~i~~d~~tg~~rG~aFV~f~~~-~a~~Ai~~l~g~~~~~~~~gr   98 (131)
T 2m2b_A           20 ENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTI-EAAQLLQILQALHPPLTIDGK   98 (131)
T ss_dssp             SCCCCEEEECSCCTTCCSHHHHHHHGGGCCCCTTTEECCBCSSSSSBCSCEEEECCHH-HHHHHHHHHTTCCCSCCGGGC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeEEEEEcCCCCCcceEEEEEECCH-HHHHHHHHhcCCCCCccCCCE
Confidence            346789999999999999999999999999977  999998854  899999999999 9999998 9999    99999


Q ss_pred             eEEEeecCCC
Q 022058          184 PVRVLPSKTA  193 (303)
Q Consensus       184 ~i~v~~~~~~  193 (303)
                      .|.|.++.+.
T Consensus        99 ~l~V~~a~~~  108 (131)
T 2m2b_A           99 TINVEFAKGS  108 (131)
T ss_dssp             CCCCEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998654

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.68  E-value=2.2e-16  Score=115.88  Aligned_cols=76  Identities=26%  Similarity=0.459  Sum_probs=70.2

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .+...++|||+|||+++++++|+++|+.||.|.+|.+++      |||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus         5 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~~~------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a   78 (90)
T 2dnp_A            5 SSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVK------DYAFVHMEKEADAKAAIAQLNGKEVKGKRINVELS   78 (90)
T ss_dssp             SSCCSCCEEEESCCTTCCHHHHHHHHHHHSCEEEEEECS------SCEEEEESCHHHHHHHHHHHTTCEETTEECEEEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHcCCCEEEEEEEC------CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEC
Confidence            344678999999999999999999999999999999973      599999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        79 ~~~   81 (90)
T 2dnp_A           79 TKG   81 (90)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.67  E-value=3.3e-16  Score=117.03  Aligned_cols=78  Identities=17%  Similarity=0.283  Sum_probs=72.0

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|..|.+.+++    |||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~v~~~~~k----g~afV~f~~~~~a~~a~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpj_A           13 TQRSRLFVGNLPPDITEEEMRKLFEKY--GKAGEVFIHKDK----GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA   86 (99)
T ss_dssp             CCTTEEEEESCCTTCCHHHHHHHTSTT--CCCSEEEEETTT----TEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhc--CCeEEEEEecCC----CEEEEEECCHHHHHHHHHHhCCCEeCCceEEEEEc
Confidence            355899999999999999999999999  999999998764    699999999999999998 9999999999999999


Q ss_pred             CCCCC
Q 022058          290 KTPVR  294 (303)
Q Consensus       290 ~~~~~  294 (303)
                      ++...
T Consensus        87 ~~~~~   91 (99)
T 2cpj_A           87 CHSAS   91 (99)
T ss_dssp             SCCSC
T ss_pred             CCCCC
Confidence            87643

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=4.2e-16  Score=114.85  Aligned_cols=76  Identities=22%  Similarity=0.361  Sum_probs=70.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+|||+++++++|+++|+.||.|.+|.+++      +||||+|.+.++|.+|+. ||+..+.|+.|.|.++
T Consensus         6 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~v~~~~------~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a   79 (92)
T 2dgt_A            6 SGKASTKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK------DYAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS   79 (92)
T ss_dssp             CCCSSEEEEEESCCSSCCHHHHHHHHHTTSCCCEEEECS------SEEEEEESCHHHHHHHHHHHTTEEETTEEEEEEES
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEC------CEEEEEECCHHHHHHHHHHhCCCeeCCcEEEEEEc
Confidence            344678999999999999999999999999999999973      599999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        80 ~~~   82 (92)
T 2dgt_A           80 TSR   82 (92)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            654

>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=99.67  E-value=4e-16  Score=116.28  Aligned_cols=76  Identities=13%  Similarity=0.231  Sum_probs=70.1

Q ss_pred             ccccceEEEcCCCC-CCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          210 EMCSRTVYCTNIDK-KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       210 ~~~~~~l~V~nL~~-~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      ..+.++|||+|||. .+++++|+++|++|  |.|..+.+.      +|||||+|.+.++|.+|+. |||..++|+.|+|.
T Consensus        19 ~~~~~~l~V~nLp~~~~t~~~L~~~F~~~--G~v~~v~i~------~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~   90 (97)
T 2xnq_A           19 SHMKSRLFIGNLPLKNVSKEDLFRIFSPY--GHIMQINIK------NAFGFIQFDNPQSVRDAIEXESQEMNFGKKLILE   90 (97)
T ss_dssp             CCTTCEEEEESCCSSCCCHHHHHHHHGGG--SCEEEEEEC------SSEEEEEESSHHHHHHHHHHHTTSEETTEECEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhc--CCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCEECCEEEEEE
Confidence            34568999999998 99999999999999  999999994      5799999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 022058          288 PSKTPV  293 (303)
Q Consensus       288 ~a~~~~  293 (303)
                      ++++..
T Consensus        91 ~a~~~~   96 (97)
T 2xnq_A           91 VSSSNA   96 (97)
T ss_dssp             ECCCCC
T ss_pred             ecCCCC
Confidence            998653

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.67  E-value=7.5e-17  Score=123.00  Aligned_cols=77  Identities=16%  Similarity=0.182  Sum_probs=69.1

Q ss_pred             CCCCCEEEEcCCCCC-CCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC--CcccCCeeEEEe
Q 022058          113 DSVRRTVYVSDIDQN-ITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG--GTMLGYYPVRVL  188 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~--g~~~~g~~i~v~  188 (303)
                      ....++|||+|||++ +++++|+++|+.||.|.+|.|++    ++|||||+|.+.++|.+|++ ||  +..+.|++|.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~fG~V~~v~i~~----~kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~V~   97 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMR----MKSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKVD   97 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEEE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhcCCEEEEEEec----CCCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            446889999999998 99999999999999999999974    36899999999999999998 75  466999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      +++..
T Consensus        98 ~a~~~  102 (112)
T 1x4f_A           98 LSEKY  102 (112)
T ss_dssp             EECSC
T ss_pred             ECccc
Confidence            98654

>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=99.67  E-value=3e-16  Score=118.48  Aligned_cols=80  Identities=28%  Similarity=0.228  Sum_probs=73.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE-EEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR-LRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~-v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+.+++++|+++|++|  |.|.. |.|+.+. |+++|||||+|.+.++|.+|+.+|+..++|+.|.|.++
T Consensus        14 ~~~~l~V~nLp~~~te~~l~~~F~~~--G~v~~~v~i~~~~~g~~~G~afV~F~~~~~a~~A~~~~~~~~~gr~i~v~~~   91 (104)
T 1wg5_A           14 NDGFVRLRGLPFGCSKEEIVQFFSGL--EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTC--CEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCcceeEEEEECCCCCcceEEEEEECCHHHHHHHHHhCcchhCCcEEEEEEC
Confidence            45899999999999999999999999  99987 8888874 78999999999999999999988999999999999998


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      .+..
T Consensus        92 ~~~~   95 (104)
T 1wg5_A           92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7554

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.67  E-value=5.9e-17  Score=121.55  Aligned_cols=78  Identities=18%  Similarity=0.204  Sum_probs=71.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.. .++.+.  +.++|||||+|.+.++|.+|+.|||..+.|+.|+|.++
T Consensus        16 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a   92 (101)
T 1fj7_A           16 TPFNLFIGNLNPNKSVAELKVAISEL--FAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   92 (101)
T ss_dssp             CSEEEEEECCCTTSCHHHHHHHHHHH--HHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEc
Confidence            45899999999999999999999999  99988 555553  78899999999999999999999999999999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      ++.
T Consensus        93 ~~~   95 (101)
T 1fj7_A           93 KGR   95 (101)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            854

>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=99.67  E-value=2.2e-16  Score=119.19  Aligned_cols=78  Identities=19%  Similarity=0.192  Sum_probs=69.8

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCC--ceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSG--MVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g--~~~~g~~l~v~  287 (303)
                      .+.++|||+|||..+++++|+++|++|  |.|.+|.++++    +|||||+|.+.++|.+|+. |++  ..+.|+.|.|.
T Consensus        13 ~p~~~l~V~nLp~~~te~~L~~~F~~f--G~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~i~Gr~l~V~   86 (104)
T 1wex_A           13 SVSPVVHVRGLCESVVEADLVEALEKF--GTICYVMMMPF----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTT--SCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhC--CCEEEEEEECC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEEEE
Confidence            356899999999999999999999999  99999999876    4699999999999999998 865  45999999999


Q ss_pred             ecCCCCC
Q 022058          288 PSKTPVR  294 (303)
Q Consensus       288 ~a~~~~~  294 (303)
                      |+++...
T Consensus        87 ~a~~~~~   93 (104)
T 1wex_A           87 YSTSKRI   93 (104)
T ss_dssp             ECSSSSC
T ss_pred             EccCccc
Confidence            9986543

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=3.4e-16  Score=115.03  Aligned_cols=79  Identities=23%  Similarity=0.314  Sum_probs=73.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|   .|..|.|+++. |+++|||||+|.+.++|.+|+.|||..++|+.|.|.+++
T Consensus         9 ~~~~l~v~nLp~~~t~~~l~~~F~~~---~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~A~~~~g~~~~gr~i~v~~a~   85 (91)
T 2dgw_A            9 TCHTVKLRGAPFNVTEKNVMEFLAPL---KPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREK   85 (91)
T ss_dssp             CCCEEEEECCCSSCCHHHHHHHHTTS---CCSEEEEEECTTSCEEEEEEEECSSHHHHHHHHHSCSEEETTEEEEEEEES
T ss_pred             CccEEEEECCCCCCCHHHHHHHHhhC---CceEEEEEECCCCCCceEEEEEECCHHHHHHHHHhCCceeCCcEEEEEECC
Confidence            45899999999999999999999997   68999999884 789999999999999999999999999999999999998


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      +..
T Consensus        86 ~~~   88 (91)
T 2dgw_A           86 SGP   88 (91)
T ss_dssp             SCC
T ss_pred             cCC
Confidence            653

>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=99.67  E-value=6.7e-17  Score=114.38  Aligned_cols=73  Identities=15%  Similarity=0.332  Sum_probs=69.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      +|||+|||..+++++|+++|++|  |.|.++.+++++  +.++|||||+|.+.++|.+|+.+++..+.|+.|.|.+|
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 KIFVGGLSPDTPEEKIREYFGGF--GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             CEEESCCCSSCCHHHHHHHHHHH--SCCSEECCCCSCCCSSSCCCEEEECSSSHHHHHHHTTSSCCBTTBCCCEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCCcCCEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            58999999999999999999999  999999999885  68899999999999999999998999999999999875

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=99.67  E-value=2e-16  Score=122.28  Aligned_cols=78  Identities=19%  Similarity=0.202  Sum_probs=73.0

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcc---eeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGE---VTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~---i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ..++|||+|||+.+++++|+++|++|  |.   |..|.|+.+. |+++|||||+|.+.++|.+|+.|||..|+|+.|+|.
T Consensus        16 ~~~~l~V~nLp~~~te~~l~~~F~~~--G~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~   93 (118)
T 2db1_A           16 EGYVVKLRGLPWSCSIEDVQNFLSDC--TIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF   93 (118)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTS--CBTTGGGGEEEEECSSSCEEEEEEEEBSSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHc--CCccCceeEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEE
Confidence            45889999999999999999999998  98   8999999885 789999999999999999999999999999999999


Q ss_pred             ecCC
Q 022058          288 PSKT  291 (303)
Q Consensus       288 ~a~~  291 (303)
                      ++.+
T Consensus        94 ~a~~   97 (118)
T 2db1_A           94 KSHR   97 (118)
T ss_dssp             EECH
T ss_pred             ECCH
Confidence            8754

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=3.6e-16  Score=116.41  Aligned_cols=77  Identities=25%  Similarity=0.415  Sum_probs=69.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|. +.++.+  .++|||||+|.+.++|.+|+. |||..+.|+.|+|.+++
T Consensus        18 ~~~~l~V~nL~~~~t~~~l~~~F~~~--G~v~-~~~~~~--~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~V~~a~   92 (97)
T 2e5j_A           18 LAADVYVGNLPRDARVSDLKRALREL--GSVP-LRLTWQ--GPRRRAFLHYPDSAAAQQAVSCLQGLRLGTDTLRVALAR   92 (97)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHHHT--TCCC-SEEEEE--TTTTEEEEECSSHHHHHHHHHHHTTCCSSSSCCEEEECC
T ss_pred             CCCEEEEeCCCCcCcHHHHHHHHHhc--CCEE-EEEEcC--CCCcEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            45899999999999999999999999  9997 666654  567899999999999999998 99999999999999998


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      ++.
T Consensus        93 ~~~   95 (97)
T 2e5j_A           93 QQR   95 (97)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            653

>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=99.67  E-value=6.6e-17  Score=126.06  Aligned_cols=79  Identities=20%  Similarity=0.224  Sum_probs=70.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+||.+|+..|.|+.|.|.++.
T Consensus        23 ~~~~~l~V~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a~  102 (124)
T 1wel_A           23 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT  102 (124)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEECC
Confidence            35789999999999999999999999999988655554433  7999999999999999999999999999999999974


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      .
T Consensus       103 ~  103 (124)
T 1wel_A          103 K  103 (124)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.67  E-value=1.4e-15  Score=113.61  Aligned_cols=84  Identities=24%  Similarity=0.364  Sum_probs=72.0

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...++|||+|||..+++++|+++|++|..|.|..+.+.      +|||||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   86 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            35689999999999999999999999822468888775      3599999999999999999 9999999999999999


Q ss_pred             CCCCCCCCCCC
Q 022058          290 KTPVRPRVTRP  300 (303)
Q Consensus       290 ~~~~~~r~~r~  300 (303)
                      ++..+.+..+.
T Consensus        87 ~~~~~~~~~~~   97 (99)
T 2cpd_A           87 KPVDKDSSGPS   97 (99)
T ss_dssp             CCCCCCCCCCS
T ss_pred             CCCCCCCCCCC
Confidence            98765544433

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.67  E-value=2.6e-16  Score=119.83  Aligned_cols=76  Identities=22%  Similarity=0.335  Sum_probs=71.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      ..+|||+|||+.+++++|+++|++|   .|.+|.|+.|+ |+++|||||+|.+.++|.+|+.||+..|+||.|.|..+.+
T Consensus        16 ~~~v~V~nLp~~~te~dl~~~F~~~---~v~~v~i~~d~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~~a~~   92 (109)
T 2dnn_A           16 DLYVSVHGMPFSAMENDVRDFFHGL---RVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATE   92 (109)
T ss_dssp             HHEEEEECCCSSCCHHHHHHHTTTS---CCCEEEECCCTTCCCCSEEEEECSSHHHHHHHHHTTTEEETTEEEEEEECCH
T ss_pred             CCEEEEeCCCCCCCHHHHHHHhccC---CeeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCeECCeEEEEEECCc
Confidence            4799999999999999999999998   58999999885 8899999999999999999999999999999999988854

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ...

Probab=99.67  E-value=1.5e-16  Score=118.39  Aligned_cols=79  Identities=27%  Similarity=0.411  Sum_probs=72.7

Q ss_pred             ccceEEEcCCCCCCCHHHHH----HHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVK----QFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~----~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      +.++|||+|||..+++++|+    ++|++|  |.|..|.+.. .|.++|||||+|.+.++|.+|+. |||..+.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~--G~i~~v~i~~-~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            7 PNHTIYINNLNEKIKKDELKKSLHAIFSRF--GQILDILVSR-SLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGG--SCEEEEECCH-HHHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHHHhC--CCEEEEEEEc-CCCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            56899999999999999999    999999  9999999874 35677899999999999999998 9999999999999


Q ss_pred             eecCCCC
Q 022058          287 SPSKTPV  293 (303)
Q Consensus       287 ~~a~~~~  293 (303)
                      .|+++..
T Consensus        84 ~~a~~~~   90 (97)
T 1nu4_A           84 QYAKTDS   90 (97)
T ss_dssp             EECSSCC
T ss_pred             EEccCCC
Confidence            9998764

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.67  E-value=5.5e-16  Score=114.74  Aligned_cols=77  Identities=29%  Similarity=0.381  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~  193 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|  +.+..+.+ ||||+|.+.++|.+|+.||+..+.|+.|.|.++...
T Consensus         6 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~v~~v--~~~~~~g~-~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~~   82 (94)
T 2e5g_A            6 SGLRSVFVSGFPRGVDSAQLSEYFLAFGPVASV--VMDKDKGV-FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQK   82 (94)
T ss_dssp             TTCCEEEEECCCTTCCHHHHHHHGGGTSCEEEE--EECSSSCC-EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCCS
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHhcCCeEEE--EEcCCCCc-EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCcC
Confidence            356799999999999999999999999999987  55555444 999999999999999999999999999999987544

>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=99.66  E-value=4.9e-16  Score=112.60  Aligned_cols=73  Identities=16%  Similarity=0.407  Sum_probs=68.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h-CCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C-SGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l-~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..+.++++    +|||||+|.+.++|.+|+. | ||..+.|+.|+|.|+
T Consensus        11 ~~~~l~V~~l~~~~t~~~l~~~f~~~--G~i~~~~~~~~----kg~afV~f~~~~~A~~a~~~l~~~~~~~g~~l~v~~a   84 (85)
T 2ytc_A           11 TITTLYVGGLGDTITETDLRNHFYQF--GEIRTITVVQR----QQCAFIQFATRQAAEVAAEKSFNKLIVNGRRLNVKWG   84 (85)
T ss_dssp             SCCCEEEECCTTTSCHHHHHHHHHTT--SCEEEEEEEGG----GTEEEEEESSHHHHHHHHHTTTTTCEETTEECCEEEC
T ss_pred             CccEEEEcCCCCCCCHHHHHHHHHhC--CCEeEEEEECC----CCEEEEEECCHHHHHHHHHHhcCCeeECCCEEEEEec
Confidence            45899999999999999999999999  99999999975    4699999999999999998 8 999999999999998


Q ss_pred             C
Q 022058          290 K  290 (303)
Q Consensus       290 ~  290 (303)
                      +
T Consensus        85 k   85 (85)
T 2ytc_A           85 R   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.66  E-value=1e-16  Score=113.94  Aligned_cols=73  Identities=19%  Similarity=0.266  Sum_probs=69.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ++|||+|||..+++++|+++|++|  |.|..+.+++++  +.++|||||+|.+.++|.+|+. ++ ..+.|+.|+|.+|
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 CKMFIGGLSWQTTQEGLREYFGQF--GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSR-HELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT--SCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTT-CCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEecCCCCCCcCceEEEEEcCHHHHHHHHHhCC-CccCCEEEEEEec
Confidence            479999999999999999999999  999999999985  7889999999999999999999 88 9999999999987

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens}

Probab=99.66  E-value=4.8e-16  Score=123.36  Aligned_cols=78  Identities=26%  Similarity=0.364  Sum_probs=72.5

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ....++|||+|||..+++++|+++|++|  |.|..+.|++++  +.++|||||+|.+.++|.+|+. |||..+.|+.|+|
T Consensus        60 ~~~~~~l~v~nlp~~~~~~~l~~~f~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v  137 (140)
T 2ku7_A           60 ATTKRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRV  137 (140)
T ss_dssp             CSSCCEEEEECCCTTCCHHHHHHHHGGG--SCEEEEECCCCTTTCCCCSEEEEEESCHHHHHHHHHHSTEEEETTEEEEE
T ss_pred             CCCCcEEEEEeCCCCCCHHHHHHHHHhc--CCEEEEEEeecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            3456899999999999999999999999  999999999984  6889999999999999999998 9999999999999


Q ss_pred             eec
Q 022058          287 SPS  289 (303)
Q Consensus       287 ~~a  289 (303)
                      .+|
T Consensus       138 ~~A  140 (140)
T 2ku7_A          138 NLA  140 (140)
T ss_dssp             EC-
T ss_pred             EeC
Confidence            986

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A

Probab=99.66  E-value=1.3e-16  Score=124.43  Aligned_cols=78  Identities=24%  Similarity=0.292  Sum_probs=70.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCcee--EEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVV--DCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      ....++|||+|||+++|+++|+++|+.| .|.  +|+|+.|+.+ ++|||||+|.+.++|++||++++..|+||.|.|.+
T Consensus        39 ~~~~~~lfVgnLp~~~te~dL~~~F~~~-~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~  117 (126)
T 2hgm_A           39 SANDGFVRLRGLPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFK  117 (126)
T ss_dssp             SSSCCEEEEECCCTTCCHHHHHHHTTTS-CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcC-CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEE
Confidence            3457889999999999999999999999 566  8999988766 89999999999999999999788999999999988


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      +.
T Consensus       118 a~  119 (126)
T 2hgm_A          118 SS  119 (126)
T ss_dssp             EC
T ss_pred             CC
Confidence            64

>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=99.66  E-value=3.7e-16  Score=119.97  Aligned_cols=79  Identities=19%  Similarity=0.260  Sum_probs=73.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..|.|+.+. .++|||||+|.+.++|.+|+. |||..+.|+.|+|.|++
T Consensus         7 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~v~i~~~~-~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a~   83 (115)
T 3lqv_A            7 VNRILYIRNLPYKITAEEMYDIFGKY--GPIRQIRVGNTP-ETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVLYYN   83 (115)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEECST-TTTTCEEEEESSHHHHHHHHHHHTTCBSSSCBCEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEeeCC-CCCcEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEEec
Confidence            45899999999999999999999999  999999999874 468999999999999999999 99999999999999998


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      +..
T Consensus        84 ~~~   86 (115)
T 3lqv_A           84 ANR   86 (115)
T ss_dssp             HHH
T ss_pred             CCh
Confidence            643

>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=99.66  E-value=5.9e-16  Score=116.56  Aligned_cols=75  Identities=23%  Similarity=0.403  Sum_probs=69.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.++      +|||||+|.+.++|.+|+. ||+..+.|++|.|.++.+
T Consensus         9 ~~~~~l~V~nl~~~~t~~~l~~~F~~~G~i~~v~~~------~~~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   82 (103)
T 2dgu_A            9 AKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKL------KDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKP   82 (103)
T ss_dssp             CCCCCEEEECCCTTCCHHHHHHHHHHHSCEEEEEEC------SSCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECCC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCEEEEEEE------CCEEEEEeCCHHHHHHHHHHHCCCccCCCEEEEEEcCC
Confidence            356889999999999999999999999999999987      4699999999999999999 999999999999999876


Q ss_pred             CC
Q 022058          193 AI  194 (303)
Q Consensus       193 ~~  194 (303)
                      ..
T Consensus        83 ~~   84 (103)
T 2dgu_A           83 PD   84 (103)
T ss_dssp             CC
T ss_pred             Cc
Confidence            54

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.66  E-value=9.5e-16  Score=114.50  Aligned_cols=74  Identities=27%  Similarity=0.432  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcC--CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSC--GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~--G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.|  |.|.++.++      +|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus        13 ~~~~~l~V~nLp~~~t~~~l~~~F~~~g~g~v~~~~~~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v~~a   86 (99)
T 2cpd_A           13 SSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKI------RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA   86 (99)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEEC------SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECC
T ss_pred             CCcCEEEEeCCCCCCCHHHHHHHHHhcCCcceEEEEEe------CCeEEEEeCCHHHHHHHHHHhCCCEeCCcEEEEEEC
Confidence            357899999999999999999999999  999999875      5799999999999999999 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ++.
T Consensus        87 ~~~   89 (99)
T 2cpd_A           87 KPV   89 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.66  E-value=1.1e-16  Score=119.15  Aligned_cols=80  Identities=28%  Similarity=0.435  Sum_probs=71.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHH----HHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          113 DSVRRTVYVSDIDQNITEERLA----GLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~----~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      ....++|||+|||+++++++|+    ++|+.||.|.+|.++.. +.++|||||+|.+.++|.+|+. |||..+.|++|.|
T Consensus         5 ~~~~~~l~V~nLp~~~~~~~l~~~l~~~f~~~G~i~~v~i~~~-~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~v   83 (97)
T 1nu4_A            5 TRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS-LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   83 (97)
T ss_dssp             -CCCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH-HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHHHHhCCCEEEEEEEcC-CCcCcEEEEEeCCHHHHHHHHHHhCCCEECCcEEEE
Confidence            3467899999999999999999    99999999999998742 2267999999999999999998 9999999999999


Q ss_pred             eecCCC
Q 022058          188 LPSKTA  193 (303)
Q Consensus       188 ~~~~~~  193 (303)
                      .++.+.
T Consensus        84 ~~a~~~   89 (97)
T 1nu4_A           84 QYAKTD   89 (97)
T ss_dssp             EECSSC
T ss_pred             EEccCC
Confidence            998643

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae}

Probab=99.66  E-value=2.4e-16  Score=117.23  Aligned_cols=75  Identities=17%  Similarity=0.317  Sum_probs=68.8

Q ss_pred             CCCCCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+ ++++++|+++|+.||.|.+|.+.      +|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus         7 ~~~~~~l~V~nlp~~~~t~~~l~~~F~~~G~v~~v~i~------~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a   80 (96)
T 2kvi_A            7 IPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIK------NAFGFIQFDNPQSVRDAIECESQEMNFGKKLILEVS   80 (96)
T ss_dssp             --CCEEEEEESSTTSCCCHHHHHHHHTTTCCCCEEEEE------TTEEEEEESCHHHHHHHHHHHTCSSCBTTTBCEEEE
T ss_pred             CCCCCEEEEeCCCcccCCHHHHHHHHHhcCCEEEEEEe------CCEEEEEECCHHHHHHHHHHcCCCeeCCcEEEEEEc
Confidence            34688999999998 99999999999999999999995      6899999999999999999 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ...
T Consensus        81 ~~~   83 (96)
T 2kvi_A           81 SSN   83 (96)
T ss_dssp             ECC
T ss_pred             CcC
Confidence            654

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.66  E-value=1.3e-16  Score=124.08  Aligned_cols=78  Identities=22%  Similarity=0.195  Sum_probs=71.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCce----eEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEe
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQV----VDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVL  188 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i----~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~  188 (303)
                      ...++|||+|||+++|+++|+++|+.||.|    .+|.|+.+..+ ++|||||+|.+.++|.+||+.|+..++||.|.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~V~  100 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF  100 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTTSCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEECCE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEEEE
Confidence            457899999999999999999999999975    68999998654 7999999999999999999989999999999998


Q ss_pred             ecC
Q 022058          189 PSK  191 (303)
Q Consensus       189 ~~~  191 (303)
                      .+.
T Consensus       101 ~a~  103 (123)
T 2dha_A          101 RST  103 (123)
T ss_dssp             EEC
T ss_pred             ECC
Confidence            764

>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=99.65  E-value=1.3e-16  Score=126.34  Aligned_cols=78  Identities=17%  Similarity=0.181  Sum_probs=73.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcc---eeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGE---VTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~---i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ...+|||+|||+++|+++|+++|++|  |.   |..|.|++|+ |+++|||||+|.+.++|.+|+.|||..|+|+.|.|.
T Consensus        43 ~~~~lfVgnLp~~~te~dL~~~F~~~--G~v~~v~~v~i~~d~~g~srG~aFV~F~~~e~a~~Al~~~g~~l~gr~i~V~  120 (136)
T 2hgl_A           43 EGFVVKLRGLPWSCSVEDVQNFLSDC--TIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF  120 (136)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHTTTC--CCSSSSTTEEEEECSSSCEEEEEEEECSSHHHHHHHHTTTEEESSSSEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCcCceeEEEEEECCCCCCCeEEEEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            45899999999999999999999999  99   8899999885 889999999999999999999999999999999999


Q ss_pred             ecCC
Q 022058          288 PSKT  291 (303)
Q Consensus       288 ~a~~  291 (303)
                      ++.+
T Consensus       121 ~a~~  124 (136)
T 2hgl_A          121 KSHR  124 (136)
T ss_dssp             ECCH
T ss_pred             ECCh
Confidence            9864

>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=99.65  E-value=2.4e-16  Score=135.84  Aligned_cols=78  Identities=19%  Similarity=0.271  Sum_probs=72.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCC--ceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCG--QVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G--~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ..++|||+|||+++|+++|+++|+.||  .|.+|+|++++.+  ++|||||+|.+.++|.+||+ ||+..|.|+.|.|.+
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V~~  146 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSLGVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVVTP  146 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTTTCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEEEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHHCCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEEEE
Confidence            467899999999999999999999999  9999999998754  79999999999999999999 999999999999999


Q ss_pred             cCC
Q 022058          190 SKT  192 (303)
Q Consensus       190 ~~~  192 (303)
                      +..
T Consensus       147 a~~  149 (229)
T 3q2s_C          147 VNK  149 (229)
T ss_dssp             CCH
T ss_pred             CCC
Confidence            753

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.65  E-value=4.3e-17  Score=122.30  Aligned_cols=79  Identities=16%  Similarity=0.203  Sum_probs=70.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC--CCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH--SVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~--~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ...++|||+|||+++++++|+++|+.||.|.. .++.+..  .++|||||+|.+.++|.+|++||+..+.|+.|.|.++.
T Consensus        15 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~-~~~~~~~~g~~~g~afV~f~~~~~a~~A~~l~g~~~~g~~l~V~~a~   93 (101)
T 1fj7_A           15 TTPFNLFIGNLNPNKSVAELKVAISELFAKND-LAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   93 (101)
T ss_dssp             SCSEEEEEECCCTTSCHHHHHHHHHHHHHHHT-CCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGCCBTTBCCEEECCS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCcce-EEEecCCCCCcCcEEEEEECCHHHHHHHHhcCCcEECCcEEEEEEcC
Confidence            35789999999999999999999999999987 5555543  37999999999999999999999999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        94 ~~   95 (101)
T 1fj7_A           94 GR   95 (101)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A

Probab=99.65  E-value=5.4e-16  Score=118.17  Aligned_cols=73  Identities=23%  Similarity=0.481  Sum_probs=68.4

Q ss_pred             CCCEEEEcCCCCC-CCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQN-ITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||++ +++++|+++|+.||.|.+|.+      ++|||||+|.+.++|.+|+. ||+..+.|+.|.|.++..
T Consensus        26 ~~~~l~V~nl~~~~~t~~~l~~~F~~~G~v~~v~i------~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~~a~~   99 (110)
T 1wf1_A           26 INSRVFIGNLNTALVKKSDVETIFSKYGRVAGCSV------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDINMAGE   99 (110)
T ss_dssp             CSSEEEECSCCCSSCCHHHHHHHHGGGSCCSEEEE------ETTEEEEECSSSHHHHHHHHHHTTCEETTEECCEEESCC
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHHhCCCeEEEEE------eCCEEEEEECCHHHHHHHHHHcCCCEECCeEEEEEECCC
Confidence            4689999999999 999999999999999999998      46899999999999999997 999999999999999864


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus       100 ~  100 (110)
T 1wf1_A          100 P  100 (110)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.65  E-value=1.1e-16  Score=121.44  Aligned_cols=79  Identities=14%  Similarity=0.138  Sum_probs=73.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcc---eeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGE---VTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~---i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ...+|||+|||+.+++++|+++|+.|  |.   |..|.|+.+. |+++|||||+|.+.++|.+|+.|||..++|+.|.|.
T Consensus        10 ~~~~l~V~nLp~~~te~~l~~~F~~~--g~~~~v~~v~i~~~~~g~~~G~afV~F~~~~~a~~Al~~~~~~~~gr~i~V~   87 (107)
T 2lmi_A           10 DVFLIRAQGLPWSCTMEDVLNFFSDC--RIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY   87 (107)
T ss_dssp             SCCEEEEECCCSSCCSHHHHHHTTTS--CBTTTTTTEECCCCTTSTTCSEEEEEBSSHHHHHHHHTTTTCCSSSSCCCCE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHhc--CCcCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCcceeCCeEEEEE
Confidence            45899999999999999999999998  88   8999999885 789999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022058          288 PSKTP  292 (303)
Q Consensus       288 ~a~~~  292 (303)
                      ++.+.
T Consensus        88 ~a~~~   92 (107)
T 2lmi_A           88 EINNE   92 (107)
T ss_dssp             ECCHH
T ss_pred             ECCHH
Confidence            98753

>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=99.65  E-value=3.6e-16  Score=114.34  Aligned_cols=74  Identities=18%  Similarity=0.169  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..++|||+|||+++++++|+++|+.| .|.++.+.    .++|||||+|.+.++|.+|+. |||..+.|++|.|.++...
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~-~v~~~~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~~~   78 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY-DLKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS-CCCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC-CeEEEEEe----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcCCC
Confidence            56889999999999999999999999 99999885    468999999999999999999 9999999999999998544

>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=99.65  E-value=6.7e-17  Score=128.34  Aligned_cols=80  Identities=21%  Similarity=0.202  Sum_probs=72.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ....++|||+|||+++|+++|+++|+.|| |.+|.|+.++.+ ++|||||+|.+.++|++||.+|+..+.||.|.|.++.
T Consensus        43 ~~~~~~lfV~nLp~~~te~dL~~~F~~~G-i~~v~i~~d~~g~srGfaFV~F~~~e~A~~Al~~~g~~l~gR~i~V~~a~  121 (139)
T 2hgn_A           43 STTGHCVHMRGLPYKATENDIYNFFSPLN-PVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNS  121 (139)
T ss_dssp             --CCCCEECCSCCTTCCHHHHHHHHCSCC-CSEEECCCSSSSCSSCCCEEECSHHHHHHHHTTCCSCSSSSCCCCCEECC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHhcC-CeEEEEEECCCCCCceEEEEEeCCHHHHHHHHhhCCCEECCEEEEEEECC
Confidence            34578899999999999999999999999 679999998765 8999999999999999999999999999999999876


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus       122 ~~  123 (139)
T 2hgn_A          122 TT  123 (139)
T ss_dssp             CS
T ss_pred             CC
Confidence            43

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1

Probab=99.64  E-value=7.9e-16  Score=117.61  Aligned_cols=77  Identities=19%  Similarity=0.170  Sum_probs=70.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|+++    +|||||+|.+.++|.+|+. |||..+.|+.|.|.|++
T Consensus         9 ~~~~l~V~nLp~~~te~~L~~~F~~~--G~i~~v~i~~~----~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   82 (111)
T 1whx_A            9 SKTVILAKNLPAGTLAAEIQETFSRF--GSLGRVLLPEG----GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCSS----SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCEEEEEEeCC----CCEEEEEeCCHHHHHHHHHHhCCCEECCeEEEEEECC
Confidence            45799999999999999999999999  99999999864    4699999999999999998 99999999999999997


Q ss_pred             CCCC
Q 022058          291 TPVR  294 (303)
Q Consensus       291 ~~~~  294 (303)
                      ....
T Consensus        83 ~~~~   86 (111)
T 1whx_A           83 IGVF   86 (111)
T ss_dssp             TTTT
T ss_pred             CCcc
Confidence            6443

>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=99.64  E-value=2.3e-16  Score=125.98  Aligned_cols=81  Identities=22%  Similarity=0.321  Sum_probs=70.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEE--------EEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRL--------RLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQ  282 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v--------~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~  282 (303)
                      +.++|||+|||+.+++++|+.+|++|  |.|..+        .+. ..|+++|||||+|.+.++|.+|+. |||..|.|+
T Consensus        44 ~~~~l~V~nLp~~~te~~L~~~F~~~--G~i~~~~~~~~~di~~~-~~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           44 PNCRIYVKNLAKHVQEKDLKYIFGRY--VDFSSETQRIMFDIRLM-KEGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CCSEEEEEEECTTCCHHHHHHHHGGG--CCTTCHHHHHHCEEEEE-EETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCcccccccceeeEEec-cCCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            45899999999999999999999999  998774        222 247889999999999999999999 999999999


Q ss_pred             eeEEeecCCCCCC
Q 022058          283 PIRVSPSKTPVRP  295 (303)
Q Consensus       283 ~l~v~~a~~~~~~  295 (303)
                      .|+|.++++....
T Consensus       121 ~l~V~~a~~~~~~  133 (143)
T 3egn_A          121 PMVVQFARSARPK  133 (143)
T ss_dssp             ECEEEECCCSCC-
T ss_pred             EEEEEECCCCCCc
Confidence            9999999865433

>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=99.64  E-value=5.8e-16  Score=118.84  Aligned_cols=79  Identities=20%  Similarity=0.285  Sum_probs=69.8

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCce----eEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQV----VDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i----~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ...++|||+|||+++++++|+++|+.||.|    ..+.+.  ...++|||||+|.+.++|.+|+. ||+..+.|++|.|.
T Consensus        23 ~~~~~l~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~--~g~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~  100 (115)
T 2cpx_A           23 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMM--TGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIE  100 (115)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEE--CSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHhCCccceEEEEEcC--CCccceEEEEEECCHHHHHHHHHHhCCCEeCCcEEEEE
Confidence            357899999999999999999999999999    455554  33478999999999999999998 99999999999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      ++....
T Consensus       101 ~a~~~~  106 (115)
T 2cpx_A          101 FGKNKK  106 (115)
T ss_dssp             ECCCCS
T ss_pred             EccCCC
Confidence            987543

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1

Probab=99.64  E-value=3.3e-16  Score=116.23  Aligned_cols=77  Identities=21%  Similarity=0.280  Sum_probs=68.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ...++|||+|||+++++++|+++|+.||.|..+   .....++|||||+|.+.++|.+|+. |||..+.|++|.|.++.+
T Consensus        14 ~~~~~l~V~nL~~~~t~~~l~~~F~~~g~v~~~---~~~~~~~g~afV~f~~~~~a~~A~~~l~g~~~~g~~l~v~~a~~   90 (96)
T 1fjc_A           14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLV---SQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCE---EETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhCCcEEEe---CCCCCcceEEEEEECCHHHHHHHHHHhCCCEECCeEEEEEEcCC
Confidence            357899999999999999999999999998766   3333479999999999999999999 999999999999999864


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus        91 ~   91 (96)
T 1fjc_A           91 K   91 (96)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.64  E-value=4.2e-16  Score=115.05  Aligned_cols=76  Identities=22%  Similarity=0.285  Sum_probs=68.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCc-eeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCC-cccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQ-VVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGG-TMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g-~~~~g~~i~v~~  189 (303)
                      ....++|||+|||+++++++|+++|+.||. |..+.+.     ++|||||+|.+.++|.+|+. ||+ ..+.|++|.|.+
T Consensus         5 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~vv~~~~~~-----~~g~afV~f~~~~~A~~A~~~l~g~~~~~g~~l~v~~   79 (93)
T 2cqh_A            5 SSGMNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLL-----KSGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDY   79 (93)
T ss_dssp             CCCCCCEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEE-----ETTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCCcEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEEc-----CCCEEEEEECCHHHHHHHHHHccCCeeECCEEEEEEE
Confidence            346789999999999999999999999999 6666663     36899999999999999998 999 999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      +.+.
T Consensus        80 a~~~   83 (93)
T 2cqh_A           80 SVSK   83 (93)
T ss_dssp             CCCC
T ss_pred             ccCc
Confidence            8654

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.64  E-value=7.7e-16  Score=115.55  Aligned_cols=79  Identities=24%  Similarity=0.344  Sum_probs=69.9

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .....++|||+|||+++++++|+++|+.|+   .+.++.+..+  ++|||||+|.+.++|.+|+. ||+..|.|+.|.|.
T Consensus        11 ~~~~~~~l~V~nLp~~~t~~~l~~~F~~~~---~~~~~~~~~~~~~~g~afV~f~~~~~A~~A~~~l~g~~~~g~~l~V~   87 (102)
T 2fc8_A           11 RSQPSKTLFVKGLSEDTTEETLKESFDGSV---RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLD   87 (102)
T ss_dssp             SSCCCSSEEEECCCTTCCHHHHHHTSTTCS---EEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCCCEEEEeCCCCccCHHHHHHHhcCCe---EEEEEecCCCCCcCcEEEEEECCHHHHHHHHHHhCCCeECCeEEEEE
Confidence            344678999999999999999999999874   6777777644  78999999999999999998 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      ++++.
T Consensus        88 ~a~~~   92 (102)
T 2fc8_A           88 WAKPK   92 (102)
T ss_dssp             ECCCC
T ss_pred             EecCC
Confidence            98654

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.64  E-value=3.1e-16  Score=117.75  Aligned_cols=77  Identities=18%  Similarity=0.358  Sum_probs=71.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+|+. ++..+.|+.|.|.++..
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~~   85 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAIR   85 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhCCCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECCc
Confidence            4688999999999999999999999999999999998744 79999999999999999999 99999999999998754

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.64  E-value=3.6e-16  Score=119.41  Aligned_cols=75  Identities=12%  Similarity=0.227  Sum_probs=67.8

Q ss_pred             CCCCEEEE--cCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc-----CCeeE
Q 022058          114 SVRRTVYV--SDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML-----GYYPV  185 (303)
Q Consensus       114 ~~~~~l~V--~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~-----~g~~i  185 (303)
                      ...++|||  |||++++++++|+++|++||.|.+|.++.    ++|||||+|.+.++|++|++ |||.++     .|++|
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~fG~v~~v~i~~----~rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~~l   98 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITL   98 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCT----TCSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEEEC
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEEccccCCCcEE
Confidence            35788999  77999999999999999999999998864    37899999999999999998 999988     68999


Q ss_pred             EEeecCC
Q 022058          186 RVLPSKT  192 (303)
Q Consensus       186 ~v~~~~~  192 (303)
                      .|.++..
T Consensus        99 ~v~~a~~  105 (114)
T 2cq2_A           99 YLNFVEK  105 (114)
T ss_dssp             EEEEESC
T ss_pred             EEEeccc
Confidence            9999753

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.64  E-value=5e-16  Score=115.27  Aligned_cols=78  Identities=24%  Similarity=0.365  Sum_probs=70.6

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEE-EEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~-~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+| .++.++.+  |.|||+|.+.++|.+|+. |||..+.|++|.|.++.
T Consensus        13 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~v~~~~~i~~~~~~--~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   90 (96)
T 2e44_A           13 QRIRKLQIRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSET--AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYIP   90 (96)
T ss_dssp             CSCCCEEEEEECSSSCHHHHHHHHHHHSCEEEEEEECCSSSS--EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCEEEEEcCCCCCCHHHHHHHHHhcCCeEEEEEeecCCCC--CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEcC
Confidence            357889999999999999999999999999999 48877654  459999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        91 ~~   92 (96)
T 2e44_A           91 DE   92 (96)
T ss_dssp             CC
T ss_pred             cc
Confidence            54

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae}

Probab=99.64  E-value=7.8e-16  Score=115.36  Aligned_cols=74  Identities=16%  Similarity=0.271  Sum_probs=69.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.++.+.+    ++|||||+|.+.++|.+|+. |||..++|+.|+|.|++
T Consensus        26 ~~~~l~V~nlp~~~~~~~l~~~f~~~--G~i~~~~~~~----~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a~   99 (101)
T 2la4_A           26 RVTTAYIGNIPHFATEADLIPLFQNF--GFILDFKHYP----EKGCCFIKYDTHEQAAVCIVALANFPFQGRNLRTGWGK   99 (101)
T ss_dssp             SCCEEEEESCCTTCCHHHHHHHHHTT--SCCSEEEEET----TTTEEEEECSSHHHHHHHHHHHTTCEETTEECCCCBCC
T ss_pred             CCCEEEEcCCCcccCHHHHHHHHHhC--CCEEEEEEec----CCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEecc
Confidence            46899999999999999999999999  9999999984    45699999999999999998 99999999999999998


Q ss_pred             C
Q 022058          291 T  291 (303)
Q Consensus       291 ~  291 (303)
                      +
T Consensus       100 ~  100 (101)
T 2la4_A          100 E  100 (101)
T ss_dssp             C
T ss_pred             C
Confidence            6

>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=99.63  E-value=8.9e-16  Score=118.04  Aligned_cols=78  Identities=19%  Similarity=0.226  Sum_probs=67.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCee-----eE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQP-----IR  285 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~-----l~  285 (303)
                      ...+|||+|||..+++++|+++|++|  |.|..|.|+.+     |||||+|.+.++|.+||+ |||..|.|+.     |+
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~   87 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREA--GDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIR   87 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGG--SCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEecC-----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEE
Confidence            34889999999999999999999999  99999999887     699999999999999999 9999999998     88


Q ss_pred             EeecCCCCCCC
Q 022058          286 VSPSKTPVRPR  296 (303)
Q Consensus       286 v~~a~~~~~~r  296 (303)
                      |..+.+....+
T Consensus        88 v~~~~~~~~~~   98 (115)
T 3beg_B           88 VKVDGPRSPSY   98 (115)
T ss_dssp             EEECC----CC
T ss_pred             eccCCCCCCCC
Confidence            88887655433

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A

Probab=99.63  E-value=3.9e-16  Score=117.22  Aligned_cols=79  Identities=20%  Similarity=0.379  Sum_probs=73.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|+++. |.++|||||+|.+.++|.+|+. +|..++|+.|.|.++.
T Consensus         8 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~v~i~~~~~g~~~g~afV~f~~~~~a~~Ai~-~~~~~~g~~l~v~~a~   84 (102)
T 2xs2_A            8 MPNTVFVGGIDVRMDETEIRSFFARY--GSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE-SQINFHGKKLKLGPAI   84 (102)
T ss_dssp             EEEEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTSCEEEEEEEEESSCCCHHHHTT-CCCEETTEECEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhC--CCeEEEEEEECCCCCccceEEEEECCHHHHHHHHh-CCCeECCEEEEEEECC
Confidence            45899999999999999999999999  999999999986 7789999999999999999999 9999999999999986


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      +..
T Consensus        85 ~~~   87 (102)
T 2xs2_A           85 RKQ   87 (102)
T ss_dssp             ECC
T ss_pred             cCc
Confidence            543

>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=99.63  E-value=1e-15  Score=112.26  Aligned_cols=75  Identities=28%  Similarity=0.412  Sum_probs=62.6

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcc--cCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTM--LGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~--~~g~~i~v~~~  190 (303)
                      .....+|||+|||+++|+++|+++|+.||.|.+|.++++   ++|||||+|.+.++|.+   +++..  +.|+.|.|.++
T Consensus         8 ~~~~~~l~V~~Lp~~~te~~L~~~F~~~G~i~~v~i~~~---srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A            8 HHHGSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKP---FRAFAFVTFADDKVAQS---LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             ---CCEEEEESCCTTCCHHHHHHHHTTTSCEEEEECCSS---CCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEEEC
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccCCEEEEEEeeC---CCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEEEc
Confidence            346789999999999999999999999999999999875   68999999999999984   44444  46999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        82 ~~k   84 (89)
T 3d2w_A           82 EPK   84 (89)
T ss_dssp             C--
T ss_pred             CCC
Confidence            643

>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=99.63  E-value=5.1e-16  Score=133.76  Aligned_cols=79  Identities=14%  Similarity=0.200  Sum_probs=73.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCc--ceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGG--EVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G--~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ..++|||+|||..+++++|+++|++|  |  .|.+|.|++|+  ++++|||||+|.+.++|.+||. |||..|.|+.|+|
T Consensus        67 ~~~~lfVgnL~~~~te~~L~~~F~~~--G~~~v~~v~i~~d~~tg~skGfaFV~f~~~~~a~~Ai~~lng~~~~Gr~l~V  144 (229)
T 3q2s_C           67 KRIALYIGNLTWWTTDEDLTEAVHSL--GVNDILEIKFFENRANGQSKGFALVGVGSEASSKKLMDLLPKRELHGQNPVV  144 (229)
T ss_dssp             --CEEEEESCCTTCCHHHHHHHHHTT--TCCCEEEEEEEECTTTCCEEEEEEEEESCTTHHHHHHTTSTTSCBTTBCCEE
T ss_pred             CccEEEEeCCCCCCCHHHHHHHHHHH--CCcceEEEEEEecCCCCccceEEEEEECCHHHHHHHHHHcCCCeECCEEeEE
Confidence            45789999999999999999999999  9  99999999984  7899999999999999999999 9999999999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      .+++++
T Consensus       145 ~~a~~~  150 (229)
T 3q2s_C          145 TPVNKQ  150 (229)
T ss_dssp             EECCHH
T ss_pred             EECCCC
Confidence            998653

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.63  E-value=8.1e-16  Score=127.33  Aligned_cols=80  Identities=21%  Similarity=0.270  Sum_probs=74.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ...++|||+|||+.+++++|+++|+.||.|.+|.|+.+..+ ++|||||+|.+.++|.+|+. ||+..+.|++|.|.++.
T Consensus        86 ~~~~~l~V~nLp~~~te~~L~~~F~~~G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a~  165 (177)
T 2f3j_A           86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVA  165 (177)
T ss_dssp             TTCEEEEEECCCSCCCHHHHHHHHHHTSCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEES
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            35688999999999999999999999999999999998844 79999999999999999999 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus       166 ~~  167 (177)
T 2f3j_A          166 SQ  167 (177)
T ss_dssp             SG
T ss_pred             CC
Confidence            54

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.43  E-value=2.5e-17  Score=126.88  Aligned_cols=81  Identities=25%  Similarity=0.379  Sum_probs=74.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeE--------EEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVD--------CRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~--------~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      ....++|||+|||+++++++|+++|+.||.|.+        |.++.++.+  ++|||||+|.+.++|.+|+. ||+..+.
T Consensus         4 ~~~~~~l~V~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            4 NSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            346789999999999999999999999999998        889888654  79999999999999999999 9999999


Q ss_pred             CeeEEEeecCCC
Q 022058          182 YYPVRVLPSKTA  193 (303)
Q Consensus       182 g~~i~v~~~~~~  193 (303)
                      |++|.|.++.+.
T Consensus        84 g~~l~V~~a~~~   95 (116)
T 2lcw_A           84 GNPIKVSFATRR   95 (116)
Confidence            999999998654

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.62  E-value=4.3e-15  Score=110.52  Aligned_cols=76  Identities=25%  Similarity=0.351  Sum_probs=68.7

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .....++|||+||  ++++++|+++|+.||.|.+|.+.    .++|||||+|.+.++|.+|+. ||+..+.|++|.|.++
T Consensus        11 ~~~~~~~l~V~n~--~~t~~~l~~~F~~~G~i~~v~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a   84 (97)
T 1x5p_A           11 APRKGNTLYVYGE--DMTPTLLRGAFSPFGNIIDLSMD----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIA   84 (97)
T ss_dssp             CCCCCSEEEEECS--SCCHHHHHHHHTTTSCEEEEEEE----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECC
T ss_pred             CCCCCCEEEEcCC--CCCHHHHHHHHhhCCCEEEEEec----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEEC
Confidence            3446789999996  89999999999999999999984    357899999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        85 ~~~   87 (97)
T 1x5p_A           85 RKQ   87 (97)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            654

>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=99.62  E-value=1.4e-15  Score=123.20  Aligned_cols=78  Identities=22%  Similarity=0.174  Sum_probs=69.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGY--YPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g--~~i~v~~~~  191 (303)
                      .-..|||+||++.+|+++|+++|+.||.|.+|.+..+.  ++|||||+|.+.++|.+|++ |||..|.|  ++|+|.|++
T Consensus        45 ~vl~l~VgNL~~~vted~L~~~Fs~fG~V~~V~i~~k~--~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~Ak  122 (164)
T 1sjr_A           45 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN--NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK  122 (164)
T ss_dssp             CEEEEEECSCCSCCCHHHHHHHHHHHSCEEEEEEEESS--SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEECS
T ss_pred             ceEEEEEeCcCCCCCHHHHHHHHHhcCCEEEEEEEeCC--CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEec
Confidence            34569999999999999999999999999999997543  57999999999999999999 99999965  999999997


Q ss_pred             CCC
Q 022058          192 TAI  194 (303)
Q Consensus       192 ~~~  194 (303)
                      ...
T Consensus       123 ~~~  125 (164)
T 1sjr_A          123 LTS  125 (164)
T ss_dssp             SSS
T ss_pred             CCc
Confidence            653

>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=99.62  E-value=2.9e-16  Score=122.38  Aligned_cols=78  Identities=22%  Similarity=0.231  Sum_probs=70.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC--CCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD--HVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d--~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+.+++++|+++|++|  |.|..+.++.+  .|+++|||||+|.+.++|.+|+.|||..|+|+.|.|.++
T Consensus        24 ~~~~l~V~nLp~~~te~~l~~~F~~~--G~v~~~~~~~~~~~g~~~G~afV~F~~~~~a~~Al~~~g~~~~gr~i~V~~a  101 (124)
T 1wel_A           24 AGFCVYLKGLPFEAENKHVIDFFKKL--DIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI  101 (124)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSS--CBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc--CCccceEEEEECCCCCCCeEEEEEECCHHHHHHHHHhCCCeECCcEEEEEEC
Confidence            45899999999999999999999999  99988544443  378999999999999999999999999999999999998


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      .+
T Consensus       102 ~~  103 (124)
T 1wel_A          102 TK  103 (124)
T ss_dssp             CH
T ss_pred             CH
Confidence            65

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.62  E-value=1.8e-15  Score=118.09  Aligned_cols=75  Identities=24%  Similarity=0.264  Sum_probs=68.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceE-EEEEecCHHHHHHHHH-hCCcccCC--eeEEEeecCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRF-AFVEFADEHGARAALN-LGGTMLGY--YPVRVLPSKT  192 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~-~fV~f~~~~~A~~Ai~-l~g~~~~g--~~i~v~~~~~  192 (303)
                      -.|||+||++.+|+++|+++|+.||.|.+|.++.+.   +|| |||+|.+.++|.+|++ |||..|.|  ++|+|.+++.
T Consensus        29 L~I~V~NL~~~vte~~L~~lFs~yG~V~~V~i~~~~---~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~ak~  105 (130)
T 3zzy_A           29 LRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKL  105 (130)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTSSCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEECSC
T ss_pred             EEEEECCCCCCCCHHHHHHHHhCcCCEEEEEEEcCC---CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEecCC
Confidence            458899999999999999999999999999988643   588 9999999999999999 99999987  9999999976


Q ss_pred             CC
Q 022058          193 AI  194 (303)
Q Consensus       193 ~~  194 (303)
                      ..
T Consensus       106 ~~  107 (130)
T 3zzy_A          106 TS  107 (130)
T ss_dssp             SS
T ss_pred             Cc
Confidence            53

>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=99.62  E-value=2.1e-15  Score=115.14  Aligned_cols=76  Identities=12%  Similarity=0.187  Sum_probs=68.7

Q ss_pred             cccceEEE--cCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee-----CCe
Q 022058          211 MCSRTVYC--TNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL-----GSQ  282 (303)
Q Consensus       211 ~~~~~l~V--~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~-----~g~  282 (303)
                      .+.++|||  +||+..+++++|+++|++|  |.|.+|.|+++    +|||||+|.+.++|.+|++ |||..+     .|+
T Consensus        23 ~pt~~L~V~Ng~L~~~~te~~L~~~F~~f--G~v~~v~i~~~----rgfaFV~f~~~~~A~~Ai~~lnG~~~~~~lg~g~   96 (114)
T 2cq2_A           23 YATQSLVVANGGLGNGVSRNQLLPVLEKC--GLVDALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKI   96 (114)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHH--SCEEEEECCTT----CSCEEEEESSHHHHHHHHHHTTTCEEECTTSCEE
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHhc--CCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCEEccccCCCc
Confidence            35688999  6799999999999999999  99999998765    4699999999999999998 999998     789


Q ss_pred             eeEEeecCCC
Q 022058          283 PIRVSPSKTP  292 (303)
Q Consensus       283 ~l~v~~a~~~  292 (303)
                      .|.|.|++..
T Consensus        97 ~l~v~~a~~~  106 (114)
T 2cq2_A           97 TLYLNFVEKV  106 (114)
T ss_dssp             ECEEEEESCC
T ss_pred             EEEEEecccC
Confidence            9999999744

>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=99.62  E-value=5.7e-16  Score=118.11  Aligned_cols=78  Identities=18%  Similarity=0.301  Sum_probs=69.5

Q ss_pred             ccccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC--CceeCCeeeE
Q 022058          210 EMCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS--GMVLGSQPIR  285 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~--g~~~~g~~l~  285 (303)
                      ..+.++|||+|||+. +++++|+++|++|  |.|.+|.|+++    +|||||+|.+.++|.+|+. ||  +..|.|+.|.
T Consensus        22 ~~p~~~l~V~NLp~~~~te~~L~~lF~~f--G~V~~v~i~~~----kg~aFVef~~~~~A~~Ai~~l~~~~~~l~Gr~l~   95 (112)
T 1x4f_A           22 QELGRVIHLSNLPHSGYSDSAVLKLAEPY--GKIKNYILMRM----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVK   95 (112)
T ss_dssp             SCCCCEEEEESCCCSSCCSHHHHTTTTTT--SCCSEEEEETT----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCE
T ss_pred             CCCCCEEEEeCCCCccCCHHHHHHHHHhc--CCEEEEEEecC----CCEEEEEECCHHHHHHHHHHhccCCceECCEEEE
Confidence            345789999999998 9999999999999  99999999865    4699999999999999998 75  5679999999


Q ss_pred             EeecCCCC
Q 022058          286 VSPSKTPV  293 (303)
Q Consensus       286 v~~a~~~~  293 (303)
                      |.|+++..
T Consensus        96 V~~a~~~~  103 (112)
T 1x4f_A           96 VDLSEKYK  103 (112)
T ss_dssp             EEEECSCS
T ss_pred             EEECcccc
Confidence            99997543

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens}

Probab=99.62  E-value=8.9e-16  Score=122.54  Aligned_cols=80  Identities=21%  Similarity=0.285  Sum_probs=69.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEE--------EEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCe
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDC--------RVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYY  183 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~--------~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~  183 (303)
                      ....++|||+|||+++++++|+++|+.||.|.++        .+.. .+.++|||||+|.+.++|.+|+. |||..+.|+
T Consensus        42 ~~~~~~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~di~~~~-~g~~~g~afV~f~~~~~A~~Ai~~lng~~~~g~  120 (143)
T 3egn_A           42 GEPNCRIYVKNLAKHVQEKDLKYIFGRYVDFSSETQRIMFDIRLMK-EGRMKGQAFIGLPNEKAAAKALKEANGYVLFGK  120 (143)
T ss_dssp             CSCCSEEEEEEECTTCCHHHHHHHHGGGCCTTCHHHHHHCEEEEEE-ETTTEEEEEEECSSHHHHHHHHHHHTTBEETTE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCcccccccceeeEEecc-CCCcccEEEEEeCCHHHHHHHHHHhCCCEeCCc
Confidence            3467899999999999999999999999998774        2222 23489999999999999999999 999999999


Q ss_pred             eEEEeecCCC
Q 022058          184 PVRVLPSKTA  193 (303)
Q Consensus       184 ~i~v~~~~~~  193 (303)
                      +|.|.+++..
T Consensus       121 ~l~V~~a~~~  130 (143)
T 3egn_A          121 PMVVQFARSA  130 (143)
T ss_dssp             ECEEEECCCS
T ss_pred             EEEEEECCCC
Confidence            9999998653

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}

Probab=99.41  E-value=3.7e-17  Score=125.93  Aligned_cols=81  Identities=22%  Similarity=0.332  Sum_probs=75.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE--------EEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR--------LRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~--------v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..        |.|+.++  +.++|||||+|.+.++|.+|+. |||..+.
T Consensus         6 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~v~i~~~~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~   83 (116)
T 2lcw_A            6 DNNTIFVQGLGENVTIESVADYFKQI--GIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFS   83 (116)
Confidence            45899999999999999999999999  99998        8898884  6889999999999999999998 9999999


Q ss_pred             CeeeEEeecCCCCC
Q 022058          281 SQPIRVSPSKTPVR  294 (303)
Q Consensus       281 g~~l~v~~a~~~~~  294 (303)
                      |+.|+|.++++...
T Consensus        84 g~~l~V~~a~~~~~   97 (116)
T 2lcw_A           84 GNPIKVSFATRRAD   97 (116)
Confidence            99999999987643

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=4.8e-15  Score=109.58  Aligned_cols=77  Identities=25%  Similarity=0.365  Sum_probs=67.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|  +.+....+ ||||+|.+.++|.+|+.|||..|+|+.|.|.++.+
T Consensus         7 ~~~~l~V~nl~~~~t~~~l~~~F~~~--G~v~~v--~~~~~~g~-~afV~f~~~~~a~~ai~l~g~~~~g~~l~V~~a~~   81 (94)
T 2e5g_A            7 GLRSVFVSGFPRGVDSAQLSEYFLAF--GPVASV--VMDKDKGV-FAIVEMGDVGAREAVLSQSQHSLGGHRLRVRPREQ   81 (94)
T ss_dssp             TCCEEEEECCCTTCCHHHHHHHGGGT--SCEEEE--EECSSSCC-EEEEEESSHHHHHHHHTCSCCEETTEECCCBCSCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc--CCeEEE--EEcCCCCc-EEEEEECCHHHHHHHHhcCCeEECCEEEEEEECCc
Confidence            44799999999999999999999999  999998  33332222 99999999999999999999999999999999865


Q ss_pred             CC
Q 022058          292 PV  293 (303)
Q Consensus       292 ~~  293 (303)
                      ..
T Consensus        82 ~~   83 (94)
T 2e5g_A           82 KE   83 (94)
T ss_dssp             SC
T ss_pred             CC
Confidence            43

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.61  E-value=2.7e-15  Score=111.28  Aligned_cols=78  Identities=17%  Similarity=0.192  Sum_probs=70.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEE-EEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRL-RLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v-~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..| .|+.++..  |.|||+|.+.++|.+|+. |||..+.|+.|+|.++
T Consensus        14 ~~~~l~V~nlp~~~t~~~l~~~F~~~--G~v~~~~~i~~~~~~--~~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a   89 (96)
T 2e44_A           14 RIRKLQIRNIPPHLQWEVLDSLLVQY--GVVESCEQVNTDSET--AVVNVTYSSKDQARQALDKLNGFQLENFTLKVAYI   89 (96)
T ss_dssp             SCCCEEEEEECSSSCHHHHHHHHHHH--SCEEEEEEECCSSSS--EEEEEEESSHHHHHHHHHHHTTCBCSSCBCEEEEC
T ss_pred             CCCEEEEEcCCCCCCHHHHHHHHHhc--CCeEEEEEeecCCCC--CEEEEEECCHHHHHHHHHHhCCCEECCcEEEEEEc
Confidence            45889999999999999999999999  999999 58887532  349999999999999998 9999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      ++..
T Consensus        90 ~~~~   93 (96)
T 2e44_A           90 PDEM   93 (96)
T ss_dssp             CCCC
T ss_pred             Cccc
Confidence            8763

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.61  E-value=5.2e-16  Score=120.65  Aligned_cols=78  Identities=24%  Similarity=0.169  Sum_probs=71.3

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcce----eEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeE
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEV----TRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIR  285 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i----~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~  285 (303)
                      ....+|||+|||+.+|+++|+++|++|  |.|    ..|.|+.+. |+++|||||+|.+.++|.+|+.+|+..++|+.|.
T Consensus        21 ~~~~~v~V~nLp~~~te~dl~~~F~~~--g~v~g~v~~v~i~~d~~gr~~G~aFV~F~~~~~A~~Al~~~~~~l~gR~i~   98 (123)
T 2dha_A           21 ENQVIVRMRGLPFTATAEEVVAFFGQH--CPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIE   98 (123)
T ss_dssp             CSCCEEEECSCCTTCCHHHHHHHHHTT--SCCTTGGGGEEEEECTTSCEEEEEEECCSSHHHHHHHHTTTTEESSSCEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhh--CCccCCcceEEEEECCCCCEeeEEEEEECCHHHHHHHHHhCCCeeCCeEEE
Confidence            345899999999999999999999999  875    689998875 7899999999999999999999899999999999


Q ss_pred             EeecC
Q 022058          286 VSPSK  290 (303)
Q Consensus       286 v~~a~  290 (303)
                      |..+.
T Consensus        99 V~~a~  103 (123)
T 2dha_A           99 LFRST  103 (123)
T ss_dssp             CEEEC
T ss_pred             EEECC
Confidence            98875

>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=99.61  E-value=1.4e-15  Score=116.93  Aligned_cols=73  Identities=22%  Similarity=0.213  Sum_probs=65.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCee-----EEEe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYP-----VRVL  188 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~-----i~v~  188 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.|+.+     |||||+|.+.++|.+||+ ||+..|.|+.     |.|.
T Consensus        15 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~gr~~~~~~i~v~   89 (115)
T 3beg_B           15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   89 (115)
T ss_dssp             --CCEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhcCCeEEEEEecC-----CEEEEEECCHHHHHHHHHHhCCCEECCcEeeeEEEEec
Confidence            4688999999999999999999999999999999876     899999999999999999 9999999998     6776


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      ...+
T Consensus        90 ~~~~   93 (115)
T 3beg_B           90 VDGP   93 (115)
T ss_dssp             ECC-
T ss_pred             cCCC
Confidence            6544

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A

Probab=99.60  E-value=3.5e-15  Score=116.48  Aligned_cols=75  Identities=20%  Similarity=0.201  Sum_probs=68.7

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccE-EEEEEcCHHHHHHHHH-hCCceeCC--eeeEEee
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI-AFVEFAVAESAILALN-CSGMVLGS--QPIRVSP  288 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~-afV~f~~~e~A~~Ai~-l~g~~~~g--~~l~v~~  288 (303)
                      ...|||+||++.+|+++|+++|++|  |.|.+|.|..+.   +|+ |||+|.+.++|.+|++ |||..|.|  +.|+|.|
T Consensus        28 VL~I~V~NL~~~vte~~L~~lFs~y--G~V~~V~i~~~~---~gfqAFVef~~~~~A~~Ai~~LnG~~i~g~~~~LrI~~  102 (130)
T 3zzy_A           28 VLRIIVENLFYPVTLDVLHQIFSKF--GTVLKIITFTKN---NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF  102 (130)
T ss_dssp             EEEEEEESCCSCCCHHHHHHHHTTS--SCEEEEEEEEET---TEEEEEEEESCHHHHHHHHHHHTTCEEETTEEEEEEEE
T ss_pred             eEEEEECCCCCCCCHHHHHHHHhCc--CCEEEEEEEcCC---CCcEEEEEECCHHHHHHHHHHcCCCeecCCCcEEEEEe
Confidence            4568899999999999999999999  999999988653   467 9999999999999999 99999988  9999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      +++.
T Consensus       103 ak~~  106 (130)
T 3zzy_A          103 SKLT  106 (130)
T ss_dssp             CSCS
T ss_pred             cCCC
Confidence            9876

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.60  E-value=1.2e-14  Score=107.98  Aligned_cols=74  Identities=20%  Similarity=0.268  Sum_probs=67.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+||  .+++++|+++|++|  |.|.+|.|.    .++|||||+|.+.++|.+|+. |||..+.|+.|+|.|++
T Consensus        14 ~~~~l~V~n~--~~t~~~l~~~F~~~--G~i~~v~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~v~~a~   85 (97)
T 1x5p_A           14 KGNTLYVYGE--DMTPTLLRGAFSPF--GNIIDLSMD----PPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   85 (97)
T ss_dssp             CCSEEEEECS--SCCHHHHHHHHTTT--SCEEEEEEE----TTTTEEEEEESSHHHHHHHHHHTTTEEETTEEEEEECCS
T ss_pred             CCCEEEEcCC--CCCHHHHHHHHhhC--CCEEEEEec----CCCCEEEEEECCHHHHHHHHHHhCCCeECCeEEEEEECC
Confidence            4589999996  89999999999999  999999995    455799999999999999998 99999999999999998


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      +..
T Consensus        86 ~~~   88 (97)
T 1x5p_A           86 KQP   88 (97)
T ss_dssp             SCC
T ss_pred             CCC
Confidence            764

>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=99.60  E-value=3.4e-15  Score=120.91  Aligned_cols=77  Identities=19%  Similarity=0.161  Sum_probs=69.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCC--eeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGS--QPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g--~~l~v~~a  289 (303)
                      ..+|||+||++.+++++|+++|++|  |.|.+|.|..+.  ++|||||+|.+.++|.+|++ |||..|.|  +.|+|.|+
T Consensus        46 vl~l~VgNL~~~vted~L~~~Fs~f--G~V~~V~i~~k~--~rgfAFVeF~d~~~A~~Ai~~LnG~~i~g~g~~L~V~~A  121 (164)
T 1sjr_A           46 VLRIIVENLFYPVTLDVLHQIFSKF--GTVLKIITFTKN--NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFS  121 (164)
T ss_dssp             EEEEEECSCCSCCCHHHHHHHHHHH--SCEEEEEEEESS--SCEEEEEEESCHHHHHHHHHHSTTBCSSSSCSCEEEEEC
T ss_pred             eEEEEEeCcCCCCCHHHHHHHHHhc--CCEEEEEEEeCC--CCCEEEEEECCHHHHHHHHHHhCCCEecCCCcEEEEEEe
Confidence            4679999999999999999999999  999999997543  56899999999999999999 99999965  99999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      ++..
T Consensus       122 k~~~  125 (164)
T 1sjr_A          122 KLTS  125 (164)
T ss_dssp             SSSS
T ss_pred             cCCc
Confidence            8763

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus}

Probab=99.60  E-value=2.2e-15  Score=124.65  Aligned_cols=80  Identities=20%  Similarity=0.330  Sum_probs=75.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..|.|..+. +.++|||||+|.+.++|.+|+. |||..|.|+.|+|.|+
T Consensus        87 ~~~~l~V~nLp~~~te~~L~~~F~~~--G~I~~v~i~~d~~g~~kG~afV~F~~~~~A~~Ai~~lng~~l~Gr~l~V~~a  164 (177)
T 2f3j_A           87 TGAKLLVSNLDFGVSDADIQELFAEF--GTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLV  164 (177)
T ss_dssp             TCEEEEEECCCSCCCHHHHHHHHHHT--SCCSEEEECCCTTSSCSCCEEEEESCHHHHHHHHHHSTTCBCSSSBCEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCeEEEEEEECCCCCEeeEEEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            46899999999999999999999999  999999999986 7889999999999999999998 9999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      .+..
T Consensus       165 ~~~~  168 (177)
T 2f3j_A          165 ASQI  168 (177)
T ss_dssp             SSGG
T ss_pred             cCCC
Confidence            7654

>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=99.60  E-value=1.6e-15  Score=110.81  Aligned_cols=82  Identities=17%  Similarity=0.248  Sum_probs=68.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|.|+.+   ++|||||+|.+.++|++|+.. +..+.|+.|.|.++++
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~~---~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~   77 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQY--GDVMDVFIPKP---FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTT--SCCCEEECCSS---CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHc--CCeeEEEEecC---CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCC
Confidence            45899999999999999999999999  99999999876   568999999999999754332 3456899999999987


Q ss_pred             CCCCCCCC
Q 022058          292 PVRPRVTR  299 (303)
Q Consensus       292 ~~~~r~~r  299 (303)
                      .....+.+
T Consensus        78 ~~~~~~~~   85 (88)
T 1wf0_A           78 KHNSNSGP   85 (88)
T ss_dssp             CCCCCSCS
T ss_pred             CCCCCCCC
Confidence            76554443

>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=99.60  E-value=1.7e-15  Score=110.15  Aligned_cols=71  Identities=27%  Similarity=0.479  Sum_probs=66.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcC----C-------ceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCe
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSC----G-------QVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYY  183 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~----G-------~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~  183 (303)
                      ..++|||+|||+++++++|+++|+.|    |       .|.++.+..+    +|||||+|.+.++|.+|+.|||..+.|+
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~~~~~g~~~~~~~~v~~~~~~~~----kg~afV~f~~~~~a~~A~~l~g~~~~g~   80 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVDETTQAMAFDGIIFQGQ   80 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHHHHHTTCCSSSSCSEEEEEECSS----SSEEEEEESSHHHHHHHGGGTTCEETTE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhhhcccccCCCCcceEEEecCC----CcEEEEEcCCHHHHHHHHhcCCCEECCe
Confidence            46899999999999999999999999    8       9999999765    6899999999999999999999999999


Q ss_pred             eEEEee
Q 022058          184 PVRVLP  189 (303)
Q Consensus       184 ~i~v~~  189 (303)
                      .|.|..
T Consensus        81 ~l~V~r   86 (87)
T 2hzc_A           81 SLKIRR   86 (87)
T ss_dssp             ECEEEC
T ss_pred             EEEEeC
Confidence            999974

>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=99.60  E-value=9.6e-16  Score=119.51  Aligned_cols=78  Identities=28%  Similarity=0.211  Sum_probs=70.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCccee-EEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVT-RLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~-~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+.+++++|+++|++|  +.+. +|.|+.|+ |+++|||||+|.+.++|.+|+.+++..|+|+.|.|.++
T Consensus        41 ~~~~lfVgnLp~~~te~dL~~~F~~~--~i~~~~v~i~~d~~GrsrGfaFV~F~~~e~A~~Al~~~~~~l~gR~I~V~~a  118 (126)
T 2hgm_A           41 NDGFVRLRGLPFGCTKEEIVQFFSGL--EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKS  118 (126)
T ss_dssp             SCCEEEEECCCTTCCHHHHHHHTTTS--CEEEEEEECCCCSSSSSCSEEEEEESSTTHHHHHHTTTTCCBTTBCCCCEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcC--CceeeEEEEEECCCCCCceEEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            45789999999999999999999998  6443 89999885 88999999999999999999998889999999999988


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      .+
T Consensus       119 ~~  120 (126)
T 2hgm_A          119 SQ  120 (126)
T ss_dssp             CH
T ss_pred             CH
Confidence            53

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.59  E-value=4.6e-15  Score=115.20  Aligned_cols=72  Identities=18%  Similarity=0.158  Sum_probs=65.6

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceE-EEEEecCHHHHHHHHH-hCCcccCC--eeEEEeecCCCC
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRF-AFVEFADEHGARAALN-LGGTMLGY--YPVRVLPSKTAI  194 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~-~fV~f~~~~~A~~Ai~-l~g~~~~g--~~i~v~~~~~~~  194 (303)
                      |||+|||+.+++++|+++|+.||.|.+|.++..    .|| |||+|.+.++|.+|++ |||..|.|  ++|+|.++++..
T Consensus        28 l~V~NL~~~vt~~~L~~~Fs~yG~V~~v~i~~~----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~Ak~~~  103 (124)
T 2e5i_A           28 LSIQNPLYPITVDVLYTVCNPVGKVQRIVIFKR----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYARPTR  103 (124)
T ss_dssp             EEEESCCSCCCHHHHHHHHTTTSCEEEEEEEES----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECCSCSC
T ss_pred             EEEcCcCCCCCHHHHHHHHHhcCCEEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEecCCc
Confidence            789999999999999999999999999999753    286 9999999999999999 99999977  699999987653

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.59  E-value=2.5e-15  Score=115.72  Aligned_cols=75  Identities=20%  Similarity=0.336  Sum_probs=67.4

Q ss_pred             CEEEEcCC----CCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecC----HHH----HHHHHH---hCCcc
Q 022058          117 RTVYVSDI----DQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFAD----EHG----ARAALN---LGGTM  179 (303)
Q Consensus       117 ~~l~V~nl----p~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~----~~~----A~~Ai~---l~g~~  179 (303)
                      ..|||+||    |+.+++++|+++|+.||+|.+|.++.|+.+  ++|||||+|.+    +++    |.+|+.   +||..
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~fGeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng~~   82 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKYGEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSGCF   82 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTTSCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTCEE
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhcCCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcCCe
Confidence            68999999    999999999999999999999999999987  89999999996    434    788875   79999


Q ss_pred             cCCeeEEEeecC
Q 022058          180 LGYYPVRVLPSK  191 (303)
Q Consensus       180 ~~g~~i~v~~~~  191 (303)
                      |+|++|+|...+
T Consensus        83 I~Gr~irV~ln~   94 (136)
T 2j8a_A           83 IMGFKFEVILNK   94 (136)
T ss_dssp             ETTEEEEEEECC
T ss_pred             ecCcEEEEEECc
Confidence            999999999854

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.59  E-value=7.8e-15  Score=110.84  Aligned_cols=80  Identities=21%  Similarity=0.206  Sum_probs=70.8

Q ss_pred             cccceEEEcCCCC-----CCCHHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEEEEcCHHHHHHHHH-hCCceeCC
Q 022058          211 MCSRTVYCTNIDK-----KVPQAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFVEFAVAESAILALN-CSGMVLGS  281 (303)
Q Consensus       211 ~~~~~l~V~nL~~-----~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g  281 (303)
                      .++++|+|.||..     .-++++|+++|++|  |.|.+|.|++++   +.++|+|||+|.+.++|.+|+. |||+.+.|
T Consensus         6 ~~s~~l~l~Nm~~~~~l~dd~~~dl~~~f~~~--G~V~~v~i~~~~~~~~~~~G~~FV~f~~~~~A~~Ai~~lnG~~~~G   83 (105)
T 2pe8_A            6 CPTKVVLLRNMVGAGEVDEDLEVETKEECEKY--GKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGG   83 (105)
T ss_dssp             SCCSEEEEESSSCSCCC---CHHHHHHHGGGG--SCEEEEEEEECSSCCTTTSEEEEEEESSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEEcCCChHHhhHHHHHHHHHHHHhc--CCEEEEEEecCCCCCCCCcEEEEEEECCHHHHHHHHHHHCCCEECC
Confidence            4568999999963     23689999999999  999999999874   4789999999999999999998 99999999


Q ss_pred             eeeEEeecCCC
Q 022058          282 QPIRVSPSKTP  292 (303)
Q Consensus       282 ~~l~v~~a~~~  292 (303)
                      |.|+|.++.+.
T Consensus        84 r~i~v~~a~~~   94 (105)
T 2pe8_A           84 RVVKACFYNLD   94 (105)
T ss_dssp             EECEEEECCHH
T ss_pred             cEEEEEEcCHH
Confidence            99999999753

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A

Probab=99.59  E-value=5.9e-15  Score=107.77  Aligned_cols=75  Identities=17%  Similarity=0.184  Sum_probs=68.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|   .|.++.+.    +++|||||+|.+.++|.+|+. |||..++|+.|+|.++.
T Consensus         4 ~~~~l~V~nLp~~~t~~~l~~~F~~~---~v~~~~i~----~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g~~l~V~~a~   76 (88)
T 1wg1_A            4 GSSGILVKNLPQDSNCQEVHDLLKDY---DLKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS---CCCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhC---CeEEEEEe----CCCcEEEEEECCHHHHHHHHHHhCCCeECCcEEEEEEcC
Confidence            35789999999999999999999998   68888885    567899999999999999999 99999999999999996


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      ...
T Consensus        77 ~~~   79 (88)
T 1wg1_A           77 TDA   79 (88)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            543

>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=99.59  E-value=2.2e-15  Score=110.02  Aligned_cols=75  Identities=25%  Similarity=0.356  Sum_probs=65.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|.++.+   ++|||||+|.+.++|++|+.. ...+.|++|.|.++.+.
T Consensus         4 ~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~~---~~g~afV~f~~~~~a~~~~~~-~~~~~g~~l~v~~a~~~   78 (88)
T 1wf0_A            4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP---FRAFAFVTFADDQIAQSLCGE-DLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS---CCSCCEEECSCHHHHHHTTTC-EEEETTEEEEEECCCCC
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHHcCCeeEEEEecC---CCCEEEEEECCHHHHHHHhcC-CceeCCEEEEEEecCCC
Confidence            5789999999999999999999999999999999865   679999999999999865432 34558999999998654

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.59  E-value=4.2e-15  Score=108.29  Aligned_cols=70  Identities=19%  Similarity=0.214  Sum_probs=62.3

Q ss_pred             CCEEEEcCCCCCCCHHH----HHHHhhcC-CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          116 RRTVYVSDIDQNITEER----LAGLFSSC-GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~----l~~~F~~~-G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      .+.|||+|||+.+++++    |+++|++| |.|.+|.        .|+|||.|.+.++|.+|++ |||..+.||+|+|.+
T Consensus         9 ~T~lYV~NL~~~~~~~~lk~~L~~lF~~yGG~Vl~Vt--------gG~AfV~F~~~esA~~A~~~l~G~~l~gr~i~v~~   80 (96)
T 2diu_A            9 HTLLYVYNLPANKDGKSVSNRLRRLSDNCGGKVLSIT--------GCSAILRFINQDSAERAQKRMENEDVFGNRIIVSF   80 (96)
T ss_dssp             SEEEEEESCCTTSCHHHHHHHHHHHHHTTTCCEEECC--------TTCEEEEESSHHHHHHHHHHHTTCCSSSSCCEEES
T ss_pred             ceEEEEeCCCCcCCHHHHHHHHHHHHHHcCCeeEEEe--------cCEEEEEECCHHHHHHHHHHhcCCccCCceEEEEe
Confidence            34499999999999988    55899999 5999881        2899999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      ++..
T Consensus        81 A~~~   84 (96)
T 2diu_A           81 TPKN   84 (96)
T ss_dssp             SCCS
T ss_pred             cCCC
Confidence            8654

>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=99.59  E-value=5.1e-15  Score=124.19  Aligned_cols=77  Identities=18%  Similarity=0.247  Sum_probs=70.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      .++|||+|||+++++++|+++|+.||.|.+|+++++..+ ++|||||+|.+.++|.+|+...+..+.|++|.|.+...
T Consensus       109 ~~~l~V~nLp~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~  186 (193)
T 2voo_A          109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDD  186 (193)
T ss_dssp             HTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTT
T ss_pred             cCEEEecCCCCcCCHHHHHHHHhcCCCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHH
Confidence            588999999999999999999999999999999998765 79999999999999999999445699999999999754

>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=99.58  E-value=7.1e-15  Score=107.69  Aligned_cols=73  Identities=22%  Similarity=0.291  Sum_probs=62.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCce--eCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMV--LGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~--~~g~~l~v~~a  289 (303)
                      +..+|||+|||+.+++++|+++|++|  |.|.+|.|+++   ++|||||+|.+.++|.+   |+|..  +.|+.|.|.++
T Consensus        10 ~~~~l~V~~Lp~~~te~~L~~~F~~~--G~i~~v~i~~~---srGfaFV~F~~~~~A~~---~~~~~~~~~g~~v~v~~a   81 (89)
T 3d2w_A           10 HGSKVFVGRCTEDMTAEELQQFFCQY--GEVVDVFIPKP---FRAFAFVTFADDKVAQS---LCGEDLIIKGISVHISNA   81 (89)
T ss_dssp             -CCEEEEESCCTTCCHHHHHHHHTTT--SCEEEEECCSS---CCSEEEEEESCHHHHHH---HTTCEEEETTEEEEEEEC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhcc--CCEEEEEEeeC---CCCEEEEEECCHHHHHH---HcCCCcccCCEEEEEEEc
Confidence            45899999999999999999999999  99999999986   67899999999999883   44544  56999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      .|.
T Consensus        82 ~~k   84 (89)
T 3d2w_A           82 EPK   84 (89)
T ss_dssp             C--
T ss_pred             CCC
Confidence            864

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.58  E-value=6.2e-15  Score=107.44  Aligned_cols=71  Identities=18%  Similarity=0.158  Sum_probs=63.4

Q ss_pred             cce-EEEcCCCCCCCHHH----HHHHhhhhcCc-ceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          213 SRT-VYCTNIDKKVPQAE----VKQFFEAACGG-EVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       213 ~~~-l~V~nL~~~~t~~~----L~~~F~~~~~G-~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      ..+ |||+|||+.+++++    |+++|++|  | .|.+|.     +   |+|||+|.+.++|.+|++ |||..+.||.|+
T Consensus         8 ~~T~lYV~NL~~~~~~~~lk~~L~~lF~~y--GG~Vl~Vt-----g---G~AfV~F~~~esA~~A~~~l~G~~l~gr~i~   77 (96)
T 2diu_A            8 CHTLLYVYNLPANKDGKSVSNRLRRLSDNC--GGKVLSIT-----G---CSAILRFINQDSAERAQKRMENEDVFGNRII   77 (96)
T ss_dssp             SSEEEEEESCCTTSCHHHHHHHHHHHHHTT--TCCEEECC-----T---TCEEEEESSHHHHHHHHHHHTTCCSSSSCCE
T ss_pred             cceEEEEeCCCCcCCHHHHHHHHHHHHHHc--CCeeEEEe-----c---CEEEEEECCHHHHHHHHHHhcCCccCCceEE
Confidence            355 99999999999987    55899998  7 999981     2   799999999999999998 999999999999


Q ss_pred             EeecCCCC
Q 022058          286 VSPSKTPV  293 (303)
Q Consensus       286 v~~a~~~~  293 (303)
                      |.||+...
T Consensus        78 v~~A~~~s   85 (96)
T 2diu_A           78 VSFTPKNR   85 (96)
T ss_dssp             EESSCCSC
T ss_pred             EEecCCCc
Confidence            99998654

>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=99.58  E-value=1.8e-14  Score=120.79  Aligned_cols=120  Identities=18%  Similarity=0.178  Sum_probs=90.7

Q ss_pred             CHHHHHHHHH-h--CCcccCCeeEEEeecCCCCCCCCCCCCCCc--ccccccccceEEEcCCCCCCCHHHHHHHhhhhcC
Q 022058          165 DEHGARAALN-L--GGTMLGYYPVRVLPSKTAILPVNPTFLPRS--EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACG  239 (303)
Q Consensus       165 ~~~~A~~Ai~-l--~g~~~~g~~i~v~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~  239 (303)
                      +.+.+..|+. .  ....+.+....|.......       .|..  ........++|||+|||..+++++|+++|++|  
T Consensus        63 d~~~I~~Al~~S~~~~lev~ed~~~vrR~~~~p-------~p~~~~~~~~~~~~~~l~V~nLp~~~t~~~L~~~F~~~--  133 (193)
T 2voo_A           63 DFNVIVEALSKSKAELMEISEDKTKIRRSPSKP-------LPEVTDEYKNDVKNRSVYIKGFPTDATLDDIKEWLEDK--  133 (193)
T ss_dssp             CHHHHHHHHHTCSSCCEEECTTSSEEEECTTSC-------CCCCCHHHHHHHHHTEEEEECCCTTCCHHHHHHHHTTS--
T ss_pred             CHHHHHHHHhhcccceEEEecccceEEecccCC-------CcccchhhhhccccCEEEecCCCCcCCHHHHHHHHhcC--
Confidence            5677777887 5  4555555545555431110       1111  11123356899999999999999999999999  


Q ss_pred             cceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCCCC
Q 022058          240 GEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPV  293 (303)
Q Consensus       240 G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~~~  293 (303)
                      |.|..|.|+++. +.++|||||+|.+.++|.+|+.+.+..+.|+.|.|.+++.-.
T Consensus       134 G~v~~v~i~~~~~~~~kG~aFVeF~~~e~A~~A~~~~~~~~~Gr~l~V~~~~~y~  188 (193)
T 2voo_A          134 GQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKDDYF  188 (193)
T ss_dssp             CCEEEEEEEECTTCCEEEEEEEEESSHHHHHHHHHCTTCEETTEECEEEETTTC-
T ss_pred             CCEEEEEEEECCCCCcccEEEEEECCHHHHHHHHHhCCCeECCEEEEEEEhHHHH
Confidence            999999999885 788999999999999999999954569999999999987644

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=1e-14  Score=111.82  Aligned_cols=74  Identities=20%  Similarity=0.253  Sum_probs=62.4

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC-----CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH-----SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~-----~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      ...++|||+|||+++++++|+++|+.||.|. +.++.+..     .++|||||+|.+.++|++||+ ++  .+.|+.+.+
T Consensus         6 ~~~~~lfVgnLp~~~te~~L~~~F~~~G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~--~~~G~~~~~   82 (114)
T 2dnl_A            6 SGSRKVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACL--EEDGKLYLC   82 (114)
T ss_dssp             SCCCCEEEECCCTTCCHHHHHHHTTTTCCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSE--EETTEEEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhcCCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhh--hcCCcEEEe
Confidence            3578899999999999999999999999999 88877654     379999999999999999998 73  356666665


Q ss_pred             eec
Q 022058          188 LPS  190 (303)
Q Consensus       188 ~~~  190 (303)
                      ..+
T Consensus        83 ~~~   85 (114)
T 2dnl_A           83 VSS   85 (114)
T ss_dssp             ECC
T ss_pred             ccC
Confidence            543

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.56  E-value=1.5e-14  Score=112.35  Aligned_cols=74  Identities=16%  Similarity=0.154  Sum_probs=66.8

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccE-EEEEEcCHHHHHHHHH-hCCceeCC--eeeEEeec
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI-AFVEFAVAESAILALN-CSGMVLGS--QPIRVSPS  289 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~-afV~f~~~e~A~~Ai~-l~g~~~~g--~~l~v~~a  289 (303)
                      ..|||+||++.+++++|+++|++|  |.|.+|.|...    .|+ |||+|.+.++|..|+. |||..|.|  +.|+|.||
T Consensus        26 l~l~V~NL~~~vt~~~L~~~Fs~y--G~V~~v~i~~~----~Gf~aFVef~~~~~A~~A~~~LnG~~i~g~~~~l~V~~A   99 (124)
T 2e5i_A           26 LLLSIQNPLYPITVDVLYTVCNPV--GKVQRIVIFKR----NGIQAMVEFESVLCAQKAKAALNGADIYAGCCTLKIEYA   99 (124)
T ss_dssp             EEEEEESCCSCCCHHHHHHHHTTT--SCEEEEEEEES----SSEEEEEEESSHHHHHHHHHHHTTCCCBTTBSEEEEECC
T ss_pred             EEEEEcCcCCCCCHHHHHHHHHhc--CCEEEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCEecCCCeEEEEEEe
Confidence            457899999999999999999999  99999998753    276 9999999999999998 99999987  69999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      ++..
T Consensus       100 k~~~  103 (124)
T 2e5i_A          100 RPTR  103 (124)
T ss_dssp             SCSC
T ss_pred             cCCc
Confidence            8763

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A

Probab=99.56  E-value=2.1e-14  Score=108.47  Aligned_cols=79  Identities=19%  Similarity=0.177  Sum_probs=69.7

Q ss_pred             CCCCEEEEcCCCC-----CCCHHHHHHHhhcCCceeEEEEeeCCC---CCceEEEEEecCHHHHHHHHH-hCCcccCCee
Q 022058          114 SVRRTVYVSDIDQ-----NITEERLAGLFSSCGQVVDCRVCGDPH---SVLRFAFVEFADEHGARAALN-LGGTMLGYYP  184 (303)
Q Consensus       114 ~~~~~l~V~nlp~-----~~t~~~l~~~F~~~G~i~~~~i~~~~~---~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~  184 (303)
                      ..+++|+|+||..     +-++++|++.|++||.|.+|.|+.++.   .++|||||+|.+.++|.+|+. |||..+.||+
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            4678999999963     236899999999999999999999864   379999999999999999998 9999999999


Q ss_pred             EEEeecCC
Q 022058          185 VRVLPSKT  192 (303)
Q Consensus       185 i~v~~~~~  192 (303)
                      |.|.++..
T Consensus        86 i~v~~a~~   93 (105)
T 2pe8_A           86 VKACFYNL   93 (105)
T ss_dssp             CEEEECCH
T ss_pred             EEEEEcCH
Confidence            99999753

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.56  E-value=1.6e-14  Score=110.81  Aligned_cols=80  Identities=18%  Similarity=0.347  Sum_probs=66.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-----CCcccEEEEEEcCHHHHHHHHH-h---CCc-----
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-----VHSTRIAFVEFAVAESAILALN-C---SGM-----  277 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-----~~~~g~afV~f~~~e~A~~Ai~-l---~g~-----  277 (303)
                      ..++|||+|||..+++++|+++|++|  |.|. +.++.+.     |+++|||||+|.+.++|.+|++ |   ||.     
T Consensus         7 ~~~~lfVgnLp~~~te~~L~~~F~~~--G~i~-~~~~~~~~~~~~g~~~G~aFV~f~~~~~a~~Ai~~~~~~~G~~~~~~   83 (114)
T 2dnl_A            7 GSRKVFVGGLPPDIDEDEITASFRRF--GPLV-VDWPHKAESKSYFPPKGYAFLLFQEESSVQALIDACLEEDGKLYLCV   83 (114)
T ss_dssp             CCCCEEEECCCTTCCHHHHHHHTTTT--CCCC-EECTTSSSSCCCSCTTSEEEECCSSHHHHHHHHHHSEEETTEEEEEE
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhc--CCEE-EEEeecCCCCCCCCcccEEEEEECCHHHHHHHHHhhhhcCCcEEEec
Confidence            45889999999999999999999999  9999 8887764     5789999999999999999998 7   666     


Q ss_pred             ---eeCCeeeEEeecCCCCC
Q 022058          278 ---VLGSQPIRVSPSKTPVR  294 (303)
Q Consensus       278 ---~~~g~~l~v~~a~~~~~  294 (303)
                         .+.++.+.|..+.....
T Consensus        84 ~~~~~~~~~~~v~p~~~~d~  103 (114)
T 2dnl_A           84 SSPTIKDKPVQIRPWNLSDS  103 (114)
T ss_dssp             CCSSSCSEEEEEECCCCCCC
T ss_pred             cCCCcCCCeeeccCCcccCC
Confidence               34566677766554443

>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=99.53  E-value=4.7e-14  Score=102.44  Aligned_cols=71  Identities=23%  Similarity=0.452  Sum_probs=65.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCc-----------ceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGG-----------EVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLG  280 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G-----------~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~  280 (303)
                      ..++|||+|||..+++++|+++|++|  |           .|.++.+.++    +|||||+|.+.++|.+|+.|||..+.
T Consensus         5 ~~~~l~V~nLp~~~t~~~l~~~F~~~--~~~~g~~~~~~~~v~~~~~~~~----kg~afV~f~~~~~a~~A~~l~g~~~~   78 (87)
T 2hzc_A            5 SARRLYVGNIPFGITEEAMMDFFNAQ--MRLGGLTQAPGNPVLAVQINQD----KNFAFLEFRSVDETTQAMAFDGIIFQ   78 (87)
T ss_dssp             GGGEEEEESCCTTCCHHHHHHHHHHH--HHHTTCCSSSSCSEEEEEECSS----SSEEEEEESSHHHHHHHGGGTTCEET
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHH--hhhcccccCCCCcceEEEecCC----CcEEEEEcCCHHHHHHHHhcCCCEEC
Confidence            45899999999999999999999998  5           7999999876    46999999999999999999999999


Q ss_pred             CeeeEEee
Q 022058          281 SQPIRVSP  288 (303)
Q Consensus       281 g~~l~v~~  288 (303)
                      |+.|+|+.
T Consensus        79 g~~l~V~r   86 (87)
T 2hzc_A           79 GQSLKIRR   86 (87)
T ss_dssp             TEECEEEC
T ss_pred             CeEEEEeC
Confidence            99999974

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.52  E-value=2.2e-14  Score=123.53  Aligned_cols=76  Identities=24%  Similarity=0.275  Sum_probs=69.1

Q ss_pred             CCCCEEEEcCCCCCC---------CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc---
Q 022058          114 SVRRTVYVSDIDQNI---------TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML---  180 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~---------t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~---  180 (303)
                      ...++|||+|||..+         ++++|+++|++||+|++|+|+.    ++|||||+|.+.++|+.|++ |+|+.+   
T Consensus       132 ~~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~----~kG~AFV~F~~~~~Ae~A~~am~g~~l~~~  207 (240)
T 3u1l_A          132 KKNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE----SKNCGFVKFKYQANAEFAKEAMSNQTLLLP  207 (240)
T ss_dssp             CCCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG----GGTEEEEEESSHHHHHHHHHHHTTCCCCCT
T ss_pred             cCCceeecCCCChhhhcccccccCcHHHHHHHHHccCCEEEEEEEC----CCCEEEEEeCCHHHHHHHHHHhCCCEEecc
Confidence            357899999999998         7999999999999999999986    36899999999999999998 999999   


Q ss_pred             ---------CCeeEEEeecCCC
Q 022058          181 ---------GYYPVRVLPSKTA  193 (303)
Q Consensus       181 ---------~g~~i~v~~~~~~  193 (303)
                               .|+.|.|.|+...
T Consensus       208 ~~~e~~~~~~gr~L~V~wA~~~  229 (240)
T 3u1l_A          208 SDKEWDDRREGTGLLVKWANED  229 (240)
T ss_dssp             TSTTGGGGGGSCCCEEEECC--
T ss_pred             ccccccccCCCCEEEEEEccCC
Confidence                     8999999998654

>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=99.52  E-value=1.2e-13  Score=105.60  Aligned_cols=80  Identities=20%  Similarity=0.251  Sum_probs=68.7

Q ss_pred             cccceEEEcCCCCCCC-----------HHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCce
Q 022058          211 MCSRTVYCTNIDKKVP-----------QAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMV  278 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t-----------~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~  278 (303)
                      .+.++|+|+||.....           +++|+++|++|  |.|..|.| .+. .++|||||+|.+.++|.+|+. |||..
T Consensus        13 ~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~--G~v~~v~i-~~~-~~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           13 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF--GQIRKLLL-FDR-HPDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT--SCCSEEEE-ETT-CTTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHcc--CCEeEEEE-ecC-CCCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            3568999999954432           58999999999  99999966 454 378999999999999999998 99999


Q ss_pred             eCCeeeEEeecCCCCC
Q 022058          279 LGSQPIRVSPSKTPVR  294 (303)
Q Consensus       279 ~~g~~l~v~~a~~~~~  294 (303)
                      +.|+.|+|.++.+...
T Consensus        89 ~~gr~l~v~~a~~~~~  104 (112)
T 2dit_A           89 FGGRQITAQAWDGTTD  104 (112)
T ss_dssp             ETTEECEEEECCSCCC
T ss_pred             ECCcEEEEEEeCCCCC
Confidence            9999999999987543

>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=99.50  E-value=9.5e-14  Score=106.08  Aligned_cols=79  Identities=22%  Similarity=0.192  Sum_probs=67.9

Q ss_pred             CCCCCCEEEEcCCCCCCC-----------HHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcc
Q 022058          112 EDSVRRTVYVSDIDQNIT-----------EERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTM  179 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t-----------~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~  179 (303)
                      .+...++|+|.||....+           +++|+++|++||.|.+|.| .+.. ++|||||+|.+.++|.+|+. |||..
T Consensus        11 ~~~~s~~l~l~Nl~~~~~~~~~~~~~~~~e~~l~~~f~~~G~v~~v~i-~~~~-~~G~afV~f~~~~~A~~Ai~~lng~~   88 (112)
T 2dit_A           11 RMRHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLL-FDRH-PDGVASVSFRDPEEADYCIQTLDGRW   88 (112)
T ss_dssp             CCCSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEE-ETTC-TTCEEEEECSCHHHHHHHHHHSTTCE
T ss_pred             CCCCceEEEEEcCCCHHHhccCHHHHHHHHHHHHHHHHccCCEeEEEE-ecCC-CCEEEEEEECCHHHHHHHHHHcCCCE
Confidence            445689999999944332           6899999999999999966 4443 79999999999999999998 99999


Q ss_pred             cCCeeEEEeecCC
Q 022058          180 LGYYPVRVLPSKT  192 (303)
Q Consensus       180 ~~g~~i~v~~~~~  192 (303)
                      +.|++|.|.++.+
T Consensus        89 ~~gr~l~v~~a~~  101 (112)
T 2dit_A           89 FGGRQITAQAWDG  101 (112)
T ss_dssp             ETTEECEEEECCS
T ss_pred             ECCcEEEEEEeCC
Confidence            9999999999864

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}

Probab=99.50  E-value=4e-14  Score=109.00  Aligned_cols=76  Identities=16%  Similarity=0.298  Sum_probs=67.6

Q ss_pred             ceEEEcCC----CCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcC----HHH----HHHHHH---hCC
Q 022058          214 RTVYCTNI----DKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAV----AES----AILALN---CSG  276 (303)
Q Consensus       214 ~~l~V~nL----~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~----~e~----A~~Ai~---l~g  276 (303)
                      ..|||+||    |+.+++++|+.+|++|  |.|.+|.++.|+  |.|+|||||+|.+    +++    |.+|+.   |||
T Consensus         3 ~kI~VgnL~~~~~~~tte~~Lk~~Fs~f--GeV~~~~li~Dp~Tg~slGfgfVef~d~~g~~d~a~kAA~kAi~~~~lng   80 (136)
T 2j8a_A            3 CEIVVYPAQDSTTTNIQDISIKNYFKKY--GEISHFEAFNDPNSALPLHVYLIKYASSDGKINDAAKAAFSAVRKHESSG   80 (136)
T ss_dssp             CEEEEEESSSSCCCCCCHHHHHHHHHTT--SCCSEEEEEECTTTCCEEEEEEEECC------CCHHHHHHHHHHHTTTTC
T ss_pred             cEEEEeCCCCCCCCCCCHHHHHHHHHhc--CCeEEEEEEecCCCCceeeEEEEEECCCCCCcchHHHHHHHHHHHhhhcC
Confidence            68999999    9999999999999999  999999999997  7899999999996    433    788875   799


Q ss_pred             ceeCCeeeEEeecCC
Q 022058          277 MVLGSQPIRVSPSKT  291 (303)
Q Consensus       277 ~~~~g~~l~v~~a~~  291 (303)
                      ..|+|+.|+|.+.+.
T Consensus        81 ~~I~Gr~irV~ln~~   95 (136)
T 2j8a_A           81 CFIMGFKFEVILNKH   95 (136)
T ss_dssp             EEETTEEEEEEECCT
T ss_pred             CeecCcEEEEEECcc
Confidence            999999999998753

>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=99.49  E-value=7.5e-14  Score=105.43  Aligned_cols=78  Identities=14%  Similarity=0.159  Sum_probs=68.1

Q ss_pred             ccceEEEcCC--CCCCC--------HHHHHHHhhhhcCcceeEEEEecCC----CCcccEEEEEEcCHHHHHHHHH-hCC
Q 022058          212 CSRTVYCTNI--DKKVP--------QAEVKQFFEAACGGEVTRLRLLGDH----VHSTRIAFVEFAVAESAILALN-CSG  276 (303)
Q Consensus       212 ~~~~l~V~nL--~~~~t--------~~~L~~~F~~~~~G~i~~v~i~~d~----~~~~g~afV~f~~~e~A~~Ai~-l~g  276 (303)
                      +++.|.|.|+  |..+.        +++|+++|++|  |.|.+|.|+++.    +.++|+|||+|.+.++|.+|+. |||
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~--G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG   81 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY--GLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTG   81 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTT--SCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHcc--CCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCC
Confidence            5688999998  33343        37999999999  999999999885    2579999999999999999998 999


Q ss_pred             ceeCCeeeEEeecCC
Q 022058          277 MVLGSQPIRVSPSKT  291 (303)
Q Consensus       277 ~~~~g~~l~v~~a~~  291 (303)
                      +.++||.|+|.|+.+
T Consensus        82 ~~f~GR~i~v~~~~~   96 (105)
T 3v4m_A           82 RKFANRVVVTKYCDP   96 (105)
T ss_dssp             CEETTEECEEEEECH
T ss_pred             CEeCCCEEEEEEeCH
Confidence            999999999999864

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A

Probab=99.49  E-value=5.3e-14  Score=121.16  Aligned_cols=80  Identities=21%  Similarity=0.355  Sum_probs=68.6

Q ss_pred             ccceEEEcCCCCCC---------CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee--
Q 022058          212 CSRTVYCTNIDKKV---------PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL--  279 (303)
Q Consensus       212 ~~~~l~V~nL~~~~---------t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~--  279 (303)
                      ..++|||+||+..+         ++++|+.+|++|  |.|.+|.|+.+    +|||||+|.+.++|..|+. |||..|  
T Consensus       133 ~~rtLfVgnL~~~~~~~~~~~~~tEe~L~~~F~~f--G~I~~v~v~~~----kG~AFV~F~~~~~Ae~A~~am~g~~l~~  206 (240)
T 3u1l_A          133 KNKTLYVGGIDGALNSKHLKPAQIESRIRFVFSRL--GDIDRIRYVES----KNCGFVKFKYQANAEFAKEAMSNQTLLL  206 (240)
T ss_dssp             CCCEEEEECTTGGGTTCCCCHHHHHHHHHHHHHTT--SCEEEEEEEGG----GTEEEEEESSHHHHHHHHHHHTTCCCCC
T ss_pred             CCceeecCCCChhhhcccccccCcHHHHHHHHHcc--CCEEEEEEECC----CCEEEEEeCCHHHHHHHHHHhCCCEEec
Confidence            46899999999998         799999999999  99999999875    5699999999999999998 999999  


Q ss_pred             ----------CCeeeEEeecCCCCCCCC
Q 022058          280 ----------GSQPIRVSPSKTPVRPRV  297 (303)
Q Consensus       280 ----------~g~~l~v~~a~~~~~~r~  297 (303)
                                .|+.|.|.||+....|..
T Consensus       207 ~~~~e~~~~~~gr~L~V~wA~~~pnp~~  234 (240)
T 3u1l_A          207 PSDKEWDDRREGTGLLVKWANEDPDPAA  234 (240)
T ss_dssp             TTSTTGGGGGGSCCCEEEECC-------
T ss_pred             cccccccccCCCCEEEEEEccCCCCHHH
Confidence                      899999999987655543

>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=99.47  E-value=2.8e-14  Score=107.65  Aligned_cols=70  Identities=17%  Similarity=0.343  Sum_probs=62.6

Q ss_pred             EcCCCCCCCHHHHHHHh------------hcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 022058          121 VSDIDQNITEERLAGLF------------SSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVR  186 (303)
Q Consensus       121 V~nlp~~~t~~~l~~~F------------~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~  186 (303)
                      +.|||+.+++++|++.|            ++||.|.+|.|+++..+ ++|||||+|.+.++|.+|+. |||..+.||+|.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~i~   99 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIH   99 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECC
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccCCceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEEEE
Confidence            56788888888777766            99999999999987765 79999999999999999998 999999999999


Q ss_pred             Eeec
Q 022058          187 VLPS  190 (303)
Q Consensus       187 v~~~  190 (303)
                      |.++
T Consensus       100 v~~s  103 (104)
T 1jmt_A          100 AELS  103 (104)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9985

>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=99.45  E-value=2.2e-13  Score=102.82  Aligned_cols=77  Identities=16%  Similarity=0.144  Sum_probs=67.8

Q ss_pred             CCCEEEEcCC--CCCCC--------HHHHHHHhhcCCceeEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcc
Q 022058          115 VRRTVYVSDI--DQNIT--------EERLAGLFSSCGQVVDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTM  179 (303)
Q Consensus       115 ~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~  179 (303)
                      +++.|.+.|+  |..+.        +++|++.|++||.|.+|.|+++..+    ++|||||+|.+.++|.+|+. |||..
T Consensus         4 ps~vl~L~Nm~~~~~l~~d~~~~~~~~dl~~~f~k~G~V~~v~i~~~~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lnG~~   83 (105)
T 3v4m_A            4 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   83 (105)
T ss_dssp             CCSEEEEESSCCGGGSSSHHHHHHHHHHHHHHHHTTSCEEEEECCCCBTTBCCTTTTEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCeEEEEECCCCHHHccChHHHHHHHHHHHHHHHccCCEEEEEEeccCCCCCcCCcEEEEEEECCHHHHHHHHHHhCCCE
Confidence            5788999998  44443        3689999999999999999987653    68999999999999999998 99999


Q ss_pred             cCCeeEEEeecC
Q 022058          180 LGYYPVRVLPSK  191 (303)
Q Consensus       180 ~~g~~i~v~~~~  191 (303)
                      +.||+|.|.++.
T Consensus        84 f~GR~i~v~~~~   95 (105)
T 3v4m_A           84 FANRVVVTKYCD   95 (105)
T ss_dssp             ETTEECEEEEEC
T ss_pred             eCCCEEEEEEeC
Confidence            999999999864

>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=99.44  E-value=5.3e-14  Score=106.08  Aligned_cols=70  Identities=23%  Similarity=0.325  Sum_probs=60.6

Q ss_pred             EcCCCCCCCHHHHHHHh------------hhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCee
Q 022058          218 CTNIDKKVPQAEVKQFF------------EAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQP  283 (303)
Q Consensus       218 V~nL~~~~t~~~L~~~F------------~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~  283 (303)
                      +.||+..+++++|+++|            ++|  |.|.+|.|+++. ++++|||||+|.+.++|.+|+. |||+.++||.
T Consensus        20 ~~~l~~~~~~~~l~~~f~~~~edl~~~f~~~~--G~V~~v~i~~~~~~~~~G~~fV~f~~~~~A~~A~~~lng~~~~Gr~   97 (104)
T 1jmt_A           20 ADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKY--GEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQP   97 (104)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--CCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEE
T ss_pred             cCCcccccCHHHHHHHHHHHHHHHHHHhhccC--CceEEEEEEeCCCCCccEEEEEEECCHHHHHHHHHHHCCCEECCEE
Confidence            44566666666666555            999  999999999886 6889999999999999999998 9999999999


Q ss_pred             eEEeec
Q 022058          284 IRVSPS  289 (303)
Q Consensus       284 l~v~~a  289 (303)
                      |+|.|+
T Consensus        98 i~v~~s  103 (104)
T 1jmt_A           98 IHAELS  103 (104)
T ss_dssp             CCEEEC
T ss_pred             EEEEEc
Confidence            999987

>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=99.42  E-value=5.1e-13  Score=102.89  Aligned_cols=77  Identities=16%  Similarity=0.194  Sum_probs=67.4

Q ss_pred             CCCEEEEcCCC--CCC---CHHHHHHHhhcCCceeEEEEeeCCCC------CceEEEEEecCHHHHHHHHH-hCCcccCC
Q 022058          115 VRRTVYVSDID--QNI---TEERLAGLFSSCGQVVDCRVCGDPHS------VLRFAFVEFADEHGARAALN-LGGTMLGY  182 (303)
Q Consensus       115 ~~~~l~V~nlp--~~~---t~~~l~~~F~~~G~i~~~~i~~~~~~------~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g  182 (303)
                      .+++|++.|+-  .++   -+++|++.|++||.|.+|.|+.+..+      ++||+||+|.+.++|.+|+. |||..+.|
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            57899999984  233   36899999999999999999987541      57999999999999999998 99999999


Q ss_pred             eeEEEeecC
Q 022058          183 YPVRVLPSK  191 (303)
Q Consensus       183 ~~i~v~~~~  191 (303)
                      |.|.|.++.
T Consensus        99 R~i~v~~~~  107 (118)
T 3ue2_A           99 RKVVAEVYD  107 (118)
T ss_dssp             EECEEEEEC
T ss_pred             cEEEEEEcC
Confidence            999999864

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.41  E-value=1.2e-12  Score=97.72  Aligned_cols=67  Identities=25%  Similarity=0.297  Sum_probs=59.1

Q ss_pred             CCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCCCCCC
Q 022058          223 KKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTPVRPR  296 (303)
Q Consensus       223 ~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~~~~r  296 (303)
                      ..+++++|+++|++|  |.|..|.|+   ++++|||||+|.+.++|..|+. +++  +.|+.|+|.|++++...+
T Consensus        27 ~~~te~~L~~~F~~~--G~V~~v~i~---~~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~~~~~   94 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKY--GEVLNLVLS---SKKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQPQDA   94 (100)
T ss_dssp             CSCCHHHHHHHHHTT--SCEEEEEEE---SSSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCCCCCC
T ss_pred             CCCCHHHHHHHHHhc--CCEEEEEEc---cCCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCCCCCC
Confidence            568999999999999  999999998   4678899999999999999998 655  679999999998776444

>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=99.39  E-value=8.3e-13  Score=101.67  Aligned_cols=79  Identities=18%  Similarity=0.219  Sum_probs=68.4

Q ss_pred             cccceEEEcCCCC--CC---CHHHHHHHhhhhcCcceeEEEEecCC------CCcccEEEEEEcCHHHHHHHHH-hCCce
Q 022058          211 MCSRTVYCTNIDK--KV---PQAEVKQFFEAACGGEVTRLRLLGDH------VHSTRIAFVEFAVAESAILALN-CSGMV  278 (303)
Q Consensus       211 ~~~~~l~V~nL~~--~~---t~~~L~~~F~~~~~G~i~~v~i~~d~------~~~~g~afV~f~~~e~A~~Ai~-l~g~~  278 (303)
                      .++++|+|.|+-.  .+   -+++|++.|++|  |.|.+|.|+++.      +.++|++||+|.+.++|.+|+. |||+.
T Consensus        18 ~ps~vl~L~Nm~~~~el~ddleedl~eef~k~--G~V~~v~I~~~~~~~~~~~~~~G~~FV~F~~~e~A~~Ai~~LnGr~   95 (118)
T 3ue2_A           18 QESTVMVLRNMVDPKDIDDDLEGEVTEECGKF--GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRW   95 (118)
T ss_dssp             HSCCEEEEESCSCGGGCCTTHHHHHHHHHTTT--SCEEEEEEEEEEESSSTTCEEEEEEEEEESSHHHHHHHHHHHTTCE
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHHHhcc--CCEeEEEEeecCCCcccCCcceEEEEEEECCHHHHHHHHHHHCCCE
Confidence            3678999999842  22   368999999999  999999999874      2467999999999999999998 99999


Q ss_pred             eCCeeeEEeecCC
Q 022058          279 LGSQPIRVSPSKT  291 (303)
Q Consensus       279 ~~g~~l~v~~a~~  291 (303)
                      |+||.|+|.|+..
T Consensus        96 f~GR~i~v~~~~~  108 (118)
T 3ue2_A           96 FAGRKVVAEVYDQ  108 (118)
T ss_dssp             ETTEECEEEEECH
T ss_pred             ECCcEEEEEEcCh
Confidence            9999999999854

>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=99.32  E-value=6.8e-12  Score=95.89  Aligned_cols=76  Identities=14%  Similarity=0.137  Sum_probs=64.8

Q ss_pred             ccceEEEcCCCCCC----------CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          212 CSRTVYCTNIDKKV----------PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       212 ~~~~l~V~nL~~~~----------t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      ++++|.|.|+=..-          -+++|+++|++|  |.|.+|.|.++.  ++|+|||+|.+.++|.+|++ |||+.++
T Consensus         6 ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kf--G~V~~v~i~~~~--~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            6 ATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKH--GGVIHIYVDKNS--AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTT--TCCSEEEECTTC--TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCcEEEEECCCChHHccChhHHHHHHHHHHHHHhcc--CCEEEEEEecCC--CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            45788888873321          136899999999  999999998764  58899999999999999998 9999999


Q ss_pred             CeeeEEeecCC
Q 022058          281 SQPIRVSPSKT  291 (303)
Q Consensus       281 g~~l~v~~a~~  291 (303)
                      ||.|+|.|+..
T Consensus        82 GR~i~v~~~~~   92 (114)
T 3s6e_A           82 GKMITAAYVPL   92 (114)
T ss_dssp             TEECEEEEECH
T ss_pred             CEEEEEEEEcH
Confidence            99999999753

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.32  E-value=8e-12  Score=93.23  Aligned_cols=63  Identities=22%  Similarity=0.238  Sum_probs=55.9

Q ss_pred             CCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          126 QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       126 ~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..+++++|+++|++||.|.+|.|+.   .++|||||+|.+.++|.+|+. +++  +.|++|.|.|++..
T Consensus        27 ~~~te~~L~~~F~~~G~V~~v~i~~---~~rGfaFVeF~~~~~A~~Ai~~~~~--~~g~~l~V~~a~~~   90 (100)
T 2d9o_A           27 GGYSKDVLLRLLQKYGEVLNLVLSS---KKPGTAVVEFATVKAAELAVQNEVG--LVDNPLKISWLEGQ   90 (100)
T ss_dssp             CSCCHHHHHHHHHTTSCEEEEEEES---SSSSEEEEEESCHHHHHHHHHTCCB--CSSSBCEEECSSCC
T ss_pred             CCCCHHHHHHHHHhcCCEEEEEEcc---CCCCEEEEEECCHHHHHHHHHhcCC--CCCCeEEEEEccCC
Confidence            5689999999999999999999983   468999999999999999998 554  67999999998654

>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=99.31  E-value=3.6e-12  Score=115.42  Aligned_cols=75  Identities=12%  Similarity=0.218  Sum_probs=64.9

Q ss_pred             CCCCCEEEEcC--CCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC---Ce--e
Q 022058          113 DSVRRTVYVSD--IDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG---YY--P  184 (303)
Q Consensus       113 ~~~~~~l~V~n--lp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~---g~--~  184 (303)
                      ....++|||+|  |++.+|+++|+++|++||.|.+|.++.    +||||||+|++.++|++|++ |||.++.   |+  +
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~G~V~~v~~~~----~kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~~~   90 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPP----NKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKIT   90 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTTSCEEEEECCT----TCSEEEEEESSHHHHHHHHHHTTTCEEECTTSCEEE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhcCCeEEEEEeC----CCCEEEEEECCHHHHHHHHHHhCCCccccccCCceE
Confidence            44678999999  578999999999999999999988754    57999999999999999999 9999883   45  6


Q ss_pred             EEEeecC
Q 022058          185 VRVLPSK  191 (303)
Q Consensus       185 i~v~~~~  191 (303)
                      |.|.+..
T Consensus        91 ly~~~~~   97 (345)
T 3tht_A           91 LYLNFVE   97 (345)
T ss_dssp             CEEEECS
T ss_pred             EEEEEee
Confidence            7777763

>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=99.31  E-value=8.5e-12  Score=95.35  Aligned_cols=77  Identities=14%  Similarity=0.091  Sum_probs=64.9

Q ss_pred             CCCCCEEEEcCCCC--CC--------CHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          113 DSVRRTVYVSDIDQ--NI--------TEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       113 ~~~~~~l~V~nlp~--~~--------t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      +..++.|.+.|+=.  +.        -+++|++.|++||.|.+|.|.++.  ++||+||+|.+.++|.+|+. |||..++
T Consensus         4 p~ps~vv~L~Nm~~~~e~~d~~~~~el~edl~~~f~kfG~V~~v~i~~~~--~~G~~fV~f~~~e~A~~Ai~~lnG~~f~   81 (114)
T 3s6e_A            4 PLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKNS--AQGNVYVKCPSIAAAIAAVNALHGRWFA   81 (114)
T ss_dssp             CCCCSEEEEESSCCTTTCCSTTHHHHHHHHHHHHHTTTTCCSEEEECTTC--TTCCEEEECSSHHHHHHHHHHHTTCEET
T ss_pred             CCCCcEEEEECCCChHHccChhHHHHHHHHHHHHHhccCCEEEEEEecCC--CcEEEEEEECCHHHHHHHHHHhCCCEEC
Confidence            34677899988832  21        145789999999999999997653  58999999999999999998 9999999


Q ss_pred             CeeEEEeecC
Q 022058          182 YYPVRVLPSK  191 (303)
Q Consensus       182 g~~i~v~~~~  191 (303)
                      ||.|.|.++.
T Consensus        82 GR~i~v~~~~   91 (114)
T 3s6e_A           82 GKMITAAYVP   91 (114)
T ss_dssp             TEECEEEEEC
T ss_pred             CEEEEEEEEc
Confidence            9999999974

>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=99.20  E-value=3.9e-11  Score=108.63  Aligned_cols=75  Identities=15%  Similarity=0.231  Sum_probs=64.9

Q ss_pred             ccccceEEEcC--CCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC---Ce-
Q 022058          210 EMCSRTVYCTN--IDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG---SQ-  282 (303)
Q Consensus       210 ~~~~~~l~V~n--L~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~---g~-  282 (303)
                      ..++.+|||+|  |+..+|+++|+++|++|  |.|.+|.+.++    +|||||+|.+.++|++|++ |||..+.   |+ 
T Consensus        15 ~~ps~~l~VgN~gl~~~~te~~L~~~F~~~--G~V~~v~~~~~----kgfaFV~f~~~~~A~~Ai~~lnG~~~~~~~g~~   88 (345)
T 3tht_A           15 SYATQSLVVANGGLGNGVSRNQLLPVLEKC--GLVDALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEVVDDLGQK   88 (345)
T ss_dssp             SSCCSEEEEETCSGGGTCCHHHHHHHHHTT--SCEEEEECCTT----CSEEEEEESSHHHHHHHHHHTTTCEEECTTSCE
T ss_pred             CCCCCEEEEEcCCCCCCCCHHHHHHHHHhc--CCeEEEEEeCC----CCEEEEEECCHHHHHHHHHHhCCCccccccCCc
Confidence            44668999999  57899999999999999  99999888763    5799999999999999999 9999883   44 


Q ss_pred             -eeEEeecC
Q 022058          283 -PIRVSPSK  290 (303)
Q Consensus       283 -~l~v~~a~  290 (303)
                       .|.|.|+.
T Consensus        89 ~~ly~~~~~   97 (345)
T 3tht_A           89 ITLYLNFVE   97 (345)
T ss_dssp             EECEEEECS
T ss_pred             eEEEEEEee
Confidence             67888874

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.17  E-value=1.3e-10  Score=83.85  Aligned_cols=74  Identities=24%  Similarity=0.302  Sum_probs=63.2

Q ss_pred             cccceEEEcCCC----CCCCH----HHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCe
Q 022058          211 MCSRTVYCTNID----KKVPQ----AEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQ  282 (303)
Q Consensus       211 ~~~~~l~V~nL~----~~~t~----~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~  282 (303)
                      ++..||+|...+    ..+-.    .+|.+.|.+|  |.|..+++..|.      +||+|.+.++|.+|+.|||..++||
T Consensus         5 Ppd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~--G~Vi~vr~~~d~------~fVtF~d~~sAlaAi~mnG~~v~Gr   76 (91)
T 2dnr_A            5 SSGGTVLVSIKSSLPENNFFDDALIDELLQQFASF--GEVILIRFVEDK------MWVTFLEGSSALNVLSLNGKELLNR   76 (91)
T ss_dssp             CSSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTT--CCEEEEEECSSS------EEEEESSHHHHHHGGGGTTCEETTE
T ss_pred             CCCCeEEEEeccCccccccCCHHHHHHHHHHHHhC--CCeEEEEEecCC------EEEEECChHHHHHHHhcCCeEeCCe
Confidence            355778887665    23333    6799999999  999999999985      8999999999999999999999999


Q ss_pred             eeEEeecCCC
Q 022058          283 PIRVSPSKTP  292 (303)
Q Consensus       283 ~l~v~~a~~~  292 (303)
                      .|+|.++.|-
T Consensus        77 ~LkV~lkt~d   86 (91)
T 2dnr_A           77 TITIALKSPS   86 (91)
T ss_dssp             EEEEEECCCS
T ss_pred             EEEEEeCCCC
Confidence            9999998753

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.03  E-value=9.4e-10  Score=79.34  Aligned_cols=72  Identities=26%  Similarity=0.312  Sum_probs=61.0

Q ss_pred             CCCEEEEcCCC----CCCCH----HHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEE
Q 022058          115 VRRTVYVSDID----QNITE----ERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVR  186 (303)
Q Consensus       115 ~~~~l~V~nlp----~~~t~----~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~  186 (303)
                      ...+|+|.-.|    .+.-.    .+|.+.|++||.|..++++.+.      +||+|.+.++|.+||.|||..+.||.|+
T Consensus         6 pd~tv~V~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vi~vr~~~d~------~fVtF~d~~sAlaAi~mnG~~v~Gr~Lk   79 (91)
T 2dnr_A            6 SGGTVLVSIKSSLPENNFFDDALIDELLQQFASFGEVILIRFVEDK------MWVTFLEGSSALNVLSLNGKELLNRTIT   79 (91)
T ss_dssp             SSCEEEEEEECSSTTTCSCCHHHHHHHHHHHHTTCCEEEEEECSSS------EEEEESSHHHHHHGGGGTTCEETTEEEE
T ss_pred             CCCeEEEEeccCccccccCCHHHHHHHHHHHHhCCCeEEEEEecCC------EEEEECChHHHHHHHhcCCeEeCCeEEE
Confidence            46777777665    22323    5689999999999999999865      8999999999999999999999999999


Q ss_pred             EeecCC
Q 022058          187 VLPSKT  192 (303)
Q Consensus       187 v~~~~~  192 (303)
                      |..+.+
T Consensus        80 V~lkt~   85 (91)
T 2dnr_A           80 IALKSP   85 (91)
T ss_dssp             EEECCC
T ss_pred             EEeCCC
Confidence            999754

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=99.01  E-value=1.3e-09  Score=83.62  Aligned_cols=72  Identities=15%  Similarity=0.051  Sum_probs=64.5

Q ss_pred             CCCEEEEcCCCCC-CCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecC-HHHHHHHHH-hC--CcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQN-ITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFAD-EHGARAALN-LG--GTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~-~~~A~~Ai~-l~--g~~~~g~~i~v~~  189 (303)
                      ..+.|+|+||++. ++.++|+++|+.||+|..|.+..+..    .|||.|.+ .++|..|+. +|  +..|.|..+.+..
T Consensus        17 ~G~il~v~~l~~~~~sredLke~F~~~G~V~~Vd~~~g~~----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~~ev   92 (121)
T 1owx_A           17 IGCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRGAK----EGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWEV   92 (121)
T ss_dssp             CCCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTTCS----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEEE
T ss_pred             CCeEEEEecCCCCcCCHHHHHHHHHhcCCEEEEEEecCCC----EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEEEEE
Confidence            5788999999999 99999999999999999999988776    69999999 899999998 84  7888898888765


Q ss_pred             c
Q 022058          190 S  190 (303)
Q Consensus       190 ~  190 (303)
                      .
T Consensus        93 L   93 (121)
T 1owx_A           93 L   93 (121)
T ss_dssp             C
T ss_pred             C
Confidence            4

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.96  E-value=2.2e-09  Score=82.29  Aligned_cols=72  Identities=10%  Similarity=0.125  Sum_probs=64.5

Q ss_pred             cccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcC-HHHHHHHHH-h--CCceeCCeeeE
Q 022058          211 MCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV-AESAILALN-C--SGMVLGSQPIR  285 (303)
Q Consensus       211 ~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~-~e~A~~Ai~-l--~g~~~~g~~l~  285 (303)
                      ..+..|+|+||+.. ++.++|+++|++|  |.|.+|.+.++..    .|||.|.+ .++|..|+. |  ++..|.|..++
T Consensus        16 ~~G~il~v~~l~~~~~sredLke~F~~~--G~V~~Vd~~~g~~----tgfVrf~~~~~~A~~av~~ln~~~~~i~g~~~~   89 (121)
T 1owx_A           16 KIGCLLKFSGDLDDQTCREDLHILFSNH--GEIKWIDFVRGAK----EGIILFKEKAKEALGKAKDANNGNLQLRNKEVT   89 (121)
T ss_dssp             CCCCEEEEEESCCSSCCHHHHHHHTCSS--CCEEEEECCTTCS----EEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEE
T ss_pred             cCCeEEEEecCCCCcCCHHHHHHHHHhc--CCEEEEEEecCCC----EEEEEECCChHHHHHHHHHhhcCCcEEeCcEEE
Confidence            35688999999999 9999999999999  9999999999875    79999999 889999997 8  47889998888


Q ss_pred             Eee
Q 022058          286 VSP  288 (303)
Q Consensus       286 v~~  288 (303)
                      +..
T Consensus        90 ~ev   92 (121)
T 1owx_A           90 WEV   92 (121)
T ss_dssp             EEE
T ss_pred             EEE
Confidence            764

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.94  E-value=2.2e-09  Score=77.76  Aligned_cols=74  Identities=20%  Similarity=0.259  Sum_probs=63.5

Q ss_pred             ccccceEEEcCCCCC-----CCH----HHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeC
Q 022058          210 EMCSRTVYCTNIDKK-----VPQ----AEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLG  280 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~-----~t~----~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~  280 (303)
                      .++..||+|..++..     +-.    .+|.+.|.+|  |.|..+++..|+      +||+|.+.++|.+||.|||..++
T Consensus        12 GPpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~--G~Vilvr~v~d~------~fVtF~d~~sAl~AI~ldG~~v~   83 (95)
T 1ufw_A           12 GPLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSY--GTIVLVRINQGQ------MLVTFADSHSALSVLDVDGMKVK   83 (95)
T ss_dssp             CCTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHH--SCCSEEEEETTE------EEEECSCSHHHHHHHHGGGSEET
T ss_pred             CCCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHC--CCEEEEEEecCc------EEEEEcChHHHHHHHhcCCeeeC
Confidence            346688999887643     322    5789999999  999999999985      99999999999999999999999


Q ss_pred             CeeeEEeecCC
Q 022058          281 SQPIRVSPSKT  291 (303)
Q Consensus       281 g~~l~v~~a~~  291 (303)
                      ||.|+|.+..|
T Consensus        84 Gr~L~V~~k~~   94 (95)
T 1ufw_A           84 GRAVKISGPSS   94 (95)
T ss_dssp             TEEEEEECCCC
T ss_pred             CeEEEEeccCC
Confidence            99999998643

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1

Probab=98.82  E-value=4.2e-09  Score=76.30  Aligned_cols=71  Identities=25%  Similarity=0.330  Sum_probs=61.2

Q ss_pred             CCCCEEEEcCCCCC------CCH---HHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCee
Q 022058          114 SVRRTVYVSDIDQN------ITE---ERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYP  184 (303)
Q Consensus       114 ~~~~~l~V~nlp~~------~t~---~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~  184 (303)
                      ....||+|.-++.+      .++   .+|.+.|.+||.|..++++.+.      +||+|.+.++|.+||.|||..+.||.
T Consensus        13 PpD~Tv~V~~~~~~~~~~~~fd~~l~~~L~~~F~~~G~Vilvr~v~d~------~fVtF~d~~sAl~AI~ldG~~v~Gr~   86 (95)
T 1ufw_A           13 PLDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQGQ------MLVTFADSHSALSVLDVDGMKVKGRA   86 (95)
T ss_dssp             CTTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETTE------EEEECSCSHHHHHHHHGGGSEETTEE
T ss_pred             CCCCeEEEEecCCcccccccCCHHHHHHHHHHHHHCCCEEEEEEecCc------EEEEEcChHHHHHHHhcCCeeeCCeE
Confidence            45788999877643      232   4688999999999999999875      99999999999999999999999999


Q ss_pred             EEEeec
Q 022058          185 VRVLPS  190 (303)
Q Consensus       185 i~v~~~  190 (303)
                      |+|.+.
T Consensus        87 L~V~~k   92 (95)
T 1ufw_A           87 VKISGP   92 (95)
T ss_dssp             EEEECC
T ss_pred             EEEecc
Confidence            999874

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.79  E-value=1.1e-08  Score=87.06  Aligned_cols=64  Identities=19%  Similarity=0.248  Sum_probs=58.1

Q ss_pred             CHHHHHHHhhhhcCcceeEEEEecCC------CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          226 PQAEVKQFFEAACGGEVTRLRLLGDH------VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       226 t~~~L~~~F~~~~~G~i~~v~i~~d~------~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      .+++|++.|++|  |.|.++.|.++.      +.++|++||+|.+.++|.+|+. |||+.+.||.|.+.|+..
T Consensus       142 ~~~dl~~e~~~~--G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~~  212 (222)
T 3dxb_A          142 LEGEVTEECGKF--GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYDQ  212 (222)
T ss_dssp             HHHHHHHHHTTT--SCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECCH
T ss_pred             HHHHHHHHHHcc--CCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcCH
Confidence            568999999999  999999998652      3789999999999999999999 999999999999999853

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}

Probab=98.77  E-value=1.2e-08  Score=86.96  Aligned_cols=64  Identities=17%  Similarity=0.163  Sum_probs=57.2

Q ss_pred             CCHHHHHHHhhcCCceeEEEEeeCCC------CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          128 ITEERLAGLFSSCGQVVDCRVCGDPH------SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       128 ~t~~~l~~~F~~~G~i~~~~i~~~~~------~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      -.+++|++.|++||.|.++.++++..      .++|++||+|.+.++|.+|+. |||..+.||+|.+.+..
T Consensus       141 e~~~dl~~e~~~~G~v~~~~v~~~~~~~~~~~~~~G~~fv~f~~~~~a~~a~~~l~gr~~~gr~i~~~~~~  211 (222)
T 3dxb_A          141 DLEGEVTEECGKFGAVNRVIIYQEKQGEEEDAEIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEVYD  211 (222)
T ss_dssp             THHHHHHHHHTTTSCEEEEEEEEEECCSSTTCCEEEEEEEEESSHHHHHHHHHHHTTCBSSSSBCEEEECC
T ss_pred             HHHHHHHHHHHccCCeEEEEEecCCCCcccCcCceeEEEEEECCHHHHHHHHHHhcCceECCeEEEEEEcC
Confidence            35678999999999999999986543      268999999999999999999 99999999999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.56  E-value=4.8e-07  Score=66.88  Aligned_cols=72  Identities=18%  Similarity=0.229  Sum_probs=64.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhc---CcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAAC---GGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~---~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .++|-+.|||.++++..|+.+.+++-   .|.+..+.+.+|.+    -|+|+|.+...|-+|.. |||.+|.|+.|++.-
T Consensus        21 ~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~----GAivef~d~~~AgKasLaL~G~ef~gr~Lr~gT   96 (117)
T 2l9w_A           21 ETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN----GAIIIFRDSKFAAKMLMILNGSQFQGKVIRSGT   96 (117)
T ss_dssp             TSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT----EEEEECSCHHHHHHHHHHHSSEEETTEEEEEEC
T ss_pred             CcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC----ceEEEEccchhhHHHHhhcCCeeecCeEEEecC
Confidence            48899999999999999999999871   37899999999975    69999999999988886 999999999999864

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}

Probab=98.53  E-value=4.1e-07  Score=67.23  Aligned_cols=77  Identities=12%  Similarity=0.165  Sum_probs=68.7

Q ss_pred             hccCCCCCCEEEEcCCCCCCCHHHHHHHhhcC-----CceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCC
Q 022058          109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSC-----GQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGY  182 (303)
Q Consensus       109 ~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~-----G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g  182 (303)
                      +.+.....++|-+-|||..++...|+.+..++     |.|..+.+..|.+   | |+|+|.+...|-+|.- |+|.+|.|
T Consensus        14 s~~~~~~~rtiaL~~ipDtvndarIr~lve~~~~i~~g~i~KI~L~pDH~---G-Aivef~d~~~AgKasLaL~G~ef~g   89 (117)
T 2l9w_A           14 SRNSKELETLICLFPLSDKVSPSLICQFLQEEIHINEKDIRKILLVSDFN---G-AIIIFRDSKFAAKMLMILNGSQFQG   89 (117)
T ss_dssp             CCCTTTTTSCEEEECCCTTCCHHHHHHHHHHHTCCCTTTCSEEEEETTTT---E-EEEECSCHHHHHHHHHHHSSEEETT
T ss_pred             ccCCccCCcEEEEecCCCCCCHHHHHHHHhhhhccCccceeEEEEecCCC---c-eEEEEccchhhHHHHhhcCCeeecC
Confidence            33344568999999999999999999999999     9999999998876   3 9999999999999986 99999999


Q ss_pred             eeEEEee
Q 022058          183 YPVRVLP  189 (303)
Q Consensus       183 ~~i~v~~  189 (303)
                      |.|+|.-
T Consensus        90 r~Lr~gT   96 (117)
T 2l9w_A           90 KVIRSGT   96 (117)
T ss_dssp             EEEEEEC
T ss_pred             eEEEecC
Confidence            9999974

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=98.10  E-value=3.1e-05  Score=56.72  Aligned_cols=89  Identities=17%  Similarity=0.185  Sum_probs=72.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhc-----CCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEe
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSS-----CGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVL  188 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~-----~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~  188 (303)
                      ...++|.|.|||+.++++.|.-+|+.     =|+|.++....      +-|+|+|.+.+.|++.++...+.+.+.+|.|.
T Consensus         6 ~~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~------~~AvItF~d~~va~rVL~k~~H~L~~~~LsV~   79 (104)
T 2dhx_A            6 SGGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG------CGGVLTFREPADAERVLAQADHELHGAQLSLR   79 (104)
T ss_dssp             CCCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET------TEEEEEESSHHHHHHHHTCSCCBSSSSBCEEE
T ss_pred             cCccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC------CcEEEEEcChHHHHHHhcCCcceecCeEEEEE
Confidence            36789999999999999999999986     25888887754      24999999999999999876779999999998


Q ss_pred             ecCCCCCCCCCCCCCCcccccccccceEEEcCCCCCCC
Q 022058          189 PSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVP  226 (303)
Q Consensus       189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t  226 (303)
                      ...+           .       ....|++++|++.++
T Consensus        80 P~~~-----------~-------~~~r~ll~gl~~~t~   99 (104)
T 2dhx_A           80 PAPP-----------R-------APARLLLQGLPPGTS   99 (104)
T ss_dssp             ECCC-----------C-------CCCCCCCCSCCCCCC
T ss_pred             cCCC-----------C-------CcceEeeecCCCCCC
Confidence            7421           1       225688888888764

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=97.99  E-value=0.00016  Score=52.92  Aligned_cols=79  Identities=20%  Similarity=0.270  Sum_probs=66.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhh---hcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEA---ACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~---~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      ..++|.|.|||+.++++.|.-+|+.   -.||.|.++.... .     -|+|+|.+.+.|++.++-..+.|.+..|.|..
T Consensus         7 ~~~~I~V~~lPp~~~~e~L~LYFEn~rrsGGG~V~~v~~~~-~-----~AvItF~d~~va~rVL~k~~H~L~~~~LsV~P   80 (104)
T 2dhx_A            7 GGVAVEVRGLPPAVPDELLTLYFENRRRSGGGPVLSWQRLG-C-----GGVLTFREPADAERVLAQADHELHGAQLSLRP   80 (104)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHHHCTTTTCCCCEEEEEEET-T-----EEEEEESSHHHHHHHHTCSCCBSSSSBCEEEE
T ss_pred             CccEEEEECCCCCCChhHheEEEeCCCcCCCceeeEEEEcC-C-----cEEEEEcChHHHHHHhcCCcceecCeEEEEEc
Confidence            3478999999999999999999997   3458999998876 2     69999999999999998667899999999988


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      .-+....|
T Consensus        81 ~~~~~~~r   88 (104)
T 2dhx_A           81 APPRAPAR   88 (104)
T ss_dssp             CCCCCCCC
T ss_pred             CCCCCcce
Confidence            65544443

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.79  E-value=8e-05  Score=54.76  Aligned_cols=74  Identities=14%  Similarity=0.096  Sum_probs=62.9

Q ss_pred             cceEEEcCCCCCC-C----HHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          213 SRTVYCTNIDKKV-P----QAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       213 ~~~l~V~nL~~~~-t----~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      ..+|+|.||+..+ .    .+.++++|..|  +++..-...+.=.    -..|.|.+.++|.+|.. ||+..+.|+.++|
T Consensus         5 pntLiitnl~~~vF~~~~lk~~~e~Lf~~~--~~~~tF~~lkSFR----Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~   78 (104)
T 1wey_A            5 SSGLIACVANDDVFSESETRAKFESLFRTY--DKDTTFQYFKSFK----RVRINFSNPLSAADARLRLHKTEFLGKEMKL   78 (104)
T ss_dssp             CCEEEEECCCGGGGSTTTHHHHHHHHHHTT--CSSCEEEEETTTT----EEEEECSSTTHHHHHHHTSTTSEETTEECEE
T ss_pred             CceEEEecCCHHHcCCHHHHHHHHHHHHhh--CcCcceeecCcce----EEEEEeCChHHHHHHHHHhccceecCceeEE
Confidence            3789999998764 2    25789999999  8888887777743    58999999999999998 9999999999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      -|+.+.
T Consensus        79 YFgq~~   84 (104)
T 1wey_A           79 YFAQTL   84 (104)
T ss_dssp             ECCCCS
T ss_pred             EecCCC
Confidence            999754

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1

Probab=97.40  E-value=0.00076  Score=49.52  Aligned_cols=74  Identities=11%  Similarity=0.087  Sum_probs=62.6

Q ss_pred             CCCEEEEcCCCCCC-C----HHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          115 VRRTVYVSDIDQNI-T----EERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       115 ~~~~l~V~nlp~~~-t----~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ...+|+|.||+.++ .    .+.++++|..|+++.+....+.-.    -.-|.|.+.++|.+|.. ||+..+.|+.++|.
T Consensus         4 ~pntLiitnl~~~vF~~~~lk~~~e~Lf~~~~~~~tF~~lkSFR----Rirv~F~~~~~A~~AR~~Lh~~~f~g~~~r~Y   79 (104)
T 1wey_A            4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKSFK----RVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEETTTT----EEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCceEEEecCCHHHcCCHHHHHHHHHHHHhhCcCcceeecCcce----EEEEEeCChHHHHHHHHHhccceecCceeEEE
Confidence            45789999999764 3    256799999999998887776543    47999999999999998 99999999999999


Q ss_pred             ecCC
Q 022058          189 PSKT  192 (303)
Q Consensus       189 ~~~~  192 (303)
                      ++++
T Consensus        80 Fgq~   83 (104)
T 1wey_A           80 FAQT   83 (104)
T ss_dssp             CCCC
T ss_pred             ecCC
Confidence            9863

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.34  E-value=0.0016  Score=49.06  Aligned_cols=70  Identities=16%  Similarity=0.162  Sum_probs=59.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCC-eeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGS-QPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g-~~l~v~~a  289 (303)
                      ..-|.|.+.|+.. ...|.+.|++|  |.|.+.......+    +-.|.|.+..+|++|+..||..++| -.|-|.+.
T Consensus        24 ~~wVtVFGFp~~~-~~~VL~~F~~~--G~Iv~~~~~~~~N----WihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           24 DTWVTVFGFPQAS-ASYILLQFAQY--GNILKHVMSNTGN----WMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGEEEEECCCGGG-HHHHHHHHHTT--SCEEEEEECSSSS----EEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCEEEEECCCHHH-HHHHHHHHHhh--CcEEEeccCCCCC----eEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            4678888999885 67788999998  9999988743333    9999999999999999999999984 77888875

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1

Probab=97.27  E-value=0.0014  Score=49.48  Aligned_cols=71  Identities=18%  Similarity=0.237  Sum_probs=58.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCC-eeEEEeec
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGY-YPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g-~~i~v~~~  190 (303)
                      ..+.|.|-+.|+.. ...+...|++||+|.+.....    ....-.|.|.+..+|++||..||..+.| ..|-|.+.
T Consensus        23 ~~~wVtVFGFp~~~-~~~VL~~F~~~G~Iv~~~~~~----~~NWihI~Y~s~~~A~rAL~kNG~ii~g~~mIGV~p~   94 (119)
T 1wwh_A           23 DDTWVTVFGFPQAS-ASYILLQFAQYGNILKHVMSN----TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPC   94 (119)
T ss_dssp             GGGEEEEECCCGGG-HHHHHHHHHTTSCEEEEEECS----SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEEC
T ss_pred             CCCEEEEECCCHHH-HHHHHHHHHhhCcEEEeccCC----CCCeEEEEeCCHHHHHHHHHhCCeEecCCEEEEEEEC
Confidence            46789999999985 666777899999999887622    2348999999999999999999999984 66777764

>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=97.20  E-value=0.0013  Score=47.39  Aligned_cols=65  Identities=15%  Similarity=0.279  Sum_probs=54.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---C-CcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---V-HSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      .+|.|++||+++|++++++.++..  +.+.......++   + ..-.-|+|.|.+.+++..-.+ ++|+.+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~--~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC--CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCc--ccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            468899999999999999999998  888887776664   2 234579999999999988888 9999884

>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=97.16  E-value=0.0021  Score=46.25  Aligned_cols=65  Identities=12%  Similarity=0.188  Sum_probs=54.0

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      +.|.|++||+.+|++++.+.+.....+........+.+    .-.-|||.|.+.+++..... ++|..+.
T Consensus         2 ~KvVIRrLPP~LteeeF~~~l~~~~~~d~~~fv~G~~s~~~~~~SRaYi~f~~~e~v~~f~~~~~g~~F~   71 (91)
T 1uw4_A            2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             cEEEEeCCCCCCCHHHHHHHhcCcccceEEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHhCCcEEE
Confidence            46899999999999999999999988776666554322    24679999999999999998 9998774

>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=97.08  E-value=0.0014  Score=47.36  Aligned_cols=54  Identities=22%  Similarity=0.294  Sum_probs=45.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-h
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L  175 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l  175 (303)
                      ....++| ++|+++.-.||.++|+.||.| .|+.+-|.     -|||.|.+++.|..|+. +
T Consensus        15 r~HVf~l-~FP~ewKt~DI~~lFs~fggv-~I~WidDT-----sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           15 RDHVLHV-TFPKEWKTSDLYQLFSAFGNI-QISWIDDT-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             CCSEEEE-ECCTTCCHHHHHHHHTTTCSC-CCEEEETT-----EEEEECSCHHHHHHHHHHH
T ss_pred             CCeEEEE-eCChhhhhHHHHHHhhccCCE-EEEEEcCC-----eEEEEecCHHHHHHHHHhc
Confidence            3455666 899999999999999999954 47777654     59999999999999998 5

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*

Probab=96.88  E-value=0.0024  Score=46.16  Aligned_cols=52  Identities=23%  Similarity=0.394  Sum_probs=43.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C  274 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l  274 (303)
                      ..++| ++|+.+...||.++|++|  |. ..|..+.|.     .|||.|.+++.|..|+. +
T Consensus        17 HVf~l-~FP~ewKt~DI~~lFs~f--gg-v~I~WidDT-----sAlvvf~~~~~a~~al~~i   69 (100)
T 1whv_A           17 HVLHV-TFPKEWKTSDLYQLFSAF--GN-IQISWIDDT-----SAFVSLSQPEQVQIAVNTS   69 (100)
T ss_dssp             SEEEE-ECCTTCCHHHHHHHHTTT--CS-CCCEEEETT-----EEEEECSCHHHHHHHHHHH
T ss_pred             eEEEE-eCChhhhhHHHHHHhhcc--CC-EEEEEEcCC-----eEEEEecCHHHHHHHHHhc
Confidence            55666 999999999999999999  84 445566665     79999999999999998 5

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.71  E-value=0.0023  Score=46.39  Aligned_cols=53  Identities=23%  Similarity=0.367  Sum_probs=44.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS  275 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~  275 (303)
                      ..++| ++|+.+...||.++|++|  | -..|..+.|.     .|||.|.+++.|..|+. +.
T Consensus         7 HV~~l-~FP~ewKt~Di~~lFs~f--g-gv~I~WidDT-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            7 HVLHV-TFPKEWKTSDLYQLFSAF--G-NIQISWIDDT-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEEE-ECCTTCCHHHHHHHTTTS--E-EEEEEEEETT-----EEEEEEEEECHHHHHHHHHT
T ss_pred             eEEEE-eCChhhhhHHHHHHHhcc--C-CEEEEEEcCC-----eEEEEecCHHHHHHHHHhcc
Confidence            45566 999999999999999999  8 4456666665     79999999999999998 53

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}

Probab=96.64  E-value=0.0026  Score=46.15  Aligned_cols=52  Identities=23%  Similarity=0.317  Sum_probs=44.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG  176 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~  176 (303)
                      .++| ++|+++.-.||.++|+.||. ..|+++-|.     -|||.|.+++.|..|+. +.
T Consensus         8 V~~l-~FP~ewKt~Di~~lFs~fgg-v~I~WidDT-----sAlvvf~~~~~a~~al~~i~   60 (101)
T 3ctr_A            8 VLHV-TFPKEWKTSDLYQLFSAFGN-IQISWIDDT-----SAFVSLSQPEQVKIAVNTSK   60 (101)
T ss_dssp             EEEE-ECCTTCCHHHHHHHTTTSEE-EEEEEEETT-----EEEEEEEEECHHHHHHHHHT
T ss_pred             EEEE-eCChhhhhHHHHHHHhccCC-EEEEEEcCC-----eEEEEecCHHHHHHHHHhcc
Confidence            3555 99999999999999999994 457777654     59999999999999998 54

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=96.52  E-value=0.0025  Score=48.80  Aligned_cols=75  Identities=16%  Similarity=0.261  Sum_probs=56.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeE-EEEecC--------------CC-CcccEEEEEEcCHHHHHHHHHhCCc
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTR-LRLLGD--------------HV-HSTRIAFVEFAVAESAILALNCSGM  277 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~-v~i~~d--------------~~-~~~g~afV~f~~~e~A~~Ai~l~g~  277 (303)
                      .-|.|.+.|+... ..+.+.|++|  |.|.. ....++              +. ....+..|+|.+..+|.+|+.-||.
T Consensus         8 ~~VtVFGFp~~~~-~~VI~~Fs~~--G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~   84 (132)
T 3p3d_A            8 LAILVFGYPETMA-NQVIAYFQEF--GTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGA   84 (132)
T ss_dssp             CEEEEECCCGGGH-HHHHHHHGGG--SCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTC
T ss_pred             eEEEEEecCHHHH-HHHHHHHHhh--ceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCe
Confidence            4577888877664 5688899998  99876 222110              00 1245889999999999999999999


Q ss_pred             eeCCeeeEEeecCC
Q 022058          278 VLGSQPIRVSPSKT  291 (303)
Q Consensus       278 ~~~g~~l~v~~a~~  291 (303)
                      .|.|..|-|.+..+
T Consensus        85 ii~G~mIGV~Py~~   98 (132)
T 3p3d_A           85 VFNGVLLGVIPYTK   98 (132)
T ss_dssp             EETTEECEEEECCH
T ss_pred             EeCcEEEEEEECCH
Confidence            99999999988753

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.81  E-value=0.0073  Score=43.77  Aligned_cols=65  Identities=9%  Similarity=0.207  Sum_probs=49.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---C-CcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---V-HSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      -+|.|+.||+++|++++.+.+++.  -.+.+......+   + ..-.-|+|.|.+.++...-.+ .+|+.+-
T Consensus        10 ~KvVIRrLPP~Ltee~F~~~l~~~--~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A           10 HMVVIRRLPPGLTKEQLEEQLRPL--PAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCEEEECCCSCSCHHHHTTTTSCC--SSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             eeEEEeCCCCCCCHHHHHHHhCCc--CccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            578999999999999988888776  555444443332   1 123469999999999988887 9999883

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}

Probab=95.77  E-value=0.012  Score=44.96  Aligned_cols=75  Identities=15%  Similarity=0.224  Sum_probs=54.5

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEE-EEeeC----------CC-----CCceEEEEEecCHHHHHHHHHhCCcc
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGD----------PH-----SVLRFAFVEFADEHGARAALNLGGTM  179 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~-~i~~~----------~~-----~~~G~~fV~f~~~~~A~~Ai~l~g~~  179 (303)
                      ...|.|-+.|++.+..- -+.|++||.|.+- ....+          ..     +....-.|+|.+..+|.+||..||..
T Consensus         7 e~~VtVFGFp~~~~~~V-I~~Fs~~G~IlE~~~~~~~~~~~~~~~~~~k~yP~f~g~NWikItYds~~~A~rAL~~NG~i   85 (132)
T 3p3d_A            7 ELAILVFGYPETMANQV-IAYFQEFGTILEDFEVLRKPQAMTVGLQDRQFVPIFSGNSWTKITYDNPASAVDALLENGAV   85 (132)
T ss_dssp             -CEEEEECCCGGGHHHH-HHHHGGGSCBCSCCGGGCCC-----------CCCCCEETTEEEEEBSSHHHHHHHHTTTTCE
T ss_pred             ceEEEEEecCHHHHHHH-HHHHHhhceEeeeccccccccccccccccccccCccCCCcEEEEEcCCHHHHHHHHHhCCeE
Confidence            45688888877766554 5578999999662 11110          00     02357899999999999999999999


Q ss_pred             cCCeeEEEeecC
Q 022058          180 LGYYPVRVLPSK  191 (303)
Q Consensus       180 ~~g~~i~v~~~~  191 (303)
                      +.|..|-|.+.+
T Consensus        86 i~G~mIGV~Py~   97 (132)
T 3p3d_A           86 FNGVLLGVIPYT   97 (132)
T ss_dssp             ETTEECEEEECC
T ss_pred             eCcEEEEEEECC
Confidence            999988888753

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=95.55  E-value=0.0078  Score=56.21  Aligned_cols=66  Identities=21%  Similarity=0.278  Sum_probs=48.4

Q ss_pred             cCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCccc
Q 022058          111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTML  180 (303)
Q Consensus       111 ~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~  180 (303)
                      |.....++|+|. .|..+++.+|.++|++||+|.++.+..+.+   -|+.|+|.+.+++..++..-+...
T Consensus        48 r~~qa~rsv~v~-~~~~~~~~~l~~y~~~~g~i~~~~~~~~~g---~~~~vef~~~~~~~~~~~~~~~p~  113 (464)
T 3pq1_A           48 RREQAQRTVLIH-CPEKISENKFLKYLSQFGPINNHFFYESFG---LYAVVEFCQKESIGSLQNGTHTPX  113 (464)
T ss_dssp             HHHHHHTEEEEE-ECCC---CHHHHHHGGGSCCCCEEEECSSS---EEEEEECC---CCHHHHSSCCCCC
T ss_pred             HHHHhcceEEEE-cCCCCCHHHHHHHHHhcCCcceEEEEccCC---eEEEEEeCCHHHHHHHHhccCCCc
Confidence            334457889998 799999999999999999999998876554   599999999999998876433333

>2l08_A Regulator of nonsense transcripts 3A; NESG, nonsense regulator, structural genomics, PSI-2, protei structure initiative; NMR {Homo sapiens}

Probab=95.32  E-value=0.019  Score=41.55  Aligned_cols=66  Identities=12%  Similarity=0.148  Sum_probs=48.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      +-.|.|+.||+.+||+++.+.++..-.+..........+    .-.-|||.|.+.++.....+ .+|..+.
T Consensus         9 ~~KvVIRrLPP~Ltee~F~~~l~~~~~~d~~~fv~G~~s~~~~~~SRAYI~F~~~edv~~F~~~f~g~~F~   79 (97)
T 2l08_A            9 SHMVVIRRLPPGLTKEQLEEQLRPLPAHDYFEFFAADLSLYPHLYSRAYINFRNPDDILLFRDRFDGYIFL   79 (97)
T ss_dssp             CCCEEEECCCSCSCHHHHTTTTSCCSSEEECCCCCCCSSSCCSCCCCCEEEESCHHHHHHHHHHSTTEEEE
T ss_pred             ceeEEEeCCCCCCCHHHHHHHhCCcCccceEEEeCCccCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            456999999999999999888876655433332221111    12459999999999999998 9987773

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}

Probab=94.86  E-value=0.012  Score=55.06  Aligned_cols=59  Identities=22%  Similarity=0.218  Sum_probs=45.7

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHh
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNC  274 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l  274 (303)
                      .+..++|+|. .|...++.+|.++|++|  |.|.++....+.|   -||.|+|.+.+++..++..
T Consensus        50 ~qa~rsv~v~-~~~~~~~~~l~~y~~~~--g~i~~~~~~~~~g---~~~~vef~~~~~~~~~~~~  108 (464)
T 3pq1_A           50 EQAQRTVLIH-CPEKISENKFLKYLSQF--GPINNHFFYESFG---LYAVVEFCQKESIGSLQNG  108 (464)
T ss_dssp             HHHHTEEEEE-ECCC---CHHHHHHGGG--SCCCCEEEECSSS---EEEEEECC---CCHHHHSS
T ss_pred             HHhcceEEEE-cCCCCCHHHHHHHHHhc--CCcceEEEEccCC---eEEEEEeCCHHHHHHHHhc
Confidence            4456899997 78899999999999999  9999999988776   5999999999998877653

>3d45_A Poly(A)-specific ribonuclease PARN; CAP analogue, exonuclease, hydrolase, magnesium, metal nonsense-mediated mRNA decay, nucleus; HET: 7MG GDP; 3.00A {Mus musculus}

Probab=85.14  E-value=3  Score=39.34  Aligned_cols=54  Identities=24%  Similarity=0.396  Sum_probs=44.2

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CS  275 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~  275 (303)
                      ...++|+ +|..+...+|.++|+.|  |. .+|..+.|.     .|||.|.+.+.|..+++ ++
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~f--g~-v~V~widdt-----~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAF--GN-IQISWIDDT-----SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGG--CC-CEEEECSSS-----EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhc--CC-EEEEEEcCC-----eEEEEECCHHHHHHHHHHHH
Confidence            3566666 99999999999999999  84 466666665     79999999999999997 64

>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=83.90  E-value=2.6  Score=39.70  Aligned_cols=54  Identities=22%  Similarity=0.309  Sum_probs=43.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LG  176 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~  176 (303)
                      ...++|+ +|..+...+|.++|+.||.+ +|+.+.+.     .|||.|.+.+.|..++. +.
T Consensus       440 ~~vl~v~-f~~~~~~~~i~~~fs~fg~v-~V~widdt-----~a~V~~~~~~~a~~~l~~~~  494 (507)
T 3d45_A          440 DHVLHVT-FPKEWKTSDLYQLFSAFGNI-QISWIDDT-----SAFVSLSQPEQVQIAVNTSK  494 (507)
T ss_dssp             GGEEEEE-CCTTCCHHHHHHHGGGGCCC-EEEECSSS-----EEEEECSCHHHHHHHHHHHT
T ss_pred             CcEEEEe-CCCCCCHHHHHHHHHhcCCE-EEEEEcCC-----eEEEEECCHHHHHHHHHHHH
Confidence            3456666 99999999999999999954 56655443     69999999999999998 64

---

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	303
d1u1qa_	183	d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1	2e-14
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-12
d1x4ba1	103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	7e-07
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-12
d2cq4a1	101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	5e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	7e-11
d1l3ka1	84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	1e-07
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-10
d2cqia1	90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	2e-07
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-10
d1x0fa1	75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	5e-06
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	2e-10
d1uawa_	77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-07
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-10
d1b7fa2	85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	3e-07
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	3e-10
d2cqda1	103	d.58.7.1 (A:1-103) RNA-binding region containing p	1e-07
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-10
d2f9da1	114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-06
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	4e-10
d1h2vz_	93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	6e-08
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	5e-10
d2cpha1	94	d.58.7.1 (A:454-547) Probable RNA-binding protein	3e-07
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	7e-10
d2cqba1	89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	6e-07
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	8e-10
d1cvja1	80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	9e-07
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1hd0a_	75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-06
d1wf2a_	98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d1u2fa_	90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-09
d1cvja2	89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	7e-06
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-09
d1x4ga1	96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	8e-06
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	1e-08
d2cpja1	86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	6e-04
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	2e-08
d1no8a_	78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	5e-05
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-08
d2cpfa1	85	d.58.7.1 (A:362-446) Probable RNA-binding protein	5e-05
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	2e-08
d2ghpa2	75	d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicin	6e-05
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	2e-08
d2msta_	75	d.58.7.1 (A:) Neural RNA-binding protein Musashi-1	1e-06
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-08
d1x5ua1	93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	2e-07
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	3e-08
d2cqca1	83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	1e-05
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	3e-08
d1l3ka2	79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	6e-05
d1weza_	102	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	4e-08
d2cq3a1	93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	3e-05
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	4e-08
d1wf0a_	88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	0.001
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	6e-08
d1zh5a2	85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	2e-06
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-08
d1b7fa1	82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	3e-05
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	9e-08
d2cqga1	90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	1e-05
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	1e-07
d1whwa_	99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	6e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	2e-07
d1fxla2	85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	5e-05
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	2e-07
d1x5ta1	83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	4e-05
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1wexa_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	9e-06
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	2e-07
d2cpda1	86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	1e-06
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	2e-07
d1wi8a_	104	d.58.7.1 (A:) Eukaryotic translation initiation fa	5e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-07
d1nu4a_	91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	1e-06
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	4e-07
d1fjca_	96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	1e-06
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-07
d1fxla1	82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	4e-05
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	7e-07
d2u2fa_	85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-06
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	8e-07
d2cq0a1	90	d.58.7.1 (A:231-320) Eukaryotic translation initia	3e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	1e-06
d1x4aa1	95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	6e-04
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	2e-06
d2ghpa3	86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-04
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_	104	d.58.7.3 (A:) 2e-06
d1wwha1	81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	3e-06
d2disa1	96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	2e-04
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	3e-06
d2adca2	88	d.58.7.1 (A:444-531) Polypyrimidine tract-binding	5e-05
d1wg5a_	104	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-06
d1rk8a_	88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	6e-06
d2cpya1	103	d.58.7.1 (A:536-638) RNA-binding protein 12 {Human	1e-04
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	9e-06
d1wela1	112	d.58.7.1 (A:412-523) RNA-binding protein 12 {Human	1e-04
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	1e-05
d1x5oa1	101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	7e-04
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	1e-05
d2cpza1	102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	9e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	1e-05
d1x4ha1	98	d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (	3e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	2e-05
d2cpea1	101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	0.003
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	2e-05
d1x4da1	89	d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [	6e-04
d2adba1	108	d.58.7.1 (A:177-284) Polypyrimidine tract-binding	2e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	2e-05
d1p1ta_	104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	3e-05
d2ghpa1	81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	0.002
d2bz2a1	79	d.58.7.1 (A:35-113) Negative elongation factor E,	6e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	8e-05
d2cqpa1	86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	1e-04
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	9e-05
d1whya_	97	d.58.7.1 (A:) Putative RNA-binding protein 15B, Rb	5e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	1e-04
d1u6fa1	139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	2e-04
d2cqha1	80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	1e-04
d2cq1a1	88	d.58.7.1 (A:51-138) Polypyrimidine tract-binding p	1e-04
d1wg1a_	88	d.58.7.1 (A:) Probable RNA-binding protein KIAA157	2e-04
d1weya_	104	d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus)	2e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	3e-04
d2cpxa1	102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	0.003
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-04
d1x5sa1	90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	3e-04
d2cq2a1	101	d.58.7.1 (A:25-125) Alkylation repair AlkB homolog	4e-04
d2cpia1	89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	8e-04
d1x4ea1	72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	0.003

>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 = 68.5 bits (166), Expect = 2e-14
 Identities = 31/183 (16%), Positives = 60/183 (32%), Gaps = 10/183 (5%)

Query: 111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHG 168
           +E    R +++  +    T+E L   F   G + DC V  DP++     F FV +A    
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 169 ARAALNLGGTMLGYYPVRVLPSKTAILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQA 228
             AA+N     +    V    + +                  +  + ++   I +   + 
Sbjct: 61  VDAAMNARPHKVDGRVVEPKRAVSRE--------DSQRPGAHLTVKKIFVGGIKEDTEEH 112

Query: 229 EVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP 288
            ++ +FE     EV  +            AFV F   +S    +      +      V  
Sbjct: 113 HLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRK 172

Query: 289 SKT 291
           + +
Sbjct: 173 ALS 175

>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 = 61.2 bits (148), Expect = 1e-12
 Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFAD 165
           R +RE    R +++  +    TEE L   +   G++ DC V  DP S     F FV F+ 
Sbjct: 12  RKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSS 71

Query: 166 EHGARAALNLGGTMLGYYPVRV 187
                AA+      +    V  
Sbjct: 72  MAEVDAAMAARPHSIDGRVVEP 93

>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 = 44.7 bits (105), Expect = 7e-07
 Identities = 11/89 (12%), Positives = 29/89 (32%), Gaps = 1/89 (1%)

Query: 202 LPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVE 261
           L R + E+E   R ++   +  +  +  ++ ++E         +        S    FV 
Sbjct: 10  LERKKREKEQ-FRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVT 68

Query: 262 FAVAESAILALNCSGMVLGSQPIRVSPSK 290
           F+       A+      +  + +    + 
Sbjct: 69  FSSMAEVDAAMAARPHSIDGRVVEPKRAV 97

>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 = 59.3 bits (143), Expect = 5e-12
 Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADE 166
              E+   RTV+   +   I    L   FS+ G+V D R+  D +S      A+VEF + 
Sbjct: 11  LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 70

Query: 167 HGARAALNLGGTMLGYYPVRVLPSK 191
                A+ L G  L   P+ V  S+
Sbjct: 71  QSVPLAIGLTGQRLLGVPIIVQASQ 95

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA binding protein 23
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 56.6 bits (136), Expect = 5e-11
 Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 3/102 (2%)

Query: 196 PVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHST 255
           PV       S +ER+  +RTV+C  +  ++   +++ FF A       R+    +   S 
Sbjct: 3   PVREPVDNLSPEERD--ARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSK 60

Query: 256 RIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKTPVRPRV 297
            IA+VEF   +S  LA+  +G  L   PI V  S+   + R+
Sbjct: 61  GIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ-AEKNRL 101

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.4 bits (133), Expect = 7e-11
 Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHG 168
           +E    R +++  +    T+E L   F   G + DC V  DP++     F FV +A    
Sbjct: 1   KEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEE 60

Query: 169 ARAALNLGGTMLGYYPVRV 187
             AA+N     +    V  
Sbjct: 61  VDAAMNARPHKVDGRVVEP 79

>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 = 46.6 bits (110), Expect = 1e-07
 Identities = 10/73 (13%), Positives = 23/73 (31%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
           R ++   +  +     ++  FE         +    +   S    FV +A  E    A+N
Sbjct: 7   RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66

Query: 274 CSGMVLGSQPIRV 286
                +  + +  
Sbjct: 67  ARPHKVDGRVVEP 79

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 2e-10
 Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 1/82 (1%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
           +D   RT+YV ++ +++TE  +  LFS  G    C++  +  S   + FVEF +   A A
Sbjct: 4   DDGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAA 63

Query: 172 ALN-LGGTMLGYYPVRVLPSKT 192
           AL  + G  +    V+V  + T
Sbjct: 64  ALAAMNGRKILGKEVKVNWATT 85

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 22/88 (25%), Positives = 41/88 (46%), Gaps = 5/88 (5%)

Query: 206 EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA 265
           ED+ +   RT+Y  N+ + V +  + Q F     G     +++ +H  +    FVEF   
Sbjct: 3   EDDGQ--PRTLYVGNLSRDVTEVLILQLFSQI--GPCKSCKMITEHTSNDPYCFVEFYEH 58

Query: 266 ESAILALN-CSGMVLGSQPIRVSPSKTP 292
             A  AL   +G  +  + ++V+ + TP
Sbjct: 59  RDAAAALAAMNGRKILGKEVKVNWATTP 86

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALNLG 176
           ++V  +  +  EE++   F   G+V    +  D  +     F F+ F +E   +  +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 177 GTMLGYYPVRV 187
              +G     +
Sbjct: 62  YHNVGLSKCEI 72

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein D0 (AUF1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.5 bits (97), Expect = 5e-06
 Identities = 8/71 (11%), Positives = 22/71 (30%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCS 275
           ++   +    P+ +++++F      E   L +           F+ F   E     +   
Sbjct: 2   IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKK 61

Query: 276 GMVLGSQPIRV 286
              +G     +
Sbjct: 62  YHNVGLSKCEI 72

>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 = 53.8 bits (129), Expect = 2e-10
 Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLG 176
           +++  +    T+E L   F   G+V +C V  DP +     F FV F D+ G    L   
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 177 GTMLGYYPVRV 187
              L    +  
Sbjct: 63  RHELDSKTIDP 73

>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 = 44.2 bits (104), Expect = 6e-07
 Identities = 11/72 (15%), Positives = 22/72 (30%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCS 275
           ++   +  +  Q  ++++F      +   +        S    FV F         L  S
Sbjct: 3   MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQS 62

Query: 276 GMVLGSQPIRVS 287
              L S+ I   
Sbjct: 63  RHELDSKTIDPK 74

>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 = 53.8 bits (129), Expect = 3e-10
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 5/81 (6%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGA 169
           E      +YV+++ + IT+++L  +F   G +V   +  D  +      AFV +     A
Sbjct: 2   ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 61

Query: 170 RAALN-LGGTML--GYYPVRV 187
           + A++ L   +   G  P+ V
Sbjct: 62  QEAISALNNVIPEGGSQPLSV 82

>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 = 18/78 (23%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAI 269
              +Y TN+ + +   ++   F          +           +AFV +     A+ AI
Sbjct: 6   DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 65

Query: 270 LALNCSGMVLGSQPIRVS 287
            ALN      GSQP+ V 
Sbjct: 66  SALNNVIPEGGSQPLSVR 83

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.4 bits (130), Expect = 3e-10
 Identities = 14/96 (14%), Positives = 33/96 (34%)

Query: 207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAE 266
            +++     ++   +      A ++++FE     E   +        S    FV  A   
Sbjct: 4   SQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRA 63

Query: 267 SAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPGM 302
           +A  A      ++  +   V+ +    +PR  + G 
Sbjct: 64  AAERACKDPNPIIDGRKANVNLAYLGAKPRSLQTGF 99

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (111), Expect = 1e-07
 Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 2/81 (2%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCG--DPHSVLRFAFVEFADE 166
             ++D+    ++V  +  + T+  L   F   G + +  V           + FV  AD 
Sbjct: 3   GSQKDTTFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADR 62

Query: 167 HGARAALNLGGTMLGYYPVRV 187
             A  A      ++      V
Sbjct: 63  AAAERACKDPNPIIDGRKANV 83

>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 = 54.6 bits (131), Expect = 3e-10
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NL 175
           R +Y+ ++   IT E +  +F   G +   RV   P      A+V + D   A+ A  +L
Sbjct: 8   RILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPE-TRGTAYVVYEDIFDAKNACDHL 66

Query: 176 GGTMLGYYPVRVLPSKT 192
            G  +    + VL    
Sbjct: 67  SGFNVCNRYLVVLYYNA 83

>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 = 42.7 bits (100), Expect = 5e-06
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 4/80 (5%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           +R +Y  N+  K+   E+   F         R+    +       A+V +     A  A 
Sbjct: 7   NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRG---TAYVVYEDIFDAKNAC 63

Query: 273 -NCSGMVLGSQPIRVSPSKT 291
            + SG  + ++ + V     
Sbjct: 64  DHLSGFNVCNRYLVVLYYNA 83

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 53.8 bits (129), Expect = 4e-10
 Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDP--HSVLRFAFVEFADEHGARAALN 174
            T+YV ++    TEE++  LFS  G +    +  D    +   F FVE+     A  A+ 
Sbjct: 8   CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 67

Query: 175 -LGGTMLGYYPVRV 187
            + GT L    +R 
Sbjct: 68  YINGTRLDDRIIRT 81

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CBP20, 20KDa nuclear cap-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.6 bits (113), Expect = 6e-08
 Identities = 16/85 (18%), Positives = 30/85 (35%), Gaps = 1/85 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           S T+Y  N+     + ++ + F  +   +   + L      +    FVE+     A  A+
Sbjct: 7   SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 66

Query: 273 N-CSGMVLGSQPIRVSPSKTPVRPR 296
              +G  L  + IR          R
Sbjct: 67  RYINGTRLDDRIIRTDWDAGFKEGR 91

>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 = 53.4 bits (128), Expect = 5e-10
 Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 5/76 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAAL 173
             + V +I     +  +  LFS+ G++   R+            F FV+F  +  A+ A 
Sbjct: 9   SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 68

Query: 174 N--LGGTMLGYYPVRV 187
           N     T L    + +
Sbjct: 69  NALCHSTHLYGRRLVL 84

>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 = 45.7 bits (108), Expect = 3e-07
 Identities = 18/93 (19%), Positives = 37/93 (39%), Gaps = 7/93 (7%)

Query: 209 REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTR---IAFVEFAVA 265
           ++  +  +   NI  +  Q E+++ F     GE+  +RL      +       FV+F   
Sbjct: 4   KKQTTSKILVRNIPFQANQREIRELFSTF--GELKTVRLPKKMTGTGAHRGFGFVDFITK 61

Query: 266 ESAILALN--CSGMVLGSQPIRVSPSKTPVRPR 296
           + A  A N  C    L  + + +  + + V  +
Sbjct: 62  QDAKKAFNALCHSTHLYGRRLVLEWADSEVTVQ 94

>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 = 52.7 bits (126), Expect = 7e-10
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 3/81 (3%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARA 171
           + +R +YV  + + + ++ L   F   G + D ++  D  +     FAFVEF     A A
Sbjct: 3   TTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAA 62

Query: 172 AL-NLGGTMLGYYPVRVLPSK 191
           A+ N+  + L    +RV  +K
Sbjct: 63  AIDNMNESELFGRTIRVNLAK 83

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.7 bits (105), Expect = 6e-07
 Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
            R +Y   + ++V    +   F         ++ L  +       AFVEF +AE A  A+
Sbjct: 5   KRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAI 64

Query: 273 -NCSGMVLGSQPIRVSPSKTPVRPR 296
            N +   L  + IRV+ +K P+R +
Sbjct: 65  DNMNESELFGRTIRVNLAK-PMRIK 88

>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 = 52.2 bits (125), Expect = 8e-10
 Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 3/77 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRV--CGDPHSVLRFAFVEFADEHGARAALN- 174
           ++YV D+  ++TE  L   FS  G ++  RV         L +A+V F     A  AL+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 175 LGGTMLGYYPVRVLPSK 191
           +   ++   PVR++ S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 43.8 bits (103), Expect = 9e-07
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN- 273
           ++Y  ++   V +A + + F  A      R+        S   A+V F     A  AL+ 
Sbjct: 2   SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 61

Query: 274 CSGMVLGSQPIRVSPSK 290
            +  V+  +P+R+  S+
Sbjct: 62  MNFDVIKGKPVRIMWSQ 78

>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 = 51.9 bits (124), Expect = 1e-09
 Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALNLG 176
           +++  +  + T++ L   FS  G+VVDC +  DP +     F FV F +       ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 177 GTMLGYYPVRV 187
              L    +  
Sbjct: 62  EHKLNGKVIDP 72

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 12/71 (16%), Positives = 24/71 (33%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCS 275
           ++   +     + ++K +F          L+L      S    FV F  +ES    ++  
Sbjct: 2   MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61

Query: 276 GMVLGSQPIRV 286
              L  + I  
Sbjct: 62  EHKLNGKVIDP 72

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoproteins C1/C2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.2 bits (125), Expect = 1e-09
 Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 8/82 (9%)

Query: 112 EDSVRRTVYVSDIDQNITEER-LAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGAR 170
             S+   V++ +++  + ++  +  +FS  G++V C V         FAFV++ +E  AR
Sbjct: 11  PRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKG------FAFVQYVNERNAR 64

Query: 171 AAL-NLGGTMLGYYPVRVLPSK 191
           AA+    G M+    + +  + 
Sbjct: 65  AAVAGEDGRMIAGQVLDINLAA 86

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor U2AF 65 KDa subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 51.3 bits (122), Expect = 2e-09
 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-------FAFVEFADEHGA 169
           R +YV +I   ITEE +   F++  ++           +         FAF+EF      
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET 61

Query: 170 RAALNLGGTMLGYYPVRV 187
             A+   G +     +++
Sbjct: 62  TQAMAFDGIIFQGQSLKI 79

>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 = 39.7 bits (92), Expect = 3e-05
 Identities = 18/94 (19%), Positives = 33/94 (35%), Gaps = 15/94 (15%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHV-------HSTRIAFVEFAVAE 266
           R +Y  NI   + +  +  FF A     +  L     +             AF+EF   +
Sbjct: 2   RRLYVGNIPFGITEEAMMDFFNAQ--MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVD 59

Query: 267 SAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRP 300
               A+   G++   Q +++       RP   +P
Sbjct: 60  ETTQAMAFDGIIFQGQSLKIR------RPHDYQP 87

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.8 bits (121), Expect = 4e-09
 Identities = 20/80 (25%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL 173
           S    +++ ++D++I  + L   FS+ G ++ C+V  D +    + FV F  +  A  A+
Sbjct: 6   SGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAI 65

Query: 174 -NLGGTMLGYYPVRVLPSKT 192
             + G +L    V V   K+
Sbjct: 66  EKMNGMLLNDRKVFVGRFKS 85

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.6 bits (97), Expect = 7e-06
 Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 3/84 (3%)

Query: 209 REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESA 268
           R+     ++  N+DK +    +   F     G +   +++ D   S    FV F   E+A
Sbjct: 4   RKSGVGNIFIKNLDKSIDNKALYDTFS--AFGNILSCKVVCDENGSKGYGFVHFETQEAA 61

Query: 269 ILAL-NCSGMVLGSQPIRVSPSKT 291
             A+   +GM+L  + + V   K+
Sbjct: 62  ERAIEKMNGMLLNDRKVFVGRFKS 85

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolysin TIAR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.0 bits (119), Expect = 8e-09
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NL 175
            TVY   I   +T++ +   FS  GQ+++ RV  +      ++FV F+    A  A+ ++
Sbjct: 19  CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPEKG----YSFVRFSTHESAAHAIVSV 74

Query: 176 GGTMLGYYPVRV 187
            GT +  + V+ 
Sbjct: 75  NGTTIEGHVVKC 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 = 41.5 bits (97), Expect = 8e-06
 Identities = 19/92 (20%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 207 DEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAE 266
           ++    + TVYC  I   +    ++Q F     G++  +R+  +  +S  + F     A 
Sbjct: 12  NQSSPKNCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPEKGYS-FVRFSTHESAA 68

Query: 267 SAILALNCSGMVLGSQPIRVSPSKTPVRPRVT 298
            AI+++N  G  +    ++    K    P +T
Sbjct: 69  HAIVSVN--GTTIEGHVVKCYWGKE--SPDMT 96

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 49.2 bits (117), Expect = 1e-08
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 5/79 (6%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
           ++  + R  ++V ++  +ITEE +  LF   G+  +  +  D      F F+       A
Sbjct: 2   EKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG----FGFIRLETRTLA 57

Query: 170 RAALN-LGGTMLGYYPVRV 187
             A   L    L    +RV
Sbjct: 58  EIAKVELDNMPLRGKQLRV 76

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Non-POU domain-containing octamer-binding protein, NonO
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.1 bits (83), Expect = 6e-04
 Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 5/80 (6%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              ++  N+   + + E+++ FE         +           I      +AE A + L
Sbjct: 8   RSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVEL 64

Query: 273 NCSGMVLGSQPIRVSPSKTP 292
           +   M L  + +RV  +   
Sbjct: 65  D--NMPLRGKQLRVRFACHS 82

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.8 bits (116), Expect = 2e-08
 Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVC-GDPHSVLRFAFVEFADEHGARAALN-LG 176
           + VS++D  +++  +  LF+  G +    V        L  A V F  +  A  A+    
Sbjct: 3   LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 62

Query: 177 GTMLGYYPVRV 187
           G  L   P+ +
Sbjct: 63  GVPLDGRPMNI 73

>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 = 38.8 bits (90), Expect = 5e-05
 Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C 274
           +  +N+D  V  A++++ F    G              S   A V F     A+ A+   
Sbjct: 3   LLVSNLDFGVSDADIQELFA-EFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 61

Query: 275 SGMVLGSQPIRVS 287
           +G+ L  +P+ + 
Sbjct: 62  NGVPLDGRPMNIQ 74

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 21/83 (25%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 120 YVSDIDQNITEERLAGLFSSCGQV-----VDCRVCGDPHSVLRFAFVEFADEHGARAALN 174
           ++ +++ + TEE L G+FS  G +        +        + F FVE+     A+ AL 
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 175 -LGGTMLGYYPVRVLPSKTAILP 196
            L G  +  + + V  S+ A  P
Sbjct: 62  QLQGHTVDGHKLEVRISERATKP 84

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 4/83 (4%)

Query: 217 YCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRI---AFVEFAVAESAILALN 273
           +  N++    +  +K  F      +   +    +           FVE+   E A  AL 
Sbjct: 2   FIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 61

Query: 274 -CSGMVLGSQPIRVSPSKTPVRP 295
              G  +    + V  S+   +P
Sbjct: 62  QLQGHTVDGHKLEVRISERATKP 84

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 48.3 bits (114), Expect = 2e-08
 Identities = 19/70 (27%), Positives = 33/70 (47%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGG 177
           TV V ++ ++  + ++   F  CG ++   V        RFA +EFA   GA AA+    
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTH 61

Query: 178 TMLGYYPVRV 187
            ++G   + V
Sbjct: 62  KVVGQNEIIV 71

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 75

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.3 bits (88), Expect = 6e-05
 Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNC 274
           TV   N+ K   Q +V ++F+      +  + +      + R A +EFA  + A+ A+  
Sbjct: 2   TVLVKNLPKSYNQNKVYKYFKHCG--PIIHVDVADSLKKNFRFARIEFARYDGALAAITK 59

Query: 275 SGMVLGSQPIRVS 287
           +  V+G   I VS
Sbjct: 60  THKVVGQNEIIVS 72

>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 = 48.2 bits (114), Expect = 2e-08
 Identities = 14/71 (19%), Positives = 22/71 (30%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCR--VCGDPHSVLRFAFVEFADEHGARAALNLG 176
           ++V  +  N T E +   F   G+V D         +    F FV F  E        + 
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 177 GTMLGYYPVRV 187
              +    V  
Sbjct: 62  FHEINNKMVEC 72

>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 = 43.2 bits (101), Expect = 1e-06
 Identities = 8/71 (11%), Positives = 19/71 (26%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCS 275
           ++   +       +VK +FE     +   L             FV F   +         
Sbjct: 2   IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61

Query: 276 GMVLGSQPIRV 286
              + ++ +  
Sbjct: 62  FHEINNKMVEC 72

>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 = 48.9 bits (116), Expect = 2e-08
 Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 3/79 (3%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGA 169
           E +   TVYV  +D+ ++E  L  LF   G VV+  +  D  +     + FVEF  E  A
Sbjct: 5   ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDA 64

Query: 170 RAAL-NLGGTMLGYYPVRV 187
             A+  +    L   P+RV
Sbjct: 65  DYAIKIMDMIKLYGKPIRV 83

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor 3B subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.2 bits (109), Expect = 2e-07
 Identities = 24/89 (26%), Positives = 37/89 (41%), Gaps = 4/89 (4%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
           P SE  ++    TVY   +D+KV +  + + F  A     T +             FVEF
Sbjct: 2   PISERNQD---ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEF 58

Query: 263 AVAESAILAL-NCSGMVLGSQPIRVSPSK 290
              E A  A+     + L  +PIRV+ + 
Sbjct: 59  LSEEDADYAIKIMDMIKLYGKPIRVNKAS 87

>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 = 48.2 bits (114), Expect = 3e-08
 Identities = 21/74 (28%), Positives = 29/74 (39%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAAL- 173
             + V  +    TE  L  +FS  G + D  +  D  S     FAFV F +   A+ A  
Sbjct: 10  CCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 69

Query: 174 NLGGTMLGYYPVRV 187
              G  L    +RV
Sbjct: 70  RANGMELDGRRIRV 83

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.8 bits (95), Expect = 1e-05
 Identities = 14/75 (18%), Positives = 26/75 (34%), Gaps = 1/75 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           +  +    +     + ++++ F          +        S   AFV F   + A  A 
Sbjct: 9   NCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAK 68

Query: 273 -NCSGMVLGSQPIRV 286
              +GM L  + IRV
Sbjct: 69  ERANGMELDGRRIRV 83

>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 = 47.8 bits (113), Expect = 3e-08
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN 174
           + ++V  I ++  E  L   F   G++    +  D  S     FAFV F D       + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 175 LGGTMLGYYPVRV 187
                +  +   V
Sbjct: 63  QKYHTVNGHNCEV 75

>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 = 38.5 bits (89), Expect = 6e-05
 Identities = 11/73 (15%), Positives = 23/73 (31%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
           + ++   I +   +  ++ +FE     EV  +            AFV F   +S    + 
Sbjct: 3   KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVI 62

Query: 274 CSGMVLGSQPIRV 286
                +      V
Sbjct: 63  QKYHTVNGHNCEV 75

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.2 bits (114), Expect = 4e-08
 Identities = 18/85 (21%), Positives = 31/85 (36%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHG 168
           +  + +    V++  +    TE  +   FS    +      G    V   A VEFA    
Sbjct: 8   SSFQSTTGHCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHED 67

Query: 169 ARAALNLGGTMLGYYPVRVLPSKTA 193
           A AA+      + +  V +  + TA
Sbjct: 68  AVAAMAKDKANMQHRYVELFLNSTA 92

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 4e-08
 Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
             S  + ++VS+I     +  L  +F   G+++D  +  +      F FV F +   A  
Sbjct: 7   SKSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADR 66

Query: 172 ALN-LGGTMLGYYPVRVLPSK 191
           A   L GT++    + V  + 
Sbjct: 67  AREKLHGTVVEGRKIEVNNAT 87

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 9
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 15/84 (17%), Positives = 35/84 (41%), Gaps = 3/84 (3%)

Query: 208 EREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAES 267
           E +   + ++ +NI  +    +++Q F      ++  + ++ +   S    FV F  +  
Sbjct: 6   ESKSTPKRLHVSNIPFRFRDPDLRQMFGQFG--KILDVEIIFNERGSKGFGFVTFENSAD 63

Query: 268 AILALN-CSGMVLGSQPIRVSPSK 290
           A  A     G V+  + I V+ + 
Sbjct: 64  ADRAREKLHGTVVEGRKIEVNNAT 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 = 47.7 bits (113), Expect = 4e-08
 Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 4/75 (5%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLG 176
             V+V     ++TE+ L   FS  G V+D  +     +   FAFV FAD+  A++     
Sbjct: 6   SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRA---FAFVTFADDQIAQSLCGED 62

Query: 177 GTMLGYYPVRVLPSK 191
             + G   V +  ++
Sbjct: 63  LIIKG-ISVHISNAE 76

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.4 bits (81), Expect = 0.001
 Identities = 16/89 (17%), Positives = 33/89 (37%), Gaps = 7/89 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           S  V+       + + E+++FF     G+V  +            AFV FA  + A    
Sbjct: 5   SSGVFVGRCTGDMTEDELREFFS--QYGDVMDVF---IPKPFRAFAFVTFADDQIAQSLC 59

Query: 273 NCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
               +++    + +S ++ P     + P 
Sbjct: 60  G-EDLIIKGISVHISNAE-PKHNSNSGPS 86

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (112), Expect = 6e-08
 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 111 REDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV-LRFAFVEFADEHGA 169
           + D   R+VY+     + T + +       GQV++ ++    H       FV F     A
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESA 60

Query: 170 RAALNLGGTMLGYYPVRVLPSK 191
           +  +   G       + +L   
Sbjct: 61  KKFVETPGQKYKETDLLILFKD 82

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 14/83 (16%), Positives = 28/83 (33%), Gaps = 1/83 (1%)

Query: 208 EREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAES 267
           + ++ +R+VY           ++K++ E        ++R    H       FV F   ES
Sbjct: 1   KNDVKNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRR-TLHKAFKGSIFVVFDSIES 59

Query: 268 AILALNCSGMVLGSQPIRVSPSK 290
           A   +   G       + +    
Sbjct: 60  AKKFVETPGQKYKETDLLILFKD 82

>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 = 46.9 bits (111), Expect = 7e-08
 Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 3/77 (3%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCR--VCGDPHSVLRFAFVEFADEHGARAALN- 174
            + V+ + Q++T+  L  LF + G +  CR            +AFV+F  E  ++ A+  
Sbjct: 4   NLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 63

Query: 175 LGGTMLGYYPVRVLPSK 191
           L G  +    ++V  ++
Sbjct: 64  LNGITVRNKRLKVSYAR 80

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

 Score = 39.6 bits (92), Expect = 3e-05
 Identities = 13/79 (16%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           +  +    + + +   E+   F A       R+       +S   AFV+F     +  A+
Sbjct: 2   NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAI 61

Query: 273 NC-SGMVLGSQPIRVSPSK 290
              +G+ + ++ ++VS ++
Sbjct: 62  KVLNGITVRNKRLKVSYAR 80

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: TAR DNA-binding protein 43, TDP-43
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.9 bits (111), Expect = 9e-08
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 3/80 (3%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEH 167
           +R       + V  +    TE+ L   FS+ G+V+  +V  D  +     F FV F +  
Sbjct: 2   KRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 61

Query: 168 GARAALNLGGTMLGYYPVRV 187
                ++    M+       
Sbjct: 62  TQVKVMS-QRHMIDGRWCDC 80

>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 = 40.7 bits (95), Expect = 1e-05
 Identities = 11/78 (14%), Positives = 29/78 (37%), Gaps = 1/78 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           +  +    +  K  + ++K++F       + +++      HS    FV F   E+ +  +
Sbjct: 8   TSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 67

Query: 273 NCSGMVLGSQPIRVSPSK 290
           +   M+ G +        
Sbjct: 68  SQRHMIDG-RWCDCKLPN 84

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.0 bits (111), Expect = 1e-07
 Identities = 17/90 (18%), Positives = 30/90 (33%), Gaps = 1/90 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           S  ++  N+     + ++++ F A          +          AFV F   E A+ A 
Sbjct: 8   SGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAY 67

Query: 273 N-CSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
               G V   + + V PS        + P 
Sbjct: 68  AEVDGQVFQGRMLHVLPSTIKKEASQSGPS 97

>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 = 44.7 bits (105), Expect = 6e-07
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 3/79 (3%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN 174
             ++V ++    +EE L  LFS+ G + +     D  +     FAFV F     A  A  
Sbjct: 9   GRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYA 68

Query: 175 -LGGTMLGYYPVRVLPSKT 192
            + G +     + VLPS  
Sbjct: 69  EVDGQVFQGRMLHVLPSTI 87

>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 = 46.2 bits (109), Expect = 2e-07
 Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 6/80 (7%)

Query: 114 SVR-RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGAR 170
           S+R   +YVS + + +T++ L  LFS  G+++  R+  D  +       F+ F     A 
Sbjct: 3   SIRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAE 62

Query: 171 AAL-NLGGTMLG--YYPVRV 187
            A+  L G        P+ V
Sbjct: 63  EAIKGLNGQKPSGATEPITV 82

>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 = 38.9 bits (90), Expect = 5e-05
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 3/77 (3%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFA---VAESAIL 270
             +Y + + K + Q E++Q F        +R+ +      S  + F+ F     AE AI 
Sbjct: 7   ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 66

Query: 271 ALNCSGMVLGSQPIRVS 287
            LN       ++PI V 
Sbjct: 67  GLNGQKPSGATEPITVK 83

>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 = 45.9 bits (108), Expect = 2e-07
 Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 4/73 (5%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARAAL-N 174
           +++ ++D  I E+ L   FS+ G ++                +AF+ FA    + AA+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 175 LGGTMLGYYPVRV 187
           + G  L   P+ V
Sbjct: 61  MNGQYLCNRPITV 73

>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 = 39.3 bits (91), Expect = 4e-05
 Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 2/77 (2%)

Query: 216 VYCTNIDKKVPQAEVKQFFEAA-CGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL-N 273
           ++  N+D ++ +  +   F A     +  ++    D  +S   AF+ FA  +++  A+  
Sbjct: 1   IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEA 60

Query: 274 CSGMVLGSQPIRVSPSK 290
            +G  L ++PI VS + 
Sbjct: 61  MNGQYLCNRPITVSYAF 77

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 13/85 (15%), Positives = 24/85 (28%), Gaps = 7/85 (8%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA 169
             + SV   V+V  + +++ E  L       G +    +          A VEF +   A
Sbjct: 9   HHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKR----QALVEFENIDSA 64

Query: 170 RAA---LNLGGTMLGYYPVRVLPSK 191
           +            +         S 
Sbjct: 65  KECVTFAADVPVYIAGQQAFFNYST 89

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.7 bits (97), Expect = 9e-06
 Identities = 14/97 (14%), Positives = 30/97 (30%), Gaps = 6/97 (6%)

Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV 264
               +   S  V+   + + V +A++ +  E         +           + F     
Sbjct: 7   GSHHKVSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMM---PFKRQALVEFENIDS 63

Query: 265 AESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           A+  +       + +  Q    + S      R+TRPG
Sbjct: 64  AKECVTFAADVPVYIAGQQAFFNYST---SKRITRPG 97

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.8 bits (108), Expect = 2e-07
 Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
           + +YV ++  + +EE +   F++       RV      +  +AFV F++   A  A+  L
Sbjct: 9   KILYVRNLMLSTSEEMIEKEFNNIKPGAVERV----KKIRDYAFVHFSNREDAVEAMKAL 64

Query: 176 GGTMLGYYPVRVLPSK 191
            G +L   P+ V  +K
Sbjct: 65  NGKVLDGSPIEVTLAK 80

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: APOBEC1 stimulating protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 6/89 (6%)

Query: 207 DEREMC-SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA 265
           DE  M   + +Y  N+     +  +++ F     G V R++ + D+       F     A
Sbjct: 1   DEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVH---FSNREDA 57

Query: 266 ESAILALNCSGMVLGSQPIRVSPSKTPVR 294
             A+ ALN  G VL   PI V+ +K   +
Sbjct: 58  VEAMKALN--GKVLDGSPIEVTLAKPVDK 84

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 2e-07
 Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL--RFAFVEFADE 166
           ++   S   T ++ ++  ++TEE +   F               +      F + EF D 
Sbjct: 8   SRLPKSPPYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDL 67

Query: 167 HGARAALNLGGTMLGYYPVRV 187
               +AL+L    LG   +RV
Sbjct: 68  DSLLSALSLNEESLGNKRIRV 88

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 4B
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (107), Expect = 5e-07
 Identities = 18/84 (21%), Positives = 32/84 (38%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
             T +  N+   V +  +K+FF       V   R   +        + EF   +S + AL
Sbjct: 15  PYTAFLGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSAL 74

Query: 273 NCSGMVLGSQPIRVSPSKTPVRPR 296
           + +   LG++ IRV  +       
Sbjct: 75  SLNEESLGNKRIRVDVADQAQDKD 98

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (107), Expect = 3e-07
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 6/81 (7%)

Query: 117 RTVYVSDIDQNITEERL----AGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAA 172
            T+Y++++++ I ++ L      +FS  GQ++D  V          AFV F +   A  A
Sbjct: 4   HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM-RGQAFVIFKEVSSATNA 62

Query: 173 LN-LGGTMLGYYPVRVLPSKT 192
           L  + G      P+R+  +KT
Sbjct: 63  LRSMQGFPFYDKPMRIQYAKT 83

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 16/84 (19%), Positives = 36/84 (42%), Gaps = 6/84 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQ----FFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESA 268
           + T+Y  N+++K+ + E+K+     F          +           + F E + A +A
Sbjct: 3   NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNA 62

Query: 269 ILALNCSGMVLGSQPIRVSPSKTP 292
           + ++   G     +P+R+  +KT 
Sbjct: 63  LRSMQ--GFPFYDKPMRIQYAKTD 84

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 45.4 bits (107), Expect = 4e-07
 Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 4/72 (5%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
           RT+   ++  NITE+ L  +F    ++      G        A++EF  E  A   L   
Sbjct: 17  RTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKG---IAYIEFKSEADAEKNLEEK 73

Query: 176 GGTMLGYYPVRV 187
            G  +    V +
Sbjct: 74  QGAEIDGRSVSL 85

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

 Score = 44.3 bits (104), Expect = 1e-06
 Identities = 19/97 (19%), Positives = 36/97 (37%), Gaps = 10/97 (10%)

Query: 205 SEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAV 264
           S+  R   +RT+   N+   + + E+K+ FE A   E+  +   G       I F   A 
Sbjct: 10  SKKVRA--ARTLLAKNLSFNITEDELKEVFEDAL--EIRLVSQDGKSKGIAYIEFKSEAD 65

Query: 265 AESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           AE  +      G  +  + + +  +      +    G
Sbjct: 66  AEKNLEEKQ--GAEIDGRSVSLYYTG----EKGGTRG 96

>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 = 45.1 bits (106), Expect = 4e-07
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 3/79 (3%)

Query: 116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAAL 173
           +  + V+ + QN+T+E    LF S G++  C++  D  +   L + FV + D   A  A+
Sbjct: 2   KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61

Query: 174 -NLGGTMLGYYPVRVLPSK 191
             L G  L    ++V  ++
Sbjct: 62  NTLNGLRLQTKTIKVSYAR 80

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.3 bits (91), Expect = 4e-05
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 213 SRT-VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA 271
           S+T +    + + + Q E +  F +    E  +L        S    FV +   + A  A
Sbjct: 1   SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60

Query: 272 L-NCSGMVLGSQPIRVSPSK 290
           +   +G+ L ++ I+VS ++
Sbjct: 61  INTLNGLRLQTKTIKVSYAR 80

>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 = 44.2 bits (104), Expect = 7e-07
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVL--RFAFVEFADEHGARAALN 174
             +++  +   + ++++  L +S G +    +  D  + L   +AF E+ D +    A+ 
Sbjct: 2   HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61

Query: 175 -LGGTMLGYYPVRV 187
            L G  LG   + V
Sbjct: 62  GLNGMQLGDKKLLV 75

>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 = 42.7 bits (100), Expect = 2e-06
 Identities = 13/79 (16%), Positives = 28/79 (35%), Gaps = 1/79 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           +  ++   +   +   +VK+   +    +   L        S   AF E+        A+
Sbjct: 1   AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 60

Query: 273 N-CSGMVLGSQPIRVSPSK 290
              +GM LG + + V  + 
Sbjct: 61  AGLNGMQLGDKKLLVQRAS 79

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 44.3 bits (104), Expect = 8e-07
 Identities = 18/85 (21%), Positives = 33/85 (38%), Gaps = 3/85 (3%)

Query: 110 QREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEH 167
            R      T+ V+++ ++  E  L  LF   G +    +  D  +     FAF+ F    
Sbjct: 2   NRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRRE 61

Query: 168 GARAALN-LGGTMLGYYPVRVLPSK 191
            A  A+  + G    +  + V  +K
Sbjct: 62  DAARAIAGVSGFGYDHLILNVEWAK 86

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Eukaryotic translation initiation factor 3 subunit 4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.7 bits (100), Expect = 3e-06
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 1/79 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           + T+  TN+ +   + ++++ F          L        S   AF+ F   E A  A+
Sbjct: 8   NATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 67

Query: 273 N-CSGMVLGSQPIRVSPSK 290
              SG       + V  +K
Sbjct: 68  AGVSGFGYDHLILNVEWAK 86

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 22/90 (24%), Positives = 36/90 (40%), Gaps = 3/90 (3%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVE 162
            G   R    ++  R +YV ++  +I  + +  +F   G + D  +         FAFVE
Sbjct: 2   GGGVIRGPAGNNDCR-IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRG-GPPFAFVE 59

Query: 163 FADEHGARAALN-LGGTMLGYYPVRVLPSK 191
           F D   A  A+    G     Y +RV   +
Sbjct: 60  FEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 89

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 11/80 (13%), Positives = 25/80 (31%), Gaps = 2/80 (2%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              +Y  N+   +   +++  F          L+          + F +   AE A+   
Sbjct: 14  DCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGR 73

Query: 273 NCSGMVLGSQPIRVSPSKTP 292
           +  G       +RV   ++ 
Sbjct: 74  D--GYDYDGYRLRVEFPRSG 91

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 43.2 bits (101), Expect = 2e-06
 Identities = 14/80 (17%), Positives = 29/80 (36%), Gaps = 4/80 (5%)

Query: 116 RRTVYVSDIDQNIT-EERLAGLFSSCGQVVDCRVCGDPHSVLR---FAFVEFADEHGARA 171
            R + + ++   +  E  L   F   G +    +             AF+ F ++  A  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 172 ALNLGGTMLGYYPVRVLPSK 191
           AL +  ++LG   + V  + 
Sbjct: 64  ALQMNRSLLGNREISVSLAD 83

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 213 SRTVYCTNIDKKVPQAEVKQ--FFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAIL 270
            R +   N+  ++    + +  F       ++       +H  +   AF+ F   +SA  
Sbjct: 4   GREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAER 63

Query: 271 ALNCSGMVLGSQPIRVSPSK 290
           AL  +  +LG++ I VS + 
Sbjct: 64  ALQMNRSLLGNREISVSLAD 83

>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 = 43.9 bits (103), Expect = 2e-06
 Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 2/71 (2%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR-FAFVEFADEHGARAALN-LG 176
           V + +      EE    +    G+V +  VC +    L    +V+F  E  A  A+  L 
Sbjct: 30  VEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLN 89

Query: 177 GTMLGYYPVRV 187
                  P+  
Sbjct: 90  NRWFNGQPIHA 100

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleoporin 35
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 13/74 (17%), Positives = 25/74 (33%), Gaps = 6/74 (8%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGG 177
            V V    Q      L   F+  G ++   +    +    +  + +  +  AR AL+  G
Sbjct: 6   WVTVFGFPQASASYILL-QFAQYGNILKHVMSNTGN----WMHIRYQSKLQARKALSKDG 60

Query: 178 TML-GYYPVRVLPS 190
            +      + V P 
Sbjct: 61  RIFGESIMIGVKPC 74

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.1 bits (101), Expect = 3e-06
 Identities = 15/77 (19%), Positives = 25/77 (32%), Gaps = 7/77 (9%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCG----QVVDCRVCGDPHSVLRFAFVEFADEHGARAA- 172
            +++  I +    E +    +        V+      D      FAFVE+     A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 173 --LNLGGTMLGYYPVRV 187
             L  G   L  + + V
Sbjct: 63  RKLMPGRIQLWGHQIAV 79

>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 = 37.7 bits (87), Expect = 2e-04
 Identities = 16/86 (18%), Positives = 28/86 (32%), Gaps = 5/86 (5%)

Query: 215 TVYCTNIDKKVPQAEVKQFFEAACGGE--VTRLRLLGDHVHSTRIAFVEFA---VAESAI 269
            ++   I K   + E+ +       G   V       D + +   AFVE+     A  A 
Sbjct: 3   RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 62

Query: 270 LALNCSGMVLGSQPIRVSPSKTPVRP 295
             L    + L    I V  ++  +  
Sbjct: 63  RKLMPGRIQLWGHQIAVDWAEPEIDV 88

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.8 bits (100), Expect = 3e-06
 Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 4/80 (5%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNL- 175
            T+++S+I  +++EE L  LFSS G VV            + A ++      A  AL   
Sbjct: 11  ATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDR--KMALIQMGSVEEAVQALIDL 68

Query: 176 -GGTMLGYYPVRVLPSKTAI 194
               +   + +RV  SK+ I
Sbjct: 69  HNHDLGENHHLRVSFSKSTI 88

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.0 bits (90), Expect = 5e-05
 Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           S T++ +NI   V + ++K  F +  G                ++A ++    E A+ AL
Sbjct: 10  SATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKF----FQKDRKMALIQMGSVEEAVQAL 65

Query: 273 NCS--GMVLGSQPIRVSPSKTPV 293
                  +  +  +RVS SK+ +
Sbjct: 66  IDLHNHDLGENHHLRVSFSKSTI 88

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein H'
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.9 bits (100), Expect = 4e-06
 Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 2/84 (2%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGA 169
           + +    V +  +    ++E +   FS    V +               AFV+FA +  A
Sbjct: 11  DTANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIA 70

Query: 170 RAALNLGGTMLGYYPVRVLPSKTA 193
             AL      +G+  + +  S  A
Sbjct: 71  EKALKKHKERIGHRYIEIFKSSRA 94

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 42.4 bits (99), Expect = 4e-06
 Identities = 15/74 (20%), Positives = 31/74 (41%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAAL- 173
             ++V+ I +   E+ +   F   G++ +  +  D  +     +A VE+     A AA  
Sbjct: 8   WILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 67

Query: 174 NLGGTMLGYYPVRV 187
            L G  +    ++V
Sbjct: 68  ALNGAEIMGQTIQV 81

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 8
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 1/85 (1%)

Query: 208 EREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAES 267
           +R +    ++ T+I ++  + E+++ F      +   L L      S   A VE+   + 
Sbjct: 2   QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 61

Query: 268 AILAL-NCSGMVLGSQPIRVSPSKT 291
           A+ A    +G  +  Q I+V     
Sbjct: 62  ALAAKEALNGAEIMGQTIQVDWCFV 86

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.1 bits (98), Expect = 6e-06
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 2/82 (2%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGA 169
            +S +   ++++I  +IT+  +           +       ++      A V+F +E  A
Sbjct: 4   VNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDA 63

Query: 170 RAALNLGGTMLGYYPVRVLPSK 191
           R +  L    L      V    
Sbjct: 64  RKSERLHRKKLNGREAFVHVVT 85

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.7 bits (89), Expect = 1e-04
 Identities = 16/96 (16%), Positives = 30/96 (31%)

Query: 206 EDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA 265
           E +        + TNI   + + +V QF E     E     L+ ++      A V+F   
Sbjct: 1   EGDVNSAKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNE 60

Query: 266 ESAILALNCSGMVLGSQPIRVSPSKTPVRPRVTRPG 301
           + A  +       L  +   V          + +  
Sbjct: 61  DDARKSERLHRKKLNGREAFVHVVTLEDMREIEKNP 96

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.8 bits (97), Expect = 9e-06
 Identities = 17/91 (18%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 103 SGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAF 160
             +  R++        VY+  +      + +   F     V D        +       F
Sbjct: 5   GQKRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGF 64

Query: 161 VEFADEHGARAALNLGGTMLGYYPVRVLPSK 191
           VEF +E   +AAL      +G   ++V P  
Sbjct: 65  VEFRNEADYKAALCRHKQYMGNRFIQVHPIT 95

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]} Length = 112

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.3 bits (88), Expect = 1e-04
 Identities = 21/88 (23%), Positives = 31/88 (35%), Gaps = 1/88 (1%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
            RS    E     VY   +  +     V  FF+     E +     G +  +T   FVEF
Sbjct: 9   SRSRSPHEA-GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEF 67

Query: 263 AVAESAILALNCSGMVLGSQPIRVSPSK 290
                   AL      +G++ I+V P  
Sbjct: 68  RNEADYKAALCRHKQYMGNRFIQVHPIT 95

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 15/85 (17%), Positives = 33/85 (38%), Gaps = 2/85 (2%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV-LRFAFVEFADEH 167
           A++++     +Y+S++  ++ E+ L  +    GQV+  R+  D         F       
Sbjct: 11  AKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTE 70

Query: 168 GARAALN-LGGTMLGYYPVRVLPSK 191
              A +    G  +   P    P++
Sbjct: 71  KCEAVIGHFNGKFIKTPPGVSAPTE 95

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 1, RBMS1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.3 bits (83), Expect = 7e-04
 Identities = 13/95 (13%), Positives = 33/95 (34%), Gaps = 5/95 (5%)

Query: 204 RSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF- 262
           +   ++E     +Y +N+   + + E++   +       TR+                  
Sbjct: 9   QMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMES 68

Query: 263 -AVAESAILALNCSGMVLGSQPIRVSPSKTPVRPR 296
               E+ I   N  G  + + P   +P++ P+  +
Sbjct: 69  TEKCEAVIGHFN--GKFIKTPPGVSAPTE-PLLCK 100

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 41.2 bits (96), Expect = 1e-05
 Identities = 19/86 (22%), Positives = 40/86 (46%), Gaps = 3/86 (3%)

Query: 109 AQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADE 166
           +Q+E      +++  + Q   ++ L  +F   G VV  +V  D  +     F FV + + 
Sbjct: 11  SQKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNP 70

Query: 167 HGARAAL-NLGGTMLGYYPVRVLPSK 191
             A+AA+ ++ G  +G   ++V   +
Sbjct: 71  VSAQAAIQSMNGFQIGMKRLKVQLKR 96

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: CUG triplet repeat RNA-binding protein 1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.9 bits (90), Expect = 9e-05
 Identities = 11/79 (13%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              ++  ++ ++    ++ Q F         ++ +      S    FV +    SA  A+
Sbjct: 18  GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 77

Query: 273 -NCSGMVLGSQPIRVSPSK 290
            + +G  +G + ++V   +
Sbjct: 78  QSMNGFQIGMKRLKVQLKR 96

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 41.0 bits (95), Expect = 1e-05
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 9/85 (10%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN 174
           +TV++ ++  +  EE L  +    G +   RV   P +      AF +F  +  A+  L 
Sbjct: 9   KTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLA 68

Query: 175 -------LGGTMLGYYPVRVLPSKT 192
                   GG  L    ++V  + T
Sbjct: 69  AASLEAEGGGLKLDGRQLKVDLAVT 93

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]} Length = 98

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 28
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.2 bits (93), Expect = 3e-05
 Identities = 21/97 (21%), Positives = 37/97 (38%), Gaps = 11/97 (11%)

Query: 202 LPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVE 261
           LP    E     +TV+  N+     +  + +  +     +  R+ L  D  HS   AF +
Sbjct: 1   LPSDVTE----GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQ 56

Query: 262 FAVAESAILALN-------CSGMVLGSQPIRVSPSKT 291
           F   E+A   L          G+ L  + ++V  + T
Sbjct: 57  FMTQEAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVT 93

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein EWS
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.9 bits (95), Expect = 2e-05
 Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 11/92 (11%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV----------LRFAFV 161
           EDS    +YV  ++ ++T + LA  F  CG V   +  G P                A V
Sbjct: 4   EDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATV 63

Query: 162 EFADEHGARAALN-LGGTMLGYYPVRVLPSKT 192
            + D   A+AA+    G       ++V  ++ 
Sbjct: 64  SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARK 95

>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 = 34.4 bits (78), Expect = 0.003
 Identities = 12/92 (13%), Positives = 32/92 (34%), Gaps = 17/92 (18%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-------------HVHSTRIAF 259
           +  +Y   ++  V   ++  FF+    G V   +  G                    +++
Sbjct: 8   NSAIYVQGLNDSVTLDDLADFFKQC--GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 65

Query: 260 VEFAVAESAILALNCSGMVLGSQPIRVSPSKT 291
            +   A++A+   +  G       ++VS ++ 
Sbjct: 66  EDPPTAKAAVEWFD--GKDFQGSKLKVSLARK 95

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 40.1 bits (93), Expect = 2e-05
 Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 10/89 (11%)

Query: 108 RAQREDSVRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADE 166
           + + E    R V++ D         +L  L    G + +  +    +     AF+E A  
Sbjct: 2   KGRVETR--RVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKIN----EAFIEMATT 55

Query: 167 HGARAALN---LGGTMLGYYPVRVLPSKT 192
             A+AA++       ++   PVRV  S+ 
Sbjct: 56  EDAQAAVDYYTTTPALVFGKPVRVHLSQK 84

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 14/85 (16%), Positives = 36/85 (42%), Gaps = 4/85 (4%)

Query: 213 SRTVYCTNIDK-KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILA 271
            R V+  +  + K  + ++ Q  E    G ++   +  + ++   I       A++A+  
Sbjct: 8   RRVVHIMDFQRGKNLRYQLLQLVEPF--GVISNHLI-LNKINEAFIEMATTEDAQAAVDY 64

Query: 272 LNCSGMVLGSQPIRVSPSKTPVRPR 296
              +  ++  +P+RV  S+   R +
Sbjct: 65  YTTTPALVFGKPVRVHLSQKYKRIK 89

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 108

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.4 bits (94), Expect = 2e-05
 Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 6/83 (7%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARA 171
           +  V R + V ++   +T + L  +FS  G V+        +     A +++AD   A+ 
Sbjct: 4   QSPVLR-IIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQ--FQALLQYADPVSAQH 60

Query: 172 ALN-LGGTMLGYY--PVRVLPSK 191
           A   L G  +      +R+  SK
Sbjct: 61  AKLSLDGQNIYNACCTLRIDFSK 83

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 40.5 bits (94), Expect = 2e-05
 Identities = 17/89 (19%), Positives = 34/89 (38%), Gaps = 1/89 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
            R+V+  NI  +  + ++K  F         RL    +        F E+   E+A+ A+
Sbjct: 8   LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67

Query: 273 -NCSGMVLGSQPIRVSPSKTPVRPRVTRP 300
            N +G     + +RV  + +       + 
Sbjct: 68  RNLNGREFSGRALRVDNAASEKNKEELKS 96

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.4 bits (91), Expect = 5e-05
 Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 3/84 (3%)

Query: 112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRF--AFVEFADEHGA 169
            D   R+V+V +I    TEE+L  +FS  G VV  R+  D  +       F E+ D+  A
Sbjct: 4   VDRSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETA 63

Query: 170 RAAL-NLGGTMLGYYPVRVLPSKT 192
            +A+ NL G       +RV  + +
Sbjct: 64  LSAMRNLNGREFSGRALRVDNAAS 87

>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 = 39.8 bits (92), Expect = 3e-05
 Identities = 13/78 (16%), Positives = 28/78 (35%), Gaps = 3/78 (3%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSV--LRFAFVEFADEHGARAALN 174
            T+++++   + T+  +  L      V               RFA+++   +  AR  + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 175 -LGGTMLGYYPVRVLPSK 191
            L G  +  Y +    S 
Sbjct: 62  KLNGLKIEGYTLVTKVSN 79

>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 = 34.8 bits (79), Expect = 0.002
 Identities = 11/78 (14%), Positives = 26/78 (33%), Gaps = 1/78 (1%)

Query: 214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN 273
            T++ TN      Q  ++   +      ++          S R A+++    E A   + 
Sbjct: 2   CTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVE 61

Query: 274 C-SGMVLGSQPIRVSPSK 290
             +G+ +    +    S 
Sbjct: 62  KLNGLKIEGYTLVTKVSN 79

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Negative elongation factor E, NELF-E
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 6e-05
 Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 7/76 (9%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
            T+YV   D  +T   L G FS  G ++D  +          AFV +     A  A+  L
Sbjct: 6   NTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPPR----NCAFVTYEKMESADQAVAEL 59

Query: 176 GGTMLGYYPVRVLPSK 191
            GT +    ++V  ++
Sbjct: 60  NGTQVESVQLKVNIAR 75

>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 = 38.5 bits (89), Expect = 8e-05
 Identities = 13/76 (17%), Positives = 27/76 (35%), Gaps = 1/76 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              +   N+   V   E+  FF        +      +    T  A V F   + A  A+
Sbjct: 9   PTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAV 68

Query: 273 -NCSGMVLGSQPIRVS 287
            + +   +GS+ +++ 
Sbjct: 69  IDLNDRPIGSRKVKLV 84

>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 = 38.1 bits (88), Expect = 1e-04
 Identities = 9/74 (12%), Positives = 24/74 (32%), Gaps = 3/74 (4%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFAD-EHGARAAL 173
             + V ++   ++ + +   F     +            +    A V F   +    A +
Sbjct: 10  TIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVI 69

Query: 174 NLGGTMLGYYPVRV 187
           +L    +G   V++
Sbjct: 70  DLNDRPIGSRKVKL 83

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 38.5 bits (89), Expect = 9e-05
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 7/79 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
             ++V  +  N +   LA  F   G +              FA++++     A+AA   +
Sbjct: 18  TRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDS----FAYIQYESLDAAQAACAKM 73

Query: 176 GGTMLGYY--PVRVLPSKT 192
            G  LG     +RV  +K+
Sbjct: 74  RGFPLGGPDRRLRVDFAKS 92

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]} Length = 97

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 36.6 bits (84), Expect = 5e-04
 Identities = 8/83 (9%), Positives = 25/83 (30%), Gaps = 3/83 (3%)

Query: 209 REMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESA 268
           +   +  ++   +      A + + F+                     I +     A++A
Sbjct: 13  KANPTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHV---KGDSFAYIQYESLDAAQAA 69

Query: 269 ILALNCSGMVLGSQPIRVSPSKT 291
              +    +    + +RV  +K+
Sbjct: 70  CAKMRGFPLGGPDRRLRVDFAKS 92

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 39.5 bits (91), Expect = 1e-04
 Identities = 18/88 (20%), Positives = 34/88 (38%), Gaps = 3/88 (3%)

Query: 108 RAQREDSVRRTVYVSDIDQNITEERLAGLFS--SCGQVVDCRVCGDPHSVLRFAFVEFAD 165
           +   E  V R + V+ I   + E +L  LF      + V      +      + FV+F  
Sbjct: 34  QMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQS 93

Query: 166 EHGARAAL-NLGGTMLGYYPVRVLPSKT 192
              A+ A+  L G  +    ++V  + +
Sbjct: 94  GSSAQQAIAGLNGFNILNKRLKVALAAS 121

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein UBP1
species: Trypanosoma cruzi [TaxId: 5693]

 Score = 38.7 bits (89), Expect = 2e-04
 Identities = 20/101 (19%), Positives = 40/101 (39%), Gaps = 5/101 (4%)

Query: 203 PRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEF 262
           P   +      R +    I   V + +++Q FE     E  ++    +   S    FV+F
Sbjct: 32  PTQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKF 91

Query: 263 AVAESAILAL-NCSGMVLGSQPIRVSPSKTPVRPRVTRPGM 302
               SA  A+   +G  + ++ ++V+ +         RPG+
Sbjct: 92  QSGSSAQQAIAGLNGFNILNKRLKVALAA----SGHQRPGI 128

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 1e-04
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 6/76 (7%)

Query: 118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNL-- 175
            +Y+ ++   +T + L  LF      +  +V         +AFV++ D++ A  A+    
Sbjct: 3   KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSG----YAFVDYPDQNWAIRAIETLS 58

Query: 176 GGTMLGYYPVRVLPSK 191
           G   L    + V  S 
Sbjct: 59  GKVELHGKIMEVDYSV 74

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.9 bits (87), Expect = 1e-04
 Identities = 11/78 (14%), Positives = 24/78 (30%), Gaps = 3/78 (3%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           SR ++   +  +V + EV              +       +   +       A + +   
Sbjct: 8   SRVLHIRKLPGEVTETEVIALGLPFGKVTNILML---KGKNQAFLELATEEAAITMVNYY 64

Query: 273 NCSGMVLGSQPIRVSPSK 290
           +     L +QPI +  S 
Sbjct: 65  SAVTPHLRNQPIYIQYSN 82

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]} Length = 88

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.4 bits (86), Expect = 2e-04
 Identities = 12/86 (13%), Positives = 25/86 (29%), Gaps = 7/86 (8%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAAL-NL 175
             + V ++ Q+   + +  L                 +     FV   +   A+ A+   
Sbjct: 6   SGILVKNLPQDSNCQEVHDLLKDYDLKYCYVDRNKRTA-----FVTLLNGEQAQNAIQMF 60

Query: 176 GGTMLGYYPVRVLPSKT-AILPVNPT 200
                    + V    T A+L   P+
Sbjct: 61  HQYSFRGKDLIVQLQPTDALLCSGPS 86

>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 = 37.5 bits (86), Expect = 2e-04
 Identities = 10/86 (11%), Positives = 26/86 (30%), Gaps = 10/86 (11%)

Query: 113 DSVRRTVYVSDIDQNITEER-----LAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEH 167
            S    +     + ++  E         LF +  +    +         +   + F++  
Sbjct: 2   SSGSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFKS----FKRVRINFSNPL 57

Query: 168 GARAAL-NLGGTMLGYYPVRVLPSKT 192
            A  A   L  T      +++  ++T
Sbjct: 58  SAADARLRLHKTEFLGKEMKLYFAQT 83

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.5 bits (86), Expect = 3e-04
 Identities = 11/79 (13%), Positives = 25/79 (31%), Gaps = 3/79 (3%)

Query: 117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFAD---EHGARAAL 173
           + +Y+ ++   +TE  L  LF+   +     +     +              E   +A  
Sbjct: 19  KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 78

Query: 174 NLGGTMLGYYPVRVLPSKT 192
            + G  L    + +   K 
Sbjct: 79  LVNGYKLYGKILVIEFGKN 97

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.4 bits (78), Expect = 0.003
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 1/80 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
           ++ +Y  N+  +V + ++   F      +   ++           AF+ F   E A  AL
Sbjct: 18  NKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQAL 77

Query: 273 NC-SGMVLGSQPIRVSPSKT 291
           +  +G  L  + + +   K 
Sbjct: 78  HLVNGYKLYGKILVIEFGKN 97

>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 = 37.0 bits (85), Expect = 3e-04
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLR--FAFVEFADEHGARA 171
           S    ++V  +  +  E+ L  +FS  GQ+ +  V  D  +     F FV F +   A+ 
Sbjct: 3   SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 62

Query: 172 AL-NLGGTMLGYYPVRV 187
           A+  + G  +    +RV
Sbjct: 63  AMMAMNGKSVDGRQIRV 79

>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 = 36.6 bits (84), Expect = 3e-04
 Identities = 13/85 (15%), Positives = 27/85 (31%), Gaps = 1/85 (1%)

Query: 213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILAL 272
              ++   +     +  ++Q F          +    +   S    FV F   + A  A+
Sbjct: 5   EGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 64

Query: 273 -NCSGMVLGSQPIRVSPSKTPVRPR 296
              +G  +  + IRV  +      R
Sbjct: 65  MAMNGKSVDGRQIRVDQAGKSSDNR 89

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]} Length = 101

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.0 bits (85), Expect = 4e-04
 Identities = 8/76 (10%), Positives = 21/76 (27%), Gaps = 4/76 (5%)

Query: 99  RKRLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRF 158
              L           +    V    +   ++  +L  +   CG V    +  +      +
Sbjct: 3   HTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP----Y 58

Query: 159 AFVEFADEHGARAALN 174
           +F  +     ++ A  
Sbjct: 59  SFARYRTTEESKRAYV 74

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 35.6 bits (81), Expect = 8e-04
 Identities = 7/81 (8%), Positives = 21/81 (25%), Gaps = 9/81 (11%)

Query: 116 RRTVYVSDIDQNITEERLAGLF---SSCGQVVDCRVCGDPHSVLRFAFVEFADEHGA--- 169
           +  V+V  + Q + +  +          G++    +               A        
Sbjct: 8   KNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSE 67

Query: 170 ---RAALNLGGTMLGYYPVRV 187
              RA   +   ++    ++ 
Sbjct: 68  DALRAIQCVNNVVVDGRTLKA 88

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.6 bits (76), Expect = 0.003
 Identities = 12/66 (18%), Positives = 27/66 (40%), Gaps = 3/66 (4%)

Query: 119 VYVSDIDQNITEERLAGLFSSCGQVVD--CRVCGDPHSVLRFAFVEFADEHGARAALN-L 175
           +Y+  +    T++ L  L    G++V     +    +    + FV+F     A+ A+  L
Sbjct: 1   LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTAL 60

Query: 176 GGTMLG 181
             + + 
Sbjct: 61  KASGVQ 66

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	303
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	100.0
d1u1qa_	183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.96
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.83
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.83
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.83
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.83
d2cqia1	90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.82
d1b7fa1	82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.82
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.82
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.82
d1fxla1	82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.82
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.82
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.81
d1h2vz_	93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.81
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.81
d1rk8a_	88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.81
d2cq0a1	90	Eukaryotic translation initiation factor 3 subunit	99.81
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.81
d2cq3a1	93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.81
d1cvja1	80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.81
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.8
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.8
d1cvja2	89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.8
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.8
d2cqba1	89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.8
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.8
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.8
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.8
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.8
d1no8a_	78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.79
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.79
d2cpza1	102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.79
d1x5ua1	93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d1whwa_	99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.79
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.79
d2cpha1	94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.79
d2cqda1	103	RNA-binding region containing protein 1 {Human (Ho	99.79
d2ghpa1	81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d2u2fa_	85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.79
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.79
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.79
d1x5sa1	90	Cold-inducible RNA-binding protein {Human (Homo sa	99.79
d1l3ka1	84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.78
d2cpfa1	85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.78
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d1u6fa1	139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.78
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.78
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.77
d1fxla2	85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.77
d2ghpa3	86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.77
d1x4ba1	103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.77
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.77
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.77
d2cqca1	83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.77
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.77
d1b7fa2	85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.77
d2cq4a1	101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.77
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.77
d1uawa_	77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.77
d1x5ta1	83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.76
d1hd0a_	75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.76
d2cqga1	90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.76
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.76
d1l3ka2	79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.76
d1p1ta_	104	Cleavage stimulation factor, 64 kda subunit {Human	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.75
d1x0fa1	75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.75
d1x4ga1	96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.75
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.75
d1zh5a2	85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.75
d2ghpa2	75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.75
d1fjeb1	91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.74
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.74
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.74
d2f9da1	114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.74
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.74
d1x5oa1	101	RNA-binding motif, single-stranded-interacting pro	99.74
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.73
d2msta_	75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.73
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.73
d1x4ha1	98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.73
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.73
d1x4aa1	95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.73
d2b0ga1	83	Splicesomal U1A protein {Drosophila melanogaster [	99.73
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.73
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.72
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.72
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.72
d2adca2	88	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1wi8a_	104	Eukaryotic translation initiation factor 4B {Human	99.72
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.72
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.72
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d2cpea1	101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.72
d1weza_	102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.72
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.71
d2adca1	109	Polypyrimidine tract-binding protein {Human (Homo	99.71
d2disa1	96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.71
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.71
d2cpja1	86	Non-POU domain-containing octamer-binding protein,	99.71
d1wf2a_	98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.71
d2cpda1	86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.71
d2cpxa1	102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.71
d1whxa_	111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.7
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.7
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.7
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.7
d2bz2a1	79	Negative elongation factor E, NELF-E {Human (Homo	99.69
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.69
d1fjca_	96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.69
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.69
d2cpia1	89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.69
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.69
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.68
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.68
d2cqha1	80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.68
d2cqpa1	86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.68
d3begb1	87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.68
d1wf0a_	88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.68
d1nu4a_	91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.68
d1x4ea1	72	RNA-binding motif, single-stranded-interacting pro	99.68
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.68
d1wg5a_	104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.67
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.67
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.67
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.67
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.66
d2adba1	108	Polypyrimidine tract-binding protein {Human (Homo	99.66
d1whya_	97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.65
d2cq1a1	88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.65
d1wg1a_	88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.65
d1wi6a1	75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.65
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.64
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.64
d2cpya1	103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.64
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.63
d1wg4a_	98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.62
d1wexa_	104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.62
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.62
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.61
d1x4da1	89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.6
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.6
d1x4fa1	99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.59
d1wela1	112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.59
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.58
d1u2fa_	90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.57
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	99.54
d1weya_	104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.53
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	99.52
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.44
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.43
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.41
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.4
d2cq2a1	101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.39
d1owxa_	113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.39
d2dita1	99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.38
d1wwha1	81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.35
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.33
d1o0pa_	104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.31
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.68
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	97.67
d1ufwa_	95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	97.3
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.17
d1uw4a_	91	RNA processing protein UPF3x, RRM domain {Human (H	97.14
d2dgxa1	73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.98
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	95.4
d1whva_	100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	94.32

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear ribonucleoprotein A1 (RNP A1, UP1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.4e-32  Score=226.25  Aligned_cols=167  Identities=18%  Similarity=0.292  Sum_probs=146.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++|+++|+++|++||.|.++.++.+..+  ++|||||+|.+.++|.+|+.+++..+.++.+.+.+...
T Consensus         5 ~~r~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f~~~~~a~~a~~~~~~~~~~~~~~~~~~~~   84 (183)
T d1u1qa_           5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVS   84 (183)
T ss_dssp             HHHEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceecccCCHHHHHHHHHhcCCcccccchhhhhhhh
Confidence            3478999999999999999999999999999999998765  78999999999999999999888888999988887533


Q ss_pred             CCCCCCCCCCCCcccccccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHH
Q 022058          193 AILPVNPTFLPRSEDEREMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAIL  270 (303)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~  270 (303)
                      ...        ..........++|||+|||..+++++|+++|+.|  |.|..+.|+.|.  |.++|||||+|.+.++|.+
T Consensus        85 ~~~--------~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~--G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~~  154 (183)
T d1u1qa_          85 RED--------SQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK  154 (183)
T ss_dssp             TTG--------GGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESCHHHHHH
T ss_pred             ccc--------ccccccccccceeEEccCCCcCCHHHHhhhhccC--CceeeeeeecccccCccceeEEEEECCHHHHHH
Confidence            211        1111123345899999999999999999999999  999999999875  6899999999999999999


Q ss_pred             HHHhCCceeCCeeeEEeecCC
Q 022058          271 ALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       271 Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      |+.+++..+.|+.|+|.+|.|
T Consensus       155 Al~~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         155 IVIQKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             HHTSSCEEETTEEEEEEECCC
T ss_pred             HHHhCCCeECCEEEEEEecCC
Confidence            999899999999999999875

>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=99.96  E-value=5.5e-29  Score=205.78  Aligned_cols=155  Identities=17%  Similarity=0.145  Sum_probs=129.1

Q ss_pred             CCcccccchhhhHHHHHHHHhccCCcceeeeccCCCCCCCc---eeeeecchhhhhhchhhhccccchHHhhhhccc---
Q 022058           24 NLETKKSESEFTVQKLVDMFTKLNPLAKEFFPSYYHQHTDH---HFSVINNNFADDNKQSAIDNFNNNRRRRNNFNQ---   97 (303)
Q Consensus        24 ~~~~~nl~~~~t~~~L~~~F~~~G~v~~v~i~~~~~~~~~~---~v~f~~~~~~~~~~~~~~~~~~~A~~a~~~~~~---   97 (303)
                      +|||+|||+++|+++|+++|++||+|.++.++.+..++.++   ||+|     .+     .+    +|.+|+...+.   
T Consensus         8 ~lfV~nLp~~~te~~L~~~F~~~G~v~~~~~~~~~~~~~~~g~afv~f-----~~-----~~----~a~~a~~~~~~~~~   73 (183)
T d1u1qa_           8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTY-----AT-----VE----EVDAAMNARPHKVD   73 (183)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEE-----SS-----HH----HHHHHHHTCSCEET
T ss_pred             EEEEECCCCCCCHHHHHHHHHHcCCEEEEEeeecccCCCccCceeccc-----CC-----HH----HHHHHHHhcCCccc
Confidence            79999999999999999999999999999999988766655   9999     77     77    78888776654   


Q ss_pred             CCC-----CCCchhhhhccCCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHH
Q 022058           98 GRK-----RLSGRAFRAQREDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGAR  170 (303)
Q Consensus        98 g~~-----~~~~~~~~~~~~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~  170 (303)
                      ++.     ................++|||+|||+.+|+++|+++|+.||.|..+.++.+..+  ++|||||+|.+.++|.
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~V~~lp~~~te~~L~~~f~~~G~v~~~~i~~~~~~~~~~g~~fV~f~~~e~A~  153 (183)
T d1u1qa_          74 GRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVD  153 (183)
T ss_dssp             TEECEEEECCCTTGGGSTTTTCCCSEEEEECCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESCHHHHH
T ss_pred             ccchhhhhhhhcccccccccccccceeEEccCCCcCCHHHHhhhhccCCceeeeeeecccccCccceeEEEEECCHHHHH
Confidence            111     111111112223346789999999999999999999999999999999998764  7899999999999999


Q ss_pred             HHHHhCCcccCCeeEEEeecCC
Q 022058          171 AALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       171 ~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      +|+++++..+.|++|.|.++.+
T Consensus       154 ~Al~~~~~~~~G~~i~V~~A~~  175 (183)
T d1u1qa_         154 KIVIQKYHTVNGHNCEVRKALS  175 (183)
T ss_dssp             HHHTSSCEEETTEEEEEEECCC
T ss_pred             HHHHhCCCeECCEEEEEEecCC
Confidence            9999888999999999999743

>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=99.83  E-value=3.3e-20  Score=134.91  Aligned_cols=82  Identities=24%  Similarity=0.407  Sum_probs=76.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+|||..+++++|+++|++|  |.|.+|.|+++....+|||||+|.+.++|.+|+. |||..+.|+.|+|.||+
T Consensus         7 ~~~tl~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           7 QPRTLYVGNLSRDVTEVLILQLFSQI--GPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHHH--SCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhc--CCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            45799999999999999999999999  9999999999987778999999999999999998 99999999999999998


Q ss_pred             CCCCC
Q 022058          291 TPVRP  295 (303)
Q Consensus       291 ~~~~~  295 (303)
                      ++...
T Consensus        85 ~~~~~   89 (90)
T d2cqia1          85 TPSSQ   89 (90)
T ss_dssp             CTTCC
T ss_pred             CCCCC
Confidence            76543

>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=99.83  E-value=3.4e-20  Score=138.31  Aligned_cols=88  Identities=17%  Similarity=0.302  Sum_probs=81.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|.|++|+  |.++|||||+|.+.++|.+|++ +|+ .|.|+.|.|.+
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~   85 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGF--GDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNL   85 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTT--SCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEE
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhc--ccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEE
Confidence            44789999999999999999999999  999999999985  7899999999999999999999 765 79999999999


Q ss_pred             cCCCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRPGM  302 (303)
Q Consensus       289 a~~~~~~r~~r~~~  302 (303)
                      +.+..+||..|+|.
T Consensus        86 a~~~~~pr~~~~g~   99 (103)
T d2cqda1          86 AYLGAKPRSLQTGF   99 (103)
T ss_dssp             STTTCCCCCCCCCC
T ss_pred             cCCCCCCCCCCCCC
Confidence            99988888888774

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.83  E-value=1.2e-20  Score=134.91  Aligned_cols=77  Identities=25%  Similarity=0.477  Sum_probs=72.6

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      +++|||+|||+++++++|+++|++||.|.++++++++.+  ++|||||+|.+.++|++|++ |||..+.|++|+|.|+++
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a~p   81 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYARP   81 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            578999999999999999999999999999999997664  79999999999999999998 999999999999999864

>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=99.83  E-value=2.1e-20  Score=133.51  Aligned_cols=77  Identities=29%  Similarity=0.529  Sum_probs=72.2

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      +++|||+|||+++++++|+++|+.||.|.+|+++++..+  ++|||||+|.+.++|++|+. |||..+.|++|.|.|+++
T Consensus         2 ~t~l~V~nLp~~~te~~l~~~f~~~G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~AkP   81 (82)
T d1fxla1           2 KTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYARP   81 (82)
T ss_dssp             CSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHhCCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEeeC
Confidence            467999999999999999999999999999999987654  78999999999999999998 999999999999999864

>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=99.82  E-value=3.4e-20  Score=134.86  Aligned_cols=81  Identities=31%  Similarity=0.452  Sum_probs=75.8

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ....++|||+|||+++|+++|+++|+.||+|.+|.++.+..+.+|||||+|.+.++|.+|+. +||..+.|++|+|.|+.
T Consensus         5 ~~~~~tl~V~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~g~~i~v~~a~   84 (90)
T d2cqia1           5 DGQPRTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNGRKILGKEVKVNWAT   84 (90)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHHHHHSCEEEEEEECCCCSSCCEEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHhcCCceeeeeecccCccceeeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            34578999999999999999999999999999999999988889999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ++
T Consensus        85 ~~   86 (90)
T d2cqia1          85 TP   86 (90)
T ss_dssp             CT
T ss_pred             CC
Confidence            43

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Sex-lethal protein
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.82  E-value=1.8e-20  Score=133.97  Aligned_cols=77  Identities=19%  Similarity=0.351  Sum_probs=72.9

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .++|||+|||+.+++++|+++|++|  |.|.++.|.+++  |.++|||||+|.+.++|.+|++ |||..+.|+.|+|.||
T Consensus         2 ~t~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~~~~g~~~g~afV~f~~~~~A~~ai~~lng~~~~g~~l~v~~a   79 (82)
T d1b7fa1           2 NTNLIVNYLPQDMTDRELYALFRAI--GPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRLKVSYA   79 (82)
T ss_dssp             CSEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCEETTTTEECSEEEEEESSHHHHHHHHHHHTTCEETTEECEEEEC
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh--CCcceeeeeeecccCCccccceEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            3689999999999999999999999  999999999874  7899999999999999999998 9999999999999999


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      +|
T Consensus        80 ~p   81 (82)
T d1b7fa1          80 RP   81 (82)
T ss_dssp             CC
T ss_pred             CC
Confidence            86

>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=99.82  E-value=6.9e-20  Score=134.03  Aligned_cols=81  Identities=22%  Similarity=0.339  Sum_probs=76.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ....++|||+|||+++++++|+++|+.||+|.+|.++.+..+++|||||+|.+.++|.+|+. ||+..+.|+.|.|.+++
T Consensus         8 ~~~~~~l~v~nLp~~~t~~~L~~~F~~~G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1           8 KSTPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             SCCCCEEEEESCCTTCCHHHHHHHGGGTSCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHhhcceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            34577899999999999999999999999999999999988899999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        88 ~r   89 (93)
T d2cq3a1          88 AR   89 (93)
T ss_dssp             SS
T ss_pred             cC
Confidence            54

>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=99.82  E-value=6.2e-20  Score=135.88  Aligned_cols=88  Identities=23%  Similarity=0.371  Sum_probs=79.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ...+|||+|||+.+++++|+++|++|  |.|.+|.|++|+  ++++|||||+|.+.++|.+|++ |||..|+|+.|+|.+
T Consensus         7 ~~~~lfV~nL~~~~t~~~l~~~F~~~--g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~   84 (99)
T d1whwa_           7 GSGRLFVRNLSYTSSEEDLEKLFSAY--GPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLP   84 (99)
T ss_dssp             SCEEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHhc--CCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34789999999999999999999999  999999999885  7899999999999999999998 999999999999999


Q ss_pred             cCCCCCCCCCCCC
Q 022058          289 SKTPVRPRVTRPG  301 (303)
Q Consensus       289 a~~~~~~r~~r~~  301 (303)
                      +++........|+
T Consensus        85 a~~~~~~~~~gps   97 (99)
T d1whwa_          85 STIKKEASQSGPS   97 (99)
T ss_dssp             CCCCSTTCCCCCC
T ss_pred             CCCCCccCCCCCC
Confidence            9987655555444

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=4.7e-20  Score=131.70  Aligned_cols=77  Identities=23%  Similarity=0.408  Sum_probs=72.9

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ++|||+|||..+++++|+++|++|  |.|.+|+|+++.  +.++|||||+|.+.++|.+|++ |||..++|+.|+|.||+
T Consensus         3 t~l~V~nLp~~~te~~l~~~f~~~--G~v~~v~i~~~~~~~~~~g~afv~f~~~~~a~~a~~~l~g~~~~g~~l~v~~Ak   80 (82)
T d1fxla1           3 TNLIVNYLPQNMTQEEFRSLFGSI--GEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTIKVSYAR   80 (82)
T ss_dssp             SEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHh--CCcccccceeeccCCCceeeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            579999999999999999999999  999999999874  6899999999999999999998 99999999999999998


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      |.
T Consensus        81 Ps   82 (82)
T d1fxla1          81 PS   82 (82)
T ss_dssp             CC
T ss_pred             Cc
Confidence            63

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.82  E-value=3.2e-20  Score=131.94  Aligned_cols=74  Identities=32%  Similarity=0.559  Sum_probs=70.8

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +|||+|||+++|+++|+++|+.||+|.+++|++++.+  ++|||||+|.+.++|..|++ |||..+.|++|+|.|++
T Consensus         2 slfV~nL~~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~aFV~f~~~~~a~~ai~~l~g~~~~gr~i~v~~a~   78 (80)
T d1cvja1           2 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHhCCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            6999999999999999999999999999999998775  78999999999999999998 99999999999999985

>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=99.81  E-value=2e-20  Score=135.75  Aligned_cols=79  Identities=27%  Similarity=0.385  Sum_probs=74.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||+|.+|.++.|+.+  ++|||||+|.+.++|.+|+. +||..++|++|.|.+++
T Consensus         4 ~~~tlfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a~   83 (89)
T d2cqba1           4 TKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK   83 (89)
T ss_dssp             CCSCEEEESCCSSCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCcEEEEeCCCCcCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            4689999999999999999999999999999999998764  89999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        84 p~   85 (89)
T d2cqba1          84 PM   85 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.81  E-value=4.8e-20  Score=133.44  Aligned_cols=79  Identities=23%  Similarity=0.283  Sum_probs=73.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ...+|||+|||..+++++|+++|++|  |.|.+|+|++|+  |.++|||||+|.+.++|.+|+. |||..+.|+.|+|+|
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~--G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~   83 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDY--GEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDW   83 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc--CCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45899999999999999999999999  999999999875  7899999999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      |.+.
T Consensus        84 a~~k   87 (88)
T d1rk8a_          84 CFVK   87 (88)
T ss_dssp             SEEC
T ss_pred             ecCC
Confidence            9753

>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=99.81  E-value=3.6e-20  Score=134.73  Aligned_cols=79  Identities=22%  Similarity=0.307  Sum_probs=74.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|++ |||..+.|+.|.|.|+
T Consensus         6 ~~~~~i~V~nLp~~~t~~~l~~~f~~~G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~a   85 (90)
T d2cq0a1           6 DDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWA   85 (90)
T ss_dssp             SSSEEEEEESCCTTCCHHHHHTTSTTTCCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHhcccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEee
Confidence            35678999999999999999999999999999999998764  79999999999999999998 9999999999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ++
T Consensus        86 kp   87 (90)
T d2cq0a1          86 KP   87 (90)
T ss_dssp             SC
T ss_pred             eC
Confidence            64

>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=99.81  E-value=9.8e-20  Score=133.17  Aligned_cols=83  Identities=20%  Similarity=0.269  Sum_probs=76.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      .+++|||+|||..+|+++|+++|++|  |.|.+|.|++++  +.++|||||+|.+.++|..|++ |||..++|+.|+|.|
T Consensus         6 ~s~tlfV~nlp~~~te~~l~~~F~~~--G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~   83 (93)
T d1h2vz_           6 KSCTLYVGNLSFYTTEEQIYELFSKS--GDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDW   83 (93)
T ss_dssp             TCCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHH--CCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            45799999999999999999999999  999999999885  6789999999999999999998 999999999999999


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      +.....+|
T Consensus        84 a~~~~~gr   91 (93)
T d1h2vz_          84 DAGFKEGR   91 (93)
T ss_dssp             ESCCCTTC
T ss_pred             cCCCCCCC
Confidence            97654443

>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=99.81  E-value=7.9e-20  Score=133.68  Aligned_cols=79  Identities=27%  Similarity=0.325  Sum_probs=74.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..+++|||+|||+++|+++|+++|+.||+|.+|.++.++.+  ++|||||+|.+.++|..|++ |||..+.|++|.|.|+
T Consensus         5 ~~s~tlfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V~~a   84 (93)
T d1h2vz_           5 KKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWD   84 (93)
T ss_dssp             TTCCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHTTTSEETTEECEEEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHHHCCcceeccccccccccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEc
Confidence            35789999999999999999999999999999999998765  78999999999999999998 9999999999999997


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ..
T Consensus        85 ~~   86 (93)
T d1h2vz_          85 AG   86 (93)
T ss_dssp             SC
T ss_pred             CC
Confidence            53

>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=99.81  E-value=4.7e-20  Score=132.27  Aligned_cols=80  Identities=25%  Similarity=0.372  Sum_probs=73.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      ++...++|||+|||+++|+++|+++|+.||.|.++.|+.|+.+  ++|||||+|.+.++|++|++++++.|.|+.|.|..
T Consensus         2 epe~~~~lfV~nlp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~   81 (84)
T d1l3ka1           2 EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKR   81 (84)
T ss_dssp             CCGGGGEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEE
T ss_pred             CCCCCcEEEEECCCCCCCHHHHHHHHHhhccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEe
Confidence            3445688999999999999999999999999999999998774  79999999999999999999999999999999987


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      +.
T Consensus        82 A~   83 (84)
T d1l3ka1          82 AV   83 (84)
T ss_dssp             CC
T ss_pred             ee
Confidence            63

>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=99.81  E-value=5.6e-20  Score=133.12  Aligned_cols=78  Identities=19%  Similarity=0.259  Sum_probs=72.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||+|.+|++++|+.+  ++|||||+|.+.++|++|+. |||..+.|++|.|.|+.
T Consensus         6 ~~~~l~V~nL~~~~t~~~l~~~F~~~G~i~~v~i~~d~~tg~~~g~afV~f~~~~~A~~A~~~lng~~l~g~~l~V~~a~   85 (88)
T d1rk8a_           6 EGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCF   85 (88)
T ss_dssp             -CEEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTSSEEEEEEEEESSHHHHHHHHHHHTTCEETTEECEEEESE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCcccccccccccccccccceeEEECCHHHHHHHHHHcCCCEECCEEEEEEEec
Confidence            5678999999999999999999999999999999998764  79999999999999999998 99999999999999985


Q ss_pred             C
Q 022058          192 T  192 (303)
Q Consensus       192 ~  192 (303)
                      +
T Consensus        86 ~   86 (88)
T d1rk8a_          86 V   86 (88)
T ss_dssp             E
T ss_pred             C
Confidence            4

>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=99.81  E-value=5.7e-20  Score=133.65  Aligned_cols=79  Identities=24%  Similarity=0.368  Sum_probs=74.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +..+|||+|||..+++++|+++|++|  |.|.++.|++|.  |.++|||||+|.+.++|.+|++ |||..++|+.|+|.|
T Consensus         7 ~~~~i~V~nLp~~~t~~~l~~~f~~~--G~v~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~v~~   84 (90)
T d2cq0a1           7 DNATIRVTNLSEDTRETDLQELFRPF--GSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEW   84 (90)
T ss_dssp             SSEEEEEESCCTTCCHHHHHTTSTTT--CCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHh--cccccccccccccccccccceeEEECCHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            44789999999999999999999999  999999999885  7899999999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      |+|.
T Consensus        85 akp~   88 (90)
T d2cq0a1          85 AKPS   88 (90)
T ss_dssp             SSCC
T ss_pred             eeCC
Confidence            9865

>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=99.81  E-value=3.9e-20  Score=134.25  Aligned_cols=78  Identities=24%  Similarity=0.467  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ...+|||+|||+++++++|+++|+.||.|.++.++.+..+++|||||+|.+.++|++|++ |||..+.|++|.|.++++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~~   85 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKS   85 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTTSCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            356799999999999999999999999999999999988899999999999999999998 999999999999999864

>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=99.81  E-value=5e-20  Score=134.75  Aligned_cols=79  Identities=30%  Similarity=0.402  Sum_probs=73.9

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++|+++|+++|+.||.|.++++++++.+  ++|||||+|.+.++|++|++ |||..+.|++|+|.|+.
T Consensus         8 ~~~tlfV~nLp~~~t~~~l~~~F~~~G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A~   87 (93)
T d1x5ua1           8 QDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKAS   87 (93)
T ss_dssp             TTTEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEETT
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhCCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            4679999999999999999999999999999999998764  89999999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        88 ~~   89 (93)
T d1x5ua1          88 AH   89 (93)
T ss_dssp             TT
T ss_pred             CC
Confidence            43

>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=99.81  E-value=2e-19  Score=131.46  Aligned_cols=79  Identities=19%  Similarity=0.307  Sum_probs=74.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||+.+++++|+++|++|  |.|.+|.++.+.+.++|||||+|.+.++|.+|+. |||..++|+.|+|.+|+
T Consensus        10 ~~~~l~v~nLp~~~t~~~L~~~F~~~--G~v~~v~~~~~~~~~kg~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~A~   87 (93)
T d2cq3a1          10 TPKRLHVSNIPFRFRDPDLRQMFGQF--GKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNAT   87 (93)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHGGGT--SCEEEEEEECCTTTTCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc--ceeeeccccccccCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEecC
Confidence            45789999999999999999999999  9999999999987789999999999999999998 99999999999999998


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        88 ~r   89 (93)
T d2cq3a1          88 AR   89 (93)
T ss_dssp             SS
T ss_pred             cC
Confidence            64

>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=99.81  E-value=9.5e-20  Score=129.46  Aligned_cols=74  Identities=26%  Similarity=0.376  Sum_probs=71.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +|||+|||+.+|+++|+++|++|  |.|.+++|++|+  |+++|||||+|.++++|..|++ |||..+.|+.|+|.|++
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 SLYVGDLHPDVTEAMLYEKFSPA--GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQ   78 (80)
T ss_dssp             EEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHTTSTTCEETTEECEEEECC
T ss_pred             EEEEeCCCCcCCHHHHHHHHHHh--CCEeEEEEEecccccCCCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            69999999999999999999999  999999999885  7889999999999999999998 99999999999999985

>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=99.80  E-value=1.4e-19  Score=134.72  Aligned_cols=83  Identities=17%  Similarity=0.285  Sum_probs=76.4

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~  287 (303)
                      +++++|||+|||+.+++++|+++|++|  |.|.++.++.+.  |.++|||||+|.+.++|..|++ |||..|+|+.|+|.
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~   93 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPF--GNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQ   93 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGG--SCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhh--ccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            345789999999999999999999999  999999999875  7899999999999999999998 99999999999999


Q ss_pred             ecCCCCCC
Q 022058          288 PSKTPVRP  295 (303)
Q Consensus       288 ~a~~~~~~  295 (303)
                      |+++....
T Consensus        94 ~a~~k~~~  101 (102)
T d2cpza1          94 LKRSKNDS  101 (102)
T ss_dssp             CCCCSCCC
T ss_pred             EeCCCCCC
Confidence            99876543

>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=99.80  E-value=7.7e-20  Score=131.49  Aligned_cols=75  Identities=28%  Similarity=0.516  Sum_probs=69.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-----CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-----VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      |||+|||+++|+++|+++|+.||.|.++.|++++.+     ++|||||+|.+.++|.+|++ +||..+.|++|.|.+++.
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a~~   80 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRISER   80 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTTSCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECSSC
T ss_pred             CEEcCCCCCCCHHHHHHHHHHhCCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            799999999999999999999999999999987654     58999999999999999998 999999999999999854


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus        81 ~   81 (85)
T d2cpfa1          81 A   81 (85)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.80  E-value=7.5e-20  Score=132.71  Aligned_cols=79  Identities=24%  Similarity=0.378  Sum_probs=74.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ...+|||+|||+.+++++|+++|++|  |.|..+.|+.+.+.++|||||+|.+.++|.+|++ |||..++|+.|.|.+++
T Consensus         7 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~i~~~~~~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~i~V~~a~   84 (89)
T d1cvja2           7 GVGNIFIKNLDKSIDNKALYDTFSAF--GNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFK   84 (89)
T ss_dssp             TTTEEEEESCCSSCCHHHHHHHHHTT--SCEEEEEECCBTTBCCSCEEEEESCHHHHHHHTTSSSEEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--CCceEEEEEeecCCCcceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            34689999999999999999999999  9999999999988889999999999999999998 99999999999999998


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        85 ~~   86 (89)
T d1cvja2          85 SR   86 (89)
T ss_dssp             CT
T ss_pred             CC
Confidence            54

>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=99.80  E-value=1.1e-19  Score=130.68  Aligned_cols=77  Identities=22%  Similarity=0.393  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEe
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGY--YPVRVL  188 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g--~~i~v~  188 (303)
                      ...++|||+|||+++++++|+++|+.||+|.++++++++.+  ++|||||+|.+.++|.+|++ |||..+.|  ++|.|.
T Consensus         4 ~~~t~lfV~nlp~~~te~~l~~~F~~~G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           4 IKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TTTCEEEEESCCTTCCHHHHHHHHTSSSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhCCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            35678999999999999999999999999999999998764  79999999999999999998 99999976  899999


Q ss_pred             ec
Q 022058          189 PS  190 (303)
Q Consensus       189 ~~  190 (303)
                      |+
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            85

>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=99.80  E-value=6.6e-20  Score=133.01  Aligned_cols=78  Identities=27%  Similarity=0.372  Sum_probs=73.8

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .++|||+|||..+++++|+++|++|  |.|.+|.|++|+  |.++|||||+|.+.++|.+|+. |||..++|+.|+|.+|
T Consensus         5 ~~tlfV~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~a   82 (89)
T d2cqba1           5 KRVLYVGGLAEEVDDKVLHAAFIPF--GDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA   82 (89)
T ss_dssp             CSCEEEESCCSSCCHHHHHHHHTTT--SCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEEC
T ss_pred             CcEEEEeCCCCcCCHHHHHHHHhhC--CeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEEe
Confidence            4799999999999999999999999  999999999885  7899999999999999999998 9999999999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      +|.
T Consensus        83 ~p~   85 (89)
T d2cqba1          83 KPM   85 (89)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>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=99.80  E-value=2.7e-20  Score=131.26  Aligned_cols=74  Identities=24%  Similarity=0.405  Sum_probs=70.3

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      |.|||+|||+++|+++|+++|++||.|.++.+++|+.+  ++|||||+|.+.++|++|+++|++.++|+.|.|..+
T Consensus         1 cklfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kG~aFV~f~~~~~a~~al~~~~~~i~Gr~i~V~~A   76 (77)
T d1uawa_           1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTTSCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHhCCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            57999999999999999999999999999999998875  899999999999999999999999999999999875

>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=99.80  E-value=1.3e-19  Score=131.65  Aligned_cols=83  Identities=18%  Similarity=0.309  Sum_probs=75.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..++|||+|||+.+++++|+++|++|  |.|..+.++.+.  +.++|||||+|.+.++|.+|++ |||..|+|+.|+|.+
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~--G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~   81 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKY--GQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQ   81 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHH--SCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhcc--ccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34789999999999999999999999  999999988764  7899999999999999999998 999999999999999


Q ss_pred             cCCCCCCC
Q 022058          289 SKTPVRPR  296 (303)
Q Consensus       289 a~~~~~~r  296 (303)
                      +.+...+|
T Consensus        82 a~~~~~~r   89 (90)
T d1x5sa1          82 AGKSSDNR   89 (90)
T ss_dssp             EECCCCCC
T ss_pred             cCCCCCCC
Confidence            98765544

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Arginine/serine-rich splicing factor 10
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.1e-19  Score=130.05  Aligned_cols=75  Identities=28%  Similarity=0.326  Sum_probs=70.1

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEE
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRV  187 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v  187 (303)
                      +...++|||+|||+++|+++|+++|+.||.|.+|.++.++.+  ++|||||+|.+.++|.+|+. |||..+.|++|+|
T Consensus         6 p~~~~~l~V~nL~~~~te~~l~~~F~~~G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           6 PDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             CCGGGCEEEESCCSSCCHHHHHHHHHTTSCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHHHhCCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            345688999999999999999999999999999999998764  79999999999999999998 9999999999987

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.80  E-value=1.1e-19  Score=128.46  Aligned_cols=74  Identities=23%  Similarity=0.315  Sum_probs=70.4

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      .|||+|||+++++++|+++|+.||.|.+++++.++.+ ++|||||+|.+.++|.+|++ |||..+.|++|+|.++.
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 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHHSCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            5999999999999999999999999999999998765 89999999999999999998 99999999999999874

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hu antigen D (Hud)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.80  E-value=1.3e-19  Score=130.24  Aligned_cols=76  Identities=25%  Similarity=0.409  Sum_probs=70.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGY--YPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g--~~i~v~~  189 (303)
                      ..++|||+|||+++|+++|+++|++||+|.++++++|+.+  ++|||||+|.+.++|.+|++ |||..+.|  ++|.|.|
T Consensus         5 k~~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~~   84 (85)
T d1fxla2           5 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVKF   84 (85)
T ss_dssp             TTCEEEEESCCTTCCHHHHHHHHGGGSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEEe
Confidence            3578999999999999999999999999999999998754  79999999999999999998 99999987  6699988


Q ss_pred             c
Q 022058          190 S  190 (303)
Q Consensus       190 ~  190 (303)
                      +
T Consensus        85 A   85 (85)
T d1fxla2          85 A   85 (85)
T ss_dssp             C
T ss_pred             C
Confidence            5

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nuclear factor Aly
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2.3e-19  Score=126.84  Aligned_cols=74  Identities=22%  Similarity=0.359  Sum_probs=71.1

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      .|||+|||+.+++++|+++|++|  |.|.+++|.+++ |+++|||||+|.+.++|.+|++ |||..++|+.|+|+++.
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 KLLVSNLDFGVSDADIQELFAEF--GTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVT   77 (78)
T ss_dssp             EEEEESCCTTCCHHHHHHHHHHH--SCEEEEEESCSSCCCSCCEEEEEESCHHHHHHHHHHHTTCEETTEECEEEEEC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHh--CCCeEEEEEEeeccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEee
Confidence            59999999999999999999999  999999999985 7899999999999999999998 99999999999999985

>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=99.79  E-value=4.3e-20  Score=137.52  Aligned_cols=79  Identities=24%  Similarity=0.350  Sum_probs=73.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++++++|+++|++||.|.++.|++|+.+  ++|||||+|.+.++|.+|+++++..|.|+.|.|.++.+
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a~~   98 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVA   98 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSSCCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECCSS
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhhCcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEECcc
Confidence            3578999999999999999999999999999999998765  89999999999999999999999999999999999764


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus        99 k   99 (103)
T d1x4ba1          99 R   99 (103)
T ss_dssp             C
T ss_pred             c
Confidence            3

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2.3e-19  Score=131.41  Aligned_cols=81  Identities=21%  Similarity=0.295  Sum_probs=74.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEEEEcCHHHHHHHHH-h-CCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFVEFAVAESAILALN-C-SGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~-l-~g~~~~g~~l~v  286 (303)
                      ...+|||+|||..+++++|+++|++|  |.|.+|.|+++.   |.++|||||+|.+.++|.+|++ | ||..+.|+.|+|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~--G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V   84 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTF--GELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVL   84 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEE
Confidence            45789999999999999999999999  999999998873   6899999999999999999998 7 999999999999


Q ss_pred             eecCCCCC
Q 022058          287 SPSKTPVR  294 (303)
Q Consensus       287 ~~a~~~~~  294 (303)
                      .||++...
T Consensus        85 ~~A~~~~~   92 (94)
T d2cpha1          85 EWADSEVT   92 (94)
T ss_dssp             EECCCCCC
T ss_pred             EEcCCCCC
Confidence            99987654

>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=99.79  E-value=5.5e-20  Score=136.50  Aligned_cols=77  Identities=31%  Similarity=0.447  Sum_probs=72.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++++..+  ++|||||+|.+.++|.+|+.|||..|.|++|.|.++.
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a~   95 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQASQ   95 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTTSCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEHH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCCCeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEECC
Confidence            3578999999999999999999999999999999998764  8999999999999999999999999999999999864

>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=99.79  E-value=1.3e-19  Score=134.73  Aligned_cols=80  Identities=21%  Similarity=0.412  Sum_probs=74.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|..||+ |||..+.|++|+|.|+
T Consensus        16 p~~~~l~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~g~~kG~afV~f~~~~~A~~Ai~~lng~~~~g~~i~V~~a   95 (102)
T d2cpza1          16 PEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQSMNGFQIGMKRLKVQLK   95 (102)
T ss_dssp             STTCCEEEESCCSSCCHHHHHHHHGGGSCCSEEEEEECSSSCSEEEEEEEECSSHHHHHHHHHHHTTCEETTEECEEECC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhhccccccceeeecccCCCccceEEEeCCHHHHHHHHHHhCCCEECCEEEEEEEe
Confidence            34678999999999999999999999999999999998765  78999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ++.
T Consensus        96 ~~k   98 (102)
T d2cpza1          96 RSK   98 (102)
T ss_dssp             CCS
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=2.1e-19  Score=131.42  Aligned_cols=79  Identities=29%  Similarity=0.386  Sum_probs=74.5

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .++|||+|||..+++++|+++|++|  |.|.++.|++++  |.++|||||+|.+.++|.+|++ |||..++|+.|+|.+|
T Consensus         9 ~~tlfV~nLp~~~t~~~l~~~F~~~--G~v~~v~~~~d~~tg~~kg~afV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~A   86 (93)
T d1x5ua1           9 DATVYVGGLDEKVSEPLLWELFLQA--GPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKA   86 (93)
T ss_dssp             TTEEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSCSBCSCEEEEESSHHHHHHHHHHSSSCBCSSCBCEEEET
T ss_pred             CCEEEEeCCCCcCCHHHHHHHHHHh--CCccccceeecccccccccceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            4789999999999999999999999  999999999885  7899999999999999999998 9999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      ++..
T Consensus        87 ~~~~   90 (93)
T d1x5ua1          87 SAHN   90 (93)
T ss_dssp             TTTS
T ss_pred             CCCC
Confidence            8654

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.79  E-value=1e-19  Score=129.62  Aligned_cols=77  Identities=17%  Similarity=0.253  Sum_probs=68.0

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .++|||+|||+++|+++|+++|+.||.|..+.++.+...  ++|||||+|.+.++|.+|++ |||..+.|++|.|.++++
T Consensus         1 d~tl~v~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~P   80 (81)
T d2ghpa1           1 ECTLWMTNFPPSYTQRNIRDLLQDINVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSNP   80 (81)
T ss_dssp             SCEEEEECCCTTCCHHHHHHHHHHTTCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECCC
T ss_pred             CcEEEEECCCCcCCHHHHHHHHHHhCcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEccC
Confidence            378999999999999999999999999988887776543  89999999999999999998 999999999999999864

>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=99.79  E-value=1.5e-19  Score=129.96  Aligned_cols=79  Identities=19%  Similarity=0.323  Sum_probs=74.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      .+|||+|||..+|+++|+++|++|  |.|.+++|++|+  |.++|||||+|.+.++|..|+. |||..++|+.|.|.+|+
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~   79 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSF--GPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS   79 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSS--SCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhc--CccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            469999999999999999999999  999999999985  7899999999999999999999 99999999999999998


Q ss_pred             CCCC
Q 022058          291 TPVR  294 (303)
Q Consensus       291 ~~~~  294 (303)
                      +..+
T Consensus        80 ~~~~   83 (85)
T d2u2fa_          80 VGAK   83 (85)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            6643

>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=99.79  E-value=2.9e-19  Score=132.21  Aligned_cols=80  Identities=28%  Similarity=0.330  Sum_probs=74.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ...++|||+|||+++++++|+++|+.||.|.+|.|+.++.+  ++|||||+|.+.++|.+||+ ||+..+.|++|+|.++
T Consensus         6 ~~~~~lfV~nL~~~~t~~~l~~~F~~~g~v~~v~i~~d~~tg~~~g~afV~f~~~~~a~~A~~~l~g~~~~gr~i~V~~a   85 (99)
T d1whwa_           6 SGSGRLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQGRMLHVLPS   85 (99)
T ss_dssp             CSCEEEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCCTTTCCCCSEEEEEESSHHHHHHHHHHTTTEESSSCEEEEEEC
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHhcCCceeeeecccccccccCcceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            35678999999999999999999999999999999998764  89999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ...
T Consensus        86 ~~~   88 (99)
T d1whwa_          86 TIK   88 (99)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            654

>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=99.79  E-value=2.3e-19  Score=127.11  Aligned_cols=75  Identities=20%  Similarity=0.275  Sum_probs=70.7

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      -++|||+|||+++|+++|+++|+.||.|..+.++.++.+  ++|||||+|.+.++|++|+++||..|+||+|.|..+
T Consensus         2 ~r~lfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           2 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             CSEEEEECCTTTCCHHHHHHHHTTTSCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CCEEEECCCCCcCCHHHHHHHHHHhccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            378999999999999999999999999999999998776  789999999999999999999999999999999875

>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=99.79  E-value=1.6e-19  Score=126.67  Aligned_cols=73  Identities=22%  Similarity=0.379  Sum_probs=68.6

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      .|||+|||+++|+++|+++|++||+|.++.++.++.+  ++|||||+|.+.++|++|+++++..+.|+.|.|..+
T Consensus         1 klfV~nl~~~~te~~l~~~F~~~G~i~~~~i~~d~~t~~~kg~afV~f~~~~~a~~Al~~~~~~l~Gr~i~V~rA   75 (75)
T d1hd0a_           1 KMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTTSCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhhccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            3899999999999999999999999999999998765  899999999999999999999999999999999753

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.79  E-value=2.3e-19  Score=131.41  Aligned_cols=79  Identities=22%  Similarity=0.289  Sum_probs=72.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC---CCceEEEEEecCHHHHHHHHH-h-CCcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH---SVLRFAFVEFADEHGARAALN-L-GGTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~---~~~G~~fV~f~~~~~A~~Ai~-l-~g~~~~g~~i~v~~  189 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|+|+++..   .++|||||+|.+.++|.+|+. | |+..+.|++|.|.|
T Consensus         7 ~~~~l~V~nLp~~~~e~~l~~~F~~~G~i~~v~i~~~~~~~g~~rg~afV~f~~~~~A~~Ai~~l~~~~~~~Gr~l~V~~   86 (94)
T d2cpha1           7 TTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYGRRLVLEW   86 (94)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCCCCSSSCSSCSEEEEEESSHHHHHHHHHHHHTCCBSSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHhCCceEEEEEeccccCCCcccEEEEEECCHHHHHHHHHHccCCcEECCEEEEEEE
Confidence            567899999999999999999999999999999988754   279999999999999999998 7 89999999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      ++..
T Consensus        87 A~~~   90 (94)
T d2cpha1          87 ADSE   90 (94)
T ss_dssp             CCCC
T ss_pred             cCCC
Confidence            8654

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding region containing protein 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=3.9e-19  Score=132.44  Aligned_cols=78  Identities=18%  Similarity=0.250  Sum_probs=71.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|.+|+++.++.+  ++|||||+|.+.++|++||+ +|+ .+.|++|.|.++.
T Consensus         9 ~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~~kg~afV~f~~~~~A~~Ai~~~~~-~l~Gr~l~V~~a~   87 (103)
T d2cqda1           9 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP-IIDGRKANVNLAY   87 (103)
T ss_dssp             SSSEEEEECCCSSCCHHHHHHHHHTTSCEEEEEESCCSSSCCCCSEEEEEESSHHHHHHHHTCSSC-EETTEECEEEEST
T ss_pred             CCcEEEEeCCCCcCcHHHHHHHHhhcccccceeccccccccccCCeEEEEECCHHHHHHHHHHCCC-cCCCEEEEEEEcC
Confidence            4578999999999999999999999999999999998764  89999999999999999999 776 7999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus        88 ~~   89 (103)
T d2cqda1          88 LG   89 (103)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.79  E-value=1.8e-19  Score=128.36  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=68.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ++|||+|||+.+|+++|+++|++|  |.|..+.++.+.  |+++|||||+|.+.++|.+|++ |||..++|+.|.|.+++
T Consensus         2 ~tl~v~nLp~~~t~~~l~~~f~~~--G~v~~~~~~~~~~~~~~~g~afV~f~~~e~A~~Ai~~l~g~~~~g~~i~V~~a~   79 (81)
T d2ghpa1           2 CTLWMTNFPPSYTQRNIRDLLQDI--NVVALSIRLPSLRFNTSRRFAYIDVTSKEDARYCVEKLNGLKIEGYTLVTKVSN   79 (81)
T ss_dssp             CEEEEECCCTTCCHHHHHHHHHHT--TCCCCEEECC-------CCEEEEECSSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cEEEEECCCCcCCHHHHHHHHHHh--CcEEeeeeecccccccccceeEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcc
Confidence            689999999999999999999999  999988877763  7899999999999999999998 99999999999999998


Q ss_pred             C
Q 022058          291 T  291 (303)
Q Consensus       291 ~  291 (303)
                      |
T Consensus        80 P   80 (81)
T d2ghpa1          80 P   80 (81)
T ss_dssp             C
T ss_pred             C
Confidence            7

>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=99.79  E-value=1.4e-19  Score=130.05  Aligned_cols=76  Identities=18%  Similarity=0.373  Sum_probs=71.8

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..|||+|||+++|+++|+++|+.||+|.++++++|+.+  ++|||||+|.+.++|..|++ |||..+.|++|.|.++..
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~~   80 (85)
T d2u2fa_           2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASV   80 (85)
T ss_dssp             CCEEEETCCSSCCSHHHHHHHTSSSCEEEEEEECCCSSSCCCCEEEEEESSSHHHHHHHHTSSSCCCSSSCCEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHhcCccceEEeeccccccccceeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            36999999999999999999999999999999998764  89999999999999999999 999999999999999864

>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=99.79  E-value=4.5e-19  Score=128.68  Aligned_cols=80  Identities=19%  Similarity=0.200  Sum_probs=71.7

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++|+++|+++|+.||.|.+|.|+.|+.+  ++|||||+|.+.++|.+||+ ++..++|+.|.|.++
T Consensus         5 ~~~~~~lfV~nLp~~~te~~l~~~F~~~G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           5 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCCCEEEESCCSSCCHHHHHHHHGGGSCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECC
T ss_pred             CcCCCeEEEECCCCCCCHHHHHHHHHhhcccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeC
Confidence            345678999999999999999999999999999999998764  89999999999999999998 334789999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      .+.
T Consensus        84 ~~k   86 (90)
T d2cqga1          84 NSK   86 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            653

>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=99.79  E-value=2.4e-19  Score=125.69  Aligned_cols=74  Identities=26%  Similarity=0.421  Sum_probs=70.6

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ++|||+|||+++++++|+++|+.||+|.+++++.++.+.+|||||+|.+.++|.+|+.+|+..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGGSCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcCCceEEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            47999999999999999999999999999999999888889999999999999999999999999999999864

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cold-inducible RNA-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.79  E-value=2.3e-19  Score=130.41  Aligned_cols=79  Identities=23%  Similarity=0.381  Sum_probs=73.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++++++|+++|+.||.|..+.++.+..+  ++|||||+|.++++|++|+. |||..+.|++|.|.++.
T Consensus         4 ~~~kifV~nLp~~~t~~~l~~~F~~~G~i~~~~~~~~~~~~~~~g~afV~f~~~~~a~~Ai~~l~~~~~~g~~l~V~~a~   83 (90)
T d1x5sa1           4 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQAG   83 (90)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHHHSCCCEEEECCCSSSCSCCSEEEEECSSHHHHHHHHHHHTTCCTTSCCCEEEEEE
T ss_pred             CCCEEEEECCCCcCCHHHHHHhhhccccccceeeccccccccccceEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            5678999999999999999999999999999998886654  89999999999999999998 99999999999999985


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        84 ~~   85 (90)
T d1x5sa1          84 KS   85 (90)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>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=99.78  E-value=7e-19  Score=126.05  Aligned_cols=76  Identities=17%  Similarity=0.269  Sum_probs=72.1

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      .++|||+|||..+++++|+++|++|  |.|.++.|++|.  |+++|||||+|.+.++|.+|++++++.|.|+.|+|..|.
T Consensus         6 ~~~lfV~nlp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg~~kG~afV~f~~~~~a~~ai~~~~~~i~Gr~i~V~~A~   83 (84)
T d1l3ka1           6 LRKLFIGGLSFETTDESLRSHFEQW--GTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV   83 (84)
T ss_dssp             GGEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHTCSCEETTEECEEEECC
T ss_pred             CcEEEEECCCCCCCHHHHHHHHHhh--ccccceeecccccCCCcccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEeee
Confidence            4789999999999999999999999  999999999885  789999999999999999999999999999999999875

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.78  E-value=4.4e-19  Score=127.45  Aligned_cols=78  Identities=21%  Similarity=0.362  Sum_probs=71.3

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--C---CcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--V---HSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       216 l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~---~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      |||+|||.++|+++|+++|++|  |.|.++.|++++  +   .++|||||+|.+.++|.+|++ |||..++|+.|.|.|+
T Consensus         1 LfV~nLp~~~t~~~l~~~F~~~--G~v~~v~i~~~~~~~~~~~~kG~afV~f~~~~~A~~A~~~~~~~~~~g~~i~V~~a   78 (85)
T d2cpfa1           1 LFIKNLNFSTTEETLKGVFSKV--GAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTVDGHKLEVRIS   78 (85)
T ss_dssp             EEEESCCTTCCHHHHHHHHHTT--SCEEEEEEEEEECTTCCEEEEEEEEEEESSHHHHHHHHHHSTTCEETTEECEEECS
T ss_pred             CEEcCCCCCCCHHHHHHHHHHh--CCccccceecccccccccccceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            7999999999999999999999  999999999874  2   468999999999999999998 9999999999999999


Q ss_pred             CCCCCC
Q 022058          290 KTPVRP  295 (303)
Q Consensus       290 ~~~~~~  295 (303)
                      ++..+|
T Consensus        79 ~~~~kp   84 (85)
T d2cpfa1          79 ERATKP   84 (85)
T ss_dssp             SCSSCC
T ss_pred             CCCCCC
Confidence            765443

>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=99.78  E-value=4.1e-19  Score=127.56  Aligned_cols=77  Identities=18%  Similarity=0.239  Sum_probs=72.2

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++|+++|+++|+.||.|.+|.++.+..+ ++|||||+|.+.++|.+||++++..+.|++|.|.|.+
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTSCCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHhcccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            3678999999999999999999999999999999987765 7999999999999999999999999999999999864

>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=99.78  E-value=1.1e-18  Score=137.17  Aligned_cols=80  Identities=21%  Similarity=0.366  Sum_probs=74.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|.|++|+  |+++|||||+|.+.++|.+|+. |||..|+|+.|+|.+
T Consensus        41 ~~~~l~V~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~t~~~rg~afV~f~~~~~A~~Ai~~lng~~~~gr~l~V~~  118 (139)
T d1u6fa1          41 VLRNLMVNYIPTTVDEVQLRQLFERY--GPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVAL  118 (139)
T ss_dssp             TTSEEEEESCSTTCCHHHHHHHHHHH--SCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhh--ccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            34789999999999999999999999  999999999885  6799999999999999999998 999999999999999


Q ss_pred             cCCCC
Q 022058          289 SKTPV  293 (303)
Q Consensus       289 a~~~~  293 (303)
                      +++..
T Consensus       119 a~~~~  123 (139)
T d1u6fa1         119 AASGH  123 (139)
T ss_dssp             SSCCC
T ss_pred             cCCCC
Confidence            97543

>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=99.78  E-value=5.6e-19  Score=138.79  Aligned_cols=82  Identities=23%  Similarity=0.365  Sum_probs=75.6

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      .+...++|||+|||+++|+++|+++|+.||.|.+|.|+.++.+  ++|||||+|.+.++|.+||+ |||..|.|+.|+|.
T Consensus        38 ~~~~~~~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          38 EPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILNKRLKVA  117 (139)
T ss_dssp             CTTTTSEEEEESCSTTCCHHHHHHHHHHHSCEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHTTTEECSSCEEEEE
T ss_pred             CCCCCCEEEEeCCCCCCCHHHHHHHHHhhccccccccccccccccccceeeEEECCHHHHHHHHHHhCCCEECCEEEEEE
Confidence            3445678999999999999999999999999999999998765  79999999999999999998 99999999999999


Q ss_pred             ecCCC
Q 022058          189 PSKTA  193 (303)
Q Consensus       189 ~~~~~  193 (303)
                      ++...
T Consensus       118 ~a~~~  122 (139)
T d1u6fa1         118 LAASG  122 (139)
T ss_dssp             ESSCC
T ss_pred             EcCCC
Confidence            98644

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: U4/U6 snRNA-associated-splicing factor PRP24
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.78  E-value=3.3e-19  Score=128.37  Aligned_cols=79  Identities=22%  Similarity=0.340  Sum_probs=70.9

Q ss_pred             ccceEEEcCCCCCCC-HHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEe
Q 022058          212 CSRTVYCTNIDKKVP-QAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVS  287 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t-~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~  287 (303)
                      ..++|||+|||.+++ +++|+++|++|  |.|.+|.|+.+.   ++++|||||+|.+.++|.+|++|||..++|+.|+|+
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~--G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~   80 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGF--GSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVS   80 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGG--SCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEE
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhh--hhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEE
Confidence            358999999999976 56699999999  999999998753   678999999999999999999999999999999999


Q ss_pred             ecCCC
Q 022058          288 PSKTP  292 (303)
Q Consensus       288 ~a~~~  292 (303)
                      ++++.
T Consensus        81 ~a~~k   85 (86)
T d2ghpa3          81 LADKK   85 (86)
T ss_dssp             ECCCC
T ss_pred             EcCCC
Confidence            99864

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Cleavage stimulation factor, 64 kda subunit
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.77  E-value=3.4e-19  Score=133.00  Aligned_cols=77  Identities=31%  Similarity=0.477  Sum_probs=72.3

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .++|||+|||+++++++|+++|+.||.|.+|+++.++.+  ++|||||+|.+.++|.+|++ |||..+.|++|.|.++.+
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a~~   87 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS   87 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTTSCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEETTC
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhccccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            468999999999999999999999999999999998765  79999999999999999998 999999999999999753

>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=99.77  E-value=7.9e-19  Score=126.08  Aligned_cols=75  Identities=25%  Similarity=0.397  Sum_probs=70.0

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCC--eeeEEe
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGS--QPIRVS  287 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g--~~l~v~  287 (303)
                      .++|||+|||+.+|+++|+++|++|  |.|.+++|++|+  |.++|||||+|.+.++|.+|++ |||..+.|  ++|.|+
T Consensus         6 ~~~lfV~nLp~~~te~~L~~~F~~~--G~v~~v~i~~d~~~g~~kg~afV~f~~~~~a~~Ai~~lng~~~~G~~~~i~V~   83 (85)
T d1fxla2           6 DANLYVSGLPKTMTQKELEQLFSQY--GRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSGATEPITVK   83 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHHh--CCccccccccccccccCCCeeEEEEcCHHHHHHHHHHhCCCEeCCCCEEEEEE
Confidence            4789999999999999999999999  999999999875  7899999999999999999998 99999987  559999


Q ss_pred             ec
Q 022058          288 PS  289 (303)
Q Consensus       288 ~a  289 (303)
                      ||
T Consensus        84 ~A   85 (85)
T d1fxla2          84 FA   85 (85)
T ss_dssp             EC
T ss_pred             eC
Confidence            86

>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=99.77  E-value=3e-19  Score=128.62  Aligned_cols=78  Identities=18%  Similarity=0.309  Sum_probs=69.9

Q ss_pred             CCCEEEEcCCCCCCC-HHHHHHHhhcCCceeEEEEeeCCC-C--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          115 VRRTVYVSDIDQNIT-EERLAGLFSSCGQVVDCRVCGDPH-S--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t-~~~l~~~F~~~G~i~~~~i~~~~~-~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      ..++|||+|||++++ +++|+++|+.||.|.+|+|+.+.. +  ++|||||+|.+.++|.+|+++|+..+.|++|.|.++
T Consensus         3 e~~~l~V~nLp~~~t~ed~l~~~F~~~G~i~~v~i~~~~~~~~~~kg~afV~f~~~~~a~~Al~~n~~~~~gr~l~V~~a   82 (86)
T d2ghpa3           3 EGREIMIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFMVFENKDSAERALQMNRSLLGNREISVSLA   82 (86)
T ss_dssp             TTTEEEEEEECTTTCCHHHHHHHHGGGSCEEEEECCSCCC---CCCEEEEEEESSHHHHHHHGGGTTEEETTEEEEEEEC
T ss_pred             CCCEEEEECCCCCcccHHHHHHHHHhhhhccceeeecccCCccccceeeeEEECCHHHHHHHHhcCCCEECCEEEEEEEc
Confidence            478999999999875 667999999999999999987542 2  799999999999999999999999999999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      ++
T Consensus        83 ~~   84 (86)
T d2ghpa3          83 DK   84 (86)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.77  E-value=9.4e-19  Score=130.16  Aligned_cols=79  Identities=13%  Similarity=0.239  Sum_probs=74.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||+++++++|+++|++|  |.|..+.|++|+  +.++|||||+|.+.++|.+|+.++|+.|.|+.|.|.+|
T Consensus        19 ~~~~lfVgnLp~~~te~~L~~~F~~~--G~i~~~~i~~d~~~~~~kg~aFV~f~~~~~a~~al~~~~~~l~G~~i~V~~a   96 (103)
T d1x4ba1          19 QFRKLFIGGLSFETTEESLRNYYEQW--GKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRA   96 (103)
T ss_dssp             HHTEEEEECCTTCCCHHHHHHHHTSS--CCCSEEEEECCTTTSSCCSEEEEECSSHHHHHHHHTSCSEEETTEEEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHhh--CcccceeecccccCCCccCeEEEEECCHHHHHHHHHhCCCeECCEEEEEEEC
Confidence            34789999999999999999999999  999999999985  57899999999999999999999999999999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      +|.
T Consensus        97 ~~k   99 (103)
T d1x4ba1          97 VAR   99 (103)
T ss_dssp             SSC
T ss_pred             ccc
Confidence            854

>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=9.2e-19  Score=132.83  Aligned_cols=78  Identities=26%  Similarity=0.375  Sum_probs=71.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +..+++|||+|||+++++++|+++|+.||+|.+|++..+. .++|||||+|.+.++|..|++ |||..|.|++|.|.++.
T Consensus         4 p~~~r~l~V~nLp~~~te~~l~~~F~~~G~v~~i~~~~~~-~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           4 PEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTP-ETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             TTCCSEEEEESCCTTCCHHHHHHHHHTTSCEEEEEEECST-TTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             cCCCCEEEEECCCCCCCHHHHHHHHhhcCCeEeecccccC-CcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            3467899999999999999999999999999999998654 368999999999999999998 99999999999999974

>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=99.77  E-value=1.7e-19  Score=126.30  Aligned_cols=73  Identities=16%  Similarity=0.331  Sum_probs=68.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      .|||+|||+++|+++|+++|++||+|.+|+|+.++.+  ++|||||+|.+.++|++||+.++..++|+.|.|..+
T Consensus         1 klfVgnLp~~~te~~l~~~F~~~G~I~~v~i~~d~~t~~~rG~~FV~f~~~~~a~~al~~~~~~i~g~~i~vk~A   75 (75)
T d1x0fa1           1 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHHSCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHhCCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            4899999999999999999999999999999998765  899999999999999999997888999999998753

>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=99.77  E-value=9.6e-19  Score=125.08  Aligned_cols=73  Identities=22%  Similarity=0.311  Sum_probs=69.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      +.++|||+|||..+|+++|+++|++|  |.|.+|.|++++  +.++|||||+|.+.++|.+|+. |||..|+|+.|+|
T Consensus         8 ~~~~l~V~nL~~~~te~~l~~~F~~~--G~i~~v~i~~~~~~~~~~g~afV~f~~~~~A~~Ai~~l~g~~~~gr~i~V   83 (83)
T d2cqca1           8 PNCCLGVFGLSLYTTERDLREVFSKY--GPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRV   83 (83)
T ss_dssp             GGGCEEEESCCSSCCHHHHHHHHHTT--SCEEEEEEEECSSSSSEEEEEEEEESSHHHHHHHHHHHTTEEETTEEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHh--CCCccccccccccccccccceEEEECCHHHHHHHHHHcCCCEECCEEeEC
Confidence            45789999999999999999999999  999999999875  7899999999999999999998 9999999999987

>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=99.77  E-value=4.7e-19  Score=126.73  Aligned_cols=74  Identities=26%  Similarity=0.509  Sum_probs=68.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEE-EEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~-~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      |||+|||+++|+++|+++|++||.|.++ .++++..+  ++|||||+|.+.++|.+|++ +||..+.|++|+|.|+.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTTSCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHhCceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecC
Confidence            7999999999999999999999999765 77877654  79999999999999999998 999999999999999864

>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=99.77  E-value=9.3e-19  Score=125.72  Aligned_cols=75  Identities=21%  Similarity=0.420  Sum_probs=70.4

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCC--eeeEEe
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGS--QPIRVS  287 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g--~~l~v~  287 (303)
                      .++|||+|||..+++++|+++|++|  |.|.+++|++++  |+++|||||+|.+.++|.+|++ |||..+.|  ++|+|+
T Consensus         6 ~t~lfV~nlp~~~te~~l~~~F~~~--G~i~~~~~~~d~~~g~~~g~afV~f~~~~~A~~Ai~~l~g~~~~g~~~~l~V~   83 (85)
T d1b7fa2           6 DTNLYVTNLPRTITDDQLDTIFGKY--GSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVR   83 (85)
T ss_dssp             TCEEEEESCCTTCCHHHHHHHHTSS--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHHHTTCCCTTCSSCCEEE
T ss_pred             CCEEEEeCCCCCCCHHHHHHHHHhh--CCEeeeeeecccccccCceeEEEEECCHHHHHHHHHHHCCCEeCCCCeEEEEE
Confidence            4679999999999999999999999  999999999875  7899999999999999999998 99999976  889999


Q ss_pred             ec
Q 022058          288 PS  289 (303)
Q Consensus       288 ~a  289 (303)
                      ||
T Consensus        84 ~A   85 (85)
T d1b7fa2          84 LA   85 (85)
T ss_dssp             EC
T ss_pred             EC
Confidence            87

>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=99.77  E-value=4.1e-19  Score=131.69  Aligned_cols=78  Identities=33%  Similarity=0.586  Sum_probs=73.4

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||+.+++++|+++|++|  |.|.+|.|+++.  |+++|||||+|.+.++|.+|+.|||..|+|+.|.|.++
T Consensus        17 ~~~tifV~nL~~~~te~~l~~~F~~~--G~V~~v~i~~d~~tg~~kG~afV~F~~~e~a~~A~~l~g~~~~G~~l~V~~a   94 (101)
T d2cq4a1          17 DARTVFCMQLAARIRPRDLEDFFSAV--GKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS   94 (101)
T ss_dssp             HHTEEEEESCCTTCCHHHHHHHHTTT--SCEEEEEECCSCCSSSCCCCEEEEESCGGGHHHHHHHTTEEETTEEEEEEEH
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHcCC--CeEEEEEeeecCCCccccceEEEEECCHHHHHHHHHHCCCEECCEEEEEEEC
Confidence            34789999999999999999999999  999999999984  78999999999999999999999999999999999998


Q ss_pred             CC
Q 022058          290 KT  291 (303)
Q Consensus       290 ~~  291 (303)
                      ++
T Consensus        95 ~~   96 (101)
T d2cq4a1          95 QA   96 (101)
T ss_dssp             HH
T ss_pred             CC
Confidence            63

>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=99.77  E-value=3.7e-19  Score=132.07  Aligned_cols=79  Identities=18%  Similarity=0.385  Sum_probs=72.5

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....++|||+|||+++++++|+++|+.||.|..+.+..+..+ ++|||||+|.+.++|.+|++ |||..|.|+++.|.++
T Consensus        15 ~~~~~~lfV~nLp~~~te~~L~~~F~~~G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          15 EQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CCCTTEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             cCCCCEEEEeCCCCCCCHHHHHHHHhhcccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            335689999999999999999999999999999999887655 79999999999999999998 9999999999999876


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      +
T Consensus        95 ~   95 (101)
T d1x5oa1          95 E   95 (101)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.77  E-value=2.6e-19  Score=126.08  Aligned_cols=74  Identities=20%  Similarity=0.258  Sum_probs=70.3

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ++|||+|||.++++++|+++|++|  |.|.++.|++|+  |+++|||||+|.+.++|.+|+.+|++.++|+.|+|..|
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 CKMFIGGLSWQTTQEGLREYFGQF--GEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKVLAQSRHELDSKTIDPKVA   76 (77)
T ss_dssp             CCEEEESCCSSCCSHHHHHHHTTT--SCCCCEEEECCCCSSSCSSEEEECCCCTTHHHHHHHTTTCCCSSCCCEEEEC
T ss_pred             CEEEEeCCCCcCCHHHHHHHHHHh--CCcceeeeecccCCCCccceEEEEECCHHHHHHHHHcCCCEECCeEEEEEEC
Confidence            369999999999999999999999  999999999986  78999999999999999999999999999999999876

>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=99.76  E-value=1e-18  Score=124.97  Aligned_cols=75  Identities=24%  Similarity=0.384  Sum_probs=69.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhhcCcceeEE-EEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCC
Q 022058          216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRL-RLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       216 l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v-~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~  291 (303)
                      |||+|||+++++++|+++|++|  |.|.++ .|+++.  |+++|||||+|.+.++|.+|++ |||..++|+.|+|.|+.+
T Consensus         1 lfV~nLp~~~te~~l~~~F~~~--G~i~~~~~i~~~~~~g~~~g~afV~f~~~~~a~~Ai~~~~g~~~~gr~l~v~~a~~   78 (83)
T d1x5ta1           1 IFIGNLDPEIDEKLLYDTFSAF--GVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFK   78 (83)
T ss_dssp             EEEECCCTTCCHHHHHHHHHTT--SCBSSCCEECCCTTTCSCCSEEEEEBSSHHHHHHHHHTTTTCEETTEECEEEESCC
T ss_pred             CEEcCCCCcCcHHHHHHHHHHh--CceeeeEEEEeeccccccCceEEEEECCHHHHHHHHHhCCCcEECCEEEEEEEecC
Confidence            7999999999999999999999  999765 677774  7899999999999999999998 999999999999999985


Q ss_pred             C
Q 022058          292 P  292 (303)
Q Consensus       292 ~  292 (303)
                      .
T Consensus        79 k   79 (83)
T d1x5ta1          79 K   79 (83)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.76  E-value=9.4e-19  Score=122.63  Aligned_cols=73  Identities=21%  Similarity=0.259  Sum_probs=68.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      .|||+|||+++++++|+++|++|  |.|.++.|++++  ++++|||||+|.+.++|.+|+++++..|.|+.|.|+.|
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 KMFIGGLSWDTTKKDLKDYFSKF--GEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRA   75 (75)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHTT--SCEEEEECCCBTTTTBCCSEEEEEESSHHHHHHHHHTCCCCBTTBCCEECCC
T ss_pred             CEEEeCCCCcCCHHHHHHHHHhh--ccccccccccCCCCCCcCceEEEEECCHHHHHHHHhcCCCEECCCEEEeeEC
Confidence            48999999999999999999999  999999999985  78999999999999999999999999999999999754

>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=99.76  E-value=2.3e-18  Score=124.83  Aligned_cols=78  Identities=17%  Similarity=0.278  Sum_probs=71.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+.+|+++|+++|++|  |.|.+|.|++|+  |.++|||||+|.+.++|.+|++ +++.|+|+.|.|.++
T Consensus         7 ~~~~lfV~nLp~~~te~~l~~~F~~~--G~i~~v~i~~d~~tg~srG~aFV~f~~~~~a~~al~-~~~~l~Gr~i~v~~a   83 (90)
T d2cqga1           7 KTSDLIVLGLPWKTTEQDLKEYFSTF--GEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMS-QRHMIDGRWCDCKLP   83 (90)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHHGGG--SCEEEEEEEECSSSCSEEEEEEEEESSHHHHHHHHH-SCEEETTEEEEEECC
T ss_pred             CCCeEEEECCCCCCCHHHHHHHHHhh--cccceeeeccCCCCcccCCEEEEEECCHHHHHHHHh-cCCccCCEEeEEEeC
Confidence            34789999999999999999999999  999999999985  7899999999999999999998 344899999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      .+.
T Consensus        84 ~~k   86 (90)
T d2cqga1          84 NSK   86 (90)
T ss_dssp             CTT
T ss_pred             CCC
Confidence            764

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Neural RNA-binding protein Musashi-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.76  E-value=6.5e-19  Score=123.44  Aligned_cols=73  Identities=21%  Similarity=0.245  Sum_probs=68.7

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      .|||+|||+++|+++|+++|+.||.|..+.++.++.+  ++|||||+|.+.++|++|+++||..++|++|.|.++
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTTSCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHhCCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            3899999999999999999999999999999887764  799999999999999999999999999999999874

>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=99.76  E-value=2.2e-18  Score=121.99  Aligned_cols=74  Identities=15%  Similarity=0.300  Sum_probs=70.4

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ++|||+|||+++|+++|+++|++|  |.|..+.+..++  +.++|||||+|.+.++|.+|+.|||+.|+|+.|+|+.|
T Consensus         3 r~lfV~nLp~~~te~~l~~~F~~~--G~i~~~~~~~~~~~~~~~g~afV~f~~~e~~~~al~~~~~~l~Gr~i~V~~A   78 (79)
T d1l3ka2           3 KKIFVGGIKEDTEEHHLRDYFEQY--GKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKA   78 (79)
T ss_dssp             SEEEEECCTTTCCHHHHHHHHTTT--SCEEEEEEEECTTTCCEEEEEEEEESSHHHHHHHHHCSCCEETTEECEEEEC
T ss_pred             CEEEECCCCCcCCHHHHHHHHHHh--ccccccccccCCCCcccccEEEEEEcCHHHHHHHHHhCCCEECCEEEEEEEC
Confidence            789999999999999999999999  999999999885  67899999999999999999999999999999999876

>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=99.75  E-value=6e-19  Score=131.66  Aligned_cols=78  Identities=24%  Similarity=0.431  Sum_probs=73.6

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      .++|||+|||..+++++|+++|++|  |.|.+|.|+++.  |+++|||||+|.+.++|.+|++ |||..|.|+.|+|.++
T Consensus         8 ~rtl~V~nLp~~~te~~l~~~f~~~--G~i~~v~i~~~~~tg~~~g~afV~f~~~~~a~~ai~~l~~~~~~g~~i~V~~a   85 (104)
T d1p1ta_           8 LRSVFVGNIPYEATEEQLKDIFSEV--GPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNA   85 (104)
T ss_dssp             HSCEEEESCCTTSCHHHHHHHHHTT--SCCSEEEEEEETTTTEEEEEEEEECSCHHHHHHHHHHSSSBSCSSSCBEEEET
T ss_pred             CCEEEEECCCCcCCHHHHHHhhhcc--ccccccccccccceeccCCceEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            4789999999999999999999999  999999999874  7899999999999999999998 9999999999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      .+.
T Consensus        86 ~~~   88 (104)
T d1p1ta_          86 ASE   88 (104)
T ss_dssp             TCT
T ss_pred             CCC
Confidence            765

>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=99.75  E-value=1.4e-18  Score=127.56  Aligned_cols=75  Identities=27%  Similarity=0.410  Sum_probs=70.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ...++|||+|||.++++++|+++|++||.|.+|+++.+    +|||||+|.+.++|.+|+. |||..+.|++|+|.|++.
T Consensus        16 ~~~~~l~v~nL~~~~te~~L~~~F~~fG~i~~v~i~~~----kg~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak~   91 (96)
T d1x4ga1          16 PKNCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE----KGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKE   91 (96)
T ss_dssp             SSCCEEEEECCSSCCCHHHHHHHHHHHSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHhCCceEEEEEec----ceEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCC
Confidence            35678999999999999999999999999999999876    5899999999999999998 999999999999999864

>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=99.75  E-value=1.1e-19  Score=132.39  Aligned_cols=81  Identities=17%  Similarity=0.210  Sum_probs=73.1

Q ss_pred             CCCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeec
Q 022058          112 EDSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPS  190 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~  190 (303)
                      .+....+|||+|||+++++++|+++|+.||.|.++.++.+..+ ++|||||+|.+.++|++||++||..+.|++|.|.++
T Consensus         9 ~~~~~~~ifV~nL~~~~te~~l~~~F~~~G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~a   88 (91)
T d1fjeb1           9 ESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKP   88 (91)
T ss_dssp             SCSSSEEEEEECCCTTSCHHHHHHHHHHHHHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECC
T ss_pred             CCCCCcEEEEeCccCcchHHHHHHHHhcCCcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEec
Confidence            4446778999999999999999999999999999888765443 899999999999999999999999999999999998


Q ss_pred             CC
Q 022058          191 KT  192 (303)
Q Consensus       191 ~~  192 (303)
                      +.
T Consensus        89 k~   90 (91)
T d1fjeb1          89 KG   90 (91)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.75  E-value=8.9e-19  Score=122.62  Aligned_cols=73  Identities=15%  Similarity=0.332  Sum_probs=68.9

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      .|||+|||+++|+++|+++|++|  |.|.+|.|++|+  ++++|||||+|.+.++|.+|++++++.++|+.|.|+.|
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 KIFVGGLSPDTPEEKIREYFGGF--GEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVA   75 (75)
T ss_dssp             EEEEESCCSSCCHHHHHHHHHHH--SCEEEEECCCCTTTCCTTCCEEEEESSSHHHHHHTTCSSCCBTTBCCEEECC
T ss_pred             CEEEcCCCCCCCHHHHHHHHHHh--CCcccccccccccccccccEEEEEECCHHHHHHHHhhCCCEECCEEeEEEEC
Confidence            48999999999999999999999  999999999985  78999999999999999999998888999999999875

>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=99.75  E-value=5.2e-18  Score=124.55  Aligned_cols=75  Identities=24%  Similarity=0.422  Sum_probs=70.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|+|.+++    |||||+|.+.++|.+|+. |||..|+|+.|+|.|++
T Consensus        17 ~~~~l~v~nL~~~~te~~L~~~F~~f--G~i~~v~i~~~k----g~afV~f~~~~~A~~Ai~~l~~~~i~g~~l~v~~ak   90 (96)
T d1x4ga1          17 KNCTVYCGGIASGLTDQLMRQTFSPF--GQIMEIRVFPEK----GYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGK   90 (96)
T ss_dssp             SCCEEEEECCSSCCCHHHHHHHHHHH--SCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHHh--CCceEEEEEecc----eEEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999  999999999885    599999999999999998 99999999999999997


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        91 ~~   92 (96)
T d1x4ga1          91 ES   92 (96)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.75  E-value=2.7e-18  Score=126.52  Aligned_cols=80  Identities=23%  Similarity=0.315  Sum_probs=72.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hC------CcccCCe
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LG------GTMLGYY  183 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~------g~~~~g~  183 (303)
                      ....++|||+|||+++|+++|+++|+.||.|.++.++.+..+  ++|||||+|.+.++|.+|++ +|      |..+.|+
T Consensus         5 ~~~~~tlfV~nLp~~~te~~l~~~f~~~G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           5 VTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCCCEEEESCCTTCCHHHHHHHHHTTSCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCCCEEEEcCCCCcCCHHHHHHHHhccccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            335789999999999999999999999999999999987765  79999999999999999998 76      5678899


Q ss_pred             eEEEeecCC
Q 022058          184 PVRVLPSKT  192 (303)
Q Consensus       184 ~i~v~~~~~  192 (303)
                      +|.|.++.+
T Consensus        85 ~l~v~~a~~   93 (98)
T d1x4ha1          85 QLKVDLAVT   93 (98)
T ss_dssp             EEEEECCCC
T ss_pred             EEEEEECCC
Confidence            999999864

>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=99.75  E-value=3.3e-18  Score=122.77  Aligned_cols=77  Identities=18%  Similarity=0.242  Sum_probs=72.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+|+++|+++|+.|  |.|..|.|.++. |.++|||||+|.+.++|.+|++++|..+.|+.|.|.|++
T Consensus         5 ~~rtvfV~nlp~~~te~~l~~~F~~~--G~v~~v~l~~~~~~~~kG~afV~f~~~e~a~~al~~~~~~~~g~~l~v~~~~   82 (85)
T d1zh5a2           5 KNRSVYIKGFPTDATLDDIKEWLEDK--GQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVETPGQKYKETDLLILFKD   82 (85)
T ss_dssp             HTTEEEEECCCTTCCHHHHHHHHTTS--CCEEEEEEEECTTCCEEEEEEEEESCHHHHHHHHTCCCCEETTEECEEEEGG
T ss_pred             CcCEEEEECCCCCCCHHHHHHHHHHh--cccccceeeeeccCCcceEEEEEEcCHHHHHHHHHHCCCEECCEEEEEEEcC
Confidence            34799999999999999999999999  999999998875 789999999999999999999999999999999999875

>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=99.75  E-value=3.3e-18  Score=119.72  Aligned_cols=74  Identities=27%  Similarity=0.369  Sum_probs=70.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ++|||+|||+++++++|+++|+++  |.|..+.+.++++..+++|||+|.+.++|.+|+.||+..|+|++|.|..+
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 TTVLVKNLPKSYNQNKVYKYFKHC--GPIIHVDVADSLKKNFRFARIEFARYDGALAAITKTHKVVGQNEIIVSHL   74 (75)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHGGG--SCEEEEEEEECTTSSSEEEEEEESSHHHHHHHHTTTTCEETTEECEEEEC
T ss_pred             CEEEEECCCCCCCHHHHHHHHhcC--CceEEEEEEeeccccceEEEEEEcchHHhHHHHHhcCcEECCEEEEEEEC
Confidence            479999999999999999999998  99999999999877778999999999999999999999999999999865

>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=99.74  E-value=5.2e-19  Score=128.66  Aligned_cols=78  Identities=18%  Similarity=0.238  Sum_probs=72.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      ...+|||+|||+.+++++|+++|++|  |.|..+.|+.+. |+++|||||+|.+.++|.+|++|||..++|+.|+|.+|+
T Consensus        12 ~~~~ifV~nL~~~~te~~l~~~F~~~--G~i~~~~v~~~~~g~~kg~afv~F~~~e~a~~Al~~~g~~~~g~~i~V~~ak   89 (91)
T d1fjeb1          12 TPFNLFIGNLNPNKSVAELKVAISEL--FAKNDLAVVDVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK   89 (91)
T ss_dssp             SSEEEEEECCCTTSCHHHHHHHHHHH--HHHHTCCCCEEEEETTTTEEEEEESSHHHHHHHHHGGGEEETTEEEEEECCC
T ss_pred             CCcEEEEeCccCcchHHHHHHHHhcC--CcEEEeeeeecCCCCccEEeEEeeCCHHHHHHHHhcCCcEECCEEEEEEecC
Confidence            45789999999999999999999999  999998887654 889999999999999999999999999999999999997


Q ss_pred             C
Q 022058          291 T  291 (303)
Q Consensus       291 ~  291 (303)
                      +
T Consensus        90 ~   90 (91)
T d1fjeb1          90 G   90 (91)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.74  E-value=4.5e-18  Score=126.07  Aligned_cols=79  Identities=18%  Similarity=0.298  Sum_probs=70.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCccee--------EEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVT--------RLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~--------~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      ...+|||+|||..+++++|+++|++|  |.|.        .+.+..+.  |+++|||||+|.+.++|.+|++ |||..|.
T Consensus         7 ~~~~i~V~nLp~~~te~~l~~~F~~~--G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~   84 (101)
T d2cpea1           7 DNSAIYVQGLNDSVTLDDLADFFKQC--GVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQ   84 (101)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHHTTT--SCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEET
T ss_pred             CCCEEEEECCCCcCCHHHHHHHHHHC--ceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEEC
Confidence            45899999999999999999999999  9884        45566664  6789999999999999999998 9999999


Q ss_pred             CeeeEEeecCCC
Q 022058          281 SQPIRVSPSKTP  292 (303)
Q Consensus       281 g~~l~v~~a~~~  292 (303)
                      |+.|+|+++++.
T Consensus        85 gr~i~V~~a~~~   96 (101)
T d2cpea1          85 GSKLKVSLARKK   96 (101)
T ss_dssp             TEECEEECSSCC
T ss_pred             CEEEEEEEcCCC
Confidence            999999999854

>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=99.74  E-value=5.1e-18  Score=121.23  Aligned_cols=76  Identities=21%  Similarity=0.327  Sum_probs=69.2

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC-CeeEEEeec
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG-YYPVRVLPS  190 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~-g~~i~v~~~  190 (303)
                      ..++++|||+|||+++++++|+++|+.||+|.+|+++++.   +|||||+|.+.++|..|+. |||..+. |++|+|.|+
T Consensus         5 ~pP~~tl~V~nLp~~~t~~~l~~~f~~~G~i~~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~a   81 (83)
T d2b0ga1           5 QPPNQILFLTNLPEETNEMMLSMLFNQFPGFKEVRLVPNR---HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITFA   81 (83)
T ss_dssp             CSCCSEEEEESCCTTCCHHHHHHHHTTSTTEEEEEECTTT---CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEEC
T ss_pred             CCCCCEEEEECCCCCCCHHHHHhhhccCccEEEeeeeccc---ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEEe
Confidence            3457899999999999999999999999999999997653   6899999999999999998 9999885 799999998


Q ss_pred             C
Q 022058          191 K  191 (303)
Q Consensus       191 ~  191 (303)
                      +
T Consensus        82 k   82 (83)
T d2b0ga1          82 K   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.74  E-value=5.5e-18  Score=128.46  Aligned_cols=77  Identities=19%  Similarity=0.251  Sum_probs=71.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|.+|.+..+ +.++|||||+|.+.++|..|+. |||..|.|+.|.|.++.
T Consensus         6 ~~r~l~V~nLp~~~te~~l~~~F~~~--G~v~~i~~~~~-~~~kG~afV~f~~~~~A~~Ai~~l~g~~~~gr~l~V~~a~   82 (114)
T d2f9da1           6 VNRILYIRNLPYKITAEEMYDIFGKY--GPIRQIRVGNT-PETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYN   82 (114)
T ss_dssp             CCSEEEEESCCTTCCHHHHHHHHHTT--SCEEEEEEECS-TTTTTEEEEEESSHHHHHHHHHHHTTCEETTEECEEEECC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc--CCeEeeccccc-CCcCCeEEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            34799999999999999999999999  99999999876 4578999999999999999998 99999999999999986


Q ss_pred             C
Q 022058          291 T  291 (303)
Q Consensus       291 ~  291 (303)
                      +
T Consensus        83 ~   83 (114)
T d2f9da1          83 A   83 (114)
T ss_dssp             H
T ss_pred             C
Confidence            4

>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=99.74  E-value=5.5e-18  Score=124.19  Aligned_cols=78  Identities=24%  Similarity=0.365  Sum_probs=71.0

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..+++|||+|||+++++++|+++|+.||.|..+.+..+. .++|||||+|.+.++|++||+ ||+..+.|++|+|.|++.
T Consensus        12 ~~~~~l~V~nLp~~~t~~~l~~~F~~~G~v~~~~~~~~~-~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~~   90 (95)
T d1x4aa1          12 NNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRR-GGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPRS   90 (95)
T ss_dssp             CCSSEEEEESCCTTCCHHHHHHHHGGGSCEEEEEECCSS-SSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCCC
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHhcCCceEEEEecccc-cccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEeccC
Confidence            456789999999999999999999999999999876543 468999999999999999998 999999999999999864

>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=99.74  E-value=2.6e-18  Score=127.41  Aligned_cols=79  Identities=18%  Similarity=0.337  Sum_probs=73.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|||+|||.++++++|+++|++|  |.|..+.+..+. +.++|||||+|.+.++|.+|+. |||..|.|+.+.|.++
T Consensus        17 ~~~~lfV~nLp~~~te~~L~~~F~~~--G~i~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~i~gr~~~v~~~   94 (101)
T d1x5oa1          17 DPTNLYISNLPLSMDEQELENMLKPF--GQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGHFNGKFIKTPPGVSAPT   94 (101)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEEECSSSCEEEEEEEEESCHHHHHHHHHHHBTCCCCCCTTSCCCS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc--ccccceeeecccccccccceeEEeCCHHHHHHHHHHhCCCEECCcCCccCCC
Confidence            34789999999999999999999999  999999988875 7889999999999999999998 9999999999999888


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      +|-
T Consensus        95 ~Pl   97 (101)
T d1x5oa1          95 EPL   97 (101)
T ss_dssp             SCB
T ss_pred             CCc
Confidence            753

>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=99.73  E-value=1.1e-17  Score=124.75  Aligned_cols=80  Identities=23%  Similarity=0.353  Sum_probs=71.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~  288 (303)
                      +..+|||+|||..+++++|+++|+.|  | |..+.++.+.   ++++|||||+|.+.++|++|++||+..|.|+.|+|.+
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~--g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~   90 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGL--N-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDV   90 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTS--C-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHh--c-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEE
Confidence            45899999999999999999999999  8 7788777663   6789999999999999988888999999999999999


Q ss_pred             cCCCCC
Q 022058          289 SKTPVR  294 (303)
Q Consensus       289 a~~~~~  294 (303)
                      +++...
T Consensus        91 a~~~~~   96 (104)
T d1wi8a_          91 ADQAQD   96 (104)
T ss_dssp             CCCCCC
T ss_pred             CCCCCC
Confidence            986643

>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=99.73  E-value=3.3e-18  Score=119.72  Aligned_cols=73  Identities=15%  Similarity=0.254  Sum_probs=69.0

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      .|||+|||+++|+++|+++|++|  |.|..+.+..++  +.++|||||+|.+.++|.+|++|||+.|+|+.|+|.+|
T Consensus         1 rlfV~nLp~~~te~~l~~~F~~~--G~i~~~~~~~~~~~~~~~~~afV~F~~~~~a~~al~~~~~~l~gr~i~V~~A   75 (75)
T d2msta_           1 KIFVGGLSVNTTVEDVKHYFEQF--GKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIHFHEINNKMVECKKA   75 (75)
T ss_dssp             CEEEECCCSSCCHHHHHHHHHTT--SCCSEECCBCCTTCTTSCCEEEEECSCHHHHHHHHHCSSCCBTTBCCEEEEC
T ss_pred             CEEEeCCCCCCCHHHHHHHHHHh--CCcceeeeeeeccccccCceeEEEECCHHHHHHHHhcCCCEECCeEEEEEEC
Confidence            48999999999999999999999  999999988875  68899999999999999999999999999999999876

>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=99.73  E-value=1.2e-17  Score=120.08  Aligned_cols=77  Identities=23%  Similarity=0.310  Sum_probs=70.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||..+++++|+++|++|  |.|..+.+...    +|||||+|.+.++|..|+. |||..|+|+.|+|+|++
T Consensus         7 ~~k~l~V~nLp~~~te~~l~~~F~~~--g~i~~~~~~~~----rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~ak   80 (86)
T d2cpda1           7 SVKILYVRNLMLSTSEEMIEKEFNNI--KPGAVERVKKI----RDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK   80 (86)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHHHTT--STTCEEEEEEC----SSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHhhccc--ceeeeEEEccc----cEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEecc
Confidence            34789999999999999999999999  99998888544    5699999999999999998 99999999999999999


Q ss_pred             CCCC
Q 022058          291 TPVR  294 (303)
Q Consensus       291 ~~~~  294 (303)
                      |+.+
T Consensus        81 P~~~   84 (86)
T d2cpda1          81 PVDK   84 (86)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            7754

>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=99.73  E-value=9.6e-18  Score=123.54  Aligned_cols=79  Identities=23%  Similarity=0.363  Sum_probs=72.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hC------CceeCCe
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CS------GMVLGSQ  282 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~------g~~~~g~  282 (303)
                      ..++|||+|||+.+|+++|+++|++|  |.|.++.+..+.  +.++|||||+|.+.++|.+|++ ||      |..+.|+
T Consensus         7 ~~~tlfV~nLp~~~te~~l~~~f~~~--G~v~~~~~~~~~~~~~~~g~afV~F~~~~~a~~ai~~l~~~~~~~g~~~~gr   84 (98)
T d1x4ha1           7 EGKTVFIRNLSFDSEEEALGEVLQQF--GDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQKCLAAASLEAEGGGLKLDGR   84 (98)
T ss_dssp             CCCCEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCBCSSSCCBCSEEEEEESSHHHHHHHHHHHCTTTTTCCEESSSC
T ss_pred             CCCEEEEcCCCCcCCHHHHHHHHhcc--ccceeeeeccccccccccceEEEEEcCHHHHHHHHHHcccccccCCcEECCE
Confidence            34789999999999999999999999  999999998875  6789999999999999999998 76      6789999


Q ss_pred             eeEEeecCCC
Q 022058          283 PIRVSPSKTP  292 (303)
Q Consensus       283 ~l~v~~a~~~  292 (303)
                      .|+|.++++.
T Consensus        85 ~l~v~~a~~k   94 (98)
T d1x4ha1          85 QLKVDLAVTR   94 (98)
T ss_dssp             EEEEECCCCC
T ss_pred             EEEEEECCCC
Confidence            9999999864

>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=99.73  E-value=1.2e-17  Score=120.69  Aligned_cols=77  Identities=26%  Similarity=0.311  Sum_probs=69.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee-CCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL-GSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~-~g~~l~v~~a  289 (303)
                      ++++|||+|||..+++++|+++|++|  |.|..+.+..++  ++|+|||+|.+.++|.+|+. |||..+ +|+.|+|+|+
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~--G~v~~~~~~~~~--~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~s   84 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSN--GGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFS   84 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTT--SCCEEEEEECSS--STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEEC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhcc--CCEEEEEEeeec--ccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeC
Confidence            46899999999999999999999999  999988776653  46799999999999999998 999998 5899999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      ++.
T Consensus        85 k~~   87 (88)
T d2adca2          85 KST   87 (88)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            875

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=1.6e-17  Score=121.68  Aligned_cols=78  Identities=19%  Similarity=0.277  Sum_probs=71.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.++|||+|||+.+++++|+++|++|  |.|..+.+..+ +.++|||||+|.+.++|..||+ |||..|.|+.|+|.|++
T Consensus        13 ~~~~l~V~nLp~~~t~~~l~~~F~~~--G~v~~~~~~~~-~~~~g~afV~f~~~e~a~~Ai~~l~g~~~~g~~l~V~~a~   89 (95)
T d1x4aa1          13 NDCRIYVGNLPPDIRTKDIEDVFYKY--GAIRDIDLKNR-RGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR   89 (95)
T ss_dssp             CSSEEEEESCCTTCCHHHHHHHHGGG--SCEEEEEECCS-SSSSCCEEEEESCHHHHHHHHHHHTTCEETTEECEEECCC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhcC--CceEEEEeccc-ccccceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEecc
Confidence            34689999999999999999999999  99999998665 4568999999999999999998 99999999999999997


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        90 ~~   91 (95)
T d1x4aa1          90 SG   91 (95)
T ss_dssp             CC
T ss_pred             CC
Confidence            53

>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=99.73  E-value=9.6e-18  Score=119.75  Aligned_cols=75  Identities=19%  Similarity=0.330  Sum_probs=69.1

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeC-CeeeEEee
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLG-SQPIRVSP  288 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~-g~~l~v~~  288 (303)
                      ++.++|||+|||..+++++|+++|++|  |.|.++++.++.   +|||||+|.+.++|.+|++ |||..+. |+.|+|+|
T Consensus         6 pP~~tl~V~nLp~~~t~~~l~~~f~~~--G~i~~v~~~~~~---~g~afV~f~~~~~A~~A~~~l~g~~~~~~~~i~v~~   80 (83)
T d2b0ga1           6 PPNQILFLTNLPEETNEMMLSMLFNQF--PGFKEVRLVPNR---HDIAFVEFTTELQSNAAKEALQGFKITPTHAMKITF   80 (83)
T ss_dssp             SCCSEEEEESCCTTCCHHHHHHHHTTS--TTEEEEEECTTT---CSCEEEEESSHHHHHHHHHHHTTCBSSTTCBCEEEE
T ss_pred             CCCCEEEEECCCCCCCHHHHHhhhccC--ccEEEeeeeccc---ceeEEEecCCHHHHHHHHHHhCCcEeCCCcEEEEEE
Confidence            456899999999999999999999999  999999998764   4699999999999999998 9999985 79999999


Q ss_pred             cC
Q 022058          289 SK  290 (303)
Q Consensus       289 a~  290 (303)
                      |+
T Consensus        81 ak   82 (83)
T d2b0ga1          81 AK   82 (83)
T ss_dssp             CC
T ss_pred             ec
Confidence            97

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Hypothetical protein FLJ20273
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=8.8e-18  Score=123.35  Aligned_cols=79  Identities=20%  Similarity=0.196  Sum_probs=69.4

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCc-eeEEEEeeCCC---CCceEEEEEecCHHHHHHHHH-hCC--cccCCeeEEEe
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQ-VVDCRVCGDPH---SVLRFAFVEFADEHGARAALN-LGG--TMLGYYPVRVL  188 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~-i~~~~i~~~~~---~~~G~~fV~f~~~~~A~~Ai~-l~g--~~~~g~~i~v~  188 (303)
                      ++.|||+|||.++++++|+++|+.||+ |.++.++.+..   .++|||||+|.+.++|..|++ |++  ..+.|++|.|.
T Consensus         1 n~rLyV~nLp~~~te~~l~~~f~~~g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V~   80 (96)
T d2disa1           1 NCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAVD   80 (96)
T ss_dssp             SEEEEEECCCTTSCHHHHHHHHHHHSTTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEEE
T ss_pred             CCEEEEcCCCCcCCHHHHHHHHHHhCCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEEE
Confidence            368999999999999999999999996 89999988754   289999999999999999998 864  45579999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      |+++..
T Consensus        81 ~A~p~~   86 (96)
T d2disa1          81 WAEPEI   86 (96)
T ss_dssp             ESCSSC
T ss_pred             EcCCCC
Confidence            997543

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.72  E-value=3.4e-18  Score=123.78  Aligned_cols=74  Identities=12%  Similarity=0.254  Sum_probs=67.2

Q ss_pred             CCCEEEEcCCCCCCCHHHH---HHHhhcCCceeEEEEeeCCCC-----CceEEEEEecCHHHHHHHHH-hCCcccCCeeE
Q 022058          115 VRRTVYVSDIDQNITEERL---AGLFSSCGQVVDCRVCGDPHS-----VLRFAFVEFADEHGARAALN-LGGTMLGYYPV  185 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l---~~~F~~~G~i~~~~i~~~~~~-----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i  185 (303)
                      ..++|||+|||+++++++|   +++|++||.|.+|.+++++.+     .+|||||+|.+.++|.+|++ |||..+.|++|
T Consensus         7 q~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~l   86 (89)
T d2cpia1           7 QKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTL   86 (89)
T ss_dssp             CSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEEE
T ss_pred             ecCEEEEECCCCccCHHHHHHHHHHhcccCCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEEE
Confidence            3567999999999999999   678999999999999988654     35999999999999999998 99999999999


Q ss_pred             EEe
Q 022058          186 RVL  188 (303)
Q Consensus       186 ~v~  188 (303)
                      +|.
T Consensus        87 kvS   89 (89)
T d2cpia1          87 KAS   89 (89)
T ss_dssp             EEE
T ss_pred             EEC
Confidence            974

>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=99.72  E-value=1.1e-17  Score=120.30  Aligned_cols=74  Identities=24%  Similarity=0.310  Sum_probs=69.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+|||+++++++|+++|++||+|.+|.+.++    +|||||+|.+.++|.+|+. |||..+.|++|+|.|+..
T Consensus         7 ~~~~l~V~nLp~~~~~~~l~~~F~~~G~i~~i~~~~~----k~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~   81 (86)
T d2cpja1           7 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD----KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACH   81 (86)
T ss_dssp             CTTEEEEESCCTTCCHHHHHHHTSTTCCCSEEEEETT----TTEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSC
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHHhCCceEeeeecc----cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCC
Confidence            4567999999999999999999999999999999865    5799999999999999998 999999999999999854

>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=99.72  E-value=2.5e-18  Score=127.78  Aligned_cols=79  Identities=19%  Similarity=0.216  Sum_probs=73.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC--CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD--HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d--~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      +.++|||+|||..+++++|+++|++|  |.|..+.+..+  .|+++|||||+|.+.++|.+|++ |||..|.|+.|+|+|
T Consensus        17 ps~tl~V~nLp~~~t~~~l~~~f~~~--G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~   94 (102)
T d2cpxa1          17 PNKVLYLKNLSPRVTERDLVSLFARF--QEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEF   94 (102)
T ss_dssp             CCSEEEEECCCTTCCHHHHHHHTHHH--HHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHhhc--cceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEe
Confidence            56899999999999999999999999  99999888776  37899999999999999999998 999999999999999


Q ss_pred             cCCC
Q 022058          289 SKTP  292 (303)
Q Consensus       289 a~~~  292 (303)
                      +++.
T Consensus        95 ak~k   98 (102)
T d2cpxa1          95 GKNK   98 (102)
T ss_dssp             CCCC
T ss_pred             CCCc
Confidence            9853

>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=99.72  E-value=1.5e-17  Score=120.06  Aligned_cols=76  Identities=30%  Similarity=0.252  Sum_probs=68.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc-CCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML-GYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~-~g~~i~v~~~~~  192 (303)
                      ++++|||+|||+++++++|+++|+.||.|..+.+....  ++|||||+|.+.++|.+|+. |||..+ +|++|+|.|+++
T Consensus         9 Ps~tL~V~NLp~~~te~~l~~~F~~~G~v~~~~~~~~~--~~~~afV~f~~~~~A~~A~~~l~~~~i~~g~~l~v~~sk~   86 (88)
T d2adca2           9 PSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQK--DRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKS   86 (88)
T ss_dssp             SCSEEEEECCCTTCCHHHHHHHHHTTSCCEEEEEECSS--STTCEEEEESSHHHHHHHHHHHTTCBSSSSCBCEEEECSS
T ss_pred             CCCEEEEECCCCCCCHHHHHHHhhccCCEEEEEEeeec--ccceeEEEECCHHHHHHHHHhccCCEecCCCEEEEEeCCC
Confidence            47899999999999999999999999999888776543  47899999999999999998 999988 589999999864

>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=99.72  E-value=1.3e-17  Score=124.26  Aligned_cols=78  Identities=24%  Similarity=0.405  Sum_probs=69.6

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC-C--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH-S--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~-~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ..++|||+|||+++|+++|+++|+.|| |.++.++.+.. +  ++|||||+|.+.++|++|+.+|+..|.|+.|+|.++.
T Consensus        14 p~~~v~V~nLp~~~te~~l~~~f~~~g-~~~~~~~~~~~~~g~~~g~afV~f~~~e~a~~~~~~~~~~~~gr~l~V~~a~   92 (104)
T d1wi8a_          14 PPYTAFLGNLPYDVTEESIKEFFRGLN-ISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEESLGNKRIRVDVAD   92 (104)
T ss_dssp             SCEEEEEESCCSSCCHHHHHHHTTTSC-EEEEECCBCSSCTTSBCSCEEEEESSHHHHHHHHGGGTCEETTEECEEEECC
T ss_pred             CCCEEEEeCCCCcCCHHHHHHHHHHhc-cccceeeeeeccCCCcceeeeEEECCHHHHHHHHHcCCCEECCEEEEEEECC
Confidence            468999999999999999999999999 77788777653 2  7899999999999999888899999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus        93 ~~   94 (104)
T d1wi8a_          93 QA   94 (104)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.72  E-value=1.4e-17  Score=125.05  Aligned_cols=75  Identities=28%  Similarity=0.381  Sum_probs=69.3

Q ss_pred             CCEEEEcCCCC-CCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          116 RRTVYVSDIDQ-NITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       116 ~~~l~V~nlp~-~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      +++|||+|||+ .+|+++|+++|+.||.|.+|.|+++.   +|||||+|.+.++|.+|++ |||..+.|++|+|.+++..
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~fG~I~~v~i~~~~---kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~~~   78 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQ   78 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHHTCEEEEEECCTT---SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCSCC
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhccccceEEEEecc---cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCC
Confidence            57899999965 59999999999999999999998875   6899999999999999998 9999999999999998644

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding motif, single-stranded-interacting protein 2, RBMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.6e-18  Score=119.36  Aligned_cols=68  Identities=19%  Similarity=0.371  Sum_probs=64.2

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCCeeEE
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGYYPVR  186 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~  186 (303)
                      |||+|||+++|+++|+++|+.||.|..+++++++.+  ++|||||+|.+.++|++|++ |||..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTTSCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhhccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            799999999999999999999999999999988765  89999999999999999998 999999999864

>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=99.72  E-value=9.5e-18  Score=124.55  Aligned_cols=81  Identities=22%  Similarity=0.185  Sum_probs=71.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      .....+|||+|||+++|+++|+++|..||. ..+.++.+..+ ++|||||+|.+.++|++|+++|+..|+||.|.|.++.
T Consensus        12 ~~~~~~v~v~nLp~~~te~dl~~~F~~~~~-~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s~   90 (102)
T d1weza_          12 STTGHCVHMRGLPYRATENDIYNFFSPLNP-MRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLNS   90 (102)
T ss_dssp             CSSSCEEEEESCCTTCCHHHHHHSSCSCCC-SEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEEC
T ss_pred             CCCCCEEEEeCCCCcCCHHHHHHHHhccCc-ceeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEcC
Confidence            335678999999999999999999999985 57888887665 7999999999999999999999999999999999986


Q ss_pred             CCC
Q 022058          192 TAI  194 (303)
Q Consensus       192 ~~~  194 (303)
                      ...
T Consensus        91 ~~~   93 (102)
T d1weza_          91 TAG   93 (102)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            543

>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=99.72  E-value=1.1e-17  Score=123.93  Aligned_cols=79  Identities=24%  Similarity=0.352  Sum_probs=69.9

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCcee--------EEEEeeCCCC--CceEEEEEecCHHHHHHHHH-hCCcccCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVV--------DCRVCGDPHS--VLRFAFVEFADEHGARAALN-LGGTMLGY  182 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~--------~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g  182 (303)
                      ...++|||+|||+++|+++|+++|+.||.|.        .+.+..+..+  ++|||||+|.+.++|.+||+ |||..+.|
T Consensus         6 ~~~~~i~V~nLp~~~te~~l~~~F~~~G~i~~~~~~~~~~~~~~~d~~~~~~~g~afV~f~~~~~a~~Ai~~l~g~~~~g   85 (101)
T d2cpea1           6 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQG   85 (101)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHHTTTSCBCBCSSSCCBSEECCBCTTTCSBCSEEEEEBSSHHHHHHHHHHHTTCEETT
T ss_pred             CCCCEEEEECCCCcCCHHHHHHHHHHCceEEEeeecccceeEEeeccccccccceeeEEecCHHHHHHHHHHhCCCEECC
Confidence            3578999999999999999999999999884        4455555543  68999999999999999998 99999999


Q ss_pred             eeEEEeecCC
Q 022058          183 YPVRVLPSKT  192 (303)
Q Consensus       183 ~~i~v~~~~~  192 (303)
                      ++|+|.++++
T Consensus        86 r~i~V~~a~~   95 (101)
T d2cpea1          86 SKLKVSLARK   95 (101)
T ss_dssp             EECEEECSSC
T ss_pred             EEEEEEEcCC
Confidence            9999999865

>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=99.72  E-value=8.9e-18  Score=124.70  Aligned_cols=83  Identities=17%  Similarity=0.151  Sum_probs=73.3

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ....+|||+|||+++|+++|+++|..+  | +..+.++.+. +.++|||||+|.+.++|++|++||+..|+||.|+|.++
T Consensus        13 ~~~~~v~v~nLp~~~te~dl~~~F~~~--~-~~~v~~~~~~~g~~~G~afVeF~~~~~a~~Al~~~~~~i~gR~I~V~~s   89 (102)
T d1weza_          13 TTGHCVHMRGLPYRATENDIYNFFSPL--N-PMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFLN   89 (102)
T ss_dssp             SSSCEEEEESCCTTCCHHHHHHSSCSC--C-CSEEEEEESSSSCEEEEEEEECSSSHHHHHHHTTSSCCSSSSCCEEEEE
T ss_pred             CCCCEEEEeCCCCcCCHHHHHHHHhcc--C-cceeeeEEecCCcceEEEEEEECCHHHHHHHHHcCCCEECCEEEEEEEc
Confidence            345799999999999999999999998  7 5577777774 78999999999999999999989999999999999999


Q ss_pred             CCCCCCC
Q 022058          290 KTPVRPR  296 (303)
Q Consensus       290 ~~~~~~r  296 (303)
                      .++...+
T Consensus        90 ~~~~~~~   96 (102)
T d1weza_          90 STAGTSG   96 (102)
T ss_dssp             CCCCCCC
T ss_pred             CCCCCCC
Confidence            8765443

>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=99.71  E-value=9e-18  Score=126.57  Aligned_cols=75  Identities=16%  Similarity=0.144  Sum_probs=69.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      .+++|||+|||+++++++|+++|+.||.|..|.|..    ++|||||+|.+.++|.+|++ |||..|.|++|.|.|+...
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~fG~I~~v~l~~----~kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~~~   84 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPE----GGITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAPIG   84 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTTSCEEEEECCS----SSSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEETT
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhccCCccEEEeec----cCceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECCCC
Confidence            457899999999999999999999999999998843    46899999999999999998 9999999999999998654

>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=99.71  E-value=2.3e-17  Score=123.86  Aligned_cols=76  Identities=26%  Similarity=0.424  Sum_probs=69.8

Q ss_pred             cceEEEcCCCC-CCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          213 SRTVYCTNIDK-KVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       213 ~~~l~V~nL~~-~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..+|||+|||+ .+++++|+++|++|  |.|.+|.|++++   +|||||+|.+.++|.+|++ |||..|.|+.|+|.|++
T Consensus         2 ~~~l~V~nL~p~~~te~~L~~~F~~f--G~I~~v~i~~~~---kg~afV~f~~~~~A~~ai~~lng~~l~g~~l~v~~s~   76 (109)
T d2adca1           2 NSVLLVSNLNPERVTPQSLFILFGVY--GDVQRVKILFNK---KENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSK   76 (109)
T ss_dssp             CSEEEEESCCTTTCCHHHHHHHHHHH--TCEEEEEECCTT---SCCEEEEESCHHHHHHHHHHHTTCBCSSSBCEEECCS
T ss_pred             CCEEEEeCCCcccCCHHHHHHHHhhc--cccceEEEEecc---cceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECC
Confidence            47899999965 59999999999999  999999999885   5799999999999999998 99999999999999997


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      ...
T Consensus        77 ~~~   79 (109)
T d2adca1          77 HQN   79 (109)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            553

>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=99.71  E-value=2.5e-17  Score=120.83  Aligned_cols=82  Identities=17%  Similarity=0.188  Sum_probs=72.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcc-eeEEEEecCC---CCcccEEEEEEcCHHHHHHHHH-hCC--ceeCCeeeEE
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGE-VTRLRLLGDH---VHSTRIAFVEFAVAESAILALN-CSG--MVLGSQPIRV  286 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~-i~~v~i~~d~---~~~~g~afV~f~~~e~A~~Ai~-l~g--~~~~g~~l~v  286 (303)
                      +.|||+|||..+++++|+++|++|  |. |..+.++++.   ++++|||||+|.+.++|..|++ |++  ..++|+.|+|
T Consensus         2 ~rLyV~nLp~~~te~~l~~~f~~~--g~~i~~v~~~~~~~~~~~~rg~aFV~F~~~~~A~~Ai~~l~~~~~~~~g~~i~V   79 (96)
T d2disa1           2 CRLFIGGIPKMKKREEILEEIAKV--TEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGRIQLWGHQIAV   79 (96)
T ss_dssp             EEEEEECCCTTSCHHHHHHHHHHH--STTEEEEECCSSSCTTTTTCCEEEEEESSHHHHHHHHTTTTTCCSCBTTBCCEE
T ss_pred             CEEEEcCCCCcCCHHHHHHHHHHh--CCcceEEEEeeeccccccCCCeEEEEEcCHHHHHHHHHHHcCCCeEECCEEEEE
Confidence            579999999999999999999999  95 8999998873   6789999999999999999998 854  5568999999


Q ss_pred             eecCCCCCCCC
Q 022058          287 SPSKTPVRPRV  297 (303)
Q Consensus       287 ~~a~~~~~~r~  297 (303)
                      .||+|...+-.
T Consensus        80 ~~A~p~~~~~~   90 (96)
T d2disa1          80 DWAEPEIDVDE   90 (96)
T ss_dssp             EESCSSCSTTT
T ss_pred             EEcCCCCCCCh
Confidence            99987655543

>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=99.71  E-value=1.3e-17  Score=122.75  Aligned_cols=73  Identities=25%  Similarity=0.508  Sum_probs=66.7

Q ss_pred             CCCEEEEcCCC-CCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDID-QNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp-~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ..++|||+||| ..+++++|+++|++||.|.+|.+.      +|||||+|.+.++|.+||. |||..+.|++|+|.++..
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~G~i~~~~i~------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~~   87 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLAAE   87 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTSSCEEEEEEE------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEETTS
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhcCCEEEEEEe------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEECCC
Confidence            45679999997 578899999999999999999983      6999999999999999998 999999999999999864


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus        88 ~   88 (98)
T d1wf2a_          88 P   88 (98)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.71  E-value=1.5e-17  Score=119.48  Aligned_cols=74  Identities=18%  Similarity=0.313  Sum_probs=69.7

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      .+|||+|||..+++++|+++|++|  |.|.+|.+.+++    |||||+|.+.++|.+|++ |||..+.|+.|+|+||.+.
T Consensus         9 ~~l~V~nLp~~~~~~~l~~~F~~~--G~i~~i~~~~~k----~~afV~f~~~~~A~~A~~~l~g~~i~g~~l~V~~A~~~   82 (86)
T d2cpja1           9 SRLFVGNLPPDITEEEMRKLFEKY--GKAGEVFIHKDK----GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS   82 (86)
T ss_dssp             TEEEEESCCTTCCHHHHHHHTSTT--CCCSEEEEETTT----TEEEEECSSSHHHHHHHHHHTTCCBTTBCCEEEESSCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHh--CCceEeeeeccc----ceEEEEECCHHHHHHHHHHhCCCEECCEEEEEEECCCc
Confidence            579999999999999999999999  999999999875    499999999999999998 9999999999999999765


Q ss_pred             C
Q 022058          293 V  293 (303)
Q Consensus       293 ~  293 (303)
                      .
T Consensus        83 ~   83 (86)
T d2cpja1          83 A   83 (86)
T ss_dssp             S
T ss_pred             C
Confidence            3

>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=99.71  E-value=2.4e-17  Score=121.36  Aligned_cols=73  Identities=19%  Similarity=0.365  Sum_probs=66.5

Q ss_pred             ccceEEEcCCC-CCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNID-KKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~-~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+||| ..+++++|+++|++|  |.|.++.|.      +|||||+|.+.++|.+|++ |||..|.|+.|+|.|+
T Consensus        14 ~~~~lfV~nL~~~~~~~~~L~~~F~~~--G~i~~~~i~------rg~aFV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a   85 (98)
T d1wf2a_          14 MNSRVFIGNLNTLVVKKSDVEAIFSKY--GKIVGCSVH------KGFAFVQYVNERNARAAVAGEDGRMIAGQVLDINLA   85 (98)
T ss_dssp             CCCCEEEEEECTTTCCHHHHHHSSTTS--SCEEEEEEE------TEEEEEEESSHHHHHHHHHTTTTCEETTEECEEEET
T ss_pred             CCcEEEEeCCCcccCCHHHHHHHHhhc--CCEEEEEEe------CCeEEEEECCHHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            34679999997 568889999999999  999999993      5799999999999999998 9999999999999999


Q ss_pred             CCC
Q 022058          290 KTP  292 (303)
Q Consensus       290 ~~~  292 (303)
                      +++
T Consensus        86 ~~~   88 (98)
T d1wf2a_          86 AEP   88 (98)
T ss_dssp             TSC
T ss_pred             CCC
Confidence            865

>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=99.71  E-value=1.5e-17  Score=119.56  Aligned_cols=74  Identities=26%  Similarity=0.379  Sum_probs=67.8

Q ss_pred             CCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          116 RRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       116 ~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      .++|||+|||+++++++|+++|+.||.|..+.+..    ++|||||+|.+.++|.+|+. |||..+.|+.|.|.|+++.
T Consensus         8 ~k~l~V~nLp~~~te~~l~~~F~~~g~i~~~~~~~----~rg~afV~f~~~~~A~~Ai~~l~~~~i~g~~i~V~~akP~   82 (86)
T d2cpda1           8 VKILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKK----IRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPV   82 (86)
T ss_dssp             CCEEEEESCCTTCCHHHHHHHHHTTSTTCEEEEEE----CSSEEEEEESSHHHHHHHHHHHSSEEETTEEEEEECCCCC
T ss_pred             CCEEEEcCCCCCCCHHHHHHhhcccceeeeEEEcc----ccEEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEeccCC
Confidence            47899999999999999999999999998887743    46899999999999999998 9999999999999998643

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 41, RBM41
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.71  E-value=2.3e-18  Score=127.94  Aligned_cols=80  Identities=19%  Similarity=0.201  Sum_probs=73.1

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCC--CCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPH--SVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~--~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ..+++|||+|||.++++++|+++|+.||.|..+.++.+..  .++|||||+|.+.++|.+|++ |||..+.|++|.|.|+
T Consensus        16 ~ps~tl~V~nLp~~~t~~~l~~~f~~~G~v~~~~~~~~~~~g~~~g~~fV~f~~~~~A~~Ai~~l~g~~~~g~~l~V~~a   95 (102)
T d2cpxa1          16 EPNKVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLVNGYKLYGKILVIEFG   95 (102)
T ss_dssp             SCCSEEEEECCCTTCCHHHHHHHTHHHHHSSSSCCEEEEECSSSCSEEEEECSSHHHHHHHHHHSTTCBCSSCBCEEEEC
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHhhccceeeEEeecccccccccccceEEeccHHHHHHHHHHhCCCEECCEEEEEEeC
Confidence            3578999999999999999999999999999998887654  389999999999999999998 9999999999999998


Q ss_pred             CCC
Q 022058          191 KTA  193 (303)
Q Consensus       191 ~~~  193 (303)
                      ++.
T Consensus        96 k~k   98 (102)
T d2cpxa1          96 KNK   98 (102)
T ss_dssp             CCC
T ss_pred             CCc
Confidence            653

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein 19, Rbm19
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.70  E-value=2.8e-17  Score=123.80  Aligned_cols=79  Identities=19%  Similarity=0.156  Sum_probs=70.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||+.+++++|+++|++|  |.|..|.|.+.    +|||||+|.+.++|.+|++ |||..|.|+.|.|.|+.
T Consensus         9 ~~~~l~V~nLp~~~t~~~L~~~F~~f--G~I~~v~l~~~----kg~afV~f~~~~~A~~A~~~lng~~~~gr~l~v~~a~   82 (111)
T d1whxa_           9 SKTVILAKNLPAGTLAAEIQETFSRF--GSLGRVLLPEG----GITAIVEFLEPLEARKAFRHLAYSKFHHVPLYLEWAP   82 (111)
T ss_dssp             EEEEEEEESCCTTCCHHHHHHHHHTT--SCEEEEECCSS----SSCEEEEESCHHHHHHHHHHHTTCBSSSSBCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHhhhhcc--CCccEEEeecc----CceEEEEEcCHHHHHHHHHHHcCCccCCCeEEEEECC
Confidence            34789999999999999999999999  99999998654    4699999999999999998 99999999999999986


Q ss_pred             CCCCCC
Q 022058          291 TPVRPR  296 (303)
Q Consensus       291 ~~~~~r  296 (303)
                      ......
T Consensus        83 ~~~~~~   88 (111)
T d1whxa_          83 IGVFGA   88 (111)
T ss_dssp             TTTTCC
T ss_pred             CCcccc
Confidence            654443

>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=99.70  E-value=2.5e-17  Score=116.43  Aligned_cols=73  Identities=22%  Similarity=0.296  Sum_probs=67.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      .+++|||+|++  +|+++|+++|++|  |.|.++.+.+++    |||||+|.+.++|..|+. |||..+.|+.|+|.|++
T Consensus         4 ~~~ti~V~~~~--~te~~L~~~F~~~--G~I~~v~~~~~~----~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           4 KGNTLYVYGED--MTPTLLRGAFSPF--GNIIDLSMDPPR----NCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCEEEEECSS--CCHHHHHHHHSTT--CCCSCEEEETTT----TEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCEEEEECCC--CCHHHHHHHHhcc--CccceeeeccCC----CEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            35799999996  8999999999999  999999998765    499999999999999998 99999999999999997


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            54

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Nucleolin
species: Golden hamster (Mesocricetus auratus) [TaxId: 10036]

Probab=99.70  E-value=2.9e-17  Score=120.54  Aligned_cols=77  Identities=22%  Similarity=0.322  Sum_probs=69.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||.++++++|+++|++|  |.|..+.   ..+.++|||||+|.+.++|.+|+. |||..|+|+.|+|.|++
T Consensus        15 ~~~~l~V~nL~~~~te~~l~~~F~~~--g~v~~~~---~~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~   89 (96)
T d1fjca_          15 AARTLLAKNLSFNITEDELKEVFEDA--LEIRLVS---QDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTG   89 (96)
T ss_dssp             GGGEEEEESCCSSCCHHHHHHHHCSE--EEECCEE---ETTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECS
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHhc--ccceeee---ecCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeC
Confidence            45899999999999999999999999  9887654   356789999999999999999998 99999999999999998


Q ss_pred             CCC
Q 022058          291 TPV  293 (303)
Q Consensus       291 ~~~  293 (303)
                      +..
T Consensus        90 ~k~   92 (96)
T d1fjca_          90 EKG   92 (96)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            543

>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=99.70  E-value=3.9e-17  Score=121.62  Aligned_cols=81  Identities=20%  Similarity=0.155  Sum_probs=71.3

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC--CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS--VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~--~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      .....|||+|||+++|+++|+++|+.+|.|..+.++.+..+  ++|||||+|.+.++|++|+++|+..|.||.|.|.++.
T Consensus        13 ~~~~~v~v~nLP~~~te~dI~~~F~~~g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~~   92 (104)
T d1wg5a_          13 ANDGFVRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS   92 (104)
T ss_dssp             SCCCEEEEESCCTTCCHHHHHHHTTTCCEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEEC
T ss_pred             CCCcEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEECC
Confidence            35667999999999999999999999999988666655443  7899999999999999999999999999999999986


Q ss_pred             CCC
Q 022058          192 TAI  194 (303)
Q Consensus       192 ~~~  194 (303)
                      ...
T Consensus        93 ~~~   95 (104)
T d1wg5a_          93 RAE   95 (104)
T ss_dssp             TTT
T ss_pred             HHH
Confidence            543

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicing factor, arginine/serine-rich 1, SFRS1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=7e-18  Score=121.57  Aligned_cols=71  Identities=17%  Similarity=0.191  Sum_probs=66.2

Q ss_pred             eEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          215 TVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       215 ~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      +|||+|||+.+++++|+++|++|  |.|.++.|.++     |||||+|.+.++|.+||. |||..|.|+.|+|.++++.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~--G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~~   73 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREA--GDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRVK   73 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGG--SCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhh--ccccccccccc-----ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEecC
Confidence            69999999999999999999999  99999999876     599999999999999998 9999999999999887544

>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=99.69  E-value=4.2e-17  Score=115.22  Aligned_cols=75  Identities=27%  Similarity=0.363  Sum_probs=67.9

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      +...++|||+|||  +|+++|+++|++||.|.++.+.++    +|||||+|.+.++|.+|+. |||..+.|++|+|.|++
T Consensus         2 p~~~~ti~V~~~~--~te~~L~~~F~~~G~I~~v~~~~~----~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~V~~a~   75 (79)
T d2bz2a1           2 PRKGNTLYVYGED--MTPTLLRGAFSPFGNIIDLSMDPP----RNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR   75 (79)
T ss_dssp             CCCCCEEEEECSS--CCHHHHHHHHSTTCCCSCEEEETT----TTEEEEECSSHHHHHHHHHHHTTCBCSSCBCEEEECC
T ss_pred             CCCCCEEEEECCC--CCHHHHHHHHhccCccceeeeccC----CCEEEEEEcccHHHHHHHHHhCCCEECCEEEEEEEec
Confidence            3457899999996  899999999999999999999754    5799999999999999998 99999999999999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      +.
T Consensus        76 ~~   77 (79)
T d2bz2a1          76 KQ   77 (79)
T ss_dssp             SS
T ss_pred             CC
Confidence            43

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.69  E-value=2.4e-17  Score=119.72  Aligned_cols=78  Identities=27%  Similarity=0.424  Sum_probs=69.8

Q ss_pred             ccceEEEcCCCCCCCHHHHH----HHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEE
Q 022058          212 CSRTVYCTNIDKKVPQAEVK----QFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRV  286 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~----~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v  286 (303)
                      +.++|||+|||+.+++++|+    ++|++|  |.|.+|.+... ++++|||||+|.+.++|.+|+. |||..++|+.|+|
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 PNHTIYINNLNEKIKKDELKKSLHAIFSRF--GQILDILVSRS-LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRI   78 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGG--SCEEEEECCHH-HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhccc--ccccceEEeee-ccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEE
Confidence            45899999999999999886    468999  99999988653 4568899999999999999998 9999999999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      .||++.
T Consensus        79 ~~ak~~   84 (91)
T d1nu4a_          79 QYAKTD   84 (91)
T ss_dssp             EECSSC
T ss_pred             EEeCCC
Confidence            999865

>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=99.69  E-value=2.1e-17  Score=121.31  Aligned_cols=77  Identities=21%  Similarity=0.267  Sum_probs=68.7

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ...++|||+|||+++|+++|+++|+.||.|..+..   ...++|||||+|.+.++|.+|+. |||..+.|++|.|.|+.+
T Consensus        14 ~~~~~l~V~nL~~~~te~~l~~~F~~~g~v~~~~~---~~~~~~~afV~f~~~~~A~~A~~~l~~~~~~gr~i~V~~a~~   90 (96)
T d1fjca_          14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQ---DGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLYYTGE   90 (96)
T ss_dssp             TGGGEEEEESCCSSCCHHHHHHHHCSEEEECCEEE---TTEEEEEEEEEESSHHHHHHHHHHTTEEEETTEEEEEEECSS
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHHHHhcccceeeee---cCccccEEEEEeCCHHHHHHHHHHcCCCEECCEEEEEEEeCC
Confidence            35688999999999999999999999999876543   33478999999999999999998 999999999999999865


Q ss_pred             C
Q 022058          193 A  193 (303)
Q Consensus       193 ~  193 (303)
                      .
T Consensus        91 k   91 (96)
T d1fjca_          91 K   91 (96)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=99.69  E-value=3e-17  Score=117.94  Aligned_cols=76  Identities=14%  Similarity=0.166  Sum_probs=67.1

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeE-EEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVD-CRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~-~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      ....|||+|||+++++++|+++|+.||.+.. +.+..+..+ ++|||||+|.+.++|++|+. ||+..+.||+|+|.++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l~   86 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLG   86 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTSCCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEES
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhcccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEEC
Confidence            3567999999999999999999999999976 455555544 79999999999999999998 9999999999999863

>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=99.69  E-value=1.9e-17  Score=119.72  Aligned_cols=73  Identities=16%  Similarity=0.423  Sum_probs=66.5

Q ss_pred             cceEEEcCCCCCCCHHHH---HHHhhhhcCcceeEEEEecCC--C---CcccEEEEEEcCHHHHHHHHH-hCCceeCCee
Q 022058          213 SRTVYCTNIDKKVPQAEV---KQFFEAACGGEVTRLRLLGDH--V---HSTRIAFVEFAVAESAILALN-CSGMVLGSQP  283 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L---~~~F~~~~~G~i~~v~i~~d~--~---~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~  283 (303)
                      .++|||+|||+.+++++|   +++|++|  |.|.+|.|++++  +   ..+|||||+|.+.++|.+|++ |||..++|+.
T Consensus         8 ~n~vyV~nLp~~~t~~~l~~~~e~F~~~--G~I~~v~i~~~~~~~~~~~~~g~aFV~f~~~~~A~~Ai~~lng~~~~gr~   85 (89)
T d2cpia1           8 KNLVFVVGLSQRLADPEVLKRPEYFGKF--GKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRT   85 (89)
T ss_dssp             SSCEEEEEECTTTCCHHHHHSTTTTTTT--SCEEEEEEECCSSCCSSSCCCEEEEEEESSHHHHHHHHHHHTTEEETTEE
T ss_pred             cCEEEEECCCCccCHHHHHHHHHHhccc--CCceEEEEeeccCcCCCCCcceEEEEecccchhHHHHHHHhCCCEECCEE
Confidence            367999999999999999   6789999  999999999885  2   346899999999999999998 9999999999


Q ss_pred             eEEe
Q 022058          284 IRVS  287 (303)
Q Consensus       284 l~v~  287 (303)
                      |+|+
T Consensus        86 lkvS   89 (89)
T d2cpia1          86 LKAS   89 (89)
T ss_dssp             EEEE
T ss_pred             EEEC
Confidence            9986

>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=99.69  E-value=2.3e-17  Score=119.10  Aligned_cols=75  Identities=25%  Similarity=0.365  Sum_probs=67.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..++|||+|||+++|+++|+++|++||.|.+|++..+   ++|||||+|.+.++|++|+. ++..|.|++|.|.++++.
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~G~v~~v~~~~~---~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~k   78 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP---FRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEPK   78 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTTSCCCEEECCSS---CCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHcCCceEEEEeec---cCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCCC
Confidence            5789999999999999999999999999999987543   57999999999999999997 778999999999998654

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.7e-17  Score=116.54  Aligned_cols=73  Identities=23%  Similarity=0.285  Sum_probs=66.0

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCc-eeCCeeeEEeecCC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGM-VLGSQPIRVSPSKT  291 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~-~~~g~~l~v~~a~~  291 (303)
                      .+|||+|||..+++++|+++|++|  |.|.++.+.+.    +|||||+|.+.++|.+|++ |||. .++|+.|+|.|+.|
T Consensus         2 n~l~V~nLp~~~te~~L~~~F~~~--G~i~~~~~~~~----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~   75 (80)
T d2cqha1           2 NKLYIGNLSPAVTADDLRQLFGDR--KLPLAGQVLLK----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVS   75 (80)
T ss_dssp             CCEEEECCCTTCCHHHHHHHHHHT--TCCCSSCEEEE----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCC
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHh--CcEEEeEEecc----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCC
Confidence            469999999999999999999999  99988777654    4699999999999999998 9996 69999999999985


Q ss_pred             C
Q 022058          292 P  292 (303)
Q Consensus       292 ~  292 (303)
                      .
T Consensus        76 k   76 (80)
T d2cqha1          76 K   76 (80)
T ss_dssp             C
T ss_pred             c
Confidence            3

>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=99.68  E-value=7.1e-17  Score=112.81  Aligned_cols=69  Identities=22%  Similarity=0.268  Sum_probs=62.0

Q ss_pred             EEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          119 VYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       119 l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      |||+|||+++++++|+++|++|| +..+.+.    .++|||||+|.+.++|.+|+. |||..+.|++|.|.+++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~g-~~~~~~~----~~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~   70 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDYE-LKYCFVD----KYKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPT   70 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTSC-EEEEEEE----TTTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCS
T ss_pred             CEEeCCCCcCCHHHHHHHHhccc-ccceeec----ccceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCC
Confidence            79999999999999999999999 5555542    357899999999999999998 999999999999999854

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: IGF-II mRNA-binding protein 2 isoform A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.1e-17  Score=117.10  Aligned_cols=72  Identities=24%  Similarity=0.315  Sum_probs=65.5

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCc-ccCCeeEEEeecCCC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGT-MLGYYPVRVLPSKTA  193 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~-~~~g~~i~v~~~~~~  193 (303)
                      +|||+|||+++|+++|+++|++||.|.++.+...    +|||||+|.+.++|.+|++ |||. .+.|++|.|.|+.+.
T Consensus         3 ~l~V~nLp~~~te~~L~~~F~~~G~i~~~~~~~~----rg~aFV~f~~~~~A~~Ai~~lng~~~~~G~~i~V~~a~~k   76 (80)
T d2cqha1           3 KLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLK----SGYAFVDYPDQNWAIRAIETLSGKVELHGKIMEVDYSVSK   76 (80)
T ss_dssp             CEEEECCCTTCCHHHHHHHHHHTTCCCSSCEEEE----TTEEEECCSCHHHHHHHHHHHTTTCEETTEECEEEECCCC
T ss_pred             EEEEECCCCCCCHHHHHHHHHHhCcEEEeEEecc----cceEEEEECCHHHHHHHHHHhCCCeEECCEEEEEEEcCCc
Confidence            5999999999999999999999999988777653    5899999999999999998 9986 699999999998653

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=4.5e-17  Score=117.00  Aligned_cols=76  Identities=18%  Similarity=0.190  Sum_probs=68.1

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE-EEEecC-CCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR-LRLLGD-HVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~-v~i~~d-~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~  288 (303)
                      ...+|||+|||.++++++|+++|+.|  |.|.. +.+..+ .+.++|+|||+|.+.++|.+|++ |||..++|+.|+|++
T Consensus         8 ~~~~l~v~nLp~~~~~~di~~~F~~~--~~~~~~~~~~~~~~g~~~G~afV~f~~~e~a~~Ai~~l~~~~l~gr~i~v~l   85 (86)
T d2cqpa1           8 GPTIIKVQNMPFTVSIDEILDFFYGY--QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVL   85 (86)
T ss_dssp             SSEEEEEESCCTTCCHHHHHHHTTTS--CCCTTTCEEEECSSSCEEEEEEEEESCHHHHHHHHHHTTTCEETTEECEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHhhc--ccceeEEEEEeCCCCCcceEEEEEEcCcHHHHHHHHHcCCCEECCEEEEEEE
Confidence            34679999999999999999999999  98876 455555 47899999999999999999998 999999999999987


Q ss_pred             c
Q 022058          289 S  289 (303)
Q Consensus       289 a  289 (303)
                      +
T Consensus        86 ~   86 (86)
T d2cqpa1          86 G   86 (86)
T ss_dssp             S
T ss_pred             C
Confidence            5

>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=99.68  E-value=1.4e-17  Score=120.01  Aligned_cols=70  Identities=20%  Similarity=0.162  Sum_probs=65.2

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      .|||+|||+++++++|+++|++||+|.++.++.+     |||||+|.+.++|++||. |||..+.|+.|.|.+.+.
T Consensus         2 rvfV~nlp~~~~~~~l~~~F~~~G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~l~g~~~~g~~i~v~~~~~   72 (87)
T d3begb1           2 RVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD-----GTGVVEFVRKEDMTYAVRKLDNTKFRSHEGETAYIRV   72 (87)
T ss_dssp             CEEEEECCSSCCTTHHHHHHGGGSCEEEEEECTT-----SEEEEEESSHHHHHHHHHHHTTCBCCCTTSCCCBCEE
T ss_pred             eEEEECCCCcCCHHHHHHHHhhhccccccccccc-----ceeeEEeCCHHHHHHHHHHhCCCEECCcEeEEeEEec
Confidence            5999999999999999999999999999998754     799999999999999998 999999999999988643

>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=99.68  E-value=4.4e-17  Score=117.55  Aligned_cols=78  Identities=18%  Similarity=0.285  Sum_probs=69.5

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecCC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSKT  291 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~~  291 (303)
                      ..++|||+|||..+|+++|+++|++|  |.|.+|++..+   ++|||||+|.+.++|++|+. +++.|+|+.|.|.+++|
T Consensus         4 ~s~~lfV~nLp~~~te~~L~~~F~~~--G~v~~v~~~~~---~~gfafV~f~~~~~a~~a~~-~~~~i~g~~l~v~~a~~   77 (88)
T d1wf0a_           4 GSSGVFVGRCTGDMTEDELREFFSQY--GDVMDVFIPKP---FRAFAFVTFADDQIAQSLCG-EDLIIKGISVHISNAEP   77 (88)
T ss_dssp             CCCEEEEESCCSSSCHHHHHHHSTTT--SCCCEEECCSS---CCSCCEEECSCHHHHHHTTT-CEEEETTEEEEEECCCC
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHc--CCceEEEEeec---cCceEEEEECCHHHHHHHHh-CCCEECCEEeEEEeCCC
Confidence            45899999999999999999999999  99999987654   46799999999999999986 78899999999999986


Q ss_pred             CCCC
Q 022058          292 PVRP  295 (303)
Q Consensus       292 ~~~~  295 (303)
                      ....
T Consensus        78 k~~~   81 (88)
T d1wf0a_          78 KHNS   81 (88)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            5433

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Splicesomal U1A protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.68  E-value=2.4e-17  Score=119.77  Aligned_cols=77  Identities=29%  Similarity=0.447  Sum_probs=68.0

Q ss_pred             CCCEEEEcCCCCCCCHHHHHH----HhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEee
Q 022058          115 VRRTVYVSDIDQNITEERLAG----LFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLP  189 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~----~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~  189 (303)
                      ++++|||+|||+++++++|++    +|++||+|.+|.+..+ ..++|||||+|.+.++|.+|+. +||..+.|++|.|.|
T Consensus         2 P~~tl~V~nLp~~~t~~dl~~~l~~~f~~~G~i~~i~~~~~-~~~~g~afV~F~~~~~A~~A~~~~~~~~~~g~~l~v~~   80 (91)
T d1nu4a_           2 PNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRS-LKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQY   80 (91)
T ss_dssp             CCSEEEEESCCTTSCHHHHHHHHHHHHGGGSCEEEEECCHH-HHHTTCEEEEESSHHHHHHHHHHHTTCEETTEECEEEE
T ss_pred             CCCEEEEeCCCCCCCHHHHHHHHHHHhcccccccceEEeee-ccCCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEE
Confidence            368999999999999999864    6899999999987542 1268999999999999999998 999999999999999


Q ss_pred             cCC
Q 022058          190 SKT  192 (303)
Q Consensus       190 ~~~  192 (303)
                      +++
T Consensus        81 ak~   83 (91)
T d1nu4a_          81 AKT   83 (91)
T ss_dssp             CSS
T ss_pred             eCC
Confidence            864

>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=99.68  E-value=1.6e-17  Score=115.33  Aligned_cols=68  Identities=13%  Similarity=0.251  Sum_probs=64.4

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       216 l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      |||+|||.++|+++|+++|++|  |.|..+.+.+++  +.++|+|||+|.+.++|.+|++ |||..+.|+.|+
T Consensus         1 lyV~nLp~~~te~~l~~~F~~~--G~v~~~~~~~~~~~~~~~g~afV~f~~~~~A~~Ai~~lng~~~~Gr~~k   71 (72)
T d1x4ea1           1 LYIRGLQPGTTDQDLVKLCQPY--GKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQAQMAK   71 (72)
T ss_dssp             EEEESCCTTCCHHHHHTTSTTT--SCEEEEEEECCSSSCSCCSEEEEEESCHHHHHHHHHHHHHHTCCEESCC
T ss_pred             CEEeCCCCcCCHHHHHHHHhhh--ccccccccccccccccccceeEEEECCHHHHHHHHHHhCCCEECCEECc
Confidence            7999999999999999999999  999999999885  6799999999999999999998 999999999874

>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=99.68  E-value=1.3e-16  Score=117.21  Aligned_cols=76  Identities=16%  Similarity=0.312  Sum_probs=69.6

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCC--eeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGS--QPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g--~~l~v~  287 (303)
                      .+.++|||+|||+.+++++|+++|++|  |.|..+.+.+++    ++|||+|.+.++|.+|++ |||..|.|  ++|+|.
T Consensus        15 ~Ps~tl~V~nLp~~~t~~~l~~~f~~~--G~i~~~~~~~~~----~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~   88 (97)
T d1whya_          15 NPTTRLWVGGLGPNTSLAALAREFDRF--GSIRTIDHVKGD----SFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVD   88 (97)
T ss_dssp             CCCSCEEEECCCSSCCHHHHHHHHHTT--SCEEEEEECSSS----CCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEE
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHhh--cccceEeeeccc----cEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEE
Confidence            356899999999999999999999999  999999998775    499999999999999998 99999976  589999


Q ss_pred             ecCCC
Q 022058          288 PSKTP  292 (303)
Q Consensus       288 ~a~~~  292 (303)
                      |+++.
T Consensus        89 ~ak~~   93 (97)
T d1whya_          89 FAKSG   93 (97)
T ss_dssp             ECCCC
T ss_pred             eCCCC
Confidence            99864

>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=99.67  E-value=2e-16  Score=117.69  Aligned_cols=80  Identities=26%  Similarity=0.173  Sum_probs=71.2

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC--CCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH--VHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~--~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+++|+++|+++|..+  |.|..+.++.+.  ++++|+|||+|.+.++|.+|+++|+..|+||.|.|.++
T Consensus        14 ~~~~v~v~nLP~~~te~dI~~~F~~~--g~v~~~v~~~~~~~~~~kG~afV~F~~~e~a~~a~~~~~~~i~gR~i~V~~~   91 (104)
T d1wg5a_          14 NDGFVRLRGLPFGCSKEEIVQFFSGL--EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKS   91 (104)
T ss_dssp             CCCEEEEESCCTTCCHHHHHHHTTTC--CEEEEEEECCBCSSSCBCSEEEEEESSHHHHHHHHTTTTCCSSSSCCEEEEE
T ss_pred             CCcEEEEeCCCCCCCHHHHHHHHHhc--CCceEEEEEEeCCCCCcceEEEEEeCCHHHHHHHHhhCCCEEcceEEEEEEC
Confidence            44679999999999999999999998  988876555543  78999999999999999999999999999999999999


Q ss_pred             CCCC
Q 022058          290 KTPV  293 (303)
Q Consensus       290 ~~~~  293 (303)
                      .+..
T Consensus        92 ~~~~   95 (104)
T d1wg5a_          92 SRAE   95 (104)
T ss_dssp             CTTT
T ss_pred             CHHH
Confidence            7653

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.2e-16  Score=115.24  Aligned_cols=74  Identities=18%  Similarity=0.174  Sum_probs=64.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ..++|||+|||+.+++++|+++|++|  | +..+.+.    .++|||||+|.+.++|.+|++ |||+.+.|+.|+|+|++
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~--G-~~~~~~~----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~   76 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDY--D-LKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQP   76 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSS--C-CCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhc--C-ceeeeee----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcC
Confidence            45789999999999999999999999  8 4445553    345799999999999999998 99999999999999996


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        77 ~~   78 (88)
T d1wg1a_          77 TD   78 (88)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=7.3e-17  Score=120.95  Aligned_cols=78  Identities=22%  Similarity=0.197  Sum_probs=70.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc--CCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML--GYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~--~g~~i~v~~~~  191 (303)
                      ....|||+|||+++|+++|+++|+.||.|.+|.++.++  ++|||||+|.+.++|.+|+. |||..+  .|+.|.|.+++
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~G~i~~~~i~~~~--~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~s~   83 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKN--NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSK   83 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTTSCEEEEEEEEET--TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEECS
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccCCcEEEEEEEeeC--CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEecC
Confidence            45679999999999999999999999999999998765  47999999999999999998 999998  47999999986


Q ss_pred             CCC
Q 022058          192 TAI  194 (303)
Q Consensus       192 ~~~  194 (303)
                      ...
T Consensus        84 ~~~   86 (108)
T d2adba1          84 LTS   86 (108)
T ss_dssp             SCS
T ss_pred             Ccc
Confidence            543

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: RNA-binding protein 12
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=4.8e-17  Score=120.92  Aligned_cols=77  Identities=19%  Similarity=0.147  Sum_probs=68.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEE-EEeeCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDC-RVCGDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~-~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      .+.+|||+|||+++|+++|+++|+.||.|..+ .++.+..+ ++|||||+|.+.++|++|+.+|+..|.|+.|.|.++.
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~~   85 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVVT   85 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTSCCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEEC
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhcccceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEECC
Confidence            46789999999999999999999999999765 44444444 8999999999999999999999999999999999864

>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=99.66  E-value=2.8e-16  Score=113.22  Aligned_cols=77  Identities=29%  Similarity=0.309  Sum_probs=70.1

Q ss_pred             ccccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h--CCceeCCeeeEE
Q 022058          210 EMCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C--SGMVLGSQPIRV  286 (303)
Q Consensus       210 ~~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l--~g~~~~g~~l~v  286 (303)
                      ..++++|||+|||..+++++|+++|++|  |.|.++.+.+++    |+|||+|.+.++|.+|++ |  ++..+.|+.|+|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~--G~i~~v~~~~~~----~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v   78 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPF--GKVTNILMLKGK----NQAFLELATEEAAITMVNYYSAVTPHLRNQPIYI   78 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTT--SCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhcc--cccccccccccc----eEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEE
Confidence            3467999999999999999999999999  999999998776    499999999999999997 4  788999999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      .|++..
T Consensus        79 ~~sk~~   84 (88)
T d2cq1a1          79 QYSNHK   84 (88)
T ss_dssp             EECSCS
T ss_pred             EECCCC
Confidence            999754

>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=99.66  E-value=8.9e-17  Score=120.47  Aligned_cols=78  Identities=19%  Similarity=0.161  Sum_probs=70.8

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee--CCeeeEEee
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL--GSQPIRVSP  288 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~--~g~~l~v~~  288 (303)
                      +..+|||+|||+.+|+++|+++|++|  |.|.++.|.+++  ++|+|||+|.+.++|.+|+. |||..|  .++.|+|.|
T Consensus         6 ~~~~v~V~NL~~~vte~~L~~~F~~~--G~i~~~~i~~~~--~~g~aFV~f~~~e~A~~Ai~~ln~~~l~~~~~~l~v~~   81 (108)
T d2adba1           6 PVLRIIVENLFYPVTLDVLHQIFSKF--GTVLKIITFTKN--NQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDF   81 (108)
T ss_dssp             CEEEEESCSCCSTTHHHHHHHHHTTT--SCEEEEEEEEET--TEEEEEEEESCHHHHHHHHHHHHSCCSSTTCCCCEEEE
T ss_pred             CeEEEEEeCcCCCCCHHHHHHHHccC--CcEEEEEEEeeC--CCCeEEEEECCHHHHHHHHHHHCCCEeccCCcEEEEEe
Confidence            45789999999999999999999999  999999998774  47899999999999999998 999998  578999999


Q ss_pred             cCCCC
Q 022058          289 SKTPV  293 (303)
Q Consensus       289 a~~~~  293 (303)
                      +++..
T Consensus        82 s~~~~   86 (108)
T d2adba1          82 SKLTS   86 (108)
T ss_dssp             CSSCS
T ss_pred             cCCcc
Confidence            97643

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Putative RNA-binding protein 15B, Rbm15b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=3.4e-16  Score=114.92  Aligned_cols=75  Identities=23%  Similarity=0.294  Sum_probs=68.4

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCC--eeEEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGY--YPVRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g--~~i~v~~~~  191 (303)
                      +.++|||+|||+++++++|+++|+.||.|..+++.++    +|||||+|.+.++|.+|++ ||+..|.|  ++|+|.|++
T Consensus        16 Ps~tl~V~nLp~~~t~~~l~~~f~~~G~i~~~~~~~~----~~~afV~f~~~~~A~~A~~~l~~~~i~g~~~~l~v~~ak   91 (97)
T d1whya_          16 PTTRLWVGGLGPNTSLAALAREFDRFGSIRTIDHVKG----DSFAYIQYESLDAAQAACAKMRGFPLGGPDRRLRVDFAK   91 (97)
T ss_dssp             CCSCEEEECCCSSCCHHHHHHHHHTTSCEEEEEECSS----SCCEEEEESSHHHHHHHHHHHTTCBCSSSSCBCEEEECC
T ss_pred             CCCEEEEcCCCCCCCHHHHHHHHHhhcccceEeeecc----ccEEEeccCCHHHHHHHHHHhCCCEeCCCceEEEEEeCC
Confidence            4689999999999999999999999999999999764    5799999999999999998 99999976  689999986


Q ss_pred             CC
Q 022058          192 TA  193 (303)
Q Consensus       192 ~~  193 (303)
                      ..
T Consensus        92 ~~   93 (97)
T d1whya_          92 SG   93 (97)
T ss_dssp             CC
T ss_pred             CC
Confidence            43

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Polypyrimidine tract-binding protein 2, PTBP2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=5.6e-16  Score=111.65  Aligned_cols=77  Identities=21%  Similarity=0.237  Sum_probs=69.4

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-h--CCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L--GGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l--~g~~~~g~~i~v~~  189 (303)
                      ..++++|||+|||+++++++|+++|+.||.|.++.+..+    +|||||+|.+.++|.+|+. +  ++..+.|++|+|.|
T Consensus         5 ~~Ps~~l~V~nLp~~~t~~~L~~~f~~~G~i~~v~~~~~----~~~afV~f~~~e~A~~a~~~~~~~~~~~~g~~l~v~~   80 (88)
T d2cq1a1           5 GAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKG----KNQAFLELATEEAAITMVNYYSAVTPHLRNQPIYIQY   80 (88)
T ss_dssp             SSCCSEEEEESCCTTCCHHHHHHTTTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCEETTEECEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHHHhccccccccccccc----ceEEEEEeCCHHHHHHHHHHHccCCCccCCCEEEEEE
Confidence            457899999999999999999999999999999998764    4799999999999999997 4  67889999999999


Q ss_pred             cCCC
Q 022058          190 SKTA  193 (303)
Q Consensus       190 ~~~~  193 (303)
                      ++..
T Consensus        81 sk~~   84 (88)
T d2cq1a1          81 SNHK   84 (88)
T ss_dssp             CSCS
T ss_pred             CCCC
Confidence            8644

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Probable RNA-binding protein KIAA1579
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.8e-16  Score=113.23  Aligned_cols=74  Identities=18%  Similarity=0.165  Sum_probs=64.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKTA  193 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~~  193 (303)
                      ..++|||+|||+++++++|+++|+.|| +..+.+.    .++|||||+|.+.++|++|+. ||+..+.|++|.|.+++..
T Consensus         4 ~s~~i~V~nLp~~~t~~~l~~lF~~~G-~~~~~~~----~~kg~afV~f~~~~~A~~Ai~~ln~~~~~G~~l~V~~a~~~   78 (88)
T d1wg1a_           4 GSSGILVKNLPQDSNCQEVHDLLKDYD-LKYCYVD----RNKRTAFVTLLNGEQAQNAIQMFHQYSFRGKDLIVQLQPTD   78 (88)
T ss_dssp             CCCCEEEESCCSSCCHHHHHHHTCSSC-CCCEEEE----GGGTEEEECCSCHHHHHHHHHHHTTEEETTEEEEEEECCCC
T ss_pred             CCCEEEEeCCCCccChHHHHHHHHhcC-ceeeeee----ccCCceEEEECCHHHHHHHHHHhCCCEECCEEEEEEEcCCC
Confidence            467899999999999999999999999 3334332    247899999999999999998 9999999999999998544

>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=99.65  E-value=5.2e-16  Score=108.31  Aligned_cols=70  Identities=19%  Similarity=0.159  Sum_probs=62.8

Q ss_pred             EEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecCCC
Q 022058          216 VYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSKTP  292 (303)
Q Consensus       216 l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~~~  292 (303)
                      |||+|||+++++++|+++|++|  | +..+.+.+    ++|||||+|.+.++|.+|++ |||..+.|+.|+|+|+++.
T Consensus         1 i~V~nLp~~~t~~~l~~~F~~~--g-~~~~~~~~----~~g~afv~f~~~~~A~~Ai~~ln~~~~~g~~l~V~~a~~d   71 (75)
T d1wi6a1           1 ILIRGLPGDVTNQEVHDLLSDY--E-LKYCFVDK----YKGTAFVTLLNGEQAEAAINTFHQSRLRERELSVQLQPTD   71 (75)
T ss_dssp             EEEECCCTTCCHHHHHHHTTTS--C-EEEEEEET----TTTEEEEEESSHHHHHHHHHHHTTEESSSCEEEEEECCST
T ss_pred             CEEeCCCCcCCHHHHHHHHhcc--c-ccceeecc----cceeEEEEECCHHHHHHHHHHhCCccCCCCEEEEEEeCCC
Confidence            7999999999999999999999  8 66666543    45799999999999999998 9999999999999999653

>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=99.64  E-value=1.9e-16  Score=116.41  Aligned_cols=73  Identities=18%  Similarity=0.108  Sum_probs=67.7

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecCC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSKT  192 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~~  192 (303)
                      ...+|||+|||+++++++|+++|+.||+|.++.+.+     +|||||+|.+.++|.+||+ |||..+.|+.|.|.+.+.
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~G~v~~~~i~~-----~g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~~   87 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQK-----DGMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIRV   87 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTSSCEEEEEEET-----TTEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhhcccccccccc-----cceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEec
Confidence            466799999999999999999999999999999864     4899999999999999998 999999999999998754

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Heterogeneous nuclear ribonucleoprotein L-like
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.64  E-value=8.4e-16  Score=114.23  Aligned_cols=79  Identities=19%  Similarity=0.176  Sum_probs=70.3

Q ss_pred             cccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h--CCceeCCeeeEEe
Q 022058          211 MCSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C--SGMVLGSQPIRVS  287 (303)
Q Consensus       211 ~~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l--~g~~~~g~~l~v~  287 (303)
                      .++++|||+|||..+++++|.++|++|  |.|.++.+.+++    |+|||+|.+.++|..|+. |  ++..++|++|+|.
T Consensus        13 ~ps~~l~v~nlp~~~te~~l~~~F~~f--G~I~~~~~~~~k----~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~   86 (104)
T d1wexa_          13 SVSPVVHVRGLCESVVEADLVEALEKF--GTICYVMMMPFK----RQALVEFENIDSAKECVTFAADVPVYIAGQQAFFN   86 (104)
T ss_dssp             CCCSEEEEESCCSSCCHHHHHHHHTTT--SCEEEEEEETTT----TEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEE
T ss_pred             CCCCEEEEeCCCCCCCHHHHHHhhhhc--ccceEEEEEecc----eeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEE
Confidence            456899999999999999999999999  999999998765    599999999999999997 6  6778899999999


Q ss_pred             ecCCCCCC
Q 022058          288 PSKTPVRP  295 (303)
Q Consensus       288 ~a~~~~~~  295 (303)
                      |++...-.
T Consensus        87 ~s~~~~~~   94 (104)
T d1wexa_          87 YSTSKRIT   94 (104)
T ss_dssp             ECSSSSCC
T ss_pred             EcCCCccC
Confidence            99764333

>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=99.64  E-value=1.4e-16  Score=118.38  Aligned_cols=77  Identities=19%  Similarity=0.145  Sum_probs=68.9

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeE-EEEecC-CCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTR-LRLLGD-HVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~-v~i~~d-~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+++|+++|+++|..|  |.|.. +.+..+ .|+++|+|||+|.+.++|.+|+.|||..|+|+.|.|.++
T Consensus         7 ~~~~v~v~nLp~~~t~~~l~~~F~~~--g~i~~~~~~~~~~~g~~~G~afV~F~s~~~a~~Al~~n~~~i~gr~i~V~~~   84 (103)
T d2cpya1           7 AKVCAHITNIPFSITKMDVLQFLEGI--PVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLHRKKLNGREAFVHVV   84 (103)
T ss_dssp             CCCEEEEESCCTTSCHHHHHHHTTTS--CCCSTTEEECCCTTSSCSSCEEEECSSHHHHHHHGGGCSEEETTEEEEEEEE
T ss_pred             CceEEEEeCCCCCCCHHHHhhhhccc--ceEEEEEEEEeCCCCCcCccEEEEECCHHHHHHHHhcCCCeECCcEEEEEEC
Confidence            34789999999999999999999999  98876 445444 488999999999999999999999999999999999986


Q ss_pred             C
Q 022058          290 K  290 (303)
Q Consensus       290 ~  290 (303)
                      .
T Consensus        85 ~   85 (103)
T d2cpya1          85 T   85 (103)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.63  E-value=1.3e-16  Score=120.29  Aligned_cols=78  Identities=22%  Similarity=0.266  Sum_probs=68.2

Q ss_pred             CCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEe-eCCCC-CceEEEEEecCHHHHHHHHHhCCcccCCeeEEEeecC
Q 022058          114 SVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVC-GDPHS-VLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       114 ~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~-~~~~~-~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~~~  191 (303)
                      ....+|||+|||+++|+++|+++|+.||.+..+.++ .+..+ ++|||||+|.+.++|++|+++|+..|+||.|.|.++.
T Consensus        16 ~~~~~i~v~nLp~~~t~~di~~~F~~~g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~~   95 (112)
T d1wela1          16 EAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPIT   95 (112)
T ss_dssp             CCCCEEEEECCCTTCCHHHHHHHSCSSCBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEEC
T ss_pred             CCCeEEEEecCCCcCcHHHHhhHHhhccccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEcC
Confidence            356789999999999999999999999999765444 34444 8999999999999999999999999999999998763

>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=99.62  E-value=6.4e-16  Score=113.57  Aligned_cols=74  Identities=18%  Similarity=0.168  Sum_probs=68.6

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      ...+|||+|||+.+++++|+++|++|  |.|.++.|.++     |||||+|.+.++|.+||+ |||..|.|+.|+|.+.+
T Consensus        14 ~~~~i~V~Nlp~~~~~~~L~~~F~~~--G~v~~~~i~~~-----g~afV~f~~~~~a~~Ai~~lng~~~~g~~i~v~~~~   86 (98)
T d1wg4a_          14 SDFRVLVSGLPPSGSWQDLKDHMREA--GDVCYADVQKD-----GMGMVEYLRKEDMEYALRKLDDTKFRSHEGETSYIR   86 (98)
T ss_dssp             CSCEEEEECCCSSCCHHHHHHHHTTS--SCEEEEEEETT-----TEEEEEESSHHHHHHHHHHHSSEEEECTTSCEEEEE
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHhh--ccccccccccc-----ceEEEEECCHHHHHHHHHHhCCCEeCCeEEEEEEEe
Confidence            34789999999999999999999999  99999999754     699999999999999998 99999999999999987


Q ss_pred             CC
Q 022058          291 TP  292 (303)
Q Consensus       291 ~~  292 (303)
                      +.
T Consensus        87 ~~   88 (98)
T d1wg4a_          87 VY   88 (98)
T ss_dssp             EE
T ss_pred             cC
Confidence            54

>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=99.62  E-value=2.9e-15  Score=111.26  Aligned_cols=78  Identities=18%  Similarity=0.120  Sum_probs=69.3

Q ss_pred             CCCCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-h--CCcccCCeeEEEee
Q 022058          113 DSVRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L--GGTMLGYYPVRVLP  189 (303)
Q Consensus       113 ~~~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l--~g~~~~g~~i~v~~  189 (303)
                      ...+++|||+|||+.+++++|+++|+.||.|..+.+.++    +|+|||+|.+.++|..|+. +  ++..+.|++|+|.|
T Consensus        12 ~~ps~~l~v~nlp~~~te~~l~~~F~~fG~I~~~~~~~~----k~~AfV~f~~~e~A~~ai~~~~~~~~~~~g~~l~v~~   87 (104)
T d1wexa_          12 VSVSPVVHVRGLCESVVEADLVEALEKFGTICYVMMMPF----KRQALVEFENIDSAKECVTFAADVPVYIAGQQAFFNY   87 (104)
T ss_dssp             CCCCSEEEEESCCSSCCHHHHHHHHTTTSCEEEEEEETT----TTEEEEEESSHHHHHHHHHHHHHSCCBSSSSBCEEEE
T ss_pred             CCCCCEEEEeCCCCCCCHHHHHHhhhhcccceEEEEEec----ceeEEEEeCCHHHHHHHHHHHcCCCcEEeeEEEEEEE
Confidence            346889999999999999999999999999999999754    5799999999999999997 6  56778899999999


Q ss_pred             cCCCC
Q 022058          190 SKTAI  194 (303)
Q Consensus       190 ~~~~~  194 (303)
                      ++...
T Consensus        88 s~~~~   92 (104)
T d1wexa_          88 STSKR   92 (104)
T ss_dssp             CSSSS
T ss_pred             cCCCc
Confidence            86543

>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=99.62  E-value=9.5e-16  Score=110.59  Aligned_cols=77  Identities=22%  Similarity=0.264  Sum_probs=69.4

Q ss_pred             cccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-h--CCceeCCeeeEE
Q 022058          211 MCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-C--SGMVLGSQPIRV  286 (303)
Q Consensus       211 ~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l--~g~~~~g~~l~v  286 (303)
                      .++++|||+|||.. +|++||.++|++|  |.|.++.+.++++    +|||+|.+.++|..|+. |  ++..+.|++|+|
T Consensus         6 ~~sr~v~v~nl~~~~~t~~eL~~lF~~f--G~I~~i~i~~~k~----~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           6 ETRRVVHIMDFQRGKNLRYQLLQLVEPF--GVISNHLILNKIN----EAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCEEEEESCCCSSSHHHHHHTTTGGG--SCEEEEEECSSSS----CEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCcEEEEECCCCCcCCHHHHHHHHHhh--CCeEEEEeeccce----EEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            35689999999986 8899999999999  9999999998765    99999999999999997 5  788999999999


Q ss_pred             eecCCCC
Q 022058          287 SPSKTPV  293 (303)
Q Consensus       287 ~~a~~~~  293 (303)
                      +||++..
T Consensus        80 ~~s~~~~   86 (89)
T d1x4da1          80 HLSQKYK   86 (89)
T ss_dssp             EEECCCT
T ss_pred             EECCCcc
Confidence            9997543

>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=99.61  E-value=7.6e-16  Score=113.38  Aligned_cols=77  Identities=16%  Similarity=0.188  Sum_probs=68.9

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH---hCCcccCCeeEEE
Q 022058          112 EDSVRRTVYVSDIDQN-ITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN---LGGTMLGYYPVRV  187 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~---l~g~~~~g~~i~v  187 (303)
                      ....+++|||+|||.+ +|+++|+++|+.||.|.++.++++    +|||||+|.+.++|.+|++   +++..+.|++|+|
T Consensus        14 ~~~~~~~l~v~nLp~~~~te~~l~~~F~~fG~V~~v~~~~~----k~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          14 KQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRM----KSQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             SSCCCCEEEEESCCCSSCCSHHHHTTTTTTSCCSEEEEETT----TTEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCCCEEEEeCCcCCccCHHHHHhhhccccceeEEEEeec----CCcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            4446789999999985 899999999999999999999865    4799999999999999995   7888999999999


Q ss_pred             eecCC
Q 022058          188 LPSKT  192 (303)
Q Consensus       188 ~~~~~  192 (303)
                      .+++.
T Consensus        90 ~~s~~   94 (99)
T d1x4fa1          90 DLSEK   94 (99)
T ss_dssp             EEECS
T ss_pred             EEcCC
Confidence            99854

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.60  E-value=1.1e-15  Score=110.29  Aligned_cols=77  Identities=25%  Similarity=0.281  Sum_probs=68.7

Q ss_pred             CCCCCCEEEEcCCCCC-CCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-h--CCcccCCeeEEE
Q 022058          112 EDSVRRTVYVSDIDQN-ITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-L--GGTMLGYYPVRV  187 (303)
Q Consensus       112 ~~~~~~~l~V~nlp~~-~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l--~g~~~~g~~i~v  187 (303)
                      ....+++|||+|||.. +|+++|+++|+.||.|.++.++.++    ++|||+|.+.++|..|+. +  ++..+.|++|.|
T Consensus         4 ~~~~sr~v~v~nl~~~~~t~~eL~~lF~~fG~I~~i~i~~~k----~~afV~f~~~~~A~~A~~~l~~~~~~~~gr~l~V   79 (89)
T d1x4da1           4 RVETRRVVHIMDFQRGKNLRYQLLQLVEPFGVISNHLILNKI----NEAFIEMATTEDAQAAVDYYTTTPALVFGKPVRV   79 (89)
T ss_dssp             CCCCCCEEEEESCCCSSSHHHHHHTTTGGGSCEEEEEECSSS----SCEEEEESSHHHHHHHHHHHHHSCCEETTEECEE
T ss_pred             CCCCCcEEEEECCCCCcCCHHHHHHHHHhhCCeEEEEeeccc----eEEEEEEcchhhHHHHHHHHhhCCCccCCceEEE
Confidence            3457899999999986 8899999999999999999998654    589999999999999997 5  678899999999


Q ss_pred             eecCC
Q 022058          188 LPSKT  192 (303)
Q Consensus       188 ~~~~~  192 (303)
                      .|++.
T Consensus        80 ~~s~~   84 (89)
T d1x4da1          80 HLSQK   84 (89)
T ss_dssp             EEECC
T ss_pred             EECCC
Confidence            99864

>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=99.60  E-value=2.3e-17  Score=119.58  Aligned_cols=75  Identities=21%  Similarity=0.338  Sum_probs=66.1

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeC-----CC--CCceEEEEEecCHHHHHHHHHhCCcccCCeeEEEee
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGD-----PH--SVLRFAFVEFADEHGARAALNLGGTMLGYYPVRVLP  189 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~-----~~--~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i~v~~  189 (303)
                      |.|||+|||+++|+++|+++|+.||.|..+.+...     ..  .++|||||+|.+.++|++|++|||..+.|++|+|.+
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V~r   81 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRR   81 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHHHTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCCBC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhhCcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEECC
Confidence            68999999999999999999999999877766432     22  279999999999999999999999999999999986


Q ss_pred             cC
Q 022058          190 SK  191 (303)
Q Consensus       190 ~~  191 (303)
                      ++
T Consensus        82 ~k   83 (90)
T d1u2fa_          82 PH   83 (90)
T ss_dssp             TT
T ss_pred             CC
Confidence            54

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Matrin 3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.59  E-value=2.8e-15  Score=110.31  Aligned_cols=76  Identities=17%  Similarity=0.259  Sum_probs=68.6

Q ss_pred             cccceEEEcCCCCC-CCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH---hCCceeCCeeeEE
Q 022058          211 MCSRTVYCTNIDKK-VPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN---CSGMVLGSQPIRV  286 (303)
Q Consensus       211 ~~~~~l~V~nL~~~-~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~---l~g~~~~g~~l~v  286 (303)
                      ..+++|||+|||.. +|+++|.++|++|  |.|.++.+.+++    |+|||+|.+.++|..|++   +++..++|+.|+|
T Consensus        16 ~~~~~l~v~nLp~~~~te~~l~~~F~~f--G~V~~v~~~~~k----~~afV~f~~~~~A~~Ai~~~~~~~~~~~gr~l~V   89 (99)
T d1x4fa1          16 ELGRVIHLSNLPHSGYSDSAVLKLAEPY--GKIKNYILMRMK----SQAFIEMETREDAMAMVDHCLKKALWFQGRCVKV   89 (99)
T ss_dssp             CCCCEEEEESCCCSSCCSHHHHTTTTTT--SCCSEEEEETTT----TEEEEECSSHHHHHHHHHHHHHSCCCSSSSCCEE
T ss_pred             CCCCEEEEeCCcCCccCHHHHHhhhccc--cceeEEEEeecC----CcEEEEecchHHHHHHHHHHhcCCceECCEEEEE
Confidence            35689999999975 8999999999999  999999998775    499999999999999995   6899999999999


Q ss_pred             eecCCC
Q 022058          287 SPSKTP  292 (303)
Q Consensus       287 ~~a~~~  292 (303)
                      +|++..
T Consensus        90 ~~s~~~   95 (99)
T d1x4fa1          90 DLSEKY   95 (99)
T ss_dssp             EEECSC
T ss_pred             EEcCCc
Confidence            999643

>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=99.59  E-value=5.3e-16  Score=116.90  Aligned_cols=77  Identities=22%  Similarity=0.206  Sum_probs=68.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEE-ec-CCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRL-LG-DHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i-~~-d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a  289 (303)
                      ...+|||+|||+.+|+++|.++|+.+  |.+..+.+ .. +.|.++|+|||+|.+.++|.+|+.|||..|+|+.|.|..+
T Consensus        17 ~~~~i~v~nLp~~~t~~di~~~F~~~--g~~~~~~~~~~~~~g~~~G~afVeF~~~e~a~~al~~~~~~i~gR~i~V~~~   94 (112)
T d1wela1          17 AGFCVYLKGLPFEAENKHVIDFFKKL--DIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVHPI   94 (112)
T ss_dssp             CCCEEEEECCCTTCCHHHHHHHSCSS--CBCTTTCEEEECTTSSEEEEEEEEBSSSHHHHHHHTSCSBCSTTSCBEEEEE
T ss_pred             CCeEEEEecCCCcCcHHHHhhHHhhc--cccccceeeecCcccceeeEEEEEECCHHHHHHHHHcCCCcCCCEEEEEEEc
Confidence            45789999999999999999999998  98876433 33 3589999999999999999999999999999999999887


Q ss_pred             C
Q 022058          290 K  290 (303)
Q Consensus       290 ~  290 (303)
                      .
T Consensus        95 ~   95 (112)
T d1wela1          95 T   95 (112)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=99.58  E-value=2.2e-15  Score=111.77  Aligned_cols=76  Identities=13%  Similarity=0.096  Sum_probs=67.7

Q ss_pred             ccceEEEcCCCCCC-CH----HHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeE
Q 022058          212 CSRTVYCTNIDKKV-PQ----AEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIR  285 (303)
Q Consensus       212 ~~~~l~V~nL~~~~-t~----~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~  285 (303)
                      ...+|||+||+..+ ++    ++|.++|++|  |.|.++.++++.    +||||+|.+.++|.+|+. |||..|.|+.|+
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~--G~i~~~~~~k~~----~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~   77 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTY--DKDTTFQYFKSF----KRVRINFSNPLSAADARLRLHKTEFLGKEMK   77 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTT--CSSCEEEEETTT----TEEEEECSSTTHHHHHHHTSTTSEETTEECE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhccc--ccceEEEEecCC----CEEEEEECCHHHHHHHHHHhcccccCCCEeE
Confidence            45789999999876 33    5799999999  999999998764    599999999999999999 999999999999


Q ss_pred             EeecCCCC
Q 022058          286 VSPSKTPV  293 (303)
Q Consensus       286 v~~a~~~~  293 (303)
                      |.|+++..
T Consensus        78 v~~a~~~~   85 (104)
T d1weya_          78 LYFAQTLH   85 (104)
T ss_dssp             EECCCCSS
T ss_pred             EeecccCC
Confidence            99997664

>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=99.57  E-value=7.5e-17  Score=116.82  Aligned_cols=76  Identities=20%  Similarity=0.374  Sum_probs=67.1

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecC-------CCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEE
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGD-------HVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRV  286 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d-------~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v  286 (303)
                      ++|||+|||..+|+++|+++|++|  |.|..+.+...       .++++|||||+|.+.++|.+|+.|||..+.|+.|+|
T Consensus         2 RrlyVgNLp~~~te~~l~~~F~~~--g~~~~~~~~~~~~~~~~~~~~~kg~afV~f~~~e~a~~a~~l~g~~~~Gr~l~V   79 (90)
T d1u2fa_           2 RRLYVGNIPFGITEEAMMDFFNAQ--MRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKI   79 (90)
T ss_dssp             CEEEECSCCTTCCTTHHHHHHHHH--HTTTTSCCSSSCSEEECCEETTTTEEEEEESSCTTTTTGGGGSSCCSSSSCCCC
T ss_pred             CEEEEcCCCCccchHHHHHHHHhh--CcEEEEEEeccceeeecccCCCceEEEEEeCCHHHHHHHHhhCCcEECCEEEEE
Confidence            689999999999999999999999  98887766532       256899999999999999999889999999999999


Q ss_pred             eecCC
Q 022058          287 SPSKT  291 (303)
Q Consensus       287 ~~a~~  291 (303)
                      +.++.
T Consensus        80 ~r~k~   84 (90)
T d1u2fa_          80 RRPHD   84 (90)
T ss_dssp             BCTTC
T ss_pred             CCCCC
Confidence            86543

>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=99.54  E-value=3.6e-16  Score=116.13  Aligned_cols=74  Identities=20%  Similarity=0.180  Sum_probs=69.5

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeec
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ..++|++++..+++++|+++|++|  |.|.+|.|+++. ++++|+|||+|.+.++|.+|+. |||++++||.|+|.|+
T Consensus        28 ~~~~v~~~~~~~~ed~l~e~f~k~--G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          28 SDVEMQEHYDEFFEEVFTEMEEKY--GEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHT--CCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             chHHhhhhhhhhhHHHHHHHhccC--CCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            468888999899999999999999  999999999875 7899999999999999999998 9999999999999986

>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=99.53  E-value=1.4e-14  Score=107.34  Aligned_cols=76  Identities=12%  Similarity=0.112  Sum_probs=67.3

Q ss_pred             CCCEEEEcCCCCCC-CH----HHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEe
Q 022058          115 VRRTVYVSDIDQNI-TE----ERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVL  188 (303)
Q Consensus       115 ~~~~l~V~nlp~~~-t~----~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~  188 (303)
                      ...+|||+||+.++ ++    ++|+++|+.||.|.++++++    ++|||||+|.+.++|.+|+. |||..+.|++|+|.
T Consensus         4 ~~~~L~v~nl~~~v~~~d~~k~~l~~lF~~~G~i~~~~~~k----~~~~afV~f~~~~~A~~Ai~~lng~~~~g~~l~v~   79 (104)
T d1weya_           4 GSSGLIACVANDDVFSESETRAKFESLFRTYDKDTTFQYFK----SFKRVRINFSNPLSAADARLRLHKTEFLGKEMKLY   79 (104)
T ss_dssp             CCCEEEEECCCGGGGSTTTHHHHHHHHHHTTCSSCEEEEET----TTTEEEEECSSTTHHHHHHHTSTTSEETTEECEEE
T ss_pred             CCceEEEEeCCchhcCcHHHHHHHHHHhcccccceEEEEec----CCCEEEEEECCHHHHHHHHHHhcccccCCCEeEEe
Confidence            56789999999875 43    56999999999999999975    35799999999999999999 99999999999999


Q ss_pred             ecCCCC
Q 022058          189 PSKTAI  194 (303)
Q Consensus       189 ~~~~~~  194 (303)
                      |++...
T Consensus        80 ~a~~~~   85 (104)
T d1weya_          80 FAQTLH   85 (104)
T ss_dssp             CCCCSS
T ss_pred             ecccCC
Confidence            986553

>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=99.52  E-value=9.2e-16  Score=113.87  Aligned_cols=73  Identities=21%  Similarity=0.296  Sum_probs=68.0

Q ss_pred             EEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC-CceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeec
Q 022058          118 TVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS-VLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       118 ~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~-~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .++|.+++.++++++|+++|++||.|.+|+|+++..+ ++|||||+|.+.++|.+|+. |||..+.||+|.|.++
T Consensus        29 ~~~v~~~~~~~~ed~l~e~f~k~G~I~~v~I~~~~~~~~~G~~fV~f~~~~~A~~Ai~~lng~~~~gr~i~v~~s  103 (104)
T d1jmta_          29 DVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELS  103 (104)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCCEEEEEECCSSSSSSEEEEEEEESCHHHHHHHHHHHTTCEETTEECCEEEC
T ss_pred             hHHhhhhhhhhhHHHHHHHhccCCCEEEEEeecCCCCCEeeEEEEEEechhHHHHHHHHHCCCEECCEEEEEEEC
Confidence            4888899999999999999999999999999887654 89999999999999999998 9999999999999975

>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=99.44  E-value=6.6e-14  Score=105.31  Aligned_cols=72  Identities=17%  Similarity=0.123  Sum_probs=62.3

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCH-HHHHHHHH-hCCcccCCeeEEEeec
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADE-HGARAALN-LGGTMLGYYPVRVLPS  190 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~-~~A~~Ai~-l~g~~~~g~~i~v~~~  190 (303)
                      .-..+||||||+++|+++|+++|++||+|.+|.|+.+    +|||||.|.+. ++|..|+. +|+..+.++.+.|.+.
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~fG~V~~v~i~~~----kg~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNHGEIKWIDFVRG----AKEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSSCCEEEEECCTT----CSEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhcCChheEEEecC----CceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            3445799999999999999999999999999999864    58999999995 78888998 9999888777777664

>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=99.43  E-value=2.1e-13  Score=100.37  Aligned_cols=63  Identities=16%  Similarity=0.272  Sum_probs=57.3

Q ss_pred             cccceEEEcC--CCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee
Q 022058          211 MCSRTVYCTN--IDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL  279 (303)
Q Consensus       211 ~~~~~l~V~n--L~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~  279 (303)
                      .+..+|+|.|  ||..+|+++|+++|++|  |.|..+.+.++++    ||||+|.+.++|.+|+. |||+.+
T Consensus        16 ~pt~~l~V~ng~L~~~vte~~L~~~F~~~--G~i~~i~~~~~k~----~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          16 YATQSLVVANGGLGNGVSRNQLLPVLEKC--GLVDALLMPPNKP----YSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SCCSEEEEETCTGGGTCCHHHHHHHHHHH--SCEEEEECCTTCS----CEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCceEEEECCCCCCCCCHHHHHHHHHhh--CcccEEeeccCcc----EEEEEECCHHHHHHHHHHhCCCCC
Confidence            3557888855  99999999999999999  9999999988764    99999999999999998 999987

>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=99.41  E-value=3.8e-13  Score=98.59  Aligned_cols=77  Identities=19%  Similarity=0.275  Sum_probs=66.5

Q ss_pred             ccceEEEcCC--CCCC---------CHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH-hCCcee
Q 022058          212 CSRTVYCTNI--DKKV---------PQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN-CSGMVL  279 (303)
Q Consensus       212 ~~~~l~V~nL--~~~~---------t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~-l~g~~~  279 (303)
                      .+++|+|+||  |..+         .+++|+..|++|  |.|..|.+..+.  ++|+|||+|.+.++|.+|+. |||..|
T Consensus         7 ~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~--G~V~~v~~~~~~--~~G~~fV~f~~~e~A~~A~~~lng~~~   82 (99)
T d2dita1           7 HERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKF--GQIRKLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWF   82 (99)
T ss_dssp             SCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGT--SCCSEEEEETTC--TTCEEEEECSCHHHHHHHHHHSTTCEE
T ss_pred             CccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCc--ccEEEEeccCCC--CccEEEEEECCHHHHHHHHHHhCCcEE
Confidence            4589999998  5432         136899999999  999999987764  56899999999999999998 999999


Q ss_pred             CCeeeEEeecCCC
Q 022058          280 GSQPIRVSPSKTP  292 (303)
Q Consensus       280 ~g~~l~v~~a~~~  292 (303)
                      +||.|+|.|+.+.
T Consensus        83 ~gr~i~v~~~~g~   95 (99)
T d2dita1          83 GGRQITAQAWDGT   95 (99)
T ss_dssp             TTEECEEEECCSC
T ss_pred             CCEEEEEEEeCCc
Confidence            9999999998654

>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=99.40  E-value=2.5e-13  Score=95.60  Aligned_cols=72  Identities=19%  Similarity=0.231  Sum_probs=61.8

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCee-EEEeecC
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYP-VRVLPSK  191 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~-i~v~~~~  191 (303)
                      +.+.|+|+++|++.+++.|+ +|++||+|.++++..    ++|||||+|.+.++|++||++||..++|+. |.|.+..
T Consensus         3 ~~~wV~V~G~p~~~~~~il~-~F~~~G~I~~~~~~~----~~~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           3 DDTWVTVFGFPQASASYILL-QFAQYGNILKHVMSN----TGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGGEEEEECCCGGGHHHHHH-HHHTTSCEEEEEECS----SSSEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             cccEEEEECCChHHHHHHHH-HHHhhhhhheEEecC----CCCEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            35779999999999976665 799999999998854    358999999999999999999999999975 5687753

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Alkylation repair AlkB homolog 8, ALKBH8
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=2.8e-13  Score=99.64  Aligned_cols=64  Identities=14%  Similarity=0.334  Sum_probs=57.0

Q ss_pred             CCCCCEEEE--cCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCccc
Q 022058          113 DSVRRTVYV--SDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTML  180 (303)
Q Consensus       113 ~~~~~~l~V--~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~  180 (303)
                      ..+.++|+|  ||||+++|+++|+++|++||.|.++.++.+    +|||||+|.+.++|.+|+. |||..+
T Consensus        15 ~~pt~~l~V~ng~L~~~vte~~L~~~F~~~G~i~~i~~~~~----k~~aFV~f~~~e~A~~A~~~lng~~i   81 (101)
T d2cq2a1          15 SYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPN----KPYSFARYRTTEESKRAYVTLNGKEV   81 (101)
T ss_dssp             SSCCSEEEEETCTGGGTCCHHHHHHHHHHHSCEEEEECCTT----CSCEEEEESSHHHHHHHHHHTTTCEE
T ss_pred             CCCCceEEEECCCCCCCCCHHHHHHHHHhhCcccEEeeccC----ccEEEEEECCHHHHHHHHHHhCCCCC
Confidence            345678888  559999999999999999999999988764    4799999999999999998 999887

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Lupus LA protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=2.9e-13  Score=101.70  Aligned_cols=73  Identities=11%  Similarity=0.169  Sum_probs=63.7

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCH-HHHHHHHH-hCCceeCCeeeEEeec
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVA-ESAILALN-CSGMVLGSQPIRVSPS  289 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~-e~A~~Ai~-l~g~~~~g~~l~v~~a  289 (303)
                      ....+||+|||+.+|+++|+++|++|  |.|.+|.|+++.    |||||.|.+. ++|..|+. ||+..+.++.+.|.++
T Consensus        10 g~~~~fvgnL~~~~tee~Lk~~F~~f--G~V~~v~i~~~k----g~gfV~F~~~~~~A~~a~~~~~~~~l~~~~~~v~~~   83 (113)
T d1owxa_          10 GCLLKFSGDLDDQTCREDLHILFSNH--GEIKWIDFVRGA----KEGIILFKEKAKEALGKAKDANNGNLQLRNKEVTWE   83 (113)
T ss_dssp             CCEEEEEESCCSSCCHHHHHHHTCSS--CCEEEEECCTTC----SEEEEEESSCHHHHHHHHHHTTTSCBCTTSSSEEEE
T ss_pred             CCeEEEECCCCCCCCHHHHHHHHHhc--CChheEEEecCC----ceEEEEecCcHHHHHHHHHHhcCCceecCceEEEEe
Confidence            45667999999999999999999999  999999999775    5999999995 78888888 9999888777777765


Q ss_pred             C
Q 022058          290 K  290 (303)
Q Consensus       290 ~  290 (303)
                      .
T Consensus        84 ~   84 (113)
T d1owxa_          84 V   84 (113)
T ss_dssp             E
T ss_pred             e
Confidence            4

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: HIV Tat-specific factor 1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.38  E-value=7.5e-13  Score=96.98  Aligned_cols=77  Identities=19%  Similarity=0.192  Sum_probs=66.4

Q ss_pred             CCCCEEEEcCC--CCCCC---------HHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          114 SVRRTVYVSDI--DQNIT---------EERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       114 ~~~~~l~V~nl--p~~~t---------~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      ..+++|+|.||  |.++.         +++|++.|+.||.|..+.+..+.  .+|||||+|.+.++|.+|+. |||..+.
T Consensus         6 ~~~r~v~l~nmf~~~~~~~~~~~~~~i~edv~~~~~~~G~V~~v~~~~~~--~~G~~fV~f~~~e~A~~A~~~lng~~~~   83 (99)
T d2dita1           6 RHERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRH--PDGVASVSFRDPEEADYCIQTLDGRWFG   83 (99)
T ss_dssp             CSCCEEEEESSCCTTHHHHCSHHHHHHHHHHHHHGGGTSCCSEEEEETTC--TTCEEEEECSCHHHHHHHHHHSTTCEET
T ss_pred             CCccEEEEccCCCHHHhhcchHHHHHHHHHHHHHhcCcccEEEEeccCCC--CccEEEEEECCHHHHHHHHHHhCCcEEC
Confidence            46789999999  55432         36799999999999999887653  57999999999999999998 9999999


Q ss_pred             CeeEEEeecCC
Q 022058          182 YYPVRVLPSKT  192 (303)
Q Consensus       182 g~~i~v~~~~~  192 (303)
                      ||+|.|.+.+.
T Consensus        84 gr~i~v~~~~g   94 (99)
T d2dita1          84 GRQITAQAWDG   94 (99)
T ss_dssp             TEECEEEECCS
T ss_pred             CEEEEEEEeCC
Confidence            99999998753

>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=99.35  E-value=1.5e-12  Score=91.60  Aligned_cols=71  Identities=15%  Similarity=0.171  Sum_probs=61.3

Q ss_pred             cceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCe-eeEEeecC
Q 022058          213 SRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQ-PIRVSPSK  290 (303)
Q Consensus       213 ~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~-~l~v~~a~  290 (303)
                      .+.|+|+++|++.+++ +.++|++|  |.|.++++.+++    |||||+|.+.++|.+|+++||..++|+ .|.|..+.
T Consensus         4 ~~wV~V~G~p~~~~~~-il~~F~~~--G~I~~~~~~~~~----~~~fV~f~~~~~A~~Al~~nG~~~~g~~~vgV~~~~   75 (81)
T d1wwha1           4 DTWVTVFGFPQASASY-ILLQFAQY--GNILKHVMSNTG----NWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCI   75 (81)
T ss_dssp             GGEEEEECCCGGGHHH-HHHHHHTT--SCEEEEEECSSS----SEEEEEESSHHHHHHHHTTTTCEETTTEECEEEECC
T ss_pred             ccEEEEECCChHHHHH-HHHHHHhh--hhhheEEecCCC----CEEEEEEcccHHHHHHHhcCCCeECCcEEEEEEeCC
Confidence            3679999999998865 44689999  999999986554    599999999999999999999999997 56788765

>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=99.33  E-value=4.9e-13  Score=98.93  Aligned_cols=79  Identities=14%  Similarity=0.152  Sum_probs=67.4

Q ss_pred             cccceEEEcCC--CCCCC--------HHHHHHHhhhhcCcceeEEEEecCC----CCcccEEEEEEcCHHHHHHHHH-hC
Q 022058          211 MCSRTVYCTNI--DKKVP--------QAEVKQFFEAACGGEVTRLRLLGDH----VHSTRIAFVEFAVAESAILALN-CS  275 (303)
Q Consensus       211 ~~~~~l~V~nL--~~~~t--------~~~L~~~F~~~~~G~i~~v~i~~d~----~~~~g~afV~f~~~e~A~~Ai~-l~  275 (303)
                      +++++|.|.|+  |..+.        .+||+..|++|  |.|.+|.|+++.    ....|++||+|.+.++|.+|+. ||
T Consensus         2 ~Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~--G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~   79 (104)
T d1o0pa_           2 HPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKY--GLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLT   79 (104)
T ss_dssp             CCCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTT--SCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHS
T ss_pred             CCCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhccc--CceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHC
Confidence            35688999999  54442        36799999999  999999998864    2356899999999999999998 99


Q ss_pred             CceeCCeeeEEeecCC
Q 022058          276 GMVLGSQPIRVSPSKT  291 (303)
Q Consensus       276 g~~~~g~~l~v~~a~~  291 (303)
                      |+.++||.|.+.|+.+
T Consensus        80 Gr~f~gR~v~v~f~~~   95 (104)
T d1o0pa_          80 GRKFANRVVVTKYCDP   95 (104)
T ss_dssp             SCCSSSSCCEEEEECH
T ss_pred             CCEECCeEEEEEEcCH
Confidence            9999999999999864

>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=99.31  E-value=1.5e-12  Score=96.20  Aligned_cols=77  Identities=16%  Similarity=0.144  Sum_probs=66.6

Q ss_pred             CCCEEEEcCC--CCCCC--------HHHHHHHhhcCCceeEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcc
Q 022058          115 VRRTVYVSDI--DQNIT--------EERLAGLFSSCGQVVDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTM  179 (303)
Q Consensus       115 ~~~~l~V~nl--p~~~t--------~~~l~~~F~~~G~i~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~  179 (303)
                      +++.|.|.|+  |..+.        .++|++.|++||.|.+|.|+++..+    ..|++||+|.+.++|.+|+. |||..
T Consensus         3 Ps~vl~l~N~~~~~~l~~~~~~~~i~edi~~e~~k~G~v~~v~I~~~~~~~~~~~~g~vfV~f~~~e~A~~A~~~l~Gr~   82 (104)
T d1o0pa_           3 PTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRK   82 (104)
T ss_dssp             CCSEEEEESSCCTTTTTSHHHHHHHHHHHHHHHTTTSCEEEEECCCCTTSSSCTTCCEEEEEESCHHHHHHHHHHHSSCC
T ss_pred             CCcEEEEeCCCCHHHcCCchhHHHHHHHHHHHhcccCceEEEEEeecCCCCccCCceEEEEEECCHHHHHHHHHHHCCCE
Confidence            5788999999  54443        3578999999999999999886654    46999999999999999998 99999


Q ss_pred             cCCeeEEEeecC
Q 022058          180 LGYYPVRVLPSK  191 (303)
Q Consensus       180 ~~g~~i~v~~~~  191 (303)
                      ++||+|.|.+..
T Consensus        83 f~gR~v~v~f~~   94 (104)
T d1o0pa_          83 FANRVVVTKYCD   94 (104)
T ss_dssp             SSSSCCEEEEEC
T ss_pred             ECCeEEEEEEcC
Confidence            999999999864

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.68  E-value=5.6e-05  Score=51.94  Aligned_cols=55  Identities=24%  Similarity=0.382  Sum_probs=50.5

Q ss_pred             HHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHHhCCceeCCeeeEEeecC
Q 022058          228 AEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALNCSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       228 ~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~l~g~~~~g~~l~v~~a~  290 (303)
                      .+|.+.|..|  |+|.-++++.|      -..|+|.+-++|.+|+.++|.++.|+.|+|....
T Consensus        39 ~~Llq~l~~~--GeViLvRFv~d------~mwVTF~dG~SAL~al~l~g~~v~G~~l~It~~~   93 (95)
T d1ufwa_          39 TELMQTLGSY--GTIVLVRINQG------QMLVTFADSHSALSVLDVDGMKVKGRAVKISGPS   93 (95)
T ss_dssp             HHHHHHHHHH--SCCSEEEEETT------EEEEECSCSHHHHHHHHGGGSEETTEEEEEECCC
T ss_pred             HHHHHHHhhC--CeEEEEEEeCC------eEEEEECCcHHHHHHhccCCeEEcceEEEEecCC
Confidence            5788999999  99999999988      5999999999999999999999999999998643

>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=97.67  E-value=0.00018  Score=46.94  Aligned_cols=59  Identities=25%  Similarity=0.268  Sum_probs=51.6

Q ss_pred             HHHHHHhhhhcCcceeEEEEecCC-CCcccEEEEEEcCHHHHHHHHH-hCCceeCCeeeEEeecC
Q 022058          228 AEVKQFFEAACGGEVTRLRLLGDH-VHSTRIAFVEFAVAESAILALN-CSGMVLGSQPIRVSPSK  290 (303)
Q Consensus       228 ~~L~~~F~~~~~G~i~~v~i~~d~-~~~~g~afV~f~~~e~A~~Ai~-l~g~~~~g~~l~v~~a~  290 (303)
                      +.|.+.|.++  |.|.++.|.+.. |..  .|-|...+..+|..|+. ||-+.+++++|.|+++.
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 QLLQEAFARH--GKVKSVELSPHTDYQL--KAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             HHHHHHHHHH--SCEEEEEECSCCSTTC--CEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             HHHHHHHHhh--eeEEEEEEEeccCCcE--EEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            5567889999  999999998763 433  69999999999999998 99999999999999974

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Synaptojanin 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=0.00014  Score=49.91  Aligned_cols=69  Identities=26%  Similarity=0.332  Sum_probs=55.2

Q ss_pred             CCCEEEEcCCCCCC------CH---HHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHHhCCcccCCeeE
Q 022058          115 VRRTVYVSDIDQNI------TE---ERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALNLGGTMLGYYPV  185 (303)
Q Consensus       115 ~~~~l~V~nlp~~~------t~---~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~l~g~~~~g~~i  185 (303)
                      ...+|.|.=..++.      ++   .+|.+.|..||+|.-++++.+      --.|+|.+-++|.+|+.++|..+.|+.|
T Consensus        14 pDgTIvV~i~~~s~e~~~~FDe~l~~~Llq~l~~~GeViLvRFv~d------~mwVTF~dG~SAL~al~l~g~~v~G~~l   87 (95)
T d1ufwa_          14 LDATVVVNLQSPTLEEKNEFPEDLRTELMQTLGSYGTIVLVRINQG------QMLVTFADSHSALSVLDVDGMKVKGRAV   87 (95)
T ss_dssp             TTCEEEEEESSCCHHHHHSCCHHHHHHHHHHHHHHSCCSEEEEETT------EEEEECSCSHHHHHHHHGGGSEETTEEE
T ss_pred             CCcEEEEEeccCCccccccCCHHHHHHHHHHHhhCCeEEEEEEeCC------eEEEEECCcHHHHHHhccCCeEEcceEE
Confidence            45666664333222      22   357788899999999999865      4899999999999999999999999999


Q ss_pred             EEee
Q 022058          186 RVLP  189 (303)
Q Consensus       186 ~v~~  189 (303)
                      .|..
T Consensus        88 ~It~   91 (95)
T d1ufwa_          88 KISG   91 (95)
T ss_dssp             EEEC
T ss_pred             EEec
Confidence            9975

>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=97.17  E-value=0.00068  Score=46.98  Aligned_cols=65  Identities=15%  Similarity=0.279  Sum_probs=55.2

Q ss_pred             ceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCC---C-CcccEEEEEEcCHHHHHHHHH-hCCceeC
Q 022058          214 RTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDH---V-HSTRIAFVEFAVAESAILALN-CSGMVLG  280 (303)
Q Consensus       214 ~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~---~-~~~g~afV~f~~~e~A~~Ai~-l~g~~~~  280 (303)
                      ++|.|++||+++|++++.+.++..  |.+.+......+   + ..-.-|+|.|.+.++...-.+ .+|+.+-
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~--~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPM--PEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSC--CCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCc--CceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            578899999999999999999998  999988877764   2 223579999999999988887 9999883

>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=97.14  E-value=0.0011  Score=45.92  Aligned_cols=65  Identities=12%  Similarity=0.188  Sum_probs=55.2

Q ss_pred             CEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCC----CceEEEEEecCHHHHHHHHH-hCCcccC
Q 022058          117 RTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHS----VLRFAFVEFADEHGARAALN-LGGTMLG  181 (303)
Q Consensus       117 ~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~----~~G~~fV~f~~~~~A~~Ai~-l~g~~~~  181 (303)
                      +.|.|+.||+++|++++.+.+...|.+........+.+    .-.-|||.|.+.++.....+ .+|..+.
T Consensus         2 tKvVvRrLPP~Lte~~F~~~l~~~~~~d~~~f~~Gk~s~~~~~~SRAYi~F~~~~~v~~F~~~f~g~~F~   71 (91)
T d1uw4a_           2 SKVVIRRLPPTLTKEQLQEHLQPMPEHDYFEFFSNDTSLYPHMYARAYINFKNQEDIILFRDRFDGYVFL   71 (91)
T ss_dssp             CEEEEEEECTTCCHHHHHHHHCSCCCEEEEEEEESCCSSTTCCCEEEEEEESSSHHHHHHHHHHTTCEEE
T ss_pred             ceEEEecCCCCCCHHHHHHHhCCcCceEEEEEeCCCcCCCCCcceEEEEEeCCHHHHHHHHHHcCCcEEE
Confidence            46899999999999999999999999988777664433    23579999999999999998 9998874

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Limkain-b1, LKAP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.98  E-value=0.0022  Score=41.60  Aligned_cols=64  Identities=19%  Similarity=0.213  Sum_probs=52.3

Q ss_pred             CCCHHH----HHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH-hCCcccCCeeEEEeecC
Q 022058          127 NITEER----LAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN-LGGTMLGYYPVRVLPSK  191 (303)
Q Consensus       127 ~~t~~~----l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~-l~g~~~~g~~i~v~~~~  191 (303)
                      .++..+    |.+.|+++|.|.++.+..-.+. .-.|-|..++.++|.-|+. |+...+++++|.|.++.
T Consensus         3 ~L~~kelqq~L~~~f~~h~~V~sv~l~~~~dg-~~~A~V~v~~~q~A~~~v~~LhR~KiG~KRI~Vs~~~   71 (73)
T d2dgxa1           3 RLSRKELQQLLQEAFARHGKVKSVELSPHTDY-QLKAVVQMENLQDAIGAVNSLHRYKIGSKKILVSLAT   71 (73)
T ss_dssp             TSCHHHHHHHHHHHHHHHSCEEEEEECSCCST-TCCEEEEESSHHHHHHHHHHHTTEEETTEEEEEEECC
T ss_pred             cCCHHHHHHHHHHHHHhheeEEEEEEEeccCC-cEEEEEEcCCHHHHHHHHHHHHHHhcCCeEEEEEEec
Confidence            445444    5568899999999998654332 3469999999999999998 99999999999999864

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.40  E-value=0.023  Score=39.22  Aligned_cols=54  Identities=24%  Similarity=0.302  Sum_probs=45.5

Q ss_pred             CCCEEEEcCCCCCCCHHHHHHHhhcCCceeEEEEeeCCCCCceEEEEEecCHHHHHHHHH
Q 022058          115 VRRTVYVSDIDQNITEERLAGLFSSCGQVVDCRVCGDPHSVLRFAFVEFADEHGARAALN  174 (303)
Q Consensus       115 ~~~~l~V~nlp~~~t~~~l~~~F~~~G~i~~~~i~~~~~~~~G~~fV~f~~~~~A~~Ai~  174 (303)
                      ....||.-..|..+...+|.++|+.||.|. |..+-|.     -|||...+.++|..++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpfG~V~-VswIddT-----Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAFGNIQ-ISWIDDT-----SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTTCSCC-CEEEETT-----EEEEECSCHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCCCceE-EEEecCc-----eEEEEecCHHHHHHHHH
Confidence            345588888999999999999999999975 5555433     49999999999999997

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Poly(A)-specific ribonuclease PARN
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.32  E-value=0.075  Score=36.57  Aligned_cols=54  Identities=24%  Similarity=0.333  Sum_probs=45.3

Q ss_pred             ccceEEEcCCCCCCCHHHHHHHhhhhcCcceeEEEEecCCCCcccEEEEEEcCHHHHHHHHH
Q 022058          212 CSRTVYCTNIDKKVPQAEVKQFFEAACGGEVTRLRLLGDHVHSTRIAFVEFAVAESAILALN  273 (303)
Q Consensus       212 ~~~~l~V~nL~~~~t~~~L~~~F~~~~~G~i~~v~i~~d~~~~~g~afV~f~~~e~A~~Ai~  273 (303)
                      ....+|.-..|..+...||.++|++|  |.|.-.-| .|.     .|||...+.++|..++.
T Consensus        14 ~RdHVf~~tFP~~Wk~~dI~~lFSpf--G~V~VswI-ddT-----Sa~V~L~~~e~~~~v~~   67 (100)
T d1whva_          14 KRDHVLHVTFPKEWKTSDLYQLFSAF--GNIQISWI-DDT-----SAFVSLSQPEQVQIAVN   67 (100)
T ss_dssp             CCCSEEEEECCTTCCHHHHHHHHTTT--CSCCCEEE-ETT-----EEEEECSCHHHHHHHHH
T ss_pred             CcceeEEEeCCcccchhHHHHHhcCC--CceEEEEe-cCc-----eEEEEecCHHHHHHHHH
Confidence            44678888999999999999999999  87765445 333     79999999999998887